Query psy4784
Match_columns 78
No_of_seqs 31 out of 33
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 17:35:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4784.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4784hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08946 Osmo_CC: Osmosensory 74.0 3.3 7.2E-05 25.1 2.2 20 2-22 22-41 (46)
2 PF07324 DGCR6: DiGeorge syndr 55.3 19 0.00041 27.1 3.6 20 42-63 152-171 (196)
3 KOG3961|consensus 50.7 5 0.00011 31.6 -0.1 11 66-76 146-156 (262)
4 PF04967 HTH_10: HTH DNA bindi 49.4 9.8 0.00021 22.9 1.1 21 41-63 3-24 (53)
5 PHA02105 hypothetical protein 46.8 8.1 0.00018 25.0 0.4 20 57-77 36-62 (68)
6 COG3413 Predicted DNA binding 40.9 15 0.00033 26.1 1.2 17 40-58 157-173 (215)
7 PF05660 DUF807: Coxiella burn 40.3 11 0.00023 27.5 0.3 18 59-76 17-34 (142)
8 PF15350 ETAA1: Ewing's tumour 39.7 16 0.00036 32.7 1.4 22 1-22 787-809 (814)
9 PF13404 HTH_AsnC-type: AsnC-t 37.9 31 0.00068 19.3 1.9 15 1-15 1-15 (42)
10 PF01731 Arylesterase: Arylest 36.6 16 0.00034 23.7 0.6 16 56-71 10-25 (86)
11 PF13645 YkuD_2: L,D-transpept 34.3 20 0.00044 26.3 0.9 20 49-68 86-105 (176)
12 PF09340 NuA4: Histone acetylt 31.7 43 0.00093 21.4 2.0 14 7-20 2-15 (80)
13 PF15209 IL31: Interleukin 31 29.9 57 0.0012 23.6 2.6 19 4-22 14-32 (137)
14 TIGR00267 conserved hypothetic 29.7 27 0.00058 24.7 0.9 15 43-57 89-103 (169)
15 PRK13741 conjugal transfer ent 25.6 68 0.0015 23.9 2.5 20 4-24 3-22 (171)
16 PRK05185 rplT 50S ribosomal pr 25.4 39 0.00085 23.2 1.1 11 4-14 89-99 (114)
17 PF14782 BBS2_C: Ciliary BBSom 25.2 74 0.0016 26.2 2.8 19 3-21 57-75 (431)
18 TIGR01032 rplT_bact ribosomal 23.5 45 0.00097 23.0 1.1 11 4-14 89-99 (113)
19 CHL00068 rpl20 ribosomal prote 23.4 44 0.00096 23.1 1.1 11 4-14 90-100 (115)
20 PRK11462 putative transporter; 23.4 72 0.0016 24.7 2.3 17 2-18 432-448 (460)
21 TIGR03412 iscX_yfhJ FeS assemb 23.3 60 0.0013 20.7 1.6 12 4-15 46-57 (63)
22 PHA00002 A DNA replication ini 23.2 86 0.0019 26.7 2.9 16 3-18 164-179 (515)
23 PF07033 Orthopox_B11R: Orthop 22.6 82 0.0018 20.4 2.1 17 6-22 8-24 (71)
24 PF06331 Tbf5: Transcription f 21.3 66 0.0014 20.3 1.5 24 38-62 11-35 (68)
25 COG0292 RplT Ribosomal protein 20.5 60 0.0013 23.0 1.3 11 3-13 89-99 (118)
26 PF11129 EIAV_Rev: Rev protein 20.4 75 0.0016 22.8 1.7 17 2-18 79-95 (134)
No 1
>PF08946 Osmo_CC: Osmosensory transporter coiled coil; InterPro: IPR015041 The osmosensory transporter coiled coil is a C-terminal domain found in various bacterial osmoprotective transporters, such as ProP, Proline/betaine transporter, Proline permease 2 and the citrate proton symporters. It adopts an antiparallel coiled-coil structure, and is essential for osmosensory and osmoprotectant transporter function []. ; PDB: 1R48_B.
