Query 031297
Match_columns 162
No_of_seqs 148 out of 245
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 12:06:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031297.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031297hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1348 Asparaginyl peptidases 100.0 3.2E-38 7E-43 279.6 8.5 119 1-120 161-290 (477)
2 PF01650 Peptidase_C13: Peptid 100.0 1E-32 2.2E-37 233.0 8.0 122 1-125 113-240 (256)
3 KOG1349 Gpi-anchor transamidas 100.0 4.7E-32 1E-36 231.4 5.6 141 1-147 145-293 (309)
4 COG5206 GPI8 Glycosylphosphati 99.9 1.3E-26 2.8E-31 200.1 4.4 146 1-150 145-296 (382)
5 PF00656 Peptidase_C14: Caspas 96.3 0.0011 2.4E-08 52.9 0.4 53 1-54 72-135 (248)
6 cd00032 CASc Caspase, interleu 88.6 0.29 6.3E-06 40.6 2.0 51 1-51 81-132 (243)
7 smart00115 CASc Caspase, inter 88.2 0.28 6E-06 40.9 1.7 50 1-50 80-130 (241)
8 KOG1546 Metacaspase involved i 83.1 2 4.3E-05 38.9 4.6 19 36-54 194-212 (362)
9 PF12770 CHAT: CHAT domain 67.0 3.4 7.4E-05 33.8 1.6 42 1-49 148-201 (287)
10 PF06866 DUF1256: Protein of u 51.7 23 0.00049 28.9 3.9 34 16-50 66-99 (163)
11 TIGR02841 spore_YyaC putative 49.0 22 0.00047 28.5 3.3 33 16-49 42-74 (140)
12 KOG1735 Actin depolymerizing f 48.6 25 0.00055 28.2 3.6 62 20-81 8-74 (146)
13 TIGR02855 spore_yabG sporulati 47.3 15 0.00032 32.5 2.3 37 17-55 178-215 (283)
14 PF14252 DUF4347: Domain of un 38.5 38 0.00083 27.2 3.3 62 2-66 54-128 (165)
15 PF10116 Host_attach: Protein 38.3 50 0.0011 25.0 3.7 39 19-57 74-112 (138)
16 cd08511 PBP2_NikA_DppA_OppA_li 29.9 51 0.0011 29.0 2.9 26 9-34 68-93 (467)
17 PF00496 SBP_bac_5: Bacterial 29.8 54 0.0012 27.4 3.0 26 10-35 28-53 (374)
18 cd08490 PBP2_NikA_DppA_OppA_li 25.6 59 0.0013 28.5 2.5 25 10-34 66-90 (470)
19 COG3407 MVD1 Mevalonate pyroph 24.7 2E+02 0.0042 26.0 5.7 45 5-66 250-294 (329)
20 cd08494 PBP2_NikA_DppA_OppA_li 24.5 62 0.0014 28.1 2.5 25 10-34 69-93 (448)
21 cd08496 PBP2_NikA_DppA_OppA_li 24.5 62 0.0014 28.4 2.5 25 10-34 68-92 (454)
22 PF08455 SNF2_assoc: Bacterial 24.0 72 0.0016 28.0 2.8 25 15-39 273-297 (377)
23 cd08492 PBP2_NikA_DppA_OppA_li 23.1 62 0.0013 28.5 2.2 24 10-33 70-93 (484)
24 cd08507 PBP2_SgrR_like The C-t 22.5 62 0.0013 28.7 2.1 27 10-36 74-100 (448)
25 TIGR00246 tRNA_RlmH_YbeA rRNA 22.1 1.5E+02 0.0033 23.5 4.0 30 14-45 74-103 (153)
26 PF08259 Periviscerokin: Periv 21.9 44 0.00094 16.0 0.6 10 5-14 1-10 (11)
27 cd08493 PBP2_DppA_like The sub 21.1 66 0.0014 28.5 2.0 24 10-33 69-92 (482)
28 PRK13626 transcriptional regul 20.5 93 0.002 28.8 2.9 27 10-36 188-214 (552)
29 TIGR02294 nickel_nikA nickel A 20.2 84 0.0018 28.1 2.5 25 10-34 73-97 (500)
30 cd08495 PBP2_NikA_DppA_OppA_li 20.2 74 0.0016 28.2 2.1 24 10-33 72-95 (482)
31 cd08491 PBP2_NikA_DppA_OppA_li 20.1 85 0.0018 27.9 2.5 25 10-34 69-93 (473)
No 1
>KOG1348 consensus Asparaginyl peptidases [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.2e-38 Score=279.56 Aligned_cols=119 Identities=20% Similarity=0.377 Sum_probs=111.1
Q ss_pred CCCCCCCCeeecCCCCccCHHHHHHHHHHHHHhCccceEEEEEeccccccccccCCC--CcEEEEeccCCCCCccceeec
Q 031297 1 MTGHGGDEFLKFQDSEELQSHDLADAVKQMKEKHRFKELLIMVDTCQAATLFSQVPV--TNFFGSVMETIHTDSAYRTTL 78 (162)
Q Consensus 1 ftgHGg~g~l~Fpd~~~L~a~dL~~~l~~M~~~krY~kmvf~vEaC~SgSmf~~l~~--~NV~a~Taa~~~e~S~ya~~~ 78 (162)
|+||||||.|.||+++.|+++||+++|++||+.|+|+|||||+|||||||||+++.+ .||||+||||++| |+|+|||
T Consensus 161 ytDHG~pGvl~mP~~~~l~akdlnevL~kmhk~k~Y~~mvfYlEACESGSmfegiLp~~lnIYatTAaNa~E-SSwgtyc 239 (477)
T KOG1348|consen 161 YTDHGGPGVLGMPTSPDLYAKDLNEVLKKMHKSKTYKKMVFYLEACESGSMFEGILPKNLNIYATTAANARE-SSWGTYC 239 (477)
T ss_pred EecCCCCceEecCCCcchhHHHHHHHHHHHHhccchheEEEEeeeccCcchhhhhccCCCcEEEeecCCccc-cccceeC
Confidence 689999999999998899999999999999999999999999999999999997665 8999999999999 8889999
Q ss_pred cCC----CCCCCCccc-----ccccchhhhcccchhhhhhhhhhhhhcccc
Q 031297 79 SRK----TSETKMPLQ-----QSVEHDESRQLINSNVQDQTSDTKIEDKQC 120 (162)
Q Consensus 79 ~~~----~~~~~~~lg-----~~~~~~e~~dL~~etl~~qf~~i~~~~~~~ 120 (162)
+.. ..++.+||| +||||||.+||++|||++|+..||.++...
