Query 031189
Match_columns 164
No_of_seqs 116 out of 126
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 10:31:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031189.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031189hhsearch_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 2.3E-27 4.9E-32 166.8 4.5 48 55-108 1-48 (64)
2 KOG4404 Tandem pore domain K+ 42.1 14 0.0003 33.9 1.4 39 29-69 31-69 (350)
3 PF14098 SSPI: Small, acid-sol 34.6 27 0.00059 25.0 1.6 34 55-101 11-44 (65)
4 PF13986 DUF4224: Domain of un 34.4 18 0.0004 23.7 0.7 13 55-67 3-15 (47)
5 PF14272 Gly_rich_SFCGS: Glyci 33.2 7.4 0.00016 30.5 -1.5 34 53-91 77-110 (115)
6 TIGR03577 EF_0830 conserved hy 32.8 7.5 0.00016 30.4 -1.6 34 53-91 77-110 (115)
7 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 32.4 32 0.0007 23.2 1.6 24 51-74 1-24 (50)
8 PF04533 Herpes_U44: Herpes vi 30.2 33 0.00071 29.6 1.7 34 40-74 14-48 (210)
9 COG4004 Uncharacterized protei 29.3 15 0.00033 28.2 -0.4 26 64-97 19-44 (96)
10 PF08920 SF3b1: Splicing facto 29.3 28 0.00061 28.0 1.1 31 30-64 66-96 (144)
11 cd04767 HTH_HspR-like_MBC Heli 28.5 27 0.00057 27.2 0.8 60 24-93 7-71 (120)
12 PF03047 ComC: COMC family; I 26.5 22 0.00047 22.1 0.0 14 52-65 11-24 (32)
13 PF03869 Arc: Arc-like DNA bin 24.7 60 0.0013 21.4 1.9 14 140-153 12-25 (50)
14 PF01180 DHO_dh: Dihydroorotat 23.9 39 0.00084 28.6 1.0 18 57-74 22-39 (295)
15 cd07684 F-BAR_srGAP3 The F-BAR 23.2 43 0.00094 29.5 1.2 17 57-73 234-250 (253)
16 PF15178 TOM_sub5: Mitochondri 23.2 1E+02 0.0023 21.1 2.8 23 134-160 8-30 (51)
17 PF11673 DUF3269: Protein of u 22.6 59 0.0013 23.9 1.6 20 50-69 39-58 (73)
18 PF14216 DUF4326: Domain of un 22.1 23 0.00049 26.0 -0.6 41 30-71 30-71 (86)
19 PF15652 Tox-SHH: HNH/Endo VII 21.9 90 0.002 24.1 2.6 33 39-71 50-83 (100)
20 PLN02826 dihydroorotate dehydr 21.0 51 0.0011 30.4 1.3 37 56-92 93-133 (409)
21 PF05416 Peptidase_C37: Southa 20.7 33 0.00072 33.0 0.0 18 51-68 249-266 (535)
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=2.3e-27 Score=166.80 Aligned_cols=48 Identities=67% Similarity=1.191 Sum_probs=46.0
Q ss_pred CChhhHHHhhhhhhhcCCCCCCCCCCCccccchhhhhhhhhhHHHHhhcccCCC
Q 031189 55 VTDEDVDELKACIELGFGFDSPAGPDQDAADQRLSDTLPALELYYAVNKHYLSK 108 (164)
Q Consensus 55 lTD~DleELKGc~DLGFgF~~~~~~d~ed~~p~L~~tLPaL~l~~av~~~~~~~ 108 (164)
|||+|||||||||||||||++ ++.+|+||+|||||++||||||+|++.
