Query 032587
Match_columns 137
No_of_seqs 98 out of 100
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 03:23:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032587.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032587hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02341 RcbX: RbcX protein; 100.0 3E-37 6.6E-42 230.0 9.5 77 56-135 7-83 (111)
2 PRK15337 type III secretion sy 64.2 47 0.001 32.1 8.7 73 63-135 494-580 (686)
3 PF12112 DUF3579: Protein of u 59.3 3.6 7.7E-05 30.3 0.3 26 75-100 61-86 (92)
4 PF12234 Rav1p_C: RAVE protein 43.4 61 0.0013 30.9 5.8 71 56-126 481-553 (631)
5 cd02518 GT2_SpsF SpsF is a gly 41.2 35 0.00075 26.5 3.3 29 70-98 196-225 (233)
6 PHA00771 head assembly protein 39.9 19 0.00042 28.6 1.7 18 39-56 62-79 (151)
7 PF02268 TFIIA_gamma_N: Transc 39.6 32 0.00069 22.6 2.4 24 105-128 18-41 (49)
8 cd06258 Peptidase_M3_like The 38.7 1E+02 0.0022 25.8 5.9 60 68-131 6-65 (365)
9 PF12290 DUF3802: Protein of u 37.2 73 0.0016 24.4 4.4 54 83-136 4-81 (113)
10 TIGR02996 rpt_mate_G_obs repea 32.8 59 0.0013 20.9 2.8 27 101-135 1-27 (42)
11 PF14677 FANCI_S3: FANCI solen 32.1 76 0.0016 26.0 4.0 25 85-110 191-215 (219)
12 PF14102 Caps_synth_CapC: Caps 31.2 69 0.0015 24.0 3.4 47 39-85 15-64 (121)
13 PF01820 Dala_Dala_lig_N: D-al 31.0 18 0.00038 26.3 0.2 23 50-80 7-29 (117)
14 TIGR01987 HI0074 nucleotidyltr 30.6 1.4E+02 0.0031 22.4 5.1 36 90-125 66-105 (123)
15 PRK09273 hypothetical protein; 30.6 93 0.002 26.0 4.4 25 101-126 185-209 (211)
16 PRK12720 secretion system appa 29.0 2.2E+02 0.0047 27.7 7.0 29 62-90 479-507 (675)
17 PF08740 BCS1_N: BCS1 N termin 29.0 1.4E+02 0.0031 22.5 4.9 20 82-101 33-52 (187)
18 cd08330 CARD_ASC_NALP1 Caspase 28.3 71 0.0015 22.1 2.9 38 82-122 43-80 (82)
19 PLN02690 Agmatine deiminase 28.2 48 0.001 29.4 2.4 28 41-68 316-343 (374)
20 PF09722 DUF2384: Protein of u 28.2 74 0.0016 19.8 2.7 30 47-80 22-51 (54)
21 PF11039 DUF2824: Protein of u 27.8 20 0.00043 28.6 -0.0 18 39-56 62-79 (151)
22 KOG0501 K+-channel KCNQ [Inorg 27.4 2.3E+02 0.005 28.1 6.9 64 49-125 439-512 (971)
23 PF11724 YvbH_ext: YvbH-like o 26.0 51 0.0011 22.5 1.7 31 75-105 24-55 (61)
24 cd00948 FBP_aldolase_I_a Fruct 25.8 36 0.00078 30.2 1.2 15 46-60 251-269 (330)
25 cd08791 DED_DEDD2 Death Effect 25.7 74 0.0016 24.1 2.7 46 73-118 18-68 (106)
26 PF10642 Tom5: Mitochondrial i 25.3 2E+02 0.0044 18.8 4.6 26 54-79 10-35 (49)
27 PF09102 Exotox-A_target: Exot 25.2 1.2E+02 0.0027 23.8 3.9 59 60-136 40-106 (143)
28 PRK06012 flhA flagellar biosyn 25.2 4.7E+02 0.01 25.3 8.5 74 61-134 498-586 (697)
29 smart00337 BCL BCL (B-Cell lym 24.9 95 0.0021 22.0 3.1 35 63-97 52-89 (100)
30 PF09280 XPC-binding: XPC-bind 24.9 1.5E+02 0.0032 19.8 3.8 19 72-90 24-42 (59)
31 PTZ00019 fructose-bisphosphate 24.0 41 0.00089 30.2 1.2 15 46-60 256-274 (355)
32 PLN02455 fructose-bisphosphate 23.6 43 0.00094 30.1 1.3 15 46-60 258-276 (358)
33 cd08327 CARD_RAIDD Caspase act 23.4 1.6E+02 0.0034 21.3 4.0 43 82-128 49-91 (94)
34 TIGR01399 hrcV type III secret 23.2 3.2E+02 0.0069 26.5 7.0 53 61-113 482-548 (677)
35 PF06540 GMAP: Galanin message 22.8 1.3E+02 0.0029 20.8 3.3 26 49-74 15-40 (62)
36 smart00351 PAX Paired Box doma 22.7 2.5E+02 0.0055 20.5 5.1 43 71-113 35-91 (125)
37 TIGR03549 conserved hypothetic 22.3 2.1E+02 0.0045 28.0 5.6 59 41-101 526-584 (718)
38 PF08563 P53_TAD: P53 transact 21.9 31 0.00068 20.0 0.1 17 3-19 4-20 (25)
39 PLN02227 fructose-bisphosphate 21.6 48 0.001 30.2 1.2 15 46-60 302-320 (399)
40 PF00619 CARD: Caspase recruit 21.3 2.5E+02 0.0054 18.3 4.7 26 86-111 48-73 (85)
41 PRK13730 conjugal transfer pil 21.2 1.4E+02 0.0031 25.1 3.8 36 77-112 42-79 (212)
42 PLN02425 probable fructose-bis 20.8 53 0.0012 29.8 1.3 15 46-60 293-311 (390)
43 PF06713 bPH_4: Bacterial PH d 20.4 77 0.0017 21.3 1.8 17 97-113 58-74 (74)
44 cd00131 PAX Paired Box domain 20.2 3.7E+02 0.008 19.9 6.7 60 60-122 24-97 (128)
No 1
>PF02341 RcbX: RbcX protein; InterPro: IPR003435 The RbcX protein has been identified as having a possible chaperonin-like function []. The rbcX gene is juxtaposed to and cotranscribed with rbcL and rbcS encoding RubisCO in Anabaena sp. (strain CA / ATCC 33047). RbcX has been shown to possess a chaperonin-like function assisting correct folding of RubisCO in Escherichia coli expression studies and is needed for RubisCO to reach its maximal activity [].; PDB: 2PEM_B 2PEI_L 2PEK_A 2Z46_E 2Z44_A 2PEJ_F 2PEN_D 2PEQ_B 2Z45_A 3Q20_A ....
Probab=100.00 E-value=3e-37 Score=229.95 Aligned_cols=77 Identities=48% Similarity=0.688 Sum_probs=73.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhccChhhHHHHHHHHhcCCCCcHHHHHHHHHhcccCCchhHHHHHHHHHHHHhhhh
Q 032587 56 EAKGAKHLHNFFTYIAVRIITAQLQSYNPEAYKELMEFLERHPLNDGDKFCADLMRESSRHKGLALRILEVSKFYLGWYL 135 (137)
Q Consensus 56 E~daAk~L~~yfTy~AvRvVl~QL~e~np~~y~wL~~Fl~~~pl~DGd~fL~~Lmre~~~~~~LAlRIMeVRe~ya~~~l 135 (137)
.+|||++|++||||+|||||++||+||||+.|.||++|+++||++|||+||++||+|+ ++||+|||+||+|||+++.
