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Conserved domains on  [gi|2462587942|ref|XP_054201601|]
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ADP-ribosylation factor-like protein 13B isoform X5 [Homo sapiens]

Protein Classification

P-loop NTPase family protein( domain architecture ID 1562424)

P-loop NTPase (nucleoside triphosphate hydrolase) family protein contains two conserved sequence signatures, the Walker A motif (the P-loop proper) and Walker B motif which bind, respectively, the beta and gamma phosphate moieties of the bound nucleotide (typically ATP or GTP), and a Mg(2+) cation

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
21-82 8.09e-31

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd04161:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 167  Bit Score: 113.64  E-value: 8.09e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462587942  21 LANKQDKEGALGEADVIECLSLEKLVNEHKCLCQIEPCSAISGYGKKIDKSIKKGLYWLLHV 82
Cdd:cd04161   106 LANKQDKKNALLGADVIEYLSLEKLVNENKSLCHIEPCSAIEGLGKKIDPSIVEGLRWLLAA 167
CCDC47 super family cl46382
PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of ...
92-134 2.46e-03

PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex, formed by CCDC47 and Asterix proteins, acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. CCDC47 is required to maintain the stability of Asterix. CCDC47 is associated with various membrane-associated processes and is component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis. It is also involved in the regulation of calcium ion homeostasis in the ER, being also required for proper protein degradation via the ERAD (ER-associated degradation) pathway.


The actual alignment was detected with superfamily member pfam07946:

Pssm-ID: 480722  Cd Length: 323  Bit Score: 39.09  E-value: 2.46e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2462587942  92 ERIQKETTEQRALEEQEKQERAERVRKLREERKQNEQEQAELD 134
Cdd:pfam07946 271 EKIKKAAEEERAEEAQEKKEEAKKKEREEKLAKLSPEEQRKYE 313
 
Name Accession Description Interval E-value
Arl2l1_Arl13_like cd04161
Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a ...
21-82 8.09e-31

Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily of the Arf family of small GTPases. Arl2l1 was identified in human cells during a search for the gene(s) responsible for Bardet-Biedl syndrome (BBS). Like Arl6, the identified BBS gene, Arl2l1 is proposed to have cilia-specific functions. Arl13 is found on the X chromosome, but its expression has not been confirmed; it may be a pseudogene.


Pssm-ID: 133361 [Multi-domain]  Cd Length: 167  Bit Score: 113.64  E-value: 8.09e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462587942  21 LANKQDKEGALGEADVIECLSLEKLVNEHKCLCQIEPCSAISGYGKKIDKSIKKGLYWLLHV 82
Cdd:cd04161   106 LANKQDKKNALLGADVIEYLSLEKLVNENKSLCHIEPCSAIEGLGKKIDPSIVEGLRWLLAA 167
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
21-83 6.88e-06

ADP-ribosylation factor family; Pfam combines a number of different Prosite families together


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 45.29  E-value: 6.88e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462587942  21 LANKQDKEGALGEADVIECLSLEKLVNEHkclCQIEPCSAISGYGkkidksIKKGLYWLLHVI 83
Cdd:pfam00025 107 LANKQDLPGAMSEAEIRELLGLHELKDRP---WEIQGCSAVTGEG------LDEGLDWLSNYI 160
CCDC47 pfam07946
PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of ...
92-134 2.46e-03

PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex, formed by CCDC47 and Asterix proteins, acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. CCDC47 is required to maintain the stability of Asterix. CCDC47 is associated with various membrane-associated processes and is component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis. It is also involved in the regulation of calcium ion homeostasis in the ER, being also required for proper protein degradation via the ERAD (ER-associated degradation) pathway.


Pssm-ID: 462322  Cd Length: 323  Bit Score: 39.09  E-value: 2.46e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2462587942  92 ERIQKETTEQRALEEQEKQERAERVRKLREERKQNEQEQAELD 134
Cdd:pfam07946 271 EKIKKAAEEERAEEAQEKKEEAKKKEREEKLAKLSPEEQRKYE 313
rne PRK10811
ribonuclease E; Reviewed
91-152 5.54e-03

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 38.48  E-value: 5.54e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462587942   91 NERIQKETTEQ-RALEEQEKQERAERVRKLREERKQNEQEQAEL--DGTSGLAELDPEPTNPFQP 152
Cdd:PRK10811   654 RESQQAEVTEKaRTQDEQQQAPRRERQRRRNDEKRQAQQEAKALnvEEQSVQETEQEERVQQVQP 718
 
Name Accession Description Interval E-value
Arl2l1_Arl13_like cd04161
Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a ...
21-82 8.09e-31

Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily of the Arf family of small GTPases. Arl2l1 was identified in human cells during a search for the gene(s) responsible for Bardet-Biedl syndrome (BBS). Like Arl6, the identified BBS gene, Arl2l1 is proposed to have cilia-specific functions. Arl13 is found on the X chromosome, but its expression has not been confirmed; it may be a pseudogene.


