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Conserved domains on  [gi|1958677287|ref|XP_038948383|]
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homeobox protein Meis1 isoform X6 [Rattus norvegicus]

Protein Classification

homeobox domain-containing protein( domain architecture ID 10531334)

homeobox domain-containing protein may be involved in the transcriptional regulation of key eukaryotic developmental processes

CATH:  1.10.10.60
Gene Ontology:  GO:0003677
SCOP:  4000291

Graphical summary

 Zoom to residue level

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List of domain hits

Name Accession Description Interval E-value
Homeobox_KN pfam05920
Homeobox KN domain; This is a homeobox transcription factor KN domain conserved from fungi to ...
128-166 2.49e-21

Homeobox KN domain; This is a homeobox transcription factor KN domain conserved from fungi to human and plants. They were first identified as TALE homeobox genes in eukaryotes, (including KNOX and MEIS genes). They have been recently classified.


:

Pssm-ID: 428673  Cd Length: 39  Bit Score: 84.49  E-value: 2.49e-21
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1958677287 128 LFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRR 166
Cdd:pfam05920   1 LYEHLHNPYPSEEEKAELAKETGLSRKQISNWFINARRR 39
PABP-1234 super family cl31127
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
163-286 3.82e-04

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


The actual alignment was detected with superfamily member TIGR01628:

Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 41.72  E-value: 3.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958677287 163 ARRRIVQPMIDQsNRAVSQGTPYnpdGQPMGGfvMDGQQHMGIRAPG--LQSMPGEYvARGGPMGVSMGQPSYTQAQMPP 240
Cdd:TIGR01628 366 QRRAHLQDQFMQ-LQPRMRQLPM---GSPMGG--AMGQPPYYGQGPQqqFNGQPLGW-PRMSMMPTPMGPGGPLRPNGLA 438
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958677287 241 HPAQLRHGPPMHTYIPGHPHHPAVM-MHGGQPHP---GMPMSASSPSVLN 286
Cdd:TIGR01628 439 PMNAVRAPSRNAQNAAQKPPMQPVMyPPNYQSLPlsqDLPQPQSTASQGG 488
 
Name Accession Description Interval E-value
Homeobox_KN pfam05920
Homeobox KN domain; This is a homeobox transcription factor KN domain conserved from fungi to ...
128-166 2.49e-21

Homeobox KN domain; This is a homeobox transcription factor KN domain conserved from fungi to human and plants. They were first identified as TALE homeobox genes in eukaryotes, (including KNOX and MEIS genes). They have been recently classified.


Pssm-ID: 428673  Cd Length: 39  Bit Score: 84.49  E-value: 2.49e-21
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1958677287 128 LFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRR 166
Cdd:pfam05920   1 LYEHLHNPYPSEEEKAELAKETGLSRKQISNWFINARRR 39
homeodomain cd00086
Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic ...
113-166 4.26e-13

Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.


Pssm-ID: 238039 [Multi-domain]  Cd Length: 59  Bit Score: 63.03  E-value: 4.26e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958677287 113 RGIFPKVATNIMRAWlFQHltHPYPSEEQKKQLAQDTGLTILQVNNWFINARRR 166
Cdd:cd00086     4 RTRFTPEQLEELEKE-FEK--NPYPSREEREELAKELGLTERQVKIWFQNRRAK 54
HOX smart00389
Homeodomain; DNA-binding factors that are involved in the transcriptional regulation of key ...
113-166 1.50e-12

Homeodomain; DNA-binding factors that are involved in the transcriptional regulation of key developmental processes


Pssm-ID: 197696 [Multi-domain]  Cd Length: 57  Bit Score: 61.50  E-value: 1.50e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958677287  113 RGIFPKVATNIMRAWlFQHltHPYPSEEQKKQLAQDTGLTILQVNNWFINARRR 166
Cdd:smart00389   5 RTSFTPEQLEELEKE-FQK--NPYPSREEREELAKKLGLSERQVKVWFQNRRAK 55
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
163-286 3.82e-04