Probab=74.00 E-value=3.3 Score=25.10 Aligned_cols=20 Identities=35% Similarity=0.483 Sum_probs=14.0
Q ss_pred hhhHHHHHHHHHHHHHHHHhc
Q psy4784 2 ELQNRKILEDLQMKKQLLLKQ 22 (78)
Q Consensus 2 e~~nrkILeeL~~kKq~LL~q 22 (78)
|+-...| +||++||+.|..|
T Consensus 22 edid~qI-aeLe~KR~~Lv~q 41 (46)
T PF08946_consen 22 EDIDEQI-AELEAKRQRLVDQ 41 (46)
T ss_dssp HHHHHHH-HHHHHHHHHHHHH
T ss_pred HHHHHHH-HHHHHHHHHHHHh
Confidence 3444444 8999999987654
No 2
>PF07324 DGCR6: DiGeorge syndrome critical region 6 (DGCR6) protein; InterPro: IPR010849 This family contains DiGeorge syndrome critical region 6 (DGCR6) proteins (approximately 200 residues long) of a number of vertebrates. DGCR6 is a candidate for involvement in the DiGeorge syndrome pathology by playing a role in neural crest cell migration into the third and fourth pharyngeal pouches, the structures from which derive the organs affected in DiGeorge syndrome []. Also found in this family is the Drosophila melanogaster gonadal protein gdl.
Probab=55.34 E-value=19 Score=27.06 Aligned_cols=20 Identities=35% Similarity=0.654 Sum_probs=17.5
Q ss_pred HHHHHHhhhhhccceeeeecCC
Q psy4784 42 HQRAALITANAQSTGFYITQDS 63 (78)
Q Consensus 42 ~q~aalq~a~s~s~GfFI~QDS 63 (78)
.|...|+.|- =+|||||.|+
T Consensus 152 dQQ~TLEkAG--VPGFyvT~nP 171 (196)
T PF07324_consen 152 DQQSTLEKAG--VPGFYVTTNP 171 (196)
T ss_pred HHHHHHHHCC--CCceeecCCH
Confidence 5888899887 8999999986
No 3
>KOG3961|consensus
Probab=50.67 E-value=5 Score=31.63 Aligned_cols=11 Identities=55% Similarity=1.108 Sum_probs=9.1
Q ss_pred CcccccccccC
Q psy4784 66 GNIVLPVLPRY 76 (78)
Q Consensus 66 GN~iLPVlPRl 76 (78)
|+.|+||||+|
T Consensus 146 g~kilpVLPqL 156 (262)
T KOG3961|consen 146 GEKILPVLPQL 156 (262)
T ss_pred ccccccccHHH
Confidence 68888888876
No 4
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=49.41 E-value=9.8 Score=22.85 Aligned_cols=21 Identities=24% Similarity=0.476 Sum_probs=16.5
Q ss_pred HHHHHHHhhhhhccceee-eecCC
Q psy4784 41 QHQRAALITANAQSTGFY-ITQDS 63 (78)
Q Consensus 41 ~~q~aalq~a~s~s~GfF-I~QDS 63 (78)
+.|+.+|..|. ..||| +|-+.
T Consensus 3 ~~Q~e~L~~A~--~~GYfd~PR~~ 24 (53)
T PF04967_consen 3 DRQREILKAAY--ELGYFDVPRRI 24 (53)
T ss_pred HHHHHHHHHHH--HcCCCCCCCcC
Confidence 57999999998 89999 34443
No 5
>PHA02105 hypothetical protein
Probab=46.79 E-value=8.1 Score=24.98 Aligned_cols=20 Identities=40% Similarity=0.712 Sum_probs=14.3
Q ss_pred eeeecCCC-------CCcccccccccCC
Q psy4784 57 FYITQDSS-------FGNIVLPVLPRYD 77 (78)
Q Consensus 57 fFI~QDS~-------fGN~iLPVlPRl~ 77 (78)
|=|||=-+ | |+|+|.+||..