T Consensus 1 lTd~dldELkGc~dLGFgF~~------~~~~p~L~~tlPaL~lyyavn~q~~~~ 48 (64)
T PF07939_consen 1 LTDDDLDELKGCIDLGFGFDE------EDLDPRLCDTLPALELYYAVNRQYSDH 48 (64)
T ss_pred CcHhHHHHHhhhhhhccccCc------cccChHHHhhhHHHHHHHHHHHHhccc
Confidence 799999999999999999986 789999999999999999999999987
No 2
>KOG4404 consensus Tandem pore domain K+ channel TASK3/THIK-1 [Inorganic ion transport and metabolism]
Probab=42.09 E-value=14 Score=33.94 Aligned_cols=39 Identities=28% Similarity=0.313 Sum_probs=32.3
Q ss_pred CCCCccchHHHHHhhhccCCCCCCCCCChhhHHHhhhhhhh
Q 031189 29 SWSPDVYRDEAWLRRKGNFKNKRSKSVTDEDVDELKACIEL 69 (164)
Q Consensus 29 s~spd~~rdeaW~rrk~~~~~rr~KSlTD~DleELKGc~DL 69 (164)
-|-.|+.+.++|++|+.+.+++-. +|++|++|+--.+.-
T Consensus 31 Ese~E~~~r~~l~~~~~~~~~kyn--~s~~d~r~~er~i~~ 69 (350)
T KOG4404|consen 31 ESENEARERERLERRLANLKRKYN--LSEEDYRELERVILK 69 (350)
T ss_pred cCcchHHHHHHHHHHHHHHHHhhC--CCHHHHHHHHHHHHh
Confidence 456799999999999988776554 999999999887753
No 3
>PF14098 SSPI: Small, acid-soluble spore protein I
Probab=34.64 E-value=27 Score=24.99 Aligned_cols=34 Identities=29% Similarity=0.455 Sum_probs=23.1
Q ss_pred CChhhHHHhhhhhhhcCCCCCCCCCCCccccchhhhhhhhhhHHHHh
Q 031189 55 VTDEDVDELKACIELGFGFDSPAGPDQDAADQRLSDTLPALELYYAV 101 (164)
Q Consensus 55 lTD~DleELKGc~DLGFgF~~~~~~d~ed~~p~L~~tLPaL~l~~av 101 (164)
|+.-.-+|||+.|+=+-.=. | -.+||||..+|-+
T Consensus 11 v~g~s~~el~~~I~daI~sg-------E------E~~LPGLGVlFE~ 44 (65)
T PF14098_consen 11 VKGSSKEELKDTIEDAIQSG-------E------EKALPGLGVLFEV 44 (65)
T ss_pred ccCCCHHHHHHHHHHHHhcc-------c------hhcCCchHHHHHH
Confidence 45556788888887643322 1 2489999998865
No 4
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=34.39 E-value=18 Score=23.72 Aligned_cols=13 Identities=38% Similarity=0.606 Sum_probs=11.1
Q ss_pred CChhhHHHhhhhh
Q 031189 55 VTDEDVDELKACI 67 (164)
Q Consensus 55 lTD~DleELKGc~ 67 (164)
||++||.||-|+.
T Consensus 3 LT~~El~elTG~k 15 (47)
T PF13986_consen 3 LTDEELQELTGYK 15 (47)
T ss_pred CCHHHHHHHHCCC
Confidence 8999999998853
No 5
>PF14272 Gly_rich_SFCGS: Glycine-rich SFCGS
Probab=33.23 E-value=7.4 Score=30.47 Aligned_cols=34 Identities=29% Similarity=0.439 Sum_probs=23.3
Q ss_pred CCCChhhHHHhhhhhhhcCCCCCCCCCCCccccchhhhh
Q 031189 53 KSVTDEDVDELKACIELGFGFDSPAGPDQDAADQRLSDT 91 (164)
Q Consensus 53 KSlTD~DleELKGc~DLGFgF~~~~~~d~ed~~p~L~~t 91 (164)
||+-+-----=.||.=|||||= |.|++..||+..
T Consensus 77 RSv~~GvTAi~~G~~VlGFGFm-----D~EeLG~rlve~ 110 (115)
T PF14272_consen 77 RSVDEGVTAINEGKKVLGFGFM-----DKEELGRRLVEA 110 (115)
T ss_pred cchhhhHHHHHcCCeEEeeccc-----cHHHHHHHHHHH
Confidence 4443333333458999999996 678888888754
No 6
>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=32.84 E-value=7.5 Score=30.44 Aligned_cols=34 Identities=29% Similarity=0.456 Sum_probs=23.8
Q ss_pred CCCChhhHHHhhhhhhhcCCCCCCCCCCCccccchhhhh
Q 031189 53 KSVTDEDVDELKACIELGFGFDSPAGPDQDAADQRLSDT 91 (164)
Q Consensus 53 KSlTD~DleELKGc~DLGFgF~~~~~~d~ed~~p~L~~t 91 (164)
||+-+-----=.||.=|||||= |.|++..+|+..
