zinc finger HIT (zf-HIT) found in INO80 complex subunit B (INO80B) and similar proteins; INO80B, also called high mobility group AT-hook 1-like 4 (HMGA1L4), or IES2 homolog, or PAP-1-associated protein 1 (PAPA-1), or zinc finger HIT domain-containing protein 4 (ZNHIT4), is a nucleolar protein that induces growth and cell cycle arrests at the G1 phase of the cell cycle. It is a core component of the chromatin remodeling INO80 complex, which is involved in transcriptional regulation, DNA replication and probably DNA repair. INO80B harbors a zf-HIT domain which is characterized by a fold in "treble-clef" through interleaved CCCC and CCHC ZnF motifs that both bind a zinc atom. The yeast counterpart of INO80B is Ies2p (Ino eighty subunit 2), which doesn't have zf-HIT domain.

                         10        20        30
                 ....*....|....*....|....*....|...
gi 548842150 590 EKCAGPSCTNIYKYRDSKSNLPLCSLQCYRAIH 622
Cdd:cd23021    1 ELCSVPGCTNPKKYRCSKTGVPVCSLECYKKNL 33

zinc finger HIT (zf-HIT) found in INO80 complex subunit B (INO80B) and similar proteins; INO80B, also called high mobility group AT-hook 1-like 4 (HMGA1L4), or IES2 homolog, or PAP-1-associated protein 1 (PAPA-1), or zinc finger HIT domain-containing protein 4 (ZNHIT4), is a nucleolar protein that induces growth and cell cycle arrests at the G1 phase of the cell cycle. It is a core component of the chromatin remodeling INO80 complex, which is involved in transcriptional regulation, DNA replication and probably DNA repair. INO80B harbors a zf-HIT domain which is characterized by a fold in "treble-clef" through interleaved CCCC and CCHC ZnF motifs that both bind a zinc atom. The yeast counterpart of INO80B is Ies2p (Ino eighty subunit 2), which doesn't have zf-HIT domain.

                         10        20        30
                 ....*....|....*....|....*....|...
gi 548842150 590 EKCAGPSCTNIYKYRDSKSNLPLCSLQCYRAIH 622
Cdd:cd23021    1 ELCSVPGCTNPKKYRCSKTGVPVCSLECYKKNL 33

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 548842150  477 QKKKKEKMTEVEQQLKKAEAAQRRRMQVEKANKElEAEAIRKiLGQDSNRKKREDKIRKHQDElAQAKAATA 548
Cdd:TIGR02794 103 AAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKA-EAEAERK-AKEEAAKQAEEEAKAKAAAE-AKKKAEEA 171

Caldesmon;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548842150  383 RRRGKSRGVKRRPFEGEVDEDGYEEELTSVNDDIDNSEFGAEG-KSSKKRKETVDSLVDEKKEFSLTTRQRALQSGKDSG 461
Cdd:pfam02029 141 QENKWSTEVRQAEEEGEEEEDKSEEAEEVPTENFAKEEVKDEKiKKEKKVKYESKVFLDQKRGHPEVKSQNGEEEVTKLK 220

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548842150  462 VAANLIEFPDGLPATQKKKKEKMTEVEQQLKK-------AEAAQRRRMQVEKANKELEAEAIRKILGQDSNRKKREDKIR 534
Cdd:pfam02029 221 VTTKRRQGGLSQSQEREEEAEVFLEAEQKLEElrrrrqeKESEEFEKLRQKQQEAELELEELKKKREERRKLLEEEEQRR 300

                         170
                  ....*....|
gi 548842150  535 KHQDELAQAK 544
Cdd:pfam02029 301 KQEEAERKLR 310

zinc finger HIT (zf-HIT) found in INO80 complex subunit B (INO80B) and similar proteins; INO80B, also called high mobility group AT-hook 1-like 4 (HMGA1L4), or IES2 homolog, or PAP-1-associated protein 1 (PAPA-1), or zinc finger HIT domain-containing protein 4 (ZNHIT4), is a nucleolar protein that induces growth and cell cycle arrests at the G1 phase of the cell cycle. It is a core component of the chromatin remodeling INO80 complex, which is involved in transcriptional regulation, DNA replication and probably DNA repair. INO80B harbors a zf-HIT domain which is characterized by a fold in "treble-clef" through interleaved CCCC and CCHC ZnF motifs that both bind a zinc atom. The yeast counterpart of INO80B is Ies2p (Ino eighty subunit 2), which doesn't have zf-HIT domain.

                         10        20        30
                 ....*....|....*....|....*....|...
gi 548842150 590 EKCAGPSCTNIYKYRDSKSNLPLCSLQCYRAIH 622
Cdd:cd23021    1 ELCSVPGCTNPKKYRCSKTGVPVCSLECYKKNL 33

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 548842150  477 QKKKKEKMTEVEQQLKKAEAAQRRRMQVEKANKElEAEAIRKiLGQDSNRKKREDKIRKHQDElAQAKAATA 548
Cdd:TIGR02794 103 AAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKA-EAEAERK-AKEEAAKQAEEEAKAKAAAE-AKKKAEEA 171

Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548842150 477 QKKKKEKMTEVEQQLKKAEAAQRRRMQVEKANKEL-----EAEAIRKILGQDSNRKKRE--DKIRKHQDELAQAKAATAM 549
Cdd:COG2268  256 EAETARAEAEAAYEIAEANAEREVQRQLEIAEREReielqEKEAEREEAELEADVRKPAeaEKQAAEAEAEAEAEAIRAK 335

                 ...
gi 548842150 550 TLA 552
Cdd:COG2268  336 GLA 338

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548842150   382 NRRRGKSRGVKRRPFEGEVDEDGYEEELTSVNDDIDNSEFGAEGKSsKKRKETVDSLVDEKKEFSLTTRQRAlqsgkdsg 461
Cdd:TIGR02169  332 DKLLAEIEELEREIEEERKRRDKLTEEYAELKEELEDLRAELEEVD-KEFAETRDELKDYREKLEKLKREIN-------- 402

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548842150   462 vaaNLIEFPDGLPATQKKKKEKMTEVEQQLKKAEAAQ------RRRMQVEKANKELEAEAIRKILGQDSNRKKR------ 529
Cdd:TIGR02169  403 ---ELKRELDRLQEELQRLSEELADLNAAIAGIEAKIneleeeKEDKALEIKKQEWKLEQLAADLSKYEQELYDlkeeyd 479

                          170
                   ....*....|....*...
gi 548842150   530 --EDKIRKHQDELAQAKA 545
Cdd:TIGR02169  480 rvEKELSKLQRELAEAEA 497

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 548842150  477 QKKKKEKMTEVEQQLKKAEAAQRRRMQVEkanKELEAEAIRKILGQDSNRKKREDKIRKHQDELAQAKA 545
Cdd:pfam13868 118 AEEKLEKQRQLREEIDEFNEEQAEWKELE---KEEEREEDERILEYLKEKAEREEEREAEREEIEEEKE 183