T Consensus 7 ~kdtak~L~~yfTy~Avr~Vl~QL~etnp~~~~wL~~F~~~~~~~DGd~fl~~L~~e~---~~LA~RIM~vR~~la~~~~ 83 (111)
T PF02341_consen 7 AKDTAKVLQSYFTYQAVRTVLAQLYETNPPAYIWLYNFLSRNPLQDGDAFLEALMREN---QELALRIMEVREHLAEEVF 83 (111)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHSTCSSHHHHHHHHHCC----HHHHHHHHHHHHHHHHHHG
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCccHHHHHHHHHHHC---HHHHHHHHHHHHHHHHHHH
Confidence 3899999999999999999999999999999999999999999999999999999998 9999999999999999864
No 2
>PRK15337 type III secretion system protein InvA; Provisional
Probab=64.22 E-value=47 Score=32.07 Aligned_cols=73 Identities=19% Similarity=0.279 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHHHHHHhhccChhhHHHHHH-------------HH-hcCCCCcHHHHHHHHHhcccCCchhHHHHHHHHH
Q 032587 63 LHNFFTYIAVRIITAQLQSYNPEAYKELME-------------FL-ERHPLNDGDKFCADLMRESSRHKGLALRILEVSK 128 (137)
Q Consensus 63 L~~yfTy~AvRvVl~QL~e~np~~y~wL~~-------------Fl-~~~pl~DGd~fL~~Lmre~~~~~~LAlRIMeVRe 128 (137)
...+|+++-|+-.++++++.+|..-.+|-+ -+ ++.|++|=-.-+|.|....+..++...=.=-||.
T Consensus 494 a~ellg~qev~~Lld~l~~~~p~Lv~elp~~l~l~~i~~VLq~LL~E~VsIRdl~~IlE~l~d~~~~~kd~~~LtE~VR~ 573 (686)
T PRK15337 494 INEFFGIQETKHLLDQLEKKYPDLLKEVYRHATVQRISEVLQRLLSERISIRNMKLIMEALALWAPREKDVIMLVEHVRG 573 (686)
T ss_pred HHHHcCHHHHHHHHHHHHHHCHHHHHHHhccCCHHHHHHHHHHHHhcCCccccHHHHHHHHHHHhccCCCHHHHHHHHHH
Confidence 678999999999999999999976655422 22 3345566556666665443333333222224677
Q ss_pred HHHhhhh
Q 032587 129 FYLGWYL 135 (137)
Q Consensus 129 ~ya~~~l 135 (137)
+++..|.
T Consensus 574 ~L~r~I~ 580 (686)
T PRK15337 574 ALARYIC 580 (686)
T ss_pred HHHHHHH
Confidence 7666553
No 3
>PF12112 DUF3579: Protein of unknown function (DUF3579); InterPro: IPR021969 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 98 to 126 amino acids in length. This protein has a conserved FRP sequence motif. ; PDB: 2L9D_A.
Probab=59.27 E-value=3.6 Score=30.30 Aligned_cols=26 Identities=23% Similarity=0.506 Sum_probs=21.9
Q ss_pred HHHHhhccChhhHHHHHHHHhcCCCC
Q 032587 75 ITAQLQSYNPEAYKELMEFLERHPLN 100 (137)
Q Consensus 75 Vl~QL~e~np~~y~wL~~Fl~~~pl~ 100 (137)
|=.+|+..||.+|..+++|...|.|+
T Consensus 61 Vd~~L~~~~P~af~fvm~FA~dN~L~ 86 (92)
T PF12112_consen 61 VDERLRDIEPMAFDFVMNFAKDNDLQ 86 (92)
T ss_dssp EETHHHHH-HHHHHHHHHHHHHHTEE
T ss_pred EccHhhhcChHHHHHHHHHHHHCCCe
Confidence 44789999999999999999998874
No 4
>PF12234 Rav1p_C: RAVE protein 1 C terminal; InterPro: IPR022033 This domain family is found in eukaryotes, and is typically between 621 and 644 amino acids in length. This family is the C-terminal region of the protein RAVE (regulator of the ATPase of vacuolar and endosomal membranes). Rav1p is involved in regulating the glucose dependent assembly and disassembly of vacuolar ATPase V1 and V0 subunits.
Probab=43.42 E-value=61 Score=30.94 Aligned_cols=71 Identities=18% Similarity=0.126 Sum_probs=44.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhcc-ChhhHHHHH-HHHhcCCCCcHHHHHHHHHhcccCCchhHHHHHHH
Q 032587 56 EAKGAKHLHNFFTYIAVRIITAQLQSY-NPEAYKELM-EFLERHPLNDGDKFCADLMRESSRHKGLALRILEV 126 (137)
Q Consensus 56 E~daAk~L~~yfTy~AvRvVl~QL~e~-np~~y~wL~-~Fl~~~pl~DGd~fL~~Lmre~~~~~~LAlRIMeV 126 (137)
=+||..++.+++-=.-.=++++-|+|- |.|.+.+|. +++--.-+.+||.|++...-=.=.+.+.|.|.+..
T Consensus 481 l~dAv~V~~~~l~D~qLAi~i~Rl~e~d~gp~~~~ll~~~vLp~a~~~~d~wl~s~~~W~L~~~~~ai~~Li~ 553 (631)
T PF12234_consen 481 LKDAVNVCLRQLNDPQLAIAIARLYEGDNGPVLKKLLEEHVLPEAIKEGDRWLASWAFWMLGDYDEAIRALIS 553 (631)
T ss_pred HHHHHHHHHHHccChhHHHHHHHHHcCCCchHHHHHHHHhhhccccccCCHHHHHHHHHhcCCHHHHHHHHhc
Confidence 466666666666555555666666553 456665544 56555556799999998754333336788887743
No 5
>cd02518 GT2_SpsF SpsF is a glycosyltrnasferase implicated in the synthesis of the spore coat. Spore coat polysaccharide biosynthesis protein F (spsF) is a glycosyltransferase implicated in the synthesis of the spore coat in a variety of bacteria challenged by stress as starvation. The spsF gene is expressed in the late stage of coat development responsible for a terminal step in coat formation that involves the glycosylation of the coat. SpsF gene mutation resulted in spores that appeared normal. But, the spores tended to aggregate and had abnormal adsorption properties, indicating a surface alteration.
Probab=41.17 E-value=35 Score=26.46 Aligned_cols=29 Identities=24% Similarity=0.574 Sum_probs=20.1
Q ss_pred HHHHHHHHHhhccChh-hHHHHHHHHhcCC
Q 032587 70 IAVRIITAQLQSYNPE-AYKELMEFLERHP 98 (137)
Q Consensus 70 ~AvRvVl~QL~e~np~-~y~wL~~Fl~~~p 98 (137)
..++.+...|+..|++ .+.|+.+|+++||
T Consensus 196 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~p 225 (233)
T cd02518 196 ELIKEIYEALYPKNPDFSLEDIIELLDKNP 225 (233)
T ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHHhCh
Confidence 3445556667766665 6788888888776
No 6
>PHA00771 head assembly protein
Probab=39.87 E-value=19 Score=28.60 Aligned_cols=18 Identities=39% Similarity=0.722 Sum_probs=15.9
Q ss_pred ccccCceeecCCCCCChh
Q 032587 39 TIHCQKMYVPGFGEASPE 56 (137)
Q Consensus 39 ~~~~~km~Vp~fGG~sPE 56 (137)
-++|+-||-|+|-|.|.|
T Consensus 62 ~~ecHa~y~P~fRG~ya~ 79 (151)
T PHA00771 62 TFDCHAMYLPEIRGFSKE 79 (151)
T ss_pred EEEEEeeeCccccchhHH
Confidence 479999999999999873
No 7
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=39.62 E-value=32 Score=22.55 Aligned_cols=24 Identities=25% Similarity=0.353 Sum_probs=18.3
Q ss_pred HHHHHHhcccCCchhHHHHHHHHH
Q 032587 105 FCADLMRESSRHKGLALRILEVSK 128 (137)
Q Consensus 105 fL~~Lmre~~~~~~LAlRIMeVRe 128 (137)
=|.+|..++.-.|.||++||+.=.
