Query 046700
Match_columns 154
No_of_seqs 103 out of 123
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 03:36:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046700.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046700hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07939 DUF1685: Protein of u 99.9 2.9E-28 6.4E-33 169.4 3.1 53 50-104 1-53 (64)
2 KOG4404 Tandem pore domain K+ 44.5 14 0.0003 33.6 1.7 39 22-64 31-69 (350)
3 cd04767 HTH_HspR-like_MBC Heli 43.8 5.7 0.00012 30.6 -0.7 50 17-68 7-58 (120)
4 PF15178 TOM_sub5: Mitochondri 40.6 34 0.00074 23.1 2.7 23 123-148 8-30 (51)
5 PF13986 DUF4224: Domain of un 38.4 15 0.00032 23.9 0.7 19 50-68 3-31 (47)
6 PF05416 Peptidase_C37: Southa 37.0 11 0.00025 35.6 0.0 19 46-64 249-267 (535)
7 cd01104 HTH_MlrA-CarA Helix-Tu 35.0 38 0.00083 21.8 2.3 45 18-64 7-53 (68)
8 COG4004 Uncharacterized protei 32.7 16 0.00035 27.6 0.2 27 59-89 19-45 (96)
9 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 32.2 26 0.00056 23.3 1.1 23 46-68 1-23 (50)
10 PF04533 Herpes_U44: Herpes vi 32.0 23 0.00051 30.1 1.1 18 52-69 31-48 (210)
11 PF08920 SF3b1: Splicing facto 29.3 26 0.00057 27.9 0.9 30 23-58 66-95 (144)
12 PF03047 ComC: COMC family; I 28.9 19 0.0004 22.1 0.0 14 47-60 11-24 (32)
13 PF15636 Tox-GHH: GHH signatur 28.3 43 0.00094 24.0 1.8 31 29-59 16-46 (79)
14 PF04328 DUF466: Protein of un 26.8 43 0.00094 23.2 1.5 23 131-153 1-23 (65)
15 cd07684 F-BAR_srGAP3 The F-BAR 25.9 32 0.0007 30.0 0.9 17 52-68 234-250 (253)
16 PF01180 DHO_dh: Dihydroorotat 25.5 30 0.00066 29.0 0.7 17 52-68 22-38 (295)
17 PF03869 Arc: Arc-like DNA bin 25.0 56 0.0012 21.3 1.7 14 128-141 12-25 (50)
18 TIGR03577 EF_0830 conserved hy 22.7 7.6 0.00016 30.0 -3.1 33 48-81 77-109 (115)
19 cd07682 F-BAR_srGAP2 The F-BAR 22.2 41 0.0009 29.5 0.9 16 53-68 245-260 (263)
20 PF11673 DUF3269: Protein of u 22.1 49 0.0011 24.0 1.1 19 46-64 40-58 (73)
21 PLN02826 dihydroorotate dehydr 22.1 44 0.00096 30.4 1.1 18 51-68 93-110 (409)
22 PF14272 Gly_rich_SFCGS: Glyci 22.0 8.1 0.00017 29.9 -3.1 33 48-81 77-109 (115)
23 smart00153 VHP Villin headpiec 21.7 45 0.00097 20.7 0.8 12 50-61 2-13 (36)
24 PF14098 SSPI: Small, acid-sol 20.8 50 0.0011 23.4 0.9 34 50-92 11-44 (65)
25 PF02209 VHP: Villin headpiece 20.5 46 0.001 20.8 0.6 12 50-61 2-13 (36)
No 1
>PF07939 DUF1685: Protein of unknown function (DUF1685); InterPro: IPR012881 The members of this family are hypothetical eukaryotic proteins of unknown function. The region in question is approximately 100 amino acid residues long.