T Consensus 36 fsipqi~yvyls~~e~-~si~p~ip~~s 62 (68)
T PHA02105 36 FSIPQIKYVYLSYEEF-NSIMPFIPRRS 62 (68)
T ss_pred ccccceEEEEEeHHHh-ccccccccccc
Confidence 55666432 5 89999999963
No 6
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=40.86 E-value=15 Score=26.09 Aligned_cols=17 Identities=24% Similarity=0.362 Sum_probs=15.3
Q ss_pred hHHHHHHHhhhhhccceee
Q psy4784 40 LQHQRAALITANAQSTGFY 58 (78)
Q Consensus 40 ~~~q~aalq~a~s~s~GfF 58 (78)
++.|+.+|+.|. ..|||
T Consensus 157 TdrQ~~vL~~A~--~~GYF 173 (215)
T COG3413 157 TDRQLEVLRLAY--KMGYF 173 (215)
T ss_pred CHHHHHHHHHHH--HcCCC
Confidence 459999999998 89999
No 7
>PF05660 DUF807: Coxiella burnetii protein of unknown function (DUF807); InterPro: IPR008525 This family consists of several proteins of unknown function from Coxiella burnetii (the causative agent of a zoonotic disease called Q fever).
Probab=40.25 E-value=11 Score=27.46 Aligned_cols=18 Identities=39% Similarity=0.397 Sum_probs=11.4
Q ss_pred eecCCCCCcccccccccC
Q psy4784 59 ITQDSSFGNIVLPVLPRY 76 (78)
Q Consensus 59 I~QDS~fGN~iLPVlPRl 76 (78)
|-.||||||.=-=.=||+
T Consensus 17 i~p~syfgn~gai~~p~I 34 (142)
T PF05660_consen 17 IDPDSYFGNPGAIMDPEI 34 (142)
T ss_pred cCchhccCCCccccChhh
Confidence 567999999643333443
No 8
>PF15350 ETAA1: Ewing's tumour-associated antigen 1 homologue
Probab=39.74 E-value=16 Score=32.74 Aligned_cols=22 Identities=41% Similarity=0.401 Sum_probs=18.1
Q ss_pred ChhhHHH-HHHHHHHHHHHHHhc
Q psy4784 1 MELQNRK-ILEDLQMKKQLLLKQ 22 (78)
Q Consensus 1 ~e~~nrk-ILeeL~~kKq~LL~q 22 (78)
.|+.||| ..||||+|||.-|..
T Consensus 787 eEEKNRKcSpEEIqRKRQEALvR 809 (814)
T PF15350_consen 787 EEEKNRKCSPEEIQRKRQEALVR 809 (814)
T ss_pred hhhhhccCCHHHHHHHHHHHHHH
Confidence 3778888 589999999987754
No 9
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=37.91 E-value=31 Score=19.34 Aligned_cols=15 Identities=40% Similarity=0.463 Sum_probs=10.5
Q ss_pred ChhhHHHHHHHHHHH
Q psy4784 1 MELQNRKILEDLQMK 15 (78)
Q Consensus 1 ~e~~nrkILeeL~~k 15 (78)
|.+..++||+.|++-
T Consensus 1 lD~~D~~Il~~Lq~d 15 (42)
T PF13404_consen 1 LDELDRKILRLLQED 15 (42)
T ss_dssp --HHHHHHHHHHHH-
T ss_pred CCHHHHHHHHHHHHc
Confidence 456789999999875
No 10
>PF01731 Arylesterase: Arylesterase; InterPro: IPR002640 The serum paraoxonases/arylesterases are enzymes that catalyse the hydrolysis of the toxic metabolites of a variety of organophosphorus insecticides. The enzymes hydrolyse a broad spectrum of organophosphate substrates, including paraoxon and a number of aromatic carboxylic acid esters (e.g., phenyl acetate), and hence confer resistance to organophosphate toxicity []. Mammals have 3 distinct paraoxonase types, termed PON1-3 [, ]. In mice and humans, the PON genes are found on the same chromosome in close proximity. PON activity has been found in variety of tissues, with highest levels in liver and serum - the source of serum PON is thought to be the liver. Unlike mammals, fish and avian species lack paraoxonase activity. Human and rabbit PONs appear to have two