T Consensus 18 tLDeli~~~~I~p~La~kVL~~FD 41 (49)
T PF02268_consen 18 TLDELIQEGKITPQLAMKVLEQFD 41 (49)
T ss_dssp HHHHHHHTTSS-HHHHHHHHHHHH
T ss_pred HHHHHHHcCCCCHHHHHHHHHHHH
Confidence 367788888778999999997533
No 8
>cd06258 Peptidase_M3_like The peptidase M3-like family, also called neurolysin-like family, is part of the "zincins" metallopeptidases, and includes M3, M2 and M32 families of metallopeptidases. The M3 family is subdivided into two subfamilies: the widespread M3A, which comprises a number of high-molecular mass endo- and exopeptidases from bacteria, archaea, protozoa, fungi, plants and animals, and the small M3B, whose members are enzymes primarily from bacteria. Well-known mammalian/eukaryotic M3A endopeptidases are the thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (alias endopeptidase 3.4.24.16), and the mitochondrial intermediate peptidase. The first two are intracellular oligopeptidases, which act only on relatively short substrates of less than 20 amino acid residues, while the latter cleaves N-terminal octapeptides from proteins during their import into the mitochondria. The M3A subfamily also contains several bacterial endopeptidases, collectively called olig
Probab=38.72 E-value=1e+02 Score=25.80 Aligned_cols=60 Identities=18% Similarity=0.134 Sum_probs=47.0
Q ss_pred HHHHHHHHHHHhhccChhhHHHHHHHHhcCCCCcHHHHHHHHHhcccCCchhHHHHHHHHHHHH
Q 032587 68 TYIAVRIITAQLQSYNPEAYKELMEFLERHPLNDGDKFCADLMRESSRHKGLALRILEVSKFYL 131 (137)
Q Consensus 68 Ty~AvRvVl~QL~e~np~~y~wL~~Fl~~~pl~DGd~fL~~Lmre~~~~~~LAlRIMeVRe~ya 131 (137)
.++-+|.-++|+-+++...-.+|.++... .+.+=++|++.|-+.- ..++.++++....++
T Consensus 6 ~lv~lr~e~A~~lGy~~~~d~~l~~~~~~-~~e~v~~f~~~l~~~~---~p~~~~~~~~l~~~~ 65 (365)
T cd06258 6 ELVSLRNQLARLLGYENFADYKLALQEAK-SPETVEGFFEELKRKL---RPLLAKLREEISAAK 65 (365)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHhcC-CHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH
Confidence 35667888999999976777778777775 6788899999998776 678888888766543
No 9
>PF12290 DUF3802: Protein of unknown function (DUF3802); InterPro: IPR020979 This family of proteins is found in bacteria and are typically between 114 and 143 amino acids in length. There is a conserved KNLFD sequence motif. The annotation with this family suggests that it may be the B subunit of bacterial type IIA DNA topoisomerase but there is no evidence to support this annotation.
Probab=37.23 E-value=73 Score=24.38 Aligned_cols=54 Identities=24% Similarity=0.455 Sum_probs=32.1
Q ss_pred ChhhHHHHHHHHhcC--------CCCcHHHHHHHHHhc---------ccCCchh--HHHHHHHHHH----H-Hhhhhc
Q 032587 83 NPEAYKELMEFLERH--------PLNDGDKFCADLMRE---------SSRHKGL--ALRILEVSKF----Y-LGWYLT 136 (137)
Q Consensus 83 np~~y~wL~~Fl~~~--------pl~DGd~fL~~Lmre---------~~~~~~L--AlRIMeVRe~----y-a~~~l~ 136 (137)
+.+.|..|.+|+..| +-..|+.=++.++.+ =..||+| +.|-+.+||+ | -++||.
T Consensus 4 dtdGY~~LI~yLte~L~lFe~~~~~~~~~~Tv~d~vee~ia~~im~vc~Qnp~L~~~~R~~iirE~Daiv~DLeEVLa 81 (113)
T PF12290_consen 4 DTDGYDALIEYLTENLSLFESSQSGDTGDETVEDVVEEQIASQIMAVCEQNPELEFSQRFQIIREADAIVYDLEEVLA 81 (113)
T ss_pred CchhHHHHHHHHHHhHHHhcCCCCCCcccchHHHHHHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456677777776543 223455544444433 1224787 9999999997 2 456654
No 10
>TIGR02996 rpt_mate_G_obs repeat-companion domain TIGR02996. This model describes an abundant paralogous domain of Gemmata obscuriglobus UQM 2246, a member of the Planctomycetes. The domain also occurs, although rarely, in Myxococcus xanthus DK 1622 and related species. Most member proteins have extensive repeats similar to the leucine-rich repeat, or another repeat class or region of low-complexity sequence. This domain is not repeated, and in Gemmata is usually found at the protein N-terminus.
Probab=32.80 E-value=59 Score=20.87 Aligned_cols=27 Identities=11% Similarity=0.261 Sum_probs=18.8
Q ss_pred cHHHHHHHHHhcccCCchhHHHHHHHHHHHHhhhh
Q 032587 101 DGDKFCADLMRESSRHKGLALRILEVSKFYLGWYL 135 (137)
Q Consensus 101 DGd~fL~~Lmre~~~~~~LAlRIMeVRe~ya~~~l 135 (137)
|-++|++++....+ +- +.|.+||.|.-
T Consensus 1 d~~all~AI~~~P~---dd-----t~RLvYADWL~ 27 (42)
T TIGR02996 1 DEEALLRAILAHPD---DD-----TPRLVYADWLD 27 (42)
T ss_pred CcHHHHHHHHhCCC---Cc-----chHHHHHHHHH
Confidence 34678888888763 22 46788999864
No 11
>PF14677 FANCI_S3: FANCI solenoid 3; PDB: 3S51_A 3S4Z_A 3S4W_A.
Probab=32.07 E-value=76 Score=26.00 Aligned_cols=25 Identities=24% Similarity=0.578 Sum_probs=16.3
Q ss_pred hhHHHHHHHHhcCCCCcHHHHHHHHH
Q 032587 85 EAYKELMEFLERHPLNDGDKFCADLM 110 (137)
Q Consensus 85 ~~y~wL~~Fl~~~pl~DGd~fL~~Lm 110 (137)
+.|.|+.+|..++++.|- .++.+|+
T Consensus 191 q~~~W~~~~ck~~~l~d~-~~~k~ll 215 (219)
T PF14677_consen 191 QMLSWTLKFCKENSLEDS-SFCKGLL 215 (219)
T ss_dssp HHHHHHHHHHHS---S-H-HHHHHHH
T ss_pred HHHHHHHHHHHhcCCCcH-HHHHHHH
Confidence 368999999999999886 4666665
No 12
>PF14102 Caps_synth_CapC: Capsule biosynthesis CapC
Probab=31.20 E-value=69 Score=23.97 Aligned_cols=47 Identities=21% Similarity=0.313 Sum_probs=38.4
Q ss_pred ccccCceeecCC---CCCChhHHHHHHHHHHHHHHHHHHHHHHhhccChh
Q 032587 39 TIHCQKMYVPGF---GEASPEAKGAKHLHNFFTYIAVRIITAQLQSYNPE 85 (137)
Q Consensus 39 ~~~~~km~Vp~f---GG~sPE~daAk~L~~yfTy~AvRvVl~QL~e~np~ 85 (137)
-.+|+.++|||+ -=.+|.+-....+.+..||..+|.+..-.-=+...