Probab=99.94 E-value=2.9e-28 Score=169.43 Aligned_cols=53 Identities=64% Similarity=1.097 Sum_probs=48.9
Q ss_pred CCchhhHhhhhhhhcCCcCCCCCCCCCcccccccccchhhhhhhccccccccCCC
Q 046700 50 VTDEDLQELKGSIELGFGFQADSPELDPKLTDTLPALGFYCAVNKHYNDRLSRCS 104 (154)
Q Consensus 50 lTD~DleELKGc~DLGFgF~~~~~d~~p~L~~tLPaL~l~~a~~~~~~~~~s~~s 104 (154)
|||+||||||||||||||| ++++.+|+||+|||||++||||||||++..++++
T Consensus 1 lTd~dldELkGc~dLGFgF--~~~~~~p~L~~tlPaL~lyyavn~q~~~~~~~~s 53 (64)
T PF07939_consen 1 LTDDDLDELKGCIDLGFGF--DEEDLDPRLCDTLPALELYYAVNRQYSDHKSRSS 53 (64)
T ss_pred CcHhHHHHHhhhhhhcccc--CccccChHHHhhhHHHHHHHHHHHHhccccCCCC
Confidence 7999999999999999999 6788999999999999999999999999865443
No 2
>KOG4404 consensus Tandem pore domain K+ channel TASK3/THIK-1 [Inorganic ion transport and metabolism]
Probab=44.55 E-value=14 Score=33.61 Aligned_cols=39 Identities=26% Similarity=0.272 Sum_probs=31.5
Q ss_pred CCCcchhHHHHHHHhhccccccccCCCCCCchhhHhhhhhhhc
Q 046700 22 SWAPDAEREEAWLRRKGNHQIRRRRSQSVTDEDLQELKGSIEL 64 (154)
Q Consensus 22 s~s~d~~reeaw~rrk~~~~~~~rrskSlTD~DleELKGc~DL 64 (154)
-|-.|+.+.++|++|+.+.++ .=.+|++|++|+--.+.-
T Consensus 31 Ese~E~~~r~~l~~~~~~~~~----kyn~s~~d~r~~er~i~~ 69 (350)
T KOG4404|consen 31 ESENEARERERLERRLANLKR----KYNLSEEDYRELERVILK 69 (350)
T ss_pred cCcchHHHHHHHHHHHHHHHH----hhCCCHHHHHHHHHHHHh
Confidence 456799999999999987764 345999999999887753
No 3
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=43.75 E-value=5.7 Score=30.58 Aligned_cols=50 Identities=22% Similarity=0.310 Sum_probs=36.5
Q ss_pred cccccCCCcchhHHHHHHHhhccccccccCCCCCCchhhHhhhhhhhc-C-CcC
Q 046700 17 LYKQRSWAPDAEREEAWLRRKGNHQIRRRRSQSVTDEDLQELKGSIEL-G-FGF 68 (154)
Q Consensus 17 l~kq~s~s~d~~reeaw~rrk~~~~~~~rrskSlTD~DleELKGc~DL-G-FgF 68 (154)
+.++...+|.+-| .|+++-...+.+.+..+-.|+.|++-|+-.+.| - +||
T Consensus 7 VA~~~GVs~~TLR--~wE~~GLl~p~r~~G~R~Ys~~dv~rL~~I~~L~~e~G~ 58 (120)
T cd04767 7 VAELLNIHPETLR--IWERHGLIKPARRNGQRLYSNNDLKRLRFIKKLINEKGL 58 (120)
T ss_pred HHHHHCcCHHHHH--HHHHCCCCCCcCCCCcEEECHHHHHHHHHHHHHHHHcCC
Confidence 3456677888888 899874444444456788999999999988777 3 666
No 4
>PF15178 TOM_sub5: Mitochondrial import receptor subunit TOM5 homolog
Probab=40.56 E-value=34 Score=23.14 Aligned_cols=23 Identities=35% Similarity=0.560 Sum_probs=18.0
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHhhhc
Q 046700 123 DPGDGPETVKMRLKQWAQVVACSVRQ 148 (154)
Q Consensus 123 spgD~p~dvK~rLK~WAqaVA~sVrq 148 (154)
.|.-||++||.+.| +-|-++||.