distinct Ca2+ binding sites, one required for stability and one required for catalytic activity. The Ca2+ dependency of PONs suggests a mechanism of hydrolysis where Ca2+ acts as the electrophillic catalyst, like that proposed for phospholipase A2. The paraoxonase enzymes, PON1 and PON3, are high density lipoprotein (HDL)- associated proteins capable of preventing oxidative modification of low density lipoproteins (LPL) []. Although PON2 has oxidative properties, the enzyme does not associate with HDL. Within a given species, PON1, PON2 and PON3 share ~60% amino acid sequence identity, whereas between mammalian species particular PONs (1,2 or 3) share 79-90% identity at the amino acid level. Human PON1 and PON3 share numerous conserved phosphorylation and N-glycosylation sites; however, it is not known whether the PON proteins are modified at these sites, or whether modification at these sites is required for activity in vivo []. This family consists of arylesterases (Also known as serum paraoxonase) 3.1.1.2 from EC. These enzymes hydrolyse organophosphorus esters such as paraoxon and are found in the liver and blood. They confer resistance to organophosphate toxicity []. Human arylesterase (PON1) P27169 from SWISSPROT is associated with HDL and may protect against LDL oxidation [].; GO: 0004064 arylesterase activity
Probab=36.63 E-value=16 Score=23.68 Aligned_cols=16 Identities=38% Similarity=0.683 Sum_probs=13.5
Q ss_pred eeeeecCCCCCccccc
Q psy4784 56 GFYITQDSSFGNIVLP 71 (78)
Q Consensus 56 GfFI~QDS~fGN~iLP 71 (78)
-||+|.|-+|++.+|-
T Consensus 10 sFy~TNDhyf~~~~l~ 25 (86)
T PF01731_consen 10 SFYVTNDHYFTDPFLR 25 (86)
T ss_pred cEEEECchhhCcHHHH
Confidence 4999999999987653
No 11
>PF13645 YkuD_2: L,D-transpeptidase catalytic domain
Probab=34.25 E-value=20 Score=26.34 Aligned_cols=20 Identities=30% Similarity=0.592 Sum_probs=16.2
Q ss_pred hhhhccceeeeecCCCCCcc
Q psy4784 49 TANAQSTGFYITQDSSFGNI 68 (78)
Q Consensus 49 ~a~s~s~GfFI~QDS~fGN~ 68 (78)
..+..|.|||.+-+.+.|..
T Consensus 86 ~S~~SSlG~y~tg~~Y~G~~ 105 (176)
T PF13645_consen 86 GSHQSSLGFYKTGETYYGKH 105 (176)
T ss_pred CCCCcCceeEEcCCEecCCC
Confidence 45667999999999998754
No 12
>PF09340 NuA4: Histone acetyltransferase subunit NuA4; InterPro: IPR015418 The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast []. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control [].
Probab=31.71 E-value=43 Score=21.37 Aligned_cols=14 Identities=43% Similarity=0.401 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHH
Q psy4784 7 KILEDLQMKKQLLL 20 (78)
Q Consensus 7 kILeeL~~kKq~LL 20 (78)
+=|+|+..+|+.|-
T Consensus 2 ~~L~~l~~~k~~Le 15 (80)
T PF09340_consen 2 KELKELLQKKKKLE 15 (80)
T ss_pred HHHHHHHHHHHHHH
Confidence 45778888888644
No 13
>PF15209 IL31: Interleukin 31
Probab=29.91 E-value=57 Score=23.63 Aligned_cols=19 Identities=37% Similarity=0.538 Sum_probs=15.7
Q ss_pred hHHHHHHHHHHHHHHHHhc
Q psy4784 4 QNRKILEDLQMKKQLLLKQ 22 (78)
Q Consensus 4 ~nrkILeeL~~kKq~LL~q 22 (78)
.-|||++|||..-+.||..