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 41.72  E-value: 3.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958677287 163 ARRRIVQPMIDQsNRAVSQGTPYnpdGQPMGGfvMDGQQHMGIRAPG--LQSMPGEYvARGGPMGVSMGQPSYTQAQMPP 240
Cdd:TIGR01628 366 QRRAHLQDQFMQ-LQPRMRQLPM---GSPMGG--AMGQPPYYGQGPQqqFNGQPLGW-PRMSMMPTPMGPGGPLRPNGLA 438
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958677287 241 HPAQLRHGPPMHTYIPGHPHHPAVM-MHGGQPHP---GMPMSASSPSVLN 286
Cdd:TIGR01628 439 PMNAVRAPSRNAQNAAQKPPMQPVMyPPNYQSLPlsqDLPQPQSTASQGG 488
 
Name Accession Description Interval E-value
Homeobox_KN pfam05920
Homeobox KN domain; This is a homeobox transcription factor KN domain conserved from fungi to ...
128-166 2.49e-21

Homeobox KN domain; This is a homeobox transcription factor KN domain conserved from fungi to human and plants. They were first identified as TALE homeobox genes in eukaryotes, (including KNOX and MEIS genes). They have been recently classified.


Pssm-ID: 428673  Cd Length: 39  Bit Score: 84.49  E-value: 2.49e-21
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1958677287 128 LFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRR 166
Cdd:pfam05920   1 LYEHLHNPYPSEEEKAELAKETGLSRKQISNWFINARRR 39
homeodomain cd00086
Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic ...
113-166 4.26e-13

Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.


Pssm-ID: 238039 [Multi-domain]  Cd Length: 59  Bit Score: 63.03  E-value: 4.26e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958677287 113 RGIFPKVATNIMRAWlFQHltHPYPSEEQKKQLAQDTGLTILQVNNWFINARRR 166
Cdd:cd00086     4 RTRFTPEQLEELEKE-FEK--NPYPSREEREELAKELGLTERQVKIWFQNRRAK 54
HOX smart00389
Homeodomain; DNA-binding factors that are involved in the transcriptional regulation of key ...
113-166 1.50e-12

Homeodomain; DNA-binding factors that are involved in the transcriptional regulation of key developmental processes


Pssm-ID: 197696 [Multi-domain]  Cd Length: 57  Bit Score: 61.50  E-value: 1.50e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958677287  113 RGIFPKVATNIMRAWlFQHltHPYPSEEQKKQLAQDTGLTILQVNNWFINARRR 166
Cdd:smart00389   5 RTSFTPEQLEELEKE-FQK--NPYPSREEREELAKKLGLSERQVKVWFQNRRAK 55
Homeodomain pfam00046
Homeodomain;
128-166 6.91e-06

Homeodomain;


Pssm-ID: 459649 [Multi-domain]  Cd Length: 57  Bit Score: 42.87  E-value: 6.91e-06
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1958677287 128 LFQHltHPYPSEEQKKQLAQDTGLTILQVNNWFINARRR 166
Cdd:pfam00046  18 EFQE--NPYPSAEEREELAAQLGLTERQVKVWFQNRRAK 54
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
163-286 3.82e-04

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 41.72  E-value: 3.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958677287 163 ARRRIVQPMIDQsNRAVSQGTPYnpdGQPMGGfvMDGQQHMGIRAPG--LQSMPGEYvARGGPMGVSMGQPSYTQAQMPP 240
Cdd:TIGR01628 366 QRRAHLQDQFMQ-LQPRMRQLPM---GSPMGG--AMGQPPYYGQGPQqqFNGQPLGW-PRMSMMPTPMGPGGPLRPNGLA 438
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958677287 241 HPAQLRHGPPMHTYIPGHPHHPAVM-MHGGQPHP---GMPMSASSPSVLN 286
Cdd:TIGR01628 439 PMNAVRAPSRNAQNAAQKPPMQPVMyPPNYQSLPlsqDLPQPQSTASQGG 488
 
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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