T Consensus 8 ~pk~DPeE~k~kmR---~dvissvrn 30 (51)
T PF15178_consen 8 GPKMDPEEMKRKMR---EDVISSVRN 30 (51)
T ss_pred CCCCCHHHHHHHHH---HHHHHHHHH
Confidence 56779999999987 467777764
No 5
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=38.43 E-value=15 Score=23.86 Aligned_cols=19 Identities=53% Similarity=0.744 Sum_probs=15.2
Q ss_pred CCchhhHhhhhh----------hhcCCcC
Q 046700 50 VTDEDLQELKGS----------IELGFGF 68 (154)
Q Consensus 50 lTD~DleELKGc----------~DLGFgF 68 (154)
||++||.||=|+ ...|+.|
T Consensus 3 LT~~El~elTG~k~~~~Q~~~L~~~Gi~~ 31 (47)
T PF13986_consen 3 LTDEELQELTGYKRPSKQIRWLRRNGIPF 31 (47)
T ss_pred CCHHHHHHHHCCCCHHHHHHHHHHCCCee
Confidence 899999999875 4567776
No 6
>PF05416 Peptidase_C37: Southampton virus-type processing peptidase; InterPro: IPR001665 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C37, (clan PA(C)). The type example is calicivirin from Southampton virus, an endopeptidase that cleaves the polyprotein at sites N-terminal to itself, liberating the polyprotein helicase. Southampton virus is a positive-stranded ssRNA virus belonging to the Caliciviruses, which are viruses that cause gastroenteritis. The calicivirus genome contains two open reading frames, ORF1 and ORF2. ORF1 encodes a non-structural polypeptide, which has RNA helicase, cysteine protease and RNA polymerase activity []. The regions of the polyprotein in which these activities lie are similar to proteins produced by the picornaviruses []. ORF2 encodes a structural, capsid protein. Two different families of caliciviruses can be distinguished on the basis of sequence similarity, namely the Norwalk-like viruses or small round structured viruses (SRSVs), and those classed as non-SRSVs.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 2FYQ_A 2FYR_A 1WQS_D 4ASH_A 2IPH_B.
Probab=37.00 E-value=11 Score=35.59 Aligned_cols=19 Identities=32% Similarity=0.377 Sum_probs=0.0
Q ss_pred CCCCCCchhhHhhhhhhhc
Q 046700 46 RSQSVTDEDLQELKGSIEL 64 (154)
Q Consensus 46 rskSlTD~DleELKGc~DL 64 (154)
++|.|||+|+||-|-.++=
T Consensus 249 s~rGLSDEEYDEyKkiREe 267 (535)
T PF05416_consen 249 SSRGLSDEEYDEYKKIREE 267 (535)
T ss_dssp -------------------
T ss_pred cccCCChhHHHHHHHHHHH
Confidence 4789999999999877654
No 7
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=35.01 E-value=38 Score=21.79 Aligned_cols=45 Identities=27% Similarity=0.350 Sum_probs=29.4
Q ss_pred ccccCCCcchhHHHHHHHhhccccc-c-ccCCCCCCchhhHhhhhhhhc
Q 046700 18 YKQRSWAPDAEREEAWLRRKGNHQI-R-RRRSQSVTDEDLQELKGSIEL 64 (154)
Q Consensus 18 ~kq~s~s~d~~reeaw~rrk~~~~~-~-~rrskSlTD~DleELKGc~DL 64 (154)
.+....++.+-| .|.++-+.... + ....+..|+.|+++|+..+.|
T Consensus 7 a~~~gvs~~tlr--~w~~~~g~~~~~r~~~~~r~yt~~~v~~l~~i~~l 53 (68)
T cd01104 7 ARLTGVSPDTLR--AWERRYGLPAPQRTDGGHRLYSEADVARLRLIRRL 53 (68)
T ss_pred HHHHCcCHHHHH--HHHHhCCCCCCCcCCCCCeecCHHHHHHHHHHHHH
Confidence 445566666666 58766444332 1 235688999999998877766
No 8
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.67 E-value=16 Score=27.64 Aligned_cols=27 Identities=30% Similarity=0.492 Sum_probs=21.6
Q ss_pred hhhhhcCCcCCCCCCCCCcccccccccchhh
Q 046700 59 KGSIELGFGFQADSPELDPKLTDTLPALGFY 89 (154)
Q Consensus 59 KGc~DLGFgF~~~~~d~~p~L~~tLPaL~l~ 89 (154)
+|.-+|||+| +.+.| +++-.+||.++.