T Consensus 14 d~kkIi~eLq~~Sk~Lled 32 (137)
T PF15209_consen 14 DIKKIIEELQALSKKLLED 32 (137)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4589999999988888754
No 14
>TIGR00267 conserved hypothetical protein TIGR00267. This family is represented in three of the first four completed archaeal genomes, with two members in A. fulgidus.
Probab=29.71 E-value=27 Score=24.67 Aligned_cols=15 Identities=13% Similarity=0.071 Sum_probs=9.3
Q ss_pred HHHHHhhhhhcccee
Q psy4784 43 QRAALITANAQSTGF 57 (78)
Q Consensus 43 q~aalq~a~s~s~Gf 57 (78)
-.+|+-++-|...|.
T Consensus 89 ~~aAl~sgls~~~g~ 103 (169)
T TIGR00267 89 YMSGFIDGFSTFMGS 103 (169)
T ss_pred HHHHHHHHHHHHHHH
Confidence 556676666655555
No 15
>PRK13741 conjugal transfer entry exclusion protein TraS; Provisional
Probab=25.61 E-value=68 Score=23.90 Aligned_cols=20 Identities=20% Similarity=0.350 Sum_probs=17.3
Q ss_pred hHHHHHHHHHHHHHHHHhcCC
Q psy4784 4 QNRKILEDLQMKKQLLLKQGA 24 (78)
Q Consensus 4 ~nrkILeeL~~kKq~LL~qg~ 24 (78)
||+.|.+|.++=|+. |+.|-
T Consensus 3 T~k~I~~E~e~Lk~~-Lk~ge 22 (171)
T PRK13741 3 THKDIKTETEKLKDV-LSVGE 22 (171)
T ss_pred chHHHHHHHHHHHHH-hhcCC
Confidence 799999999999994 77765
No 16
>PRK05185 rplT 50S ribosomal protein L20; Provisional
Probab=25.39 E-value=39 Score=23.25 Aligned_cols=11 Identities=45% Similarity=0.770 Sum_probs=8.9
Q ss_pred hHHHHHHHHHH
Q psy4784 4 QNRKILEDLQM 14 (78)
Q Consensus 4 ~nrkILeeL~~ 14 (78)
-|||||.||-.
T Consensus 89 LNRK~La~lAi 99 (114)
T PRK05185 89 IDRKVLADLAV 99 (114)
T ss_pred ccHHHHHHHHh
Confidence 48999999854
No 17
>PF14782 BBS2_C: Ciliary BBSome complex subunit 2, C-terminal
Probab=25.15 E-value=74 Score=26.18 Aligned_cols=19 Identities=37% Similarity=0.420 Sum_probs=16.0
Q ss_pred hhHHHHHHHHHHHHHHHHh
Q psy4784 3 LQNRKILEDLQMKKQLLLK 21 (78)
Q Consensus 3 ~~nrkILeeL~~kKq~LL~ 21 (78)
...+..|+||..|||.|++
T Consensus 57 ~~~~~~lreL~qkKQ~Ll~ 75 (431)
T PF14782_consen 57 SDEQEALRELSQKKQNLLL 75 (431)
T ss_pred hhHHHHHHHHHHHHHHHHH
Confidence 4567889999999999884
No 18
>TIGR01032 rplT_bact ribosomal protein L20. This protein binds directly to 23s ribosomal RNA and is necessary for the in vitro assembly process of the 50s ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. GO process changed accordingly
Probab=23.51 E-value=45 Score=22.99 Aligned_cols=11 Identities=45% Similarity=0.791 Sum_probs=8.9
Q ss_pred hHHHHHHHHHH
Q psy4784 4 QNRKILEDLQM 14 (78)
Q Consensus 4 ~nrkILeeL~~ 14 (78)
-|||||.||-.