T Consensus 77 RSveeGvTAi~eG~~VlGFGFm-----D~EeLG~rlvea 110 (115)
T TIGR03577 77 RSVEEGVTAINEGKNVLGFGFM-----DKEELGKRLTEA 110 (115)
T ss_pred cchhhhHHHHhcCCeEEeeccc-----cHHHHHHHHHHH
Confidence 4544433334469999999996 678888888754
No 7
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=32.45 E-value=32 Score=23.18 Aligned_cols=24 Identities=25% Similarity=0.524 Sum_probs=15.4
Q ss_pred CCCCCChhhHHHhhhhhhhcCCCC
Q 031189 51 RSKSVTDEDVDELKACIELGFGFD 74 (164)
Q Consensus 51 r~KSlTD~DleELKGc~DLGFgF~ 74 (164)
|.+.|||.|=-.|-+..+|||-..
T Consensus 1 RG~~Lt~~Eqaqid~m~qlG~s~~ 24 (50)
T PF11427_consen 1 RGKTLTDAEQAQIDVMHQLGMSLR 24 (50)
T ss_dssp -S----HHHHHHHHHHHHTT--HH
T ss_pred CCCcCCHHHHHHHHHHHHhchhHH
Confidence 568899999999999999987664
No 8
>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=30.16 E-value=33 Score=29.57 Aligned_cols=34 Identities=29% Similarity=0.272 Sum_probs=22.4
Q ss_pred HHhhhccCCC-CCCCCCChhhHHHhhhhhhhcCCCC
Q 031189 40 WLRRKGNFKN-KRSKSVTDEDVDELKACIELGFGFD 74 (164)
Q Consensus 40 W~rrk~~~~~-rr~KSlTD~DleELKGc~DLGFgF~ 74 (164)
|.+-|-..+= +..-+. |.+.+||+.|+|+||.-.
T Consensus 14 ~~fg~~~~~Y~~L~~~~-~~~~~~l~~ei~~~~ppG 48 (210)
T PF04533_consen 14 WPFGKPRADYVLLQDSE-DVCPERLQAEIEMGFPPG 48 (210)
T ss_pred cccCCCCCCeeecCCcc-ccCHHHHHHHHHccCCCC
Confidence 5554433321 333344 899999999999998753
No 9
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=29.32 E-value=15 Score=28.15 Aligned_cols=26 Identities=23% Similarity=0.477 Sum_probs=21.1
Q ss_pred hhhhhhcCCCCCCCCCCCccccchhhhhhhhhhH
Q 031189 64 KACIELGFGFDSPAGPDQDAADQRLSDTLPALEL 97 (164)
Q Consensus 64 KGc~DLGFgF~~~~~~d~ed~~p~L~~tLPaL~l 97 (164)
+|.-+|||+|++ +.+ +++-.+||.+.
T Consensus 19 ~~l~e~g~~v~~-------eGD-~ivas~pgis~ 44 (96)
T COG4004 19 RGLSELGWTVSE-------EGD-RIVASSPGISR 44 (96)
T ss_pred HHHHHhCeeEee-------ccc-EEEEecCCceE
Confidence 577889999983 455 99999999875
No 10
>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=29.25 E-value=28 Score=28.04 Aligned_cols=31 Identities=26% Similarity=0.652 Sum_probs=17.8
Q ss_pred CCCccchHHHHHhhhccCCCCCCCCCChhhHHHhh
Q 031189 30 WSPDVYRDEAWLRRKGNFKNKRSKSVTDEDVDELK 64 (164)
Q Consensus 30 ~spd~~rdeaW~rrk~~~~~rr~KSlTD~DleELK 64 (164)
+.|+..---.|++--. .|.|-|||+|||+|=
T Consensus 66 mtp~~~~~~~~~~eid----~RNrpLTDEELD~mL 96 (144)
T PF08920_consen 66 MTPEQYQAMRWEKEID----ERNRPLTDEELDAML 96 (144)
T ss_dssp --HHHHHHHHHHHHHH----HCTS-S-HHHHHHTS
T ss_pred cChhhhhhhccccchh----hccCcCCHHHHHHhC
Confidence 5566666566665321 456779999999973
No 11
>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=28.53 E-value=27 Score=27.21 Aligned_cols=60 Identities=18% Similarity=0.369 Sum_probs=41.5