T Consensus 19 ~~l~e~g~~v---~~eGD-~ivas~pgis~i 45 (96)
T COG4004 19 RGLSELGWTV---SEEGD-RIVASSPGISRI 45 (96)
T ss_pred HHHHHhCeeE---eeccc-EEEEecCCceEE
Confidence 5677899999 45555 999999999864
No 9
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=32.15 E-value=26 Score=23.32 Aligned_cols=23 Identities=22% Similarity=0.471 Sum_probs=15.1
Q ss_pred CCCCCCchhhHhhhhhhhcCCcC
Q 046700 46 RSQSVTDEDLQELKGSIELGFGF 68 (154)
Q Consensus 46 rskSlTD~DleELKGc~DLGFgF 68 (154)
|.+.|||.|--.|-+..+|||-.
T Consensus 1 RG~~Lt~~Eqaqid~m~qlG~s~ 23 (50)
T PF11427_consen 1 RGKTLTDAEQAQIDVMHQLGMSL 23 (50)
T ss_dssp -S----HHHHHHHHHHHHTT--H
T ss_pred CCCcCCHHHHHHHHHHHHhchhH
Confidence 56889999999999999999986
No 10
>PF04533 Herpes_U44: Herpes virus U44 protein; InterPro: IPR007619 This entry represents proteins from dsDNA beta-herpesvirinae and gamma-herpesvirinae viruses. The function is not known, and the proteins are named variously as U44, BSRF1, UL71, and M71. The entry also includes BSRF1.
Probab=31.96 E-value=23 Score=30.09 Aligned_cols=18 Identities=33% Similarity=0.431 Sum_probs=16.5
Q ss_pred chhhHhhhhhhhcCCcCC
Q 046700 52 DEDLQELKGSIELGFGFQ 69 (154)
Q Consensus 52 D~DleELKGc~DLGFgF~ 69 (154)
|.+.+||+.|+|+||.-+
T Consensus 31 ~~~~~~l~~ei~~~~ppG 48 (210)
T PF04533_consen 31 DVCPERLQAEIEMGFPPG 48 (210)
T ss_pred ccCHHHHHHHHHccCCCC
Confidence 899999999999999864
No 11
>PF08920 SF3b1: Splicing factor 3B subunit 1; InterPro: IPR015016 This group of proteins consists of several eukaryotic splicing factor 3B subunit 1 proteins, which associate with p14 through a C terminus beta-strand that interacts with beta-3 of the p14 RNA recognition motif (RRM) beta-sheet, which is in turn connected to an alpha-helix by a loop that makes extensive contacts with both the shorter C-terminal helix and RRM of p14. This subunit is required for 'A' splicing complex assembly (formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA) and 'E' splicing complex assembly []. ; PDB: 2FHO_A 3LQV_P 2PEH_D 2F9J_P 2F9D_Q.