T Consensus 240 p~~~psppse~~tcLGDlySV~WmeDSd~hdL~kETL~qQYhlVK~rt~~s 290 (477)
T KOG1348|consen 240 PGEYPSPPSEYSTCLGDLYSVNWMEDSDVHDLKKETLHQQYHLVKKRTNTS 290 (477)
T ss_pred CCCCCCChhhcccccccceeeeeeccCccccchHHHHHHHHHHHHHhcCCC
Confidence 943 337999999 999999999999999999999999988744
No 2
>PF01650 Peptidase_C13: Peptidase C13 family; InterPro: IPR001096 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 C13 (legumain family, clan CD). A type example is legumain from Canavalia ensiformis (Jack bean, Horse bean). The blood fluke parasite Schistosoma mansoni has two cysteine proteases in its digestive tract, one a cathepsin B-like protease, the other termed hemoglobinase [, ]. The latter has been hard to purify, free of cathepsin B, and expressed forms in Escherichia coli prove to be inactive, suggesting that hemoglobinase may act in association with cathepsin B [, ]. Plant vacuolar processing enzyme and legumain from legumes [] have been shown to have sequence and functional similarity to hemoglobinase. The catalytic residues of the family are currently unknown, but sequence alignments reveal one totally conserved cysteine and two totally conserved histidines.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis
Probab=99.97 E-value=1e-32 Score=232.96 Aligned_cols=122 Identities=31% Similarity=0.483 Sum_probs=110.8
Q ss_pred CCCCCCCCeeecCCCCccCHHHHHHHHHHHHHhCccceEEEEEeccccccccccCCC-CcEEEEeccCCCCCccceeecc
Q 031297 1 MTGHGGDEFLKFQDSEELQSHDLADAVKQMKEKHRFKELLIMVDTCQAATLFSQVPV-TNFFGSVMETIHTDSAYRTTLS 79 (162)
Q Consensus 1 ftgHGg~g~l~Fpd~~~L~a~dL~~~l~~M~~~krY~kmvf~vEaC~SgSmf~~l~~-~NV~a~Taa~~~e~S~ya~~~~ 79 (162)
|+||||+|+|+||+.+.|++.||+++|++|++++||+||||++|||+|||||+.|+. |||+++|||+++| ++|+|||
T Consensus 113 ~~~HG~~~~l~~~~~~~l~~~~L~~~L~~m~~~~~y~~lv~~veaC~SGs~~~~L~~~~nv~~iTAa~~~e-~Sy~~~~- 190 (256)
T PF01650_consen 113 FTGHGGPGFLKFPDGEELTADDLADALDKMHEKKRYKKLVFVVEACYSGSFFEGLLKSPNVYVITAANADE-SSYGCYC- 190 (256)
T ss_pred EeccCCCCcccCCCcccccHHHHHHHHHHHHhhCCcceEEEEEecccccchhhccCCCCCEEEEecCCccc-ccccccc-
Confidence 689999999999988899999999999999999999999999999999999999666 9999999999999 7889999
Q ss_pred CCCCCCCCccc-----ccccchhhhcccchhhhhhhhhhhhhccccccccc
Q 031297 80 RKTSETKMPLQ-----QSVEHDESRQLINSNVQDQTSDTKIEDKQCPFTQR 125 (162)
Q Consensus 80 ~~~~~~~~~lg-----~~~~~~e~~dL~~etl~~qf~~i~~~~~~~~~~~~ 125 (162)
.++.+++|+| +||++++..+++++|+++||+.++.+....++.+.
T Consensus 191 -~~~~~~~~l~d~fs~~~m~~~~~~~~~~~Tl~~~f~~v~~~~~~shv~~~ 240 (256)
T PF01650_consen 191 -SDDSIGTYLGDAFSYNWMEDSDSHPLSEETLDDQFEYVKRKTTGSHVQQY 240 (256)
T ss_pred -cccccccEeHHHHHHHhhhhhccCCccccCHHHHHHHHHHhcccchHHhc
Confidence 2335889999 99999999999999999999999988765555544
No 3
>KOG1349 consensus Gpi-anchor transamidase [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=4.7e-32 Score=231.42 Aligned_cols=141 Identities=33% Similarity=0.440 Sum_probs=125.2
Q ss_pred CCCCCCCCeeecCCCCccCHHHHHHHHHHHHHhCccceEEEEEeccccccccccCCCCcEEEEeccCCCCCccceeeccC
Q 031297 1 MTGHGGDEFLKFQDSEELQSHDLADAVKQMKEKHRFKELLIMVDTCQAATLFSQVPVTNFFGSVMETIHTDSAYRTTLSR 80 (162)
Q Consensus 1 ftgHGg~g~l~Fpd~~~L~a~dL~~~l~~M~~~krY~kmvf~vEaC~SgSmf~~l~~~NV~a~Taa~~~e~S~ya~~~~~ 80 (162)
||||||+|||||||.|+|+++||+++|++|+++|||+||+|++|||||.||++++..|||.|+.++-.+|+|+ +..