Q ss_pred cccccCCCCccchHHHHHhhhccC-C--CCCCCCCChhhHHHhhhhhhh-c-CCCCCCCCCCCccccchhhhhhh
Q 031189 24 LRKQHSWSPDVYRDEAWLRRKGNF-K--NKRSKSVTDEDVDELKACIEL-G-FGFDSPAGPDQDAADQRLSDTLP 93 (164)
Q Consensus 24 L~kq~s~spd~~rdeaW~rrk~~~-~--~rr~KSlTD~DleELKGc~DL-G-FgF~~~~~~d~ed~~p~L~~tLP 93 (164)
+.+....+|.+.| .|++. +.. . ++..+-.|+.|+.-|+-.+.| - .||+ -+++..+.+.+|
T Consensus 7 VA~~~GVs~~TLR--~wE~~-GLl~p~r~~G~R~Ys~~dv~rL~~I~~L~~e~G~~-------l~eI~~~L~l~~ 71 (120)
T cd04767 7 VAELLNIHPETLR--IWERH-GLIKPARRNGQRLYSNNDLKRLRFIKKLINEKGLN-------IAGVKQILSMYP 71 (120)
T ss_pred HHHHHCcCHHHHH--HHHHC-CCCCCcCCCCcEEECHHHHHHHHHHHHHHHHcCCC-------HHHHHHHHHhCc
Confidence 3456677788888 78886 433 2 244577999999999988887 3 6776 355666666555
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=26.47 E-value=22 Score=22.09 Aligned_cols=14 Identities=21% Similarity=0.548 Sum_probs=0.0
Q ss_pred CCCCChhhHHHhhh
Q 031189 52 SKSVTDEDVDELKA 65 (164)
Q Consensus 52 ~KSlTD~DleELKG 65 (164)
-+-|||.||+++.|
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 36799999999998
No 13
>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=24.73 E-value=60 Score=21.38 Aligned_cols=14 Identities=29% Similarity=0.615 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHH
Q 031189 140 PQTVKTRLRQWAQV 153 (164)
Q Consensus 140 p~dvK~rLK~WAqa 153 (164)
|++||++||.+|..
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 78999999999975
No 14
>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=23.87 E-value=39 Score=28.65 Aligned_cols=18 Identities=33% Similarity=0.602 Sum_probs=15.5
Q ss_pred hhhHHHhhhhhhhcCCCC
Q 031189 57 DEDVDELKACIELGFGFD 74 (164)
Q Consensus 57 D~DleELKGc~DLGFgF~ 74 (164)
+-+.++++.++|+||||=
T Consensus 22 ~~~~~~~~~~~~~G~Gav 39 (295)
T PF01180_consen 22 DKNGEEIKRLFDAGFGAV 39 (295)
T ss_dssp STSSHHHHHHHHHSSSEE
T ss_pred CCCchhhhhhhcCCccEE
Confidence 556789999999999983
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=23.20 E-value=43 Score=29.54 Aligned_cols=17 Identities=41% Similarity=0.716 Sum_probs=13.7
Q ss_pred hhhHHHhhhhhhhcCCC
Q 031189 57 DEDVDELKACIELGFGF 73 (164)
Q Consensus 57 D~DleELKGc~DLGFgF 73 (164)
..||-+|=-|+||||--
T Consensus 234 ~~dl~~l~~c~DlG~h~ 250 (253)
T cd07684 234 IHDVSDLIDCCDLGFHA 250 (253)
T ss_pred HhhHHHHHHHHhccchh
Confidence 35788889999999854
No 16
>PF15178 TOM_sub5: Mitochondrial import receptor subunit TOM5 homolog
Probab=23.19 E-value=1e+02 Score=21.13 Aligned_cols=23 Identities=35% Similarity=0.614 Sum_probs=16.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHhhhcc
Q 031189 134 GTGENDPQTVKTRLRQWAQVVACSVRQ 160 (164)
Q Consensus 134 spgD~~p~dvK~rLK~WAqaVAcsVrq 160 (164)
.|.-| |++||.+.| +-|-++||.