Pssm-ID: 133361 [Multi-domain]  Cd Length: 167  Bit Score: 113.64  E-value: 8.09e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462587942  21 LANKQDKEGALGEADVIECLSLEKLVNEHKCLCQIEPCSAISGYGKKIDKSIKKGLYWLLHV 82
Cdd:cd04161   106 LANKQDKKNALLGADVIEYLSLEKLVNENKSLCHIEPCSAIEGLGKKIDPSIVEGLRWLLAA 167
Arf_Arl cd00878
ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl ...
21-81 3.13e-11

ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thus, despite their significant sequence homologies, Arf family proteins may regulate unrelated functions.


Pssm-ID: 206644 [Multi-domain]  Cd Length: 158  Bit Score: 60.67  E-value: 3.13e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462587942  21 LANKQDKEGALGEADVIECLSLEKLvneHKCLCQIEPCSAISGYGkkidksIKKGLYWLLH 81
Cdd:cd00878   106 LANKQDLPGALTESELIELLGLESI---KGRRWHIQPCSAVTGDG------LDEGLDWLIE 157
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
21-83 6.88e-06

ADP-ribosylation factor family; Pfam combines a number of different Prosite families together


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 45.29  E-value: 6.88e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462587942  21 LANKQDKEGALGEADVIECLSLEKLVNEHkclCQIEPCSAISGYGkkidksIKKGLYWLLHVI 83
Cdd:pfam00025 107 LANKQDLPGAMSEAEIRELLGLHELKDRP---WEIQGCSAVTGEG------LDEGLDWLSNYI 160
Arfrp1 cd04160
Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a ...
21-79 7.01e-06

Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development.


Pssm-ID: 206725 [Multi-domain]  Cd Length: 168  Bit Score: 45.41  E-value: 7.01e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462587942  21 LANKQDKEGALGEADVIECLSLeKLVNEHKCLCQIEPCSAISGYGkkidksIKKGLYWL 79
Cdd:cd04160   114 LANKQDLPDALSVAEIKEVFDD-CIALIGRRDCLVQPVSALEGEG------VEEGIEWL 165
Arl5_Arl8 cd04153
Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like ...
21-81 2.90e-05

Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like Arl4 and Arl7, are localized to the nucleus and nucleolus. Arl5 is developmentally regulated during embryogenesis in mice. Human Arl5 interacts with the heterochromatin protein 1-alpha (HP1alpha), a nonhistone chromosomal protein that is associated with heterochromatin and telomeres, and prevents telomere fusion. Arl5 may also play a role in embryonic nuclear dynamics and/or signaling cascades. Arl8 was identified from a fetal cartilage cDNA library. It is found in brain, heart, lung, cartilage, and kidney. No function has been assigned for Arl8 to date.


Pssm-ID: 133353 [Multi-domain]  Cd Length: 174  Bit Score: 43.88  E-value: 2.90e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462587942  21 LANKQDKEGALGEADVIECLSLEKlVNEHKclCQIEPCSAISGygkkidKSIKKGLYWLLH 81
Cdd:cd04153   122 LANKQDLKGAMTPAEISESLGLTS-IRDHT--WHIQGCCALTG------EGLPEGLDWIAS 173
Arl1 cd04151
ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi ...
21-79 3.22e-05

ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi complex, where it is believed to recruit effector proteins to the trans-Golgi network. Like most members of the Arf family, Arl1 is myristoylated at its N-terminal helix and mutation of the myristoylation site disrupts Golgi targeting. In humans, the Golgi-localized proteins golgin-97 and golgin-245 have been identified as Arl1 effectors. Golgins are large coiled-coil proteins found in the Golgi, and these golgins contain a C-terminal GRIP domain, which is the site of Arl1 binding. Additional Arl1 effectors include the GARP (Golgi-associated retrograde protein)/VFT (Vps53) vesicle-tethering complex and Arfaptin 2. Arl1 is not required for exocytosis, but appears necessary for trafficking from the endosomes to the Golgi. In Drosophila zygotes, mutation of Arl1 is lethal, and in the host-bloodstream form of Trypanosoma brucei, Arl1 is essential for viability.