Probab=29.32 E-value=26 Score=27.89 Aligned_cols=30 Identities=23% Similarity=0.549 Sum_probs=17.5
Q ss_pred CCcchhHHHHHHHhhccccccccCCCCCCchhhHhh
Q 046700 23 WAPDAEREEAWLRRKGNHQIRRRRSQSVTDEDLQEL 58 (154)
Q Consensus 23 ~s~d~~reeaw~rrk~~~~~~~rrskSlTD~DleEL 58 (154)
+.|+..---.|++=-. .|.+-|||+|||+|
T Consensus 66 mtp~~~~~~~~~~eid------~RNrpLTDEELD~m 95 (144)
T PF08920_consen 66 MTPEQYQAMRWEKEID------ERNRPLTDEELDAM 95 (144)
T ss_dssp --HHHHHHHHHHHHHH------HCTS-S-HHHHHHT
T ss_pred cChhhhhhhccccchh------hccCcCCHHHHHHh
Confidence 5666666666665332 34567999999998
No 12
>PF03047 ComC: COMC family; InterPro: IPR004288 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. This family consists of streptococcal competence stimulating peptide precursors, which are generally up to 50 amino acid residues long. In all the members of this family, the leader sequence is cleaved after two conserved glycine residues; thus the leader sequence is of the double- glycine type []. Competence stimulating peptides (CSP) are small (less than 25 amino acid residues) cationic peptides. The N-terminal amino acid residue is negatively charged, either glutamate or aspartate. The C-terminal end is positively charged. The third residue is also positively charged: a highly conserved arginine []. Some COMC proteins and their precursors (not included in this family) do not fully follow the above description. Functionally, CSP act as pheromones, stimulating competence for genetic transformation in streptococci. In streptococci, the (CSP mediated) competence response requires exponential cell growth at a critical density, a relatively simple requirement when compared to the stationary-phase requirement of Haemophilus, or the late-logarithmic- phase of Bacillus []. All bacteria induced to competence by a particular CSP are said to belong to the same pherotype, because each CSP is recognised by a specific receptor (the signalling domain of a histidine kinase ComD). Pherotypes are not necessarily species-specific. In addition, an organism may change pherotype. There are two possible mechanisms for pherotype switching: horizontal gene transfer, and accumulation of point mutations. The biological significance of pherotypes and pherotype switching is not definitively determined. Pherotype switching occurs frequently enough in naturally competent streptococci to suggest that it may be an important contributor to genetic exchange between different bacterial species []. This entry also includes proteins that form bacteriocin-like propetides with a glycine-glycine cleavage site. The bacteriocin is initially formed as a pre-propeptide and upon cleavage at the glycine-glycine cleavage site, a leader peptide and the propeptide would be formed. The propeptide then undergoes posttranslational modification before becoming functional [].; GO: 0005186 pheromone activity; PDB: 2I2J_A 2I2H_A 2A1C_A.
Probab=28.95 E-value=19 Score=22.11 Aligned_cols=14 Identities=43% Similarity=0.800 Sum_probs=0.0
Q ss_pred CCCCCchhhHhhhh
Q 046700 47 SQSVTDEDLQELKG 60 (154)
Q Consensus 47 skSlTD~DleELKG 60 (154)
=+-|||.||+++.|
T Consensus 11 F~~lt~~eL~~I~G 24 (32)
T PF03047_consen 11 FEELTEEELQEIQG 24 (32)
T ss_dssp --------------
T ss_pred HhcCCHHHHhhccC
Confidence 46799999999988
No 13
>PF15636 Tox-GHH: GHH signature containing HNH/Endo VII superfamily nuclease toxin
Probab=28.26 E-value=43 Score=24.02 Aligned_cols=31 Identities=23% Similarity=0.309 Sum_probs=24.0
Q ss_pred HHHHHHHhhccccccccCCCCCCchhhHhhh
Q 046700 29 REEAWLRRKGNHQIRRRRSQSVTDEDLQELK 59 (154)
Q Consensus 29 reeaw~rrk~~~~~~~rrskSlTD~DleELK 59 (154)
-..||.+=|.........++..|+.|.+||-
T Consensus 16 v~~aW~~Er~~v~~g~~gtr~Wt~~Ek~ell 46 (79)
T PF15636_consen 16 VRRAWEQERQLVRSGEEGTRNWTEEEKQELL 46 (79)
T ss_pred HHHHHHHHHHHHHcCCCCcCccCHHHHHHHH
Confidence 3578888776665556678999999999984
No 14
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=26.84 E-value=43 Score=23.18 Aligned_cols=23 Identities=26% Similarity=0.212 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHhhhcccCCC
Q 046700 131 VKMRLKQWAQVVACSVRQFSGEL 153 (154)
Q Consensus 131 vK~rLK~WAqaVA~sVrq~s~~~ 153 (154)
|..+|+.|.+.|.-.||.-.|.+
T Consensus 1 M~~~l~~~~~~~~~~~r~l~G~~ 23 (65)
T PF04328_consen 1 MFQRLRRAWRRVRWYARLLVGEP 23 (65)
T ss_pred ChHHHHHHHHHHHHHHHHhcCcH
Confidence 67899999999999999988865
No 15
>cd07684 F-BAR_srGAP3 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Protein 3. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Slit-Robo GTPase Activating Proteins (srGAPs) are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are secreted proteins that control axon guidance and the migration of neurons and leukocytes. Vertebrates contain three isoforms of srGAPs. srGAP3, also called MEGAP (MEntal disorder associated GTPase-Activating Protein), is a Rho GAP with activity towards Rac1 and Cdc42. It impacts cell migration by regulating actin and microtubule cytoskeletal dynamics. The association between srGAP3 haploinsufficiency and mental retardation is under debate. srGAP3 contains an N-terminal F-BAR domain, a Rho GAP domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers wit
Probab=25.88 E-value=32 Score=29.98 Aligned_cols=17 Identities=29% Similarity=0.464 Sum_probs=13.8
Q ss_pred chhhHhhhhhhhcCCcC
Q 046700 52 DEDLQELKGSIELGFGF 68 (154)
Q Consensus 52 D~DleELKGc~DLGFgF 68 (154)
..||-+|=-|+||||--
T Consensus 234 ~~dl~~l~~c~DlG~h~ 250 (253)
T cd07684 234 IHDVSDLIDCCDLGFHA 250 (253)
T ss_pred HhhHHHHHHHHhccchh
Confidence 35788899999999953
No 16
>PF01180 DHO_dh: Dihydroorotate dehydrogenase; InterPro: IPR012135 Dihydroorotate dehydrogenase (DHOD), also known as dihydroorotate oxidase, catalyses the fourth step in de novo pyrimidine biosynthesis, the stereospecific oxidation of (S)-dihydroorotate to orotate, which is the only redox reaction in this pathway. DHODs can be divided into two mains classes: class 1 cytosolic enzymes found primarily in Gram-positive bacteria, and class 2 membrane-associated enzymes found primarily in eukaryotic mitochondria and Gram-negative bacteria []. The class 1 DHODs can be further divided into subclasses 1A and 1B, which differ in their structural organisation and use of electron acceptors. The 1A enzyme is a homodimer of two PyrD subunits where each subunit forms a TIM barrel fold with a bound FMN cofactor located near the top of the barrel []. Fumarate is the natural electron acceptor for this enzyme. The 1B enzyme, in contrast is a heterotetramer composed of a central, FMN-containing, PyrD homodimer resembling the 1A homodimer, and two additional PyrK subunits which contain FAD and a 2Fe-2S cluster []. These additional groups allow the enzyme to use NAD(+) as its natural electron acceptor. The class 2 membrane-associated enzymes are monomers which have the FMN-containing TIM barrel domain found in the class 1 PyrD subunit, and an additional N-terminal alpha helical domain [, ]. These enzymes use respiratory quinones as the physiological electron acceptor. This entry represents the FMN-binding subunit common to all classes of dihydroorotate dehydrogenase.; GO: 0004152 dihydroorotate dehydrogenase activity, 0006222 UMP biosynthetic process, 0055114 oxidation-reduction process; PDB: 3GYE_A 3GZ3_A 3MHU_B 3MJY_A 3TQ0_A 2B4G_C 1EP3_A 1EP2_A 1EP1_A 3I6R_A ....
Probab=25.46 E-value=30 Score=29.00 Aligned_cols=17 Identities=35% Similarity=0.634 Sum_probs=15.2
Q ss_pred chhhHhhhhhhhcCCcC
Q 046700 52 DEDLQELKGSIELGFGF 68 (154)
Q Consensus 52 D~DleELKGc~DLGFgF 68 (154)
+-+.++++.++|+||||
T Consensus 22 ~~~~~~~~~~~~~G~Ga 38 (295)
T PF01180_consen 22 DKNGEEIKRLFDAGFGA 38 (295)
T ss_dssp STSSHHHHHHHHHSSSE
T ss_pred CCCchhhhhhhcCCccE
Confidence 56678999999999998
No 17
>PF03869 Arc: Arc-like DNA binding domain; InterPro: IPR005569 Arc repressor act by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove [].; GO: 0003677 DNA binding; PDB: 3QOQ_D 1MNT_B 1QTG_B 1BDV_A 1PAR_C 1BDT_C 1ARR_B 1MYL_F 1MYK_A 1NLA_B ....