T Consensus 145 mtGHGgd~FlKFqd~eelts~dLadai~qm~e~~Ryneil~miDTCQaasly~~~~sPNVLav~SS~~ge~Sy----Sh~ 220 (309)
T KOG1349|consen 145 LTGHGGDGFLKFQDAEELTSDDLADAIQQMWEKKRYNEILFMIDTCQAASLYERFYSPNVLAVASSLVGEPSY----SHH 220 (309)
T ss_pred EccCCCccceecccHHHhhhHHHHHHHHHHHHhhhhceEEEEeeccchHHHHHhhcCCCeEEEeecccCCccc----ccC
Confidence 6999999999999999999999999999999999999999999999999999999999999999999999665 666
Q ss_pred CCCCCCCccc-----ccccchhhhc-ccchhhhhhhhhhhhhccccccccch--hhhhcccccccccceeeEehh
Q 031297 81 KTSETKMPLQ-----QSVEHDESRQ-LINSNVQDQTSDTKIEDKQCPFTQRW--NAFQDNLEKIERIDSLVNYGL 147 (162)
Q Consensus 81 ~~~~~~~~lg-----~~~~~~e~~d-L~~etl~~qf~~i~~~~~~~~~~~~~--~~~~~~~~~~~~~D~~~~~~~ 147 (162)
.|+++|++.- +-+++.|+.. -++.|+++.|+. ..+. .|+++++. ..+++.|.+|.+|||||++.+
T Consensus 221 ~d~~Igv~vIDrftyy~l~flek~~~~~~~~l~dl~~s-~~~~-~~~St~gvr~dl~~r~~~~v~itDFFg~vr~ 293 (309)
T KOG1349|consen 221 SDSDIGVYVIDRFTYYTLEFLEKGIGAKNRTLQDLFDS-CPKR-LLGSTPGVRTDLYQRDPKDVLITDFFGSVRI 293 (309)
T ss_pred CCcccceeeeccchHHHHHHHHhcccchhhhHHHHHHh-CChh-hhcCCcCcccccccCCcccceeeeeccccee
Confidence 6777998887 8899999955 666689999997 4444 57776666 448999999999999999983
No 4
>COG5206 GPI8 Glycosylphosphatidylinositol transamidase (GPIT), subunit GPI8 [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=1.3e-26 Score=200.09 Aligned_cols=146 Identities=31% Similarity=0.398 Sum_probs=122.3
Q ss_pred CCCCCCCCeeecCCCCccCHHHHHHHHHHHHHhCccceEEEEEeccccccccccCCCCcEEEEeccCCCCCccceeeccC
Q 031297 1 MTGHGGDEFLKFQDSEELQSHDLADAVKQMKEKHRFKELLIMVDTCQAATLFSQVPVTNFFGSVMETIHTDSAYRTTLSR 80 (162)
Q Consensus 1 ftgHGg~g~l~Fpd~~~L~a~dL~~~l~~M~~~krY~kmvf~vEaC~SgSmf~~l~~~NV~a~Taa~~~e~S~ya~~~~~ 80 (162)
|+||||++||||||.++|+++||+++|++|+++|||+|++|++|||||.+|+++...|||.|+.++..++ |+|.-+++.
T Consensus 145 mtGHGgd~FlKFqdaeemtseDladai~ql~~~kRyNeIlfmiDTCQAnaly~k~ysPNvLavgsSeig~-ssyShhsd~ 223 (382)
T COG5206 145 MTGHGGDAFLKFQDAEEMTSEDLADAISQLAAKKRYNEILFMIDTCQANALYDKSYSPNVLAVGSSEIGQ-SSYSHHSDS 223 (382)
T ss_pred EccCCCccceecccHHHhhhHHHHHHHHHHHHhhhhceEEEEeeccccchhhhhccCCceEEEeccccCC-ccccccchh
Confidence 6999999999999999999999999999999999999999999999999999999999999999998888 777666654
Q ss_pred CCCCCCCccc-----ccccchhhhc-ccchhhhhhhhhhhhhccccccccchhhhhcccccccccceeeEehhhhh
Q 031297 81 KTSETKMPLQ-----QSVEHDESRQ-LINSNVQDQTSDTKIEDKQCPFTQRWNAFQDNLEKIERIDSLVNYGLIIM 150 (162)
Q Consensus 81 ~~~~~~~~lg-----~~~~~~e~~d-L~~etl~~qf~~i~~~~~~~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~ 150 (162)
. +|+..- .-+++.|+.| -++-||++.+.....+.-.+++.-....|.|.|..+.++|||+++.-+.+
T Consensus 224 ~---IgvaVIDrFty~~l~fle~id~~skltlqDL~~s~n~e~ihS~~gv~~~~fdr~p~d~litDFF~nVqn~~l 296 (382)
T COG5206 224 L---IGVAVIDRFTYFFLKFLEKIDIGSKLTLQDLLASLNKEPIHSHVGVRELVFDRRPSDFLITDFFANVQNSAL 296 (382)
T ss_pred h---hhHHHhhcchHHHHHHHhhcCcCCeeEHHHHHHhcCcccccCCCCcccccccCCccceeehHhhhhhhhcch
Confidence 4 565444 6678888877 58889999998755544444444334457999999999999998876643
No 5
>PF00656 Peptidase_C14: Caspase domain; InterPro: IPR011600 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 sequences represent the p20 (20kDa) and p10 (10kDa) subunits of caspases, which together form the catalytic domain of the caspase and are derived from the p45 (45 kDa) precursor (IPR002398 from INTERPRO) []. Caspases (Cysteine-dependent ASPartyl-specific proteASE) are cysteine peptidases that belong to the MEROPS peptidase family C14 (caspase family, clan CD) based on the architecture of their catalytic dyad or triad []. Caspases are tightly regulated proteins that require zymogen activation to become active, and once active can be regulated by caspase inhibitors. Activated caspases act as cysteine proteases, using the sulphydryl group of a cysteine side chain