T Consensus 15 G~~~gGlivPgylAl~~~~P~~l~~~~~~s~lt~~i~~~l~~~~ilyGRr 64 (121)
T PF14102_consen 15 GWSPGGLIVPGYLALYLDQPVRLLVTLLISLLTYLIVRLLSRRTILYGRR 64 (121)
T ss_pred CCCCCCEeeHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHhhhcccHH
Confidence 568999999972 33899999999999999999998887766555554
No 13
>PF01820 Dala_Dala_lig_N: D-ala D-ala ligase N-terminus; InterPro: IPR011127 This entry represents the N-terminal region of the D-alanine--D-alanine ligase enzyme (6.3.2.4 from EC) which is thought to be involved in substrate binding []. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF) [].; GO: 0008716 D-alanine-D-alanine ligase activity, 0009252 peptidoglycan biosynthetic process, 0005618 cell wall; PDB: 4EG0_B 3E5N_A 3RFC_A 3R5F_A 1IOV_A 1IOW_A 2DLN_A 3Q1K_D 3I12_C 3N8D_B ....
Probab=30.99 E-value=18 Score=26.34 Aligned_cols=23 Identities=26% Similarity=0.307 Sum_probs=16.5
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHHHHHHHhh
Q 032587 50 FGEASPEAKGAKHLHNFFTYIAVRIITAQLQ 80 (137)
Q Consensus 50 fGG~sPE~daAk~L~~yfTy~AvRvVl~QL~ 80 (137)
|||.|+|++++- ...+.|+.+|.
T Consensus 7 fGG~S~EheVSl--------~Sa~~v~~~L~ 29 (117)
T PF01820_consen 7 FGGRSSEHEVSL--------RSARNVYEALD 29 (117)
T ss_dssp EETSSTTHHHHH--------HHHHHHHHHSH
T ss_pred eccCchhHHHHH--------HHHHHHHHHHh
Confidence 899999999863 34455666664
No 14
>TIGR01987 HI0074 nucleotidyltransferase substrate binding protein, HI0074 family. The member of this family from Haemophilus influenzae, HI0074, has been shown by crystal structure to resemble nucleotidyltransferase substrate binding proteins. It forms a complex with HI0073, encoded by the adjacent gene and containing a nucleotidyltransferase nucleotide binding domain (pfam01909).
Probab=30.61 E-value=1.4e+02 Score=22.36 Aligned_cols=36 Identities=19% Similarity=0.122 Sum_probs=23.7
Q ss_pred HHHHHhcCCCCcHHHHHHHHHhcccC----CchhHHHHHH
Q 032587 90 LMEFLERHPLNDGDKFCADLMRESSR----HKGLALRILE 125 (137)
Q Consensus 90 L~~Fl~~~pl~DGd~fL~~Lmre~~~----~~~LAlRIMe 125 (137)
+......+-+.||+.|++-+-..|.- +.+.|..|..
T Consensus 66 ir~A~~~glI~d~~~W~~ml~~RN~tsHtYde~~a~~i~~ 105 (123)
T TIGR01987 66 LKEAFRAGLIGDESLWIAMLDDRNITSHTYDQEKAREIYA 105 (123)
T ss_pred HHHHHHcCCcCCHHHHHHHHHHhCcccccCCHHHHHHHHH
Confidence 44555556679999999988555422 3456766664
No 15
>PRK09273 hypothetical protein; Provisional
Probab=30.58 E-value=93 Score=25.95 Aligned_cols=25 Identities=20% Similarity=0.406 Sum_probs=15.5
Q ss_pred cHHHHHHHHHhcccCCchhHHHHHHH
Q 032587 101 DGDKFCADLMRESSRHKGLALRILEV 126 (137)
Q Consensus 101 DGd~fL~~Lmre~~~~~~LAlRIMeV 126 (137)
.|+.|.+-++. +..+++++..|=++
T Consensus 185 ~~~~f~~~~~~-~~~~~~i~~~~~~~ 209 (211)
T PRK09273 185 SGERFQEYFFE-NCQDKEIAAYVKSV 209 (211)
T ss_pred cchhHHHHHHh-cCChHHHHHHHHHh
Confidence 57777777776 34456676655443
No 16
>PRK12720 secretion system apparatus protein SsaV; Provisional
Probab=29.05 E-value=2.2e+02 Score=27.66 Aligned_cols=29 Identities=21% Similarity=0.250 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHHHHhhccChhhHHHH
Q 032587 62 HLHNFFTYIAVRIITAQLQSYNPEAYKEL 90 (137)
Q Consensus 62 ~L~~yfTy~AvRvVl~QL~e~np~~y~wL 90 (137)
....+||++-++..+++|++.+|..-.++
T Consensus 479 ~a~ellg~qev~~Lld~l~~~~p~Lv~el 507 (675)
T PRK12720 479 YMGEFIGVQETRYLMDAMEKRYGELVKEL 507 (675)
T ss_pred HHHHHcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 36789999999999999999998876665
No 17
>PF08740 BCS1_N: BCS1 N terminal; InterPro: IPR014851 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. This domain is found at the N terminus of the mitochondrial BSC1 subfamily, belonging to the AAA ATPase family. At2g21640 and BCS1 are both highly stress responsive genes which encode mitochondrial proteins. The promoter of BCS1 was not responsive to H2O2 or rotenone, but highly responsive to salicylic acid (SA). The SA dependent pathway represented by BCS1 is one of at least three distinctive pathways to regulate mitochondrial stress response at a transcriptional level []. The BCS1 product is a mitochondrial protein required for the assembly of respiratory complex III []. BCS1, a component of the inner membrane of mitochondria, belongs to the group of proteins with internal, noncleavable import signals. It has a transmembrane domain (amino acid residues 51 to 68), a presequence type helix (residues 69 to 83), and an import auxiliary region (residues 84 to 126) [].
Probab=28.96 E-value=1.4e+02 Score=22.52 Aligned_cols=20 Identities=35% Similarity=0.635 Sum_probs=17.1
Q ss_pred cChhhHHHHHHHHhcCCCCc
Q 032587 82 YNPEAYKELMEFLERHPLND 101 (137)
Q Consensus 82 ~np~~y~wL~~Fl~~~pl~D 101 (137)
.+-+.|.||+.+++++|...
T Consensus 33 ~~D~~Y~~lm~Wls~q~~~~ 52 (187)
T PF08740_consen 33 SDDEAYDWLMRWLSSQPFSK 52 (187)
T ss_pred CCCHHHHHHHHHHhhCCccc
Confidence 45679999999999999854
No 18
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=28.34 E-value=71 Score=22.13 Aligned_cols=38 Identities=24% Similarity=0.216 Sum_probs=29.8
Q ss_pred cChhhHHHHHHHHhcCCCCcHHHHHHHHHhcccCCchhHHH
Q 032587 82 YNPEAYKELMEFLERHPLNDGDKFCADLMRESSRHKGLALR 122 (137)
Q Consensus 82 ~np~~y~wL~~Fl~~~pl~DGd~fL~~Lmre~~~~~~LAlR 122 (137)
|++.....|.+++.+...+-=+.|+..|...+ |.|+..
T Consensus 43 T~~~kar~Lld~l~~kG~~A~~~F~~~L~e~~---p~L~~~ 80 (82)
T cd08330 43 TNQEKMRKLFSFVRSWGASCKDIFYQILREEE---PYLVED 80 (82)
T ss_pred CcHHHHHHHHHHHHccCHHHHHHHHHHHHHhC---hHHHhH
Confidence 66778888999999766666789999995554 788754
No 19
>PLN02690 Agmatine deiminase
Probab=28.17 E-value=48 Score=29.37 Aligned_cols=28 Identities=21% Similarity=0.348 Sum_probs=23.7
Q ss_pred ccCceeecCCCCCChhHHHHHHHHHHHH
Q 032587 41 HCQKMYVPGFGEASPEAKGAKHLHNFFT 68 (137)
Q Consensus 41 ~~~km~Vp~fGG~sPE~daAk~L~~yfT 68 (137)
-++-++||.||-...++.|-++|+.+|-
T Consensus 316 ~N~~VivP~fgd~~~D~~A~~~l~~~fP 343 (374)
T PLN02690 316 ANGGIVAPQFGDAKWDKEAIEVLSEAFP 343 (374)
T ss_pred ECCEEEEecCCCCcccHHHHHHHHHHCC
Confidence 5678999999986668899999999885
No 20
>PF09722 DUF2384: Protein of unknown function (DUF2384); InterPro: IPR024467 This domain is found predominantly in proteobacterial proteins. Its function in unknown.