Probab=24.97 E-value=56 Score=21.28 Aligned_cols=14 Identities=43% Similarity=0.627 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHH
Q 046700 128 PETVKMRLKQWAQV 141 (154)
Q Consensus 128 p~dvK~rLK~WAqa 141 (154)
|++||++||.+|..
T Consensus 12 P~~l~~~lk~~A~~ 25 (50)
T PF03869_consen 12 PEELKEKLKERAEE 25 (50)
T ss_dssp EHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHH
Confidence 68999999999974
No 18
>TIGR03577 EF_0830 conserved hypothetical protein EF_0830/AHA_3911. Members of this family of small (about 120 amino acid), relatively rare proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The function is unknown.
Probab=22.72 E-value=7.6 Score=30.03 Aligned_cols=33 Identities=39% Similarity=0.561 Sum_probs=21.6
Q ss_pred CCCCchhhHhhhhhhhcCCcCCCCCCCCCccccc
Q 046700 48 QSVTDEDLQELKGSIELGFGFQADSPELDPKLTD 81 (154)
Q Consensus 48 kSlTD~DleELKGc~DLGFgF~~~~~d~~p~L~~ 81 (154)
||+-+-----=.||.=|||||= |.|++..+|+.
T Consensus 77 RSveeGvTAi~eG~~VlGFGFm-D~EeLG~rlve 109 (115)
T TIGR03577 77 RSVEEGVTAINEGKNVLGFGFM-DKEELGKRLTE 109 (115)
T ss_pred cchhhhHHHHhcCCeEEeeccc-cHHHHHHHHHH
Confidence 4554443344469999999995 55666666654
No 19
>cd07682 F-BAR_srGAP2 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Protein 2. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Slit-Robo GTPase Activating Proteins (srGAPs) are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are secreted proteins that control axon guidance and the migration of neurons and leukocytes. Vertebrates contain three isoforms of srGAPs. srGAP2 is expressed in zones of neuronal differentiation. It plays a role in the regeneration of neurons and axons. srGAP2 contains an N-terminal F-BAR domain, a Rho GAP domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=22.23 E-value=41 Score=29.51 Aligned_cols=16 Identities=31% Similarity=0.578 Sum_probs=13.1
Q ss_pred hhhHhhhhhhhcCCcC
Q 046700 53 EDLQELKGSIELGFGF 68 (154)
Q Consensus 53 ~DleELKGc~DLGFgF 68 (154)
.|+-.|=-|+||||--
T Consensus 245 ~dlsdLiDC~DlGfh~ 260 (263)
T cd07682 245 HDLSDLIDCCDLGYHA 260 (263)
T ss_pred hhhHHHHHHHhccchh
Confidence 4777888999999953
No 20
>PF11673 DUF3269: Protein of unknown function (DUF3269); InterPro: IPR021687 This entry is represented by Bacteriophage 92, Orf70. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.13 E-value=49 Score=23.97 Aligned_cols=19 Identities=26% Similarity=0.532 Sum_probs=16.9
Q ss_pred CCCCCCchhhHhhhhhhhc
Q 046700 46 RSQSVTDEDLQELKGSIEL 64 (154)
Q Consensus 46 rskSlTD~DleELKGc~DL 64 (154)
-.+-+||+||+++||--.|
T Consensus 40 ~~~~~T~~El~~fK~~~~L 58 (73)
T PF11673_consen 40 INKNMTDDELKKFKAKHNL 58 (73)
T ss_pred ccCcccHHHHHHHHHHHhh
Confidence 3688999999999998887
No 21
>PLN02826 dihydroorotate dehydrogenase
Probab=22.12 E-value=44 Score=30.43 Aligned_cols=18 Identities=39% Similarity=0.872 Sum_probs=15.6
Q ss_pred CchhhHhhhhhhhcCCcC
Q 046700 51 TDEDLQELKGSIELGFGF 68 (154)
Q Consensus 51 TD~DleELKGc~DLGFgF 68 (154)
.|-+-+++.++.+|||||
T Consensus 93 ~dkn~~~~~~l~~lGfG~ 110 (409)
T PLN02826 93 FDKNAEAVEGLLGLGFGF 110 (409)
T ss_pred cCCCHHHHHHHHhcCCCe
Confidence 466778999999999998
No 22
>PF14272 Gly_rich_SFCGS: Glycine-rich SFCGS
Probab=21.97 E-value=8.1 Score=29.88 Aligned_cols=33 Identities=36% Similarity=0.541 Sum_probs=21.1
Q ss_pred CCCCchhhHhhhhhhhcCCcCCCCCCCCCccccc
Q 046700 48 QSVTDEDLQELKGSIELGFGFQADSPELDPKLTD 81 (154)
Q Consensus 48 kSlTD~DleELKGc~DLGFgF~~~~~d~~p~L~~ 81 (154)
||+-+-----=.||.=|||||= |.|++..+|+.