for catalysing peptide bond cleavage at aspartyl residues in their substrates. The catalytic cysteine and histidine residues are on the p20 subunit after cleavage of the p45 precursor. Caspases are mainly involved in mediating cell death (apoptosis) [, , ]. They have two main roles within the apoptosis cascade: as initiators that trigger the cell death process, and as effectors of the process itself. Caspase-mediated apoptosis follows two main pathways, one extrinsic and the other intrinsic or mitochondrial-mediated. The extrinsic pathway involves the stimulation of various TNF (tumour necrosis factor) cell surface receptors on cells targeted to die by various TNF cytokines that are produced by cells such as cytotoxic T cells. The activated receptor transmits the signal to the cytoplasm by recruiting FADD, which forms a death-inducing signalling complex (DISC) with caspase-8. The subsequent activation of caspase-8 initiates the apoptosis cascade involving caspases 3, 4, 6, 7, 9 and 10. The intrinsic pathway arises from signals that originate within the cell as a consequence of cellular stress or DNA damage. The stimulation or inhibition of different Bcl-2 family receptors results in the leakage of cytochrome c from the mitochondria, and the formation of an apoptosome composed of cytochrome c, Apaf1 and caspase-9. The subsequent activation of caspase-9 initiates the apoptosis cascade involving caspases 3 and 7, among others. At the end of the cascade, caspases act on a variety of signal transduction proteins, cytoskeletal and nuclear proteins, chromatin-modifying proteins, DNA repair proteins and endonucleases that destroy the cell by disintegrating its contents, including its DNA. The different caspases have different domain architectures depending upon where they fit into the apoptosis cascades, however they all carry the catalytic p10 and p20 subunits. Caspases can have roles other than in apoptosis, such as caspase-1 (interleukin-1 beta convertase) (3.4.22.36 from EC), which is involved in the inflammatory process. The activation of apoptosis can sometimes lead to caspase-1 activation, providing a link between apoptosis and inflammation, such as during the targeting of infected cells. Caspases may also be involved in cell differentiation [].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 1M72_C 2NN3_C 3V4L_A 3IBF_B 2QLF_D 2QLB_C 3IBC_B 2QL9_A 3R5K_B 3H1P_A ....
Probab=96.34 E-value=0.0011 Score=52.90 Aligned_cols=53 Identities=23% Similarity=0.300 Sum_probs=33.3
Q ss_pred CCCCCCC--C----eeecCCCCccCHHH---HHHHHHHHHHhCc-cc-eEEEEEecccccccccc
Q 031297 1 MTGHGGD--E----FLKFQDSEELQSHD---LADAVKQMKEKHR-FK-ELLIMVDTCQAATLFSQ 54 (162)
Q Consensus 1 ftgHGg~--g----~l~Fpd~~~L~a~d---L~~~l~~M~~~kr-Y~-kmvf~vEaC~SgSmf~~ 54 (162)
|+|||.. + .+.-.|...+..+. +.+.|+.+..+.. -+ | +|++|+|+||.+...
T Consensus 72 fsGHG~~~~~~~~~~~~~~d~~~~~~d~~~~~~~~l~~~~~~~~~~~~k-~~ilD~C~sg~~~~~ 135 (248)
T PF00656_consen 72 FSGHGIQVDGEGGDEDSGYDGYLLPLDANLILDDELRDLLCKSLPKKPK-LFILDCCRSGGFIDG 135 (248)
T ss_dssp EESEEETETTCCSTEEEETSSEEEEHHHHEEHHHHTSTTTTGGGTTS-E-EEEEESESSSBTBCE
T ss_pred EeccccccCCccCcccccccceeeecchhhhHHHHHhhhhhhhccCCcc-EEeeccccCCccCCc
Confidence 6899965 2 22222432344444 6777777766622 22 5 999999999998765
No 6
>cd00032 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
Probab=88.59 E-value=0.29 Score=40.64 Aligned_cols=51 Identities=14% Similarity=0.225 Sum_probs=34.5
Q ss_pred CCCCCCCCeeecCCCCccCHHHHHHHHHHHHHhC-ccceEEEEEeccccccc
Q 031297 1 MTGHGGDEFLKFQDSEELQSHDLADAVKQMKEKH-RFKELLIMVDTCQAATL 51 (162)
Q Consensus 1 ftgHGg~g~l~Fpd~~~L~a~dL~~~l~~M~~~k-rY~kmvf~vEaC~SgSm 51 (162)
|.+||..|.|.-.|.+.+.-++|.+.|..-.-.. +-|-=+|+|+||...-.