Probab=28.16 E-value=74 Score=19.85 Aligned_cols=30 Identities=17% Similarity=0.121 Sum_probs=19.3
Q ss_pred ecCCCCCChhHHHHHHHHHHHHHHHHHHHHHHhh
Q 032587 47 VPGFGEASPEAKGAKHLHNFFTYIAVRIITAQLQ 80 (137)
Q Consensus 47 Vp~fGG~sPE~daAk~L~~yfTy~AvRvVl~QL~ 80 (137)
.|+|||.+|-.= +.+---...|+-.|++++
T Consensus 22 ~~~l~g~~Plel----~~t~~G~~~V~~~L~~~~ 51 (54)
T PF09722_consen 22 NPALGGRTPLEL----LRTEAGAERVLDYLDRIE 51 (54)
T ss_pred HHHhCCCCHHHH----HcChHHHHHHHHHHHHHH
Confidence 357999999743 333455566666676665
No 21
>PF11039 DUF2824: Protein of unknown function (DUF2824); InterPro: IPR022568 This family of proteins has no known function. Members of the family are found in P22-like viruses and bacteria. Some of the phage members have been annotated as head assembly proteins, but this has not been confirmed.
Probab=27.83 E-value=20 Score=28.63 Aligned_cols=18 Identities=39% Similarity=0.826 Sum_probs=14.5
Q ss_pred ccccCceeecCCCCCChh
Q 032587 39 TIHCQKMYVPGFGEASPE 56 (137)
Q Consensus 39 ~~~~~km~Vp~fGG~sPE 56 (137)
-++|+-||-|||-|.+-|
T Consensus 62 ~vecHa~y~P~fRG~a~~ 79 (151)
T PF11039_consen 62 VVECHAMYDPGFRGYALE 79 (151)
T ss_pred eEEEEeeeccccchhHHH
Confidence 479999999999884433
No 22
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=27.39 E-value=2.3e+02 Score=28.11 Aligned_cols=64 Identities=30% Similarity=0.573 Sum_probs=40.0
Q ss_pred CCCCCChhHHHHH------HHHHHHHHHH----HHHHHHHhhccChhhHHHHHHHHhcCCCCcHHHHHHHHHhcccCCch
Q 032587 49 GFGEASPEAKGAK------HLHNFFTYIA----VRIITAQLQSYNPEAYKELMEFLERHPLNDGDKFCADLMRESSRHKG 118 (137)
Q Consensus 49 ~fGG~sPE~daAk------~L~~yfTy~A----vRvVl~QL~e~np~~y~wL~~Fl~~~pl~DGd~fL~~Lmre~~~~~~ 118 (137)
|||..-|+-|..| ++..-+-|.+ |-+++.|++. |...|.++++=+. +||. |..-. ++
T Consensus 439 GFGNiA~~TD~EKiF~v~mMii~aLLYAtIFG~vTTI~QQM~s-~T~rYHeMlnnVR--------eFlK-L~evP---K~ 505 (971)
T KOG0501|consen 439 GFGNIAPNTDNEKIFGVCMMIIGALLYATIFGHVTTIIQQMTS-NTNRYHEMLNNVR--------EFLK-LYEVP---KG 505 (971)
T ss_pred cccccCCCccHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHh-hhHHHHHHHHHHH--------HHHH-HHhcc---HH
Confidence 7999999866544 4444444544 4677788775 2334655554433 5553 44444 89
Q ss_pred hHHHHHH
Q 032587 119 LALRILE 125 (137)
Q Consensus 119 LAlRIMe 125 (137)
|++|||.
T Consensus 506 LsERVMD 512 (971)
T KOG0501|consen 506 LSERVMD 512 (971)
T ss_pred HHHHHHH
Confidence 9999995
No 23
>PF11724 YvbH_ext: YvbH-like oligomerisation region; InterPro: IPR021722 This domain is found at the C terminus of a group of bacterial uncharacterised proteins. This domain is composed of a helical hairpin that appears to mediate oligomerisation based on the known structure. ; PDB: 3B77_D.
Probab=25.96 E-value=51 Score=22.47 Aligned_cols=31 Identities=26% Similarity=0.442 Sum_probs=24.1
Q ss_pred HHHHhhccChhhHHHHHHHHhcCCCCc-HHHH
Q 032587 75 ITAQLQSYNPEAYKELMEFLERHPLND-GDKF 105 (137)
Q Consensus 75 Vl~QL~e~np~~y~wL~~Fl~~~pl~D-Gd~f 105 (137)
|.+|.++.|.-++.||.+--.+...+| |+-|
T Consensus 24 ~~~~Fk~ln~~aF~Wl~~~~~~y~~KDFg~VF 55 (61)
T PF11724_consen 24 VSDQFKELNEFAFNWLEDHRKQYTVKDFGDVF 55 (61)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHS-S--HHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhccHHHHH
Confidence 557777888889999999988888888 8665
No 24
>cd00948 FBP_aldolase_I_a Fructose-1,6-bisphosphate aldolase. The enzyme catalyzes the cleavage of fructose 1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). This family includes proteins found in vertebrates, plants, and bacterial plant pathogens. Mutations in the aldolase genes in humans cause hemolytic anemia and hereditary fructose intolerance. The enzyme is a member of the class I aldolase family, which utilizes covalent catalysis through a Schiff base formed between a lysine residue of the enzyme and ketose substrates.
Probab=25.81 E-value=36 Score=30.23 Aligned_cols=15 Identities=47% Similarity=0.680 Sum_probs=10.9
Q ss_pred eecC--C--CCCChhHHHH
Q 032587 46 YVPG--F--GEASPEAKGA 60 (137)
Q Consensus 46 ~Vp~--f--GG~sPE~daA 60 (137)
-||| | ||||+|..++
T Consensus 251 avpGI~FLSGGqseeeAt~ 269 (330)
T cd00948 251 AVPGIVFLSGGQSEEEATL 269 (330)
T ss_pred cCCeeeeccCCCCHHHHHH
Confidence 4666 4 9999997554
No 25
>cd08791 DED_DEDD2 Death Effector Domain of DEDD2. Death Effector Domain (DED) found in DEDD2. DEDD2 has been shown to bind to itself, DEDD, and to the two tandem DED-containing caspases, caspase-8 and -10. It may play a role in apoptosis. In general, DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways.
Probab=25.71 E-value=74 Score=24.14 Aligned_cols=46 Identities=20% Similarity=0.353 Sum_probs=34.4
Q ss_pred HHHHHHhhccChhhHHHHHH--HHhcCCC---CcHHHHHHHHHhcccCCch
Q 032587 73 RIITAQLQSYNPEAYKELME--FLERHPL---NDGDKFCADLMRESSRHKG 118 (137)
Q Consensus 73 RvVl~QL~e~np~~y~wL~~--Fl~~~pl---~DGd~fL~~Lmre~~~~~~ 118 (137)
.||=+||.+.+-..-.+|.. +...+++ ++|=.++.+|++.+.-+++
T Consensus 18 ~iVs~qLt~~dL~~LkFLc~e~~iGk~~le~i~SGldLf~~Leer~~l~e~ 68 (106)
T cd08791 18 EVVGSQLTETCGGELAFLLDETYPGKHPLDRPKSGVELLLELERRGYCDES 68 (106)
T ss_pred HHHhhhcchhhHhHhhhhhccCccccchhhhccCHHHHHHHHHHhCcCChh
Confidence 57888999888777666665 5555544 7999999999998866544
No 26
>PF10642 Tom5: Mitochondrial import receptor subunit or translocase; InterPro: IPR019603 This entry represents a short family of yeast proteins. Tom5 is one of three very small translocases of the mitochondrial outer membrane. Tom5 links mitochondrial preprotein receptors to the general import pore []. Although Tom5 has allegedly been identified in vertebrates this could not be confirmed.