T Consensus 89 LnRKvLa~lAi 99 (113)
T TIGR01032 89 INRKVLSELAI 99 (113)
T ss_pred ccHHHHHHHHh
Confidence 48999999853
No 19
>CHL00068 rpl20 ribosomal protein L20
Probab=23.44 E-value=44 Score=23.12 Aligned_cols=11 Identities=45% Similarity=0.730 Sum_probs=8.9
Q ss_pred hHHHHHHHHHH
Q psy4784 4 QNRKILEDLQM 14 (78)
Q Consensus 4 ~nrkILeeL~~ 14 (78)
-|||||.||-.
T Consensus 90 LnRKvLa~LAi 100 (115)
T CHL00068 90 LNRKILAQIAI 100 (115)
T ss_pred ccHHHHHHHHh
Confidence 48999999853
No 20
>PRK11462 putative transporter; Provisional
Probab=23.44 E-value=72 Score=24.73 Aligned_cols=17 Identities=18% Similarity=0.259 Sum_probs=14.0
Q ss_pred hhhHHHHHHHHHHHHHH
Q psy4784 2 ELQNRKILEDLQMKKQL 18 (78)
Q Consensus 2 e~~nrkILeeL~~kKq~ 18 (78)
|++.++|.+||.+||+.
T Consensus 432 ~~~~~~i~~~l~~~~~~ 448 (460)
T PRK11462 432 THNLKTVMEQLAQGKRR 448 (460)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 56789999999888874
No 21
>TIGR03412 iscX_yfhJ FeS assembly protein IscX. Members of this protein family are YfhJ, a protein of the ISC system for iron-sulfur cluster assembly. Other genes in the system include iscSUA, hscBA, and fdx.
Probab=23.30 E-value=60 Score=20.66 Aligned_cols=12 Identities=58% Similarity=0.714 Sum_probs=9.9
Q ss_pred hHHHHHHHHHHH
Q psy4784 4 QNRKILEDLQMK 15 (78)
Q Consensus 4 ~nrkILeeL~~k 15 (78)
-|-||||.||+.
T Consensus 46 ~~EkiLEaIQ~a 57 (63)
T TIGR03412 46 CNEKILEAIQMA 57 (63)
T ss_pred ccHHHHHHHHHH
Confidence 478999999864
No 22
>PHA00002 A DNA replication initiation protein gpA
Probab=23.19 E-value=86 Score=26.75 Aligned_cols=16 Identities=38% Similarity=0.376 Sum_probs=12.2
Q ss_pred hhHHHHHHHHHHHHHH
Q psy4784 3 LQNRKILEDLQMKKQL 18 (78)
Q Consensus 3 ~~nrkILeeL~~kKq~ 18 (78)
+.-+||||++++|-++
T Consensus 164 decsK~lE~~~~ksrr 179 (515)
T PHA00002 164 DECSKILEESTMKSRR 179 (515)
T ss_pred cHHHHHHHHHhHhhhc
Confidence 4558999999998443
No 23
>PF07033 Orthopox_B11R: Orthopoxvirus B11R protein; InterPro: IPR009754 This family consists of several Orthopoxvirus B11R proteins of around 70 residues in length. The function of this family is unknown.
Probab=22.63 E-value=82 Score=20.43 Aligned_cols=17 Identities=24% Similarity=0.536 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHhc
Q psy4784 6 RKILEDLQMKKQLLLKQ 22 (78)
Q Consensus 6 rkILeeL~~kKq~LL~q 22 (78)
..|+.|++++|...|++
T Consensus 8 e~i~neidreke~ilkn 24 (71)
T PF07033_consen 8 EDIMNEIDREKEEILKN 24 (71)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 35899999999999887
No 24
>PF06331 Tbf5: Transcription factor TFIIH complex subunit Tfb5; InterPro: IPR009400 This entry represents nucleotide excision repair (NER) proteins, such as TTDA subunit of TFIIH basal transcription factor complex (also known as subunit 5 of RNA polymerase II transcription factor B), and Rex1. These proteins have a structural motif consisting of a 2-layer sandwich structure with an alpha/beta plait topology. Nucleotide excision repair is a major pathway for repairing UV light-induced DNA damage in most organisms. Transcription/repair factor IIH (TFIIH) is essential for RNA polymerase II transcription and nucleotide excision repair. The TFIIH complex consists of ten subunits: ERCC2, ERCC3, GTF2H1, GTF2H2, GTF2H3, GTF2H4, GTF2H5, MNAT1, CDK7 and CCNH. Defects in GTF2H5 cause the disease trichothiodystrophy (TTD), therefore GTF2H5 (general transcription factor 2H subunit 5) is also known as the TTD group A (TTDA) subunit (and as Tfb5) []. The TTDA subunit is responsible for the DNA repair function of the complex. TTDA is present both bound to TFIIH, and as a free fraction that shuffles between the cytoplasm and nucleus; induction of NER-type DNA lesions shifts the balance towards TTDA's more stable association with TFIIH []. TTDA is also required for the stability of the TFIIH complex and for the presence of normal levels of TFIIH in the cell. REX1 (required for excision 1) is required for DNA repair in the single-celled, photosynthetic algae Chlamydomonas reinhardtii [], and has homologues in other eukaryotes.; GO: 0003677 DNA binding, 0006289 nucleotide-excision repair; PDB: 2JNJ_B 1YDL_A 3DGP_B 3DOM_B.