T Consensus 81 ~~sHG~~~~l~~~D~~~v~l~~i~~~f~~~~~~sl~~kPKl~~iqACRg~~~ 132 (243)
T cd00032 81 ILSHGEEGGIYGTDGDVVPIDEITSLFNGDNCPSLAGKPKLFFIQACRGDEL 132 (243)
T ss_pred ECCCCCCCEEEEecCcEEEHHHHHHhhccCCCccccCCCcEEEEECCCCCcC
Confidence 4689999999988866777777766654211111 12334889999998654
No 7
>smart00115 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
Probab=88.19 E-value=0.28 Score=40.95 Aligned_cols=50 Identities=14% Similarity=0.180 Sum_probs=33.0
Q ss_pred CCCCCCCCeeecCCCCccCHHHHHHHHHHHHH-hCccceEEEEEecccccc
Q 031297 1 MTGHGGDEFLKFQDSEELQSHDLADAVKQMKE-KHRFKELLIMVDTCQAAT 50 (162)
Q Consensus 1 ftgHGg~g~l~Fpd~~~L~a~dL~~~l~~M~~-~krY~kmvf~vEaC~SgS 50 (162)
|.+||..|+|.-.|+..+.-++|.+.|.--.- .-+-|==+|+|+||...-
T Consensus 80 ~~sHG~~~~l~~~D~~~v~l~~i~~~f~~~~c~~L~~kPKlffiqACRg~~ 130 (241)
T smart00115 80 LLSHGEEGGIYGTDHSPLPLDEIFSLFNGDNCPSLAGKPKLFFIQACRGDE 130 (241)
T ss_pred EcCCCCCCeEEEecCCEEEHHHHHHhccccCChhhcCCCcEEEEeCCCCCC
Confidence 46999999999888767777777666632110 111122378899998753
No 8
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=83.11 E-value=2 Score=38.91 Aligned_cols=19 Identities=21% Similarity=0.350 Sum_probs=16.4
Q ss_pred cceEEEEEecccccccccc
Q 031297 36 FKELLIMVDTCQAATLFSQ 54 (162)
Q Consensus 36 Y~kmvf~vEaC~SgSmf~~ 54 (162)
=-|+-.++|+|+||++.+-
T Consensus 194 G~~lt~I~DSCHSGgliDl 212 (362)
T KOG1546|consen 194 GCKLTAISDSCHSGGLIDL 212 (362)
T ss_pred CceEEEEeecccCCCcccc
Confidence 3589999999999999873
No 9
>PF12770 CHAT: CHAT domain
Probab=66.97 E-value=3.4 Score=33.79 Aligned_cols=42 Identities=24% Similarity=0.493 Sum_probs=30.1
Q ss_pred CCCCCCCC-------eeecC-----CCCccCHHHHHHHHHHHHHhCccceEEEEEeccccc
Q 031297 1 MTGHGGDE-------FLKFQ-----DSEELQSHDLADAVKQMKEKHRFKELLIMVDTCQAA 49 (162)
Q Consensus 1 ftgHGg~g-------~l~Fp-----d~~~L~a~dL~~~l~~M~~~krY~kmvf~vEaC~Sg 49 (162)
|+|||... .|.+. +...+++.||.+ ++ -.+ -+ ++++-||+|+
T Consensus 148 ~a~Hg~~~~~~~~~~~l~l~~~~~~~~~~l~~~~l~~-l~---l~~--~~-lVvLsaC~s~ 201 (287)
T PF12770_consen 148 FAGHGTFDPDPPDQSGLVLSDESGQEDGLLSAEELAQ-LD---LRG--PR-LVVLSACESA 201 (287)
T ss_pred EEcccccCCCCCCCCEEEEeccCCCCCcccCHHHHHh-hc---CCC--CC-EEEecCcCCc
Confidence 57899877 88886 455899999988 21 111 33 5567899999
No 10
>PF06866 DUF1256: Protein of unknown function (DUF1256); InterPro: IPR009665 This family consists of several uncharacterised bacterial proteins, which seem to be specific to the orders Clostridia and Bacillales. Family members are typically around 180 residues in length. The function of this family is unknown.
Probab=51.69 E-value=23 Score=28.90 Aligned_cols=34 Identities=24% Similarity=0.599 Sum_probs=27.4
Q ss_pred CccCHHHHHHHHHHHHHhCccceEEEEEecccccc
Q 031297 16 EELQSHDLADAVKQMKEKHRFKELLIMVDTCQAAT 50 (162)
Q Consensus 16 ~~L~a~dL~~~l~~M~~~krY~kmvf~vEaC~SgS 50 (162)
+.++|..|.+++++.+++.. +..++-||||-+..
T Consensus 66 ~PVHA~NL~e~l~~I~~~~~-~~~IIAIDAcLG~~ 99 (163)
T PF06866_consen 66 EPVHALNLEETLNEIKKKHP-NPFIIAIDACLGRP 99 (163)
T ss_pred CCcchhhHHHHHHHHHHHCC-CCeEEEEECCCCCc
Confidence 58999999999999655433 77899999998743
No 11
>TIGR02841 spore_YyaC putative sporulation protein YyaC. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, also called YyaC, is a member of that panel and is otherwise uncharacterized. The second round of PSI-BLAST shows many similarities to the germination protease GPR, which is found in exactly the same set of organisms and has a known role in the sporulation/germination process.
Probab=49.03 E-value=22 Score=28.48 Aligned_cols=33 Identities=27% Similarity=0.619 Sum_probs=27.1
Q ss_pred CccCHHHHHHHHHHHHHhCccceEEEEEeccccc
Q 031297 16 EELQSHDLADAVKQMKEKHRFKELLIMVDTCQAA 49 (162)
Q Consensus 16 ~~L~a~dL~~~l~~M~~~krY~kmvf~vEaC~Sg 49 (162)
+.++|..|.+++++.+++.. +..++-+|||=+.
T Consensus 42 ~PVHA~NL~e~l~~I~~~~~-~~~iIAIDAcLG~ 74 (140)
T TIGR02841 42 EPVHAKNLEEKLKIIKKKHP-NPFIIAIDACLGR 74 (140)
T ss_pred CCcccccHHHHHHHHHHhCC-CCeEEEEECccCC
Confidence 47999999999999655544 6788999999874
No 12
>KOG1735 consensus Actin depolymerizing factor [Cytoskeleton]
Probab=48.59 E-value=25 Score=28.22 Aligned_cols=62 Identities=11% Similarity=0.042 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHHHhCccceEEEEEeccccccccccCCCCcE--EEEeccCC---CCCccceeeccCC
Q 031297 20 SHDLADAVKQMKEKHRFKELLIMVDTCQAATLFSQVPVTNF--FGSVMETI---HTDSAYRTTLSRK 81 (162)
Q Consensus 20 a~dL~~~l~~M~~~krY~kmvf~vEaC~SgSmf~~l~~~NV--~a~Taa~~---~e~S~ya~~~~~~ 81 (162)
+++-..++++|+.+|+++-++|.++-=.....-+.+-.++. --.++.-+ .++=.||.|=-+.