Probab=25.27 E-value=2e+02 Score=18.79 Aligned_cols=26 Identities=27% Similarity=0.135 Sum_probs=17.5
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHh
Q 032587 54 SPEAKGAKHLHNFFTYIAVRIITAQL 79 (137)
Q Consensus 54 sPE~daAk~L~~yfTy~AvRvVl~QL 79 (137)
|+|++.+-.-...+|.+-+=++-.=|
T Consensus 10 S~eE~k~~e~~A~~Tvk~a~~~a~~L 35 (49)
T PF10642_consen 10 SEEEIKAAEAQANFTVKNAAAAAALL 35 (49)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 88877777777777777655544333
No 27
>PF09102 Exotox-A_target: Exotoxin A, targeting; InterPro: IPR015186 This domain, found in Pseudomonas aeruginosa exotoxin A, is responsible for transmembrane targeting of the toxin, as well as transmembrane translocation of the catalytic domain into the cytoplasmic compartment. A furin cleavage site is present within the domain: cleavage generates a 37 kDa carboxy-terminal fragment, which includes the enzymatic domain, which is then is translocated into the cytoplasm. It adopts a helical structure, with six alpha-helices forming a bundle []. ; PDB: 1IKP_A 1IKQ_A 2Q5T_A 3Q9O_A.
Probab=25.24 E-value=1.2e+02 Score=23.79 Aligned_cols=59 Identities=24% Similarity=0.459 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhc--------cChhhHHHHHHHHhcCCCCcHHHHHHHHHhcccCCchhHHHHHHHHHHHH
Q 032587 60 AKHLHNFFTYIAVRIITAQLQS--------YNPEAYKELMEFLERHPLNDGDKFCADLMRESSRHKGLALRILEVSKFYL 131 (137)
Q Consensus 60 Ak~L~~yfTy~AvRvVl~QL~e--------~np~~y~wL~~Fl~~~pl~DGd~fL~~Lmre~~~~~~LAlRIMeVRe~ya 131 (137)
+..|.++ |+|.|+.-+|+.. ..|+....|.| |.+..+++ |+.+.-++++-..+-
T Consensus 40 ~Q~iVsL--~~A~Ri~~~~~D~V~~~~L~~~~~~vaerl~D-------------L~~~~~~~---P~~~~~~LT~A~~~~ 101 (143)
T PF09102_consen 40 AQNIVSL--FVATRILFSHLDSVFTLNLDEQEPEVAERLSD-------------LRRINENN---PGMVTQVLTVARQIY 101 (143)
T ss_dssp HHHHHHH--HHHCT--GGGHHHHHHCHHHCTTCCHHHHHHH-------------HHHHHHHS---CCHHHHHHHHHHHHH
T ss_pred HHHHHHH--HHHHHHHHHHHHHHHHHhccCCCcchhhhhhH-------------HHHHHhcC---chHHHHHHHHHHHHH
Confidence 4445554 6888988888763 44555555543 45566777 788888888877765
Q ss_pred hhhhc
Q 032587 132 GWYLT 136 (137)
Q Consensus 132 ~~~l~ 136 (137)
+.|.+
T Consensus 102 ~~~V~ 106 (143)
T PF09102_consen 102 NDYVT 106 (143)
T ss_dssp HHHHC
T ss_pred HHHHH
Confidence 55543
No 28
>PRK06012 flhA flagellar biosynthesis protein FlhA; Validated
Probab=25.23 E-value=4.7e+02 Score=25.33 Aligned_cols=74 Identities=18% Similarity=0.117 Sum_probs=51.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhccChhhHHH--------------HHHHH-hcCCCCcHHHHHHHHHhcccCCchhHHHHHH
Q 032587 61 KHLHNFFTYIAVRIITAQLQSYNPEAYKE--------------LMEFL-ERHPLNDGDKFCADLMRESSRHKGLALRILE 125 (137)
Q Consensus 61 k~L~~yfTy~AvRvVl~QL~e~np~~y~w--------------L~~Fl-~~~pl~DGd~fL~~Lmre~~~~~~LAlRIMe 125 (137)
+....+||.+-|+-.+++|++.+|..-.+ |.+-+ +..|++|=-.-+|.|....+..++...=.=-
T Consensus 498 ~~a~ellgrQEvq~LLD~L~~~~p~LVeElvp~~l~l~~Iq~VLq~LL~E~VSIRdL~tIlEaLad~a~~~kD~~~LtE~ 577 (697)
T PRK06012 498 NHAAELLGRQEVQQLLDRLAKEYPKLVEELVPKVLSLGTLQKVLQNLLKERVSIRDLRTILETLADYAPITKDPDELTEH 577 (697)
T ss_pred HhHHHHhCHHHHHHHHHHHHHhChHHHHHhccccCCHHHHHHHHHHHHhCCCccccHHHHHHHHHHHhccCCCHHHHHHH
Confidence 34678999999999999999999875444 34444 3457788888888887765444444333335
Q ss_pred HHHHHHhhh
Q 032587 126 VSKFYLGWY 134 (137)
Q Consensus 126 VRe~ya~~~ 134 (137)
||.+++..|
T Consensus 578 VR~aL~RqI 586 (697)
T PRK06012 578 VRQRLGRQI 586 (697)
T ss_pred HHHHHHHHH
Confidence 677776655
No 29
>smart00337 BCL BCL (B-Cell lymphoma); contains BH1, BH2 regions. (BH1, BH2, (BH3 (one helix only)) and not BH4(one helix only)). Involved in apoptosis regulation
Probab=24.93 E-value=95 Score=21.98 Aligned_cols=35 Identities=17% Similarity=0.252 Sum_probs=18.4
Q ss_pred HHHHHHHH---HHHHHHHHhhccChhhHHHHHHHHhcC
Q 032587 63 LHNFFTYI---AVRIITAQLQSYNPEAYKELMEFLERH 97 (137)
Q Consensus 63 L~~yfTy~---AvRvVl~QL~e~np~~y~wL~~Fl~~~ 97 (137)
+..+|+|- |++.+-.+..+.-.....|+.+|+.++
T Consensus 52 Ival~~F~~~la~~~~~~~~~~~~~~i~~~~~~~l~~~ 89 (100)
T smart00337 52 VVALLSFGGALAVKLVQKEDPDLVSRLASWLSEFLRET 89 (100)
T ss_pred HHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHH
Confidence 34455553 333333333334445667788887755
No 30
>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0043161 proteasomal ubiquitin-dependent protein catabolic process; PDB: 1PVE_A 1QZE_A 1OQY_A 1TP4_A 1X3W_B 3ESW_B 2QSG_X 2QSF_X 1X3Z_B 2QSH_X ....
Probab=24.90 E-value=1.5e+02 Score=19.77 Aligned_cols=19 Identities=21% Similarity=0.300 Sum_probs=12.4
Q ss_pred HHHHHHHhhccChhhHHHH
Q 032587 72 VRIITAQLQSYNPEAYKEL 90 (137)
Q Consensus 72 vRvVl~QL~e~np~~y~wL 90 (137)
+.-||.||..+||..+...