Pssm-ID: 206718 [Multi-domain]  Cd Length: 158  Bit Score: 43.17  E-value: 3.22e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462587942  21 LANKQDKEGALGEADVIECLSLEKLVNEHkclCQIEPCSAISGYGkkidksIKKGLYWL 79
Cdd:cd04151   106 FANKQDMPGALSEAEVAEKLGLSELKDRT---WQIFKTSATKGEG------LDEGMDWL 155
Arl2 cd04154
Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind ...
21-80 6.13e-04

Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind GDP and GTP with very low affinity. Unlike most Arf family proteins, Arl2 is not myristoylated at its N-terminal helix. The protein PDE-delta, first identified in photoreceptor rod cells, binds specifically to Arl2 and is structurally very similar to RhoGDI. Despite the high structural similarity between Arl2 and Rho proteins and between PDE-delta and RhoGDI, the interactions between the GTPases and their effectors are very different. In its GTP bound form, Arl2 interacts with the protein Binder of Arl2 (BART), and the complex is believed to play a role in mitochondrial adenine nucleotide transport. In its GDP bound form, Arl2 interacts with tubulin- folding Cofactor D; this interaction is believed to play a role in regulation of microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis.


Pssm-ID: 206720 [Multi-domain]  Cd Length: 173  Bit Score: 39.62  E-value: 6.13e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462587942  21 LANKQDKEGALGEADVIECLSLEKLVNEHKCLCqiePCSAISGYGkkidksIKKGLYWLL 80
Cdd:cd04154   121 FANKQDLPGALSPEEIREVLELDSIKSHHWRIF---GCSAVTGEN------LLDGIDWLV 171
ARLTS1 cd04156
Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), ...
19-65 1.24e-03

Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), also known as Arl11, is a member of the Arf family of small GTPases that is believed to play a major role in apoptotic signaling. ARLTS1 is widely expressed and functions as a tumor suppressor gene in several human cancers. ARLTS1 is a low-penetrance suppressor that accounts for a small percentage of familial melanoma or familial chronic lymphocytic leukemia (CLL). ARLTS1 inactivation seems to occur most frequently through biallelic down-regulation by hypermethylation of the promoter. In breast cancer, ARLTS1 alterations were typically a combination of a hypomorphic polymorphism plus loss of heterozygosity. In a case of thyroid adenoma, ARLTS1 alterations were polymorphism plus promoter hypermethylation. The nonsense polymorphism Trp149Stop occurs with significantly greater frequency in familial cancer cases than in sporadic cancer cases, and the Cys148Arg polymorphism is associated with an increase in high-risk familial breast cancer.


Pssm-ID: 133356 [Multi-domain]  Cd Length: 160  Bit Score: 38.55  E-value: 1.24e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2462587942  19 VRLANKQDKEGALGEADVIECLSLEKLVNEHKclCQIEPCSAISGYG 65
Cdd:cd04156   105 VLLANKQDLPGALTAEEITRRFKLKKYCSDRD--WYVQPCSAVTGEG 149
CCDC47 pfam07946
PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of ...
92-134 2.46e-03

PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex, formed by CCDC47 and Asterix proteins, acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. CCDC47 is required to maintain the stability of Asterix. CCDC47 is associated with various membrane-associated processes and is component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis. It is also involved in the regulation of calcium ion homeostasis in the ER, being also required for proper protein degradation via the ERAD (ER-associated degradation) pathway.


Pssm-ID: 462322  Cd Length: 323  Bit Score: 39.09  E-value: 2.46e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2462587942  92 ERIQKETTEQRALEEQEKQERAERVRKLREERKQNEQEQAELD 134
Cdd:pfam07946 271 EKIKKAAEEERAEEAQEKKEEAKKKEREEKLAKLSPEEQRKYE 313
rne PRK10811
ribonuclease E; Reviewed
91-152 5.54e-03

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 38.48  E-value: 5.54e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462587942   91 NERIQKETTEQ-RALEEQEKQERAERVRKLREERKQNEQEQAEL--DGTSGLAELDPEPTNPFQP 152
Cdd:PRK10811   654 RESQQAEVTEKaRTQDEQQQAPRRERQRRRNDEKRQAQQEAKALnvEEQSVQETEQEERVQQVQP 718
Arl3 cd04155
Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most ...
21-79 8.76e-03

Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.


Pssm-ID: 206721 [Multi-domain]  Cd Length: 174  Bit Score: 36.22  E-value: 8.76e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462587942  21 LANKQDKEGALGEADVIECLSLEKLVNEhkcLCQIEPCSAISGYGkkidksIKKGLYWL 79
Cdd:cd04155   122 FANKQDLLTAAPAEEVAEALNLHDIRDR---SWHIQACSAKTGEG------LQEGMNWV 171
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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