T Consensus 8 sde~~~~F~elk~kk~~r~ivF~i~~~~~~i~ve~~g~~~~s~~~f~~~l~~~~~~dCrYA~yDf~f 74 (146)
T KOG1735|consen 8 SDECKKVFNELKVKKRKRYVVFKISEDKKQIIVEKGGSPGASYDDFVASLPKMPEKDCRYALYDFEF 74 (146)
T ss_pred cHHHHHHHHHHHhhcceeEEEEEeccccccccccccCCCCCchhhhHHHhccCCccccceEEecceE
Confidence 46778999999999999999999987655555555433322 22333333 5667777775543
No 13
>TIGR02855 spore_yabG sporulation peptidase YabG. Members of this family are the protein YabG, demonstrated for Bacillus subtilis to be an endopeptidase able to release N-terminal peptides from a number of sporulation proteins, including CotT, CotF, and SpoIVA. It appears to be expressed under control of sigma-K.
Probab=47.33 E-value=15 Score=32.54 Aligned_cols=37 Identities=19% Similarity=0.428 Sum_probs=29.8
Q ss_pred ccCHHHHHHHHHHHHHhC-ccceEEEEEeccccccccccC
Q 031297 17 ELQSHDLADAVKQMKEKH-RFKELLIMVDTCQAATLFSQV 55 (162)
Q Consensus 17 ~L~a~dL~~~l~~M~~~k-rY~kmvf~vEaC~SgSmf~~l 55 (162)
+-+++.+.++++...+.. -|-++|++.-|||| -||.|
T Consensus 178 YrnSkyFVeaVk~aR~y~~~~D~LVIFAGACQS--~yEal 215 (283)
T TIGR02855 178 YRHSKYFVETVREARKYVPSLDQLVIFAGACQS--HFESL 215 (283)
T ss_pred hhhhHHHHHHHHHHHhcCCCcccEEEEcchhHH--HHHHH
Confidence 568899999999876655 67799999999996 45654
No 14
>PF14252 DUF4347: Domain of unknown function (DUF4347)
Probab=38.50 E-value=38 Score=27.21 Aligned_cols=62 Identities=16% Similarity=0.241 Sum_probs=41.3
Q ss_pred CCCCCCCeeecCCCCccCHHHHHHHHHHHHHhCcc----ceEEEEEeccccccc------cc---cCCCCcEEEEecc
Q 031297 2 TGHGGDEFLKFQDSEELQSHDLADAVKQMKEKHRF----KELLIMVDTCQAATL------FS---QVPVTNFFGSVME 66 (162)
Q Consensus 2 tgHGg~g~l~Fpd~~~L~a~dL~~~l~~M~~~krY----~kmvf~vEaC~SgSm------f~---~l~~~NV~a~Taa 66 (162)
..||+||-|.+.+. .|+++.|..--..+..-++. ..+++| .|..+.= .+ ++..-||.|.+-.
T Consensus 54 vsHG~~G~l~LG~~-~l~~~~L~~~~~~l~~w~~~L~~~~~IlLy--GC~vaag~~G~~fv~~L~~ltga~VAAS~~~ 128 (165)
T PF14252_consen 54 VSHGSPGALQLGNT-WLSAETLEQYADELAQWGQALADDGDILLY--GCNVAAGEEGQEFVQRLAQLTGADVAASTDL 128 (165)
T ss_pred EcCCCcceEEECCc-eeCHHHHHHHHHHHHHHHHHhCCCCcEEEE--cCccCcchhHHHHHHHHHHHHCCCEEecCCC
Confidence 47999999999886 99999988755555444432 356666 7876552 11 1445677766654
No 15
>PF10116 Host_attach: Protein required for attachment to host cells; InterPro: IPR019291 Members of this family of bacterial proteins are required for the attachment of the bacterium to host cells [, ].
Probab=38.28 E-value=50 Score=24.96 Aligned_cols=39 Identities=13% Similarity=0.270 Sum_probs=31.3
Q ss_pred CHHHHHHHHHHHHHhCccceEEEEEeccccccccccCCC
Q 031297 19 QSHDLADAVKQMKEKHRFKELLIMVDTCQAATLFSQVPV 57 (162)
Q Consensus 19 ~a~dL~~~l~~M~~~krY~kmvf~vEaC~SgSmf~~l~~ 57 (162)
-+.++++.|.+...+++|.+++++.+.=.-|-|-+.|.+
T Consensus 74 Fa~~vA~~L~~~~~~~~~~~LvlvA~p~~LG~LR~~L~~ 112 (138)
T PF10116_consen 74 FAREVADRLEKARRAGKFDRLVLVAPPRFLGLLREHLSK 112 (138)
T ss_pred HHHHHHHHHHHHHHhCCCCeEEEEECHHHHHHHHHHhCH
Confidence 468899999999999999999999877666665555533
No 16
>cd08511 PBP2_NikA_DppA_OppA_like_5 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is mos
Probab=29.93 E-value=51 Score=28.97 Aligned_cols=26 Identities=12% Similarity=0.234 Sum_probs=22.6
Q ss_pred eeecCCCCccCHHHHHHHHHHHHHhC
Q 031297 9 FLKFQDSEELQSHDLADAVKQMKEKH 34 (162)
Q Consensus 9 ~l~Fpd~~~L~a~dL~~~l~~M~~~k 34 (162)
-++|.|++.++++|+..+++.+....