T Consensus 24 L~~lLqql~~~nP~l~q~I 42 (59)
T PF09280_consen 24 LPPLLQQLGQSNPQLLQLI 42 (59)
T ss_dssp HHHHHHHHHCCSHHHHHHH
T ss_pred HHHHHHHHhccCHHHHHHH
Confidence 3456777777777765443
No 31
>PTZ00019 fructose-bisphosphate aldolase; Provisional
Probab=23.96 E-value=41 Score=30.18 Aligned_cols=15 Identities=40% Similarity=0.678 Sum_probs=10.9
Q ss_pred eecC--C--CCCChhHHHH
Q 032587 46 YVPG--F--GEASPEAKGA 60 (137)
Q Consensus 46 ~Vp~--f--GG~sPE~daA 60 (137)
-||| | ||||+|..++
T Consensus 256 avPGI~FLSGGqSeeeAt~ 274 (355)
T PTZ00019 256 ALPGVMFLSGGQSEEEASL 274 (355)
T ss_pred cCCeeeeccCCCCHHHHHH
Confidence 4666 4 9999997554
No 32
>PLN02455 fructose-bisphosphate aldolase
Probab=23.58 E-value=43 Score=30.06 Aligned_cols=15 Identities=47% Similarity=0.680 Sum_probs=10.5
Q ss_pred eecC--C--CCCChhHHHH
Q 032587 46 YVPG--F--GEASPEAKGA 60 (137)
Q Consensus 46 ~Vp~--f--GG~sPE~daA 60 (137)
-||| | ||||+|..++
T Consensus 258 avpGI~FLSGGqSeeeAt~ 276 (358)
T PLN02455 258 AVPGIVFLSGGQSEEEATL 276 (358)
T ss_pred cCCcceecCCCCcHHHHHH
Confidence 3566 4 9999987544
No 33
>cd08327 CARD_RAIDD Caspase activation and recruitment domain of RIP-associated ICH-1 homologous protein with a death domain. Caspase activation and recruitment domain (CARD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal CARD, which interacts with the caspase-2 CARD, and a C-terminal Death domain (DD), which interacts with the DD of PIDD. In general, CARDs are DDs associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodime
Probab=23.44 E-value=1.6e+02 Score=21.26 Aligned_cols=43 Identities=14% Similarity=0.148 Sum_probs=33.4
Q ss_pred cChhhHHHHHHHHhcCCCCcHHHHHHHHHhcccCCchhHHHHHHHHH
Q 032587 82 YNPEAYKELMEFLERHPLNDGDKFCADLMRESSRHKGLALRILEVSK 128 (137)
Q Consensus 82 ~np~~y~wL~~Fl~~~pl~DGd~fL~~Lmre~~~~~~LAlRIMeVRe 128 (137)
|+.+....|++.+.+--.+-=+.|+++| ++- |-||..++..++
T Consensus 49 T~~~k~~~LLdiLp~RG~~AF~~F~~aL-~e~---~~l~~~l~~~~~ 91 (94)
T cd08327 49 TSRRKTMKLLDILPSRGPKAFHAFLDSL-EEF---PWVRDKLLKLRE 91 (94)
T ss_pred ChHHHHHHHHHHHHhhChhHHHHHHHHH-HHH---HHHHHHHHHHHh
Confidence 5566778899999887777778999999 443 788888887665
No 34
>TIGR01399 hrcV type III secretion protein, HrcV family. Members of this family are closely homologous to the flagellar biosynthesis protein FlhA (TIGR01398) and should all participate in type III secretion systems. Examples include InvA (Salmonella enterica), LcrD (Yersinia enterocolitica), HrcV (Xanthomonas), etc. Type III secretion systems resemble flagellar biogenesis systems, and may share the property of translocating special classes of peptides through the membrane.
Probab=23.21 E-value=3.2e+02 Score=26.52 Aligned_cols=53 Identities=17% Similarity=0.273 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhccChhhHHHHHH-------------HH-hcCCCCcHHHHHHHHHhcc
Q 032587 61 KHLHNFFTYIAVRIITAQLQSYNPEAYKELME-------------FL-ERHPLNDGDKFCADLMRES 113 (137)
Q Consensus 61 k~L~~yfTy~AvRvVl~QL~e~np~~y~wL~~-------------Fl-~~~pl~DGd~fL~~Lmre~ 113 (137)
+....+|+.+-++-.++.|++.+|..-.++-+ -+ +..|++|=-.-+|.|....
T Consensus 482 ~~a~ellgrqe~~~Lld~l~~~~p~Lv~Elp~~~~l~~i~~VLq~LL~E~VsIRdl~~IlEtLad~~ 548 (677)
T TIGR01399 482 RNAQEFIGIQETRYLLDQMEREYPELVKEVQRVLPLQRIAEVLQRLVSEQVSIRNLRLILETLIEWA 548 (677)
T ss_pred HHHHHHcCHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHhCCCccccHHHHHHHHHHHh
Confidence 34678999999999999999999886666422 22 3445566666666665544
No 35
>PF06540 GMAP: Galanin message associated peptide (GMAP); InterPro: IPR013068 Galanin is a peptide hormone that controls various biological activities []. Galanin-like immuno-reactivity has been found in the central and peripheral nervous systems of mammals, with high concentrations demonstrated in discrete regions of the central nervous system, including the median eminence, hypothalamus, arcuate nucleus, septum, neuro-intermediate lobe of the pituitary, and the spinal cord. Its localisation within neurosecretory granules suggests that galanin may function as a neurotransmitter, and it has been shown to coexist with a variety of other peptide and amine neurotransmitters within individual neurons []. Although the precise physiological role of galanin is uncertain, it has a number of pharmacological properties: it stimulates food intake, when injected into the third ventricle of rats; it increases levels of plasma growth hormone and prolactin, and decreases dopamine levels in the median eminence []; and infusion into humans results in hyperglycemia and glucose intolerance, and inhibits pancreatic release of insulin, somatostatin and pancreatic peptide. Galanin also modulates smooth muscle contractility within the gastro-intestinal and genito-urinary tracts, all such activities suggesting that the hormone may play an important role in the nervous modulation of endocrine and smooth muscle function []. This domain represents the galanin message-associated peptide (GMAP) domain which is found C-terminal to the galanin domain in the preprogalanin precursor protein. GMAP sequences in different species show a high degree of homology, but the biological function of the GMAP peptide is not known [].
Probab=22.83 E-value=1.3e+02 Score=20.82 Aligned_cols=26 Identities=12% Similarity=0.379 Sum_probs=22.2
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHHH
Q 032587 49 GFGEASPEAKGAKHLHNFFTYIAVRI 74 (137)
Q Consensus 49 ~fGG~sPE~daAk~L~~yfTy~AvRv 74 (137)
+|+.-.||.++-.++..|+||.=.+-
T Consensus 15 ~~~r~l~d~nivrTiiEFLtfLhLKE 40 (62)
T PF06540_consen 15 SFDRPLADDNIVRTIIEFLTFLHLKE 40 (62)
T ss_pred cccCCCchhHHHHHHHHHHHHHHHHH
Confidence 37888899999999999999986654
No 36
>smart00351 PAX Paired Box domain.
Probab=22.66 E-value=2.5e+02 Score=20.51 Aligned_cols=43 Identities=26% Similarity=0.143 Sum_probs=30.3
Q ss_pred HHHHHHHHhhccChhhHHHHHHHHhcCCCCc----H----------HHHHHHHHhcc
Q 032587 71 AVRIITAQLQSYNPEAYKELMEFLERHPLND----G----------DKFCADLMRES 113 (137)
Q Consensus 71 AvRvVl~QL~e~np~~y~wL~~Fl~~~pl~D----G----------d~fL~~Lmre~ 113 (137)
..+.|-.++.=..+..|.|+..|-++..+.. | +.||.++.+++
T Consensus 35 s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~ 91 (125)
T smart00351 35 RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQEN 91 (125)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHC
Confidence 4555556665566678999999987655433 3 66888888887
No 37
>TIGR03549 conserved hypothetical protein TIGR03549. This family consists of remarkably well-conserved proteins from gamma and beta Proteobacteria, heavily skewed towards organisms of marine environments. This family has an OsmC-like N-terminal domain. It shares a central domain, modeled by pfam02624 and TIGR00702, with other families of smaller proteins. The function is unknown. Fifteen of the first sixteen members of this family are from selenouridine-positive genomes, but this correlation may be fortuitous.