T Consensus 77 RSv~~GvTAi~~G~~VlGFGFm-D~EeLG~rlve 109 (115)
T PF14272_consen 77 RSVDEGVTAINEGKKVLGFGFM-DKEELGRRLVE 109 (115)
T ss_pred cchhhhHHHHHcCCeEEeeccc-cHHHHHHHHHH
Confidence 4443333333459999999995 56667777654
No 23
>smart00153 VHP Villin headpiece domain.
Probab=21.74 E-value=45 Score=20.72 Aligned_cols=12 Identities=42% Similarity=0.758 Sum_probs=9.9
Q ss_pred CCchhhHhhhhh
Q 046700 50 VTDEDLQELKGS 61 (154)
Q Consensus 50 lTD~DleELKGc 61 (154)
|+|+||++|=|+
T Consensus 2 LsdeeF~~vfgm 13 (36)
T smart00153 2 LSDEDFEEVFGM 13 (36)
T ss_pred CCHHHHHHHHCC
Confidence 789999988665
No 24
>PF14098 SSPI: Small, acid-soluble spore protein I
Probab=20.79 E-value=50 Score=23.35 Aligned_cols=34 Identities=32% Similarity=0.394 Sum_probs=23.7
Q ss_pred CCchhhHhhhhhhhcCCcCCCCCCCCCcccccccccchhhhhh
Q 046700 50 VTDEDLQELKGSIELGFGFQADSPELDPKLTDTLPALGFYCAV 92 (154)
Q Consensus 50 lTD~DleELKGc~DLGFgF~~~~~d~~p~L~~tLPaL~l~~a~ 92 (154)
|+.-.-+||++.|+=+-.= .=-.+||||..+|-+
T Consensus 11 v~g~s~~el~~~I~daI~s---------gEE~~LPGLGVlFE~ 44 (65)
T PF14098_consen 11 VKGSSKEELKDTIEDAIQS---------GEEKALPGLGVLFEV 44 (65)
T ss_pred ccCCCHHHHHHHHHHHHhc---------cchhcCCchHHHHHH
Confidence 5556678888888765442 112489999999866
No 25
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition []. An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core []. ; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1ZV6_A 1QZP_A 1UND_A 2PPZ_A 3TJW_B 1YU8_X 2JM0_A 1WY4_A 3MYC_A 1YU5_X ....
Probab=20.54 E-value=46 Score=20.77 Aligned_cols=12 Identities=33% Similarity=0.692 Sum_probs=8.5
Q ss_pred CCchhhHhhhhh
Q 046700 50 VTDEDLQELKGS 61 (154)
Q Consensus 50 lTD~DleELKGc 61 (154)
|||+||++|=|+
T Consensus 2 Lsd~dF~~vFgm 13 (36)
T PF02209_consen 2 LSDEDFEKVFGM 13 (36)
T ss_dssp S-HHHHHHHHSS
T ss_pred cCHHHHHHHHCC
Confidence 788999888554
Done!