Probab=21.28 E-value=66 Score=20.27 Aligned_cols=24 Identities=13% Similarity=0.286 Sum_probs=17.8
Q ss_pred hhhHHHHHHHhhhhh-ccceeeeecC
Q psy4784 38 DQLQHQRAALITANA-QSTGFYITQD 62 (78)
Q Consensus 38 ~~~~~q~aalq~a~s-~s~GfFI~QD 62 (78)
.|||..|+-+-|-++ ...| ||=+|
T Consensus 11 ~CDpa~Kq~il~ld~~~~~~-FIIed 35 (68)
T PF06331_consen 11 ECDPAIKQFILHLDESMPHG-FIIED 35 (68)
T ss_dssp ES-HHHHHHHHHHHHHCCTS-SEEEE
T ss_pred EcCHHHHHHHHHHhcCCCCC-eEEEE
Confidence 478999999999998 5567 66554
No 25
>COG0292 RplT Ribosomal protein L20 [Translation, ribosomal structure and biogenesis]
Probab=20.49 E-value=60 Score=23.02 Aligned_cols=11 Identities=45% Similarity=0.637 Sum_probs=8.8
Q ss_pred hhHHHHHHHHH
Q psy4784 3 LQNRKILEDLQ 13 (78)
Q Consensus 3 ~~nrkILeeL~ 13 (78)
+-|||+|.||-
T Consensus 89 ~inRKvLadlA 99 (118)
T COG0292 89 EIDRKVLADLA 99 (118)
T ss_pred hhhHHHHHHHH
Confidence 46899999974
No 26
>PF11129 EIAV_Rev: Rev protein of equine infectious anaemia virus; InterPro: IPR021311 The sequence of this family is highly conserved and carries a nuclear export signal from residues 31-55, and RNA binding/nuclear localisation signals of RRDR at residue 76 and KRRRK at residue 159. Rev is an essential regulatory protein required for nucleocytoplasmic transport of incompletely spliced viral mRNAs that encode structural proteins. Rev has been shown to down-regulate the expression of viral late genes and alter sensitivity to Gag-specific cytotoxic-T-lymphocytes (CTL). Equine infectious anaemia virus (EIAV) exhibits a high rate of genetic variation in vivo, and results in a clinically variable disease in infected horses.
Probab=20.44 E-value=75 Score=22.76 Aligned_cols=17 Identities=29% Similarity=0.458 Sum_probs=14.4
Q ss_pred hhhHHHHHHHHHHHHHH
Q psy4784 2 ELQNRKILEDLQMKKQL 18 (78)
Q Consensus 2 e~~nrkILeeL~~kKq~ 18 (78)
|..||.|+.||+-+++.
T Consensus 79 ~~vnk~iwrel~~~~~q 95 (134)
T PF11129_consen 79 EKVNKEIWRELQYTRRQ 95 (134)
T ss_pred HHHHHHHHHHHHhhHhh
Confidence 67899999999987763
Done!