Probab=22.33 E-value=2.1e+02 Score=28.04 Aligned_cols=59 Identities=25% Similarity=0.353 Sum_probs=41.8
Q ss_pred ccCceeecCCCCCChhHHHHHHHHHHHHHHHHHHHHHHhhccChhhHHHHHHHHhcCCCCc
Q 032587 41 HCQKMYVPGFGEASPEAKGAKHLHNFFTYIAVRIITAQLQSYNPEAYKELMEFLERHPLND 101 (137)
Q Consensus 41 ~~~km~Vp~fGG~sPE~daAk~L~~yfTy~AvRvVl~QL~e~np~~y~wL~~Fl~~~pl~D 101 (137)
.+=+++|||+.+.||-.|-- ..|.=.-..+|-.+-.|.+.+.+.|..|++-++..-+-|
T Consensus 526 ~acriivPg~Seiyp~~dl~--~~N~n~~~~~r~~il~l~~~~~~~~~~l~~~l~~~~~dd 584 (718)
T TIGR03549 526 PACRILVPGYSEVYPVEDLI--WDNTNKALDYREDILNLHRLDDEALEDLLERLEESQLDN 584 (718)
T ss_pred eEEEEecCCcccccchHHhh--hhhhccchhHHHHHHhhhcCCHHHHHHHHHHHHhccccc
Confidence 44569999999999987743 233333345566677778888888888888888766643
No 38
>PF08563 P53_TAD: P53 transactivation motif; InterPro: IPR013872 The binding of this protein by regulatory proteins regulates p53 transcription activation. This entry is comprised of a single amphipathic alpha helix and contains a highly conserved motif [, ]. ; GO: 0005515 protein binding; PDB: 1YCQ_B 2Z5T_R 3DAB_B 3DAC_B 2Z5S_Q 2K8F_B 2L14_B 1YCR_B.
Probab=21.93 E-value=31 Score=20.00 Aligned_cols=17 Identities=41% Similarity=0.433 Sum_probs=9.3
Q ss_pred CCCCCCCCCccccccch
Q 032587 3 TSSILPLPQLSFLSLRL 19 (137)
Q Consensus 3 ~~~~~~~~~~s~~~~~~ 19 (137)
....+|+||=+|-+-|.
T Consensus 4 ~~~~~PLSQeTF~~LW~ 20 (25)
T PF08563_consen 4 ESPELPLSQETFSDLWN 20 (25)
T ss_dssp SS-----STCCHHHHHH
T ss_pred cCCCCCccHHHHHHHHH
Confidence 44569999999988773
No 39
>PLN02227 fructose-bisphosphate aldolase I
Probab=21.64 E-value=48 Score=30.21 Aligned_cols=15 Identities=40% Similarity=0.539 Sum_probs=10.8
Q ss_pred eecC--C--CCCChhHHHH
Q 032587 46 YVPG--F--GEASPEAKGA 60 (137)
Q Consensus 46 ~Vp~--f--GG~sPE~daA 60 (137)
-||| | ||||+|..++
T Consensus 302 AVPGI~FLSGGQSeeeAt~ 320 (399)
T PLN02227 302 AVPGIMFLSGGQSELEATL 320 (399)
T ss_pred CCCeeeecCCCCcHHHHHH
Confidence 4666 4 9999987554
No 40
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=21.30 E-value=2.5e+02 Score=18.32 Aligned_cols=26 Identities=27% Similarity=0.477 Sum_probs=13.8
Q ss_pred hHHHHHHHHhcCCCCcHHHHHHHHHh
Q 032587 86 AYKELMEFLERHPLNDGDKFCADLMR 111 (137)
Q Consensus 86 ~y~wL~~Fl~~~pl~DGd~fL~~Lmr 111 (137)
....|++-+.+......+.|+..|..
T Consensus 48 k~~~LLd~l~~kg~~a~~~F~~~L~~ 73 (85)
T PF00619_consen 48 KARKLLDILKRKGPEAFDIFCQALRE 73 (85)
T ss_dssp HHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCHHHHHHHHHHHHh
Confidence 34445555554444455556665555
No 41
>PRK13730 conjugal transfer pilus assembly protein TrbC; Provisional
Probab=21.16 E-value=1.4e+02 Score=25.08 Aligned_cols=36 Identities=19% Similarity=0.281 Sum_probs=28.9
Q ss_pred HHhhc-cChhhHHHHHHHHhcCCC-CcHHHHHHHHHhc
Q 032587 77 AQLQS-YNPEAYKELMEFLERHPL-NDGDKFCADLMRE 112 (137)
Q Consensus 77 ~QL~e-~np~~y~wL~~Fl~~~pl-~DGd~fL~~Lmre 112 (137)
.||.+ ++++.-.|+-.-+.+||+ .|+..|+.+|++.
T Consensus 42 ~~l~~~~~~~~~~~~~~~~~~npl~~~d~~~lD~l~~~ 79 (212)
T PRK13730 42 RQLREKPDHQLKAWAEKQVLENPLQRSDNHFLDELVRK 79 (212)
T ss_pred HHHHcCCChHHHHHHHHhhhcCCCCchhHHHHHHHHHH
Confidence 34444 567777889888889999 6889999999886
No 42
>PLN02425 probable fructose-bisphosphate aldolase
Probab=20.75 E-value=53 Score=29.83 Aligned_cols=15 Identities=40% Similarity=0.558 Sum_probs=10.9
Q ss_pred eecC--C--CCCChhHHHH
Q 032587 46 YVPG--F--GEASPEAKGA 60 (137)
Q Consensus 46 ~Vp~--f--GG~sPE~daA 60 (137)
-||| | ||||+|..++
T Consensus 293 AVPGI~FLSGGqseeeAt~ 311 (390)
T PLN02425 293 AVPGIMFLSGGQSEVEATL 311 (390)
T ss_pred CCCcceeccCCCcHHHHHH
Confidence 4666 4 9999997554
No 43
>PF06713 bPH_4: Bacterial PH domain; InterPro: IPR009589 This entry is represented by Bacteriophage SP-beta, YolF. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical proteins specific to Oceanobacillus and Bacillus species. Members of this family are typically around 130 residues in length. The function of this family is unknown.
Probab=20.44 E-value=77 Score=21.34 Aligned_cols=17 Identities=24% Similarity=0.436 Sum_probs=13.3
Q ss_pred CCCCcHHHHHHHHHhcc
Q 032587 97 HPLNDGDKFCADLMRES 113 (137)
Q Consensus 97 ~pl~DGd~fL~~Lmre~ 113 (137)
-.|+|=|+|+++|.+.|
T Consensus 58 IsP~~~~~FI~~L~k~n 74 (74)
T PF06713_consen 58 ISPKDKEEFIAELQKRN 74 (74)
T ss_pred EECCCHHHHHHHHHhhC
Confidence 34688899999998764
No 44
>cd00131 PAX Paired Box domain
Probab=20.16 E-value=3.7e+02 Score=19.88 Aligned_cols=60 Identities=17% Similarity=0.035 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccChhhHHHHHHHHhcCCCC--------------cHHHHHHHHHhcccCCchhHHH
Q 032587 60 AKHLHNFFTYIAVRIITAQLQSYNPEAYKELMEFLERHPLN--------------DGDKFCADLMRESSRHKGLALR 122 (137)
Q Consensus 60 Ak~L~~yfTy~AvRvVl~QL~e~np~~y~wL~~Fl~~~pl~--------------DGd~fL~~Lmre~~~~~~LAlR 122 (137)
++++.-|-.=...+.|..++.=..+..+.|+..|-++..+. +-+.||.++++++ +++-++
T Consensus 24 ~rIv~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~---p~~Tl~ 97 (128)
T cd00131 24 QRIVELAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQEN---PGMFAW 97 (128)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHC---CCCCHH
Confidence 34444444444556666666666677899999998764442 1257788888887 555333
Done!