T Consensus 8 ~pk~D-PeE~k~kmR---~dvissvrn 30 (51)
T PF15178_consen 8 GPKMD-PEEMKRKMR---EDVISSVRN 30 (51)
T ss_pred CCCCC-HHHHHHHHH---HHHHHHHHH
Confidence 35556 999999987 466666664
No 17
>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=22.58 E-value=59 Score=23.88 Aligned_cols=20 Identities=30% Similarity=0.474 Sum_probs=17.7
Q ss_pred CCCCCCChhhHHHhhhhhhh
Q 031189 50 KRSKSVTDEDVDELKACIEL 69 (164)
Q Consensus 50 rr~KSlTD~DleELKGc~DL 69 (164)
.-.+-+||+||+++||-..|
T Consensus 39 ~~~~~~T~~El~~fK~~~~L 58 (73)
T PF11673_consen 39 HINKNMTDDELKKFKAKHNL 58 (73)
T ss_pred cccCcccHHHHHHHHHHHhh
Confidence 44788999999999999888
No 18
>PF14216 DUF4326: Domain of unknown function (DUF4326)
Probab=22.08 E-value=23 Score=26.02 Aligned_cols=41 Identities=22% Similarity=0.354 Sum_probs=29.4
Q ss_pred CCCccchHHHHHhhhccCCCC-CCCCCChhhHHHhhhhhhhcC
Q 031189 30 WSPDVYRDEAWLRRKGNFKNK-RSKSVTDEDVDELKACIELGF 71 (164)
Q Consensus 30 ~spd~~rdeaW~rrk~~~~~r-r~KSlTD~DleELKGc~DLGF 71 (164)
...+..|++|-++=|.-...+ ....+..++++||+| ++||=
T Consensus 30 ~~~~~~R~~~v~~yr~~l~~~~~~~~~~~~~l~~L~G-k~L~C 71 (86)
T PF14216_consen 30 VGEDGDREEAVEKYREWLWGRLRTREILRDALEELRG-KDLGC 71 (86)
T ss_pred CCCCCCHHHHHHHHHHHHHHhccccHHHHHHHHhcCC-CceEe
Confidence 333677888777665544333 677889999999999 78873
No 19
>PF15652 Tox-SHH: HNH/Endo VII superfamily toxin with a SHH signature
Probab=21.94 E-value=90 Score=24.10 Aligned_cols=33 Identities=9% Similarity=0.153 Sum_probs=26.9
Q ss_pred HHHhhhccCCCCCCCCCChhhHHH-hhhhhhhcC
Q 031189 39 AWLRRKGNFKNKRSKSVTDEDVDE-LKACIELGF 71 (164)
Q Consensus 39 aW~rrk~~~~~rr~KSlTD~DleE-LKGc~DLGF 71 (164)
+|..||......++.+..-+||.+ ++=++|-||
T Consensus 50 ~~r~~r~~~g~gkw~t~~~~Ef~~~~~eM~dAGV 83 (100)
T PF15652_consen 50 AQRDERTAKGGGKWSTTLQEEFNNSYREMFDAGV 83 (100)
T ss_pred HHHHHHhcCCCCCccchHHHHHHHHHHHHHHcCC
Confidence 788888777666799999999999 777888653
No 20
>PLN02826 dihydroorotate dehydrogenase
Probab=21.05 E-value=51 Score=30.35 Aligned_cols=37 Identities=22% Similarity=0.391 Sum_probs=24.7
Q ss_pred ChhhHHHhhhhhhhcCCCCCCC----CCCCccccchhhhhh
Q 031189 56 TDEDVDELKACIELGFGFDSPA----GPDQDAADQRLSDTL 92 (164)
Q Consensus 56 TD~DleELKGc~DLGFgF~~~~----~~d~ed~~p~L~~tL 92 (164)
.|.+-+++.++.+|||||=+-+ .|-.....||+..+.
T Consensus 93 ~dkn~~~~~~l~~lGfG~vevgTVT~~pq~GNp~PR~frl~ 133 (409)
T PLN02826 93 FDKNAEAVEGLLGLGFGFVEIGSVTPLPQPGNPKPRVFRLR 133 (409)
T ss_pred cCCCHHHHHHHHhcCCCeEEeCCccCCCCCCCCCCcEEecC
Confidence 5667789999999999996533 122234456766555
No 21
>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=20.67 E-value=33 Score=32.97 Aligned_cols=18 Identities=39% Similarity=0.547 Sum_probs=0.0
Q ss_pred CCCCCChhhHHHhhhhhh
Q 031189 51 RSKSVTDEDVDELKACIE 68 (164)
Q Consensus 51 r~KSlTD~DleELKGc~D 68 (164)
++|.|||+|.||-|-.++
T Consensus 249 s~rGLSDEEYDEyKkiRE 266 (535)
T PF05416_consen 249 SSRGLSDEEYDEYKKIRE 266 (535)
T ss_dssp ------------------
T ss_pred cccCCChhHHHHHHHHHH
Confidence 468999999999987664
Done!