T Consensus 68 ~~~wsdG~pvTA~Dv~~s~~~~~~~~ 93 (467)
T cd08511 68 GVKFHDGTPFDAAAVKANLERLLTLP 93 (467)
T ss_pred CCCccCCCCCCHHHHHHHHHHHhCCC
Confidence 35899999999999999999987654
No 17
>PF00496 SBP_bac_5: Bacterial extracellular solute-binding proteins, family 5 Middle; InterPro: IPR000914 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into Gram-positive bacteria which are surrounded by a single membrane and therefore have no periplasmic region the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families of clusters, which generally correlate with the nature of the solute bound. Family 5 currently includes periplasmic oligopeptide-binding proteins (oppA) of Gram-negative bacteria and homologous lipoproteins in Gram-positive bacteria (oppA, amiA or appA); periplasmic dipeptide-binding proteins of Escherichia coli (dppA) and Bacillus subtilis (dppE); periplasmic murein peptide-binding protein of E. coli (mppA); periplasmic peptide-binding proteins sapA of E. coli, Salmonella typhimurium and Haemophilus influenzae; periplasmic nickel-binding protein (nikA) of E. coli; haem-binding lipoprotein (hbpA or dppA) from H. influenzae; lipoprotein xP55 from Streptomyces lividans; and hypothetical proteins from H. influenzae (HI0213) and Rhizobium sp. (strain NGR234) symbiotic plasmid (y4tO and y4wM).; GO: 0005215 transporter activity, 0006810 transport; PDB: 1B51_A 1B0H_A 1QKA_A 1B9J_A 1B6H_A 1OLA_A 1B3L_C 1JEV_A 1B5H_A 1JET_A ....
Probab=29.79 E-value=54 Score=27.45 Aligned_cols=26 Identities=23% Similarity=0.434 Sum_probs=20.3
Q ss_pred eecCCCCccCHHHHHHHHHHHHHhCc
Q 031297 10 LKFQDSEELQSHDLADAVKQMKEKHR 35 (162)
Q Consensus 10 l~Fpd~~~L~a~dL~~~l~~M~~~kr 35 (162)
++|.|++.|+++|+..+++.+.....
T Consensus 28 ~~wsDG~~lTA~Dv~~s~~~~~~~~~ 53 (374)
T PF00496_consen 28 LKWSDGEPLTAEDVVFSFERLADPDY 53 (374)
T ss_dssp -B-TTSTB-SHHHHHHHHHHHHHCCG
T ss_pred eeecCCCcceeeEEeeeehhcccCCc
Confidence 78999999999999999999886553
No 18
>cd08490 PBP2_NikA_DppA_OppA_like_3 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=25.60 E-value=59 Score=28.47 Aligned_cols=25 Identities=20% Similarity=0.399 Sum_probs=22.4
Q ss_pred eecCCCCccCHHHHHHHHHHHHHhC
Q 031297 10 LKFQDSEELQSHDLADAVKQMKEKH 34 (162)
Q Consensus 10 l~Fpd~~~L~a~dL~~~l~~M~~~k 34 (162)
++|.|++.|+++|+.-+++.+...+
T Consensus 66 ~~wsDG~plTA~Dv~~s~~~~~~~~ 90 (470)
T cd08490 66 VKFHDGTPLTAEAVKASLERALAKS 90 (470)
T ss_pred CCccCCCCCCHHHHHHHHHHHhccC
Confidence 6899999999999999999987654
No 19
>COG3407 MVD1 Mevalonate pyrophosphate decarboxylase [Lipid metabolism]
Probab=24.68 E-value=2e+02 Score=26.02 Aligned_cols=45 Identities=18% Similarity=0.315 Sum_probs=32.2
Q ss_pred CCCCeeecCCCCccCHHHHHHHHHHHHHhCccceEEEEEeccccccccccCCCCcEEEEecc
Q 031297 5 GGDEFLKFQDSEELQSHDLADAVKQMKEKHRFKELLIMVDTCQAATLFSQVPVTNFFGSVME 66 (162)
Q Consensus 5 Gg~g~l~Fpd~~~L~a~dL~~~l~~M~~~krY~kmvf~vEaC~SgSmf~~l~~~NV~a~Taa 66 (162)
++|+++.|.+. ..++.+.+++|.+.+. -..|-+|| +|||+.++-.
T Consensus 250 s~p~~~y~~~~----s~~ii~~v~~~r~~g~--~~~fT~Da-----------GPnV~v~~~~ 294 (329)
T COG3407 250 SGPPFFYLTDE----SLRIIEFVHELRKEGN--AVYFTMDA-----------GPNVKVITLE 294 (329)
T ss_pred cCCceEEECcc----HHHHHHHHHHHHhcCC--ceEEEEcC-----------CCceEEEEec
Confidence 56889999764 6789999999888743 44444443 4999987763
No 20
>cd08494 PBP2_NikA_DppA_OppA_like_6 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=24.54 E-value=62 Score=28.11 Aligned_cols=25 Identities=12% Similarity=0.363 Sum_probs=22.3
Q ss_pred eecCCCCccCHHHHHHHHHHHHHhC
Q 031297 10 LKFQDSEELQSHDLADAVKQMKEKH 34 (162)
Q Consensus 10 l~Fpd~~~L~a~dL~~~l~~M~~~k 34 (162)
++|.|++.||++|+..+++.+...+
T Consensus 69 ~~fsdG~pvTA~Dv~~s~~~~~~~~ 93 (448)
T cd08494 69 VTFHDGTPFDAADVKFSLQRARAPD 93 (448)
T ss_pred CEecCcCCCCHHHHHhHHHHHhCCC
Confidence 6899999999999999999987654
No 21
>cd08496 PBP2_NikA_DppA_OppA_like_9 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA can bind peptides of a wide range of lengths (2-35 amino-acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most
Probab=24.50 E-value=62 Score=28.43 Aligned_cols=25 Identities=20% Similarity=0.320 Sum_probs=22.2
Q ss_pred eecCCCCccCHHHHHHHHHHHHHhC
Q 031297 10 LKFQDSEELQSHDLADAVKQMKEKH 34 (162)
Q Consensus 10 l~Fpd~~~L~a~dL~~~l~~M~~~k 34 (162)
++|.|++.+|++|+..+++.+....
T Consensus 68 ~~f~DG~pvTA~Dv~~s~~~~~~~~ 92 (454)
T cd08496 68 LTFSDGTPLDAAAVKANLDRGKSTG 92 (454)
T ss_pred CCccCCCCcCHHHHHHHHHHHhCCC
Confidence 6899999999999999999987654
No 22
>PF08455 SNF2_assoc: Bacterial SNF2 helicase associated; InterPro: IPR013663 This domain is found in bacterial proteins of the SWF/SNF/SWI helicase family to the N terminus of the SNF2 family N-terminal domain (IPR000330 from INTERPRO) and together with the Helicase conserved C-terminal domain (IPR001650 from INTERPRO). The function of the domain is not clear [].
Probab=24.01 E-value=72 Score=27.95 Aligned_cols=25 Identities=32% Similarity=0.666 Sum_probs=22.8
Q ss_pred CCccCHHHHHHHHHHHHHhCccceE
Q 031297 15 SEELQSHDLADAVKQMKEKHRFKEL 39 (162)
Q Consensus 15 ~~~L~a~dL~~~l~~M~~~krY~km 39 (162)
.+.+..+||.++|+-..++|+|-++
T Consensus 273 ~~~i~~~El~~iL~a~~~kkkY~rL 297 (377)
T PF08455_consen 273 SDDIDPEELADILKAYREKKKYYRL 297 (377)
T ss_pred eCCCCHHHHHHHHHHHHhCCCEEEC
Confidence 3579999999999999999999886
No 23
>cd08492 PBP2_NikA_DppA_OppA_like_15 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=23.08 E-value=62 Score=28.51 Aligned_cols=24 Identities=13% Similarity=0.343 Sum_probs=21.7
Q ss_pred eecCCCCccCHHHHHHHHHHHHHh
Q 031297 10 LKFQDSEELQSHDLADAVKQMKEK 33 (162)
Q Consensus 10 l~Fpd~~~L~a~dL~~~l~~M~~~ 33 (162)
++|.|++.|+++|+.-+++.+...
T Consensus 70 ~~wsdG~pvTA~Dv~~s~~~~~~~ 93 (484)
T cd08492 70 VTFSDGTPLDAEAVKANFDRILDG 93 (484)
T ss_pred CEecCCCCCCHHHHHHHHHHhcCC
Confidence 689999999999999999998753
No 24
>cd08507 PBP2_SgrR_like The C-terminal solute-binding domain of DNA-binding transcriptional regulator SgrR is related to the ABC-type oligopeptide-binding proteins and contains the type 2 periplasmic-binding fold. A novel family of SgrR transcriptional regulator contains a two-domain structure with an N terminal DNA-binding domain of the winged helix family and a C-terminal solute-binding domain. The C-terminal domain shows strong homology with the ABC-type oligopeptide-binding protein family, a member of the type 2 periplasmic-binding fold protein (PBP2) superfamily that also includes the C-terminal substrate-binding domain of LysR-type transcriptional regulators. SgrR (SugaR transport-related Regulator) is negatively autoregulated and activates transcription of divergent operon SgrS, which encodes a small RNA required for recovery from glucose-phosphate stress. Hence, the small RNA SgrS and SgrR, the transcription factor that controls sgrS expression, are both required for recovery f
Probab=22.45 E-value=62 Score=28.67 Aligned_cols=27 Identities=19% Similarity=0.507 Sum_probs=23.8
Q ss_pred eecCCCCccCHHHHHHHHHHHHHhCcc
Q 031297 10 LKFQDSEELQSHDLADAVKQMKEKHRF 36 (162)
Q Consensus 10 l~Fpd~~~L~a~dL~~~l~~M~~~krY 36 (162)
++|.|++.++++|+.-.++.+.....+
T Consensus 74 v~f~DG~pvtA~DV~~s~~r~~~~~~~ 100 (448)
T cd08507 74 VRFHNGRELTAEDVVFTLLRLRELESY 100 (448)
T ss_pred CEecCCCCccHHHHHHHHHHHhccccc
Confidence 689999999999999999998876543
No 25
>TIGR00246 tRNA_RlmH_YbeA rRNA large subunit m3Psi methyltransferase RlmH. This protein, in the SPOUT methyltransferase family, previously designated YbeA in E. coli, was shown to be responsible for a further modification, a methylation, to a pseudouridine base in ribosomal large subunit RNA.
Probab=22.15 E-value=1.5e+02 Score=23.51 Aligned_cols=30 Identities=13% Similarity=0.357 Sum_probs=24.4
Q ss_pred CCCccCHHHHHHHHHHHHHhCccceEEEEEec
Q 031297 14 DSEELQSHDLADAVKQMKEKHRFKELLIMVDT 45 (162)
Q Consensus 14 d~~~L~a~dL~~~l~~M~~~krY~kmvf~vEa 45 (162)
.+..+++.+|++.|+++...+ +++.|+|-.
T Consensus 74 ~Gk~~sS~~fA~~l~~~~~~g--~~i~FvIGG 103 (153)
T TIGR00246 74 PGKPWTTPQLADTLEKWKTDG--RDVTLLIGG 103 (153)
T ss_pred CCCcCCHHHHHHHHHHHhccC--CeEEEEEcC
Confidence 456899999999999986666 479999854
No 26
>PF08259 Periviscerokin: Periviscerokinin family; InterPro: IPR013231 Perviscerokinin neuropeptides are found in the abdominal perisympathetic organs of insects. They mediate visceral muscle contractile activity (myotropic activity). CAPA, which are in the periviscerokinin and pyrokinin peptide families, has potential medical importance. This is due to its myotropic effects on, for example, heart muscles and due to its occurrence in the Ixodoidea (ticks), which are important vectors in the transmission of many animal diseases []. These peptides also have a strong diuretic or anti-diuretic effect, suggesting they have significant medical implications [].
Probab=21.89 E-value=44 Score=15.98 Aligned_cols=10 Identities=20% Similarity=0.581 Sum_probs=7.9
Q ss_pred CCCCeeecCC
Q 031297 5 GGDEFLKFQD 14 (162)
Q Consensus 5 Gg~g~l~Fpd 14 (162)
|+.|.|.||-
T Consensus 1 gssGlI~fpR 10 (11)
T PF08259_consen 1 GSSGLIPFPR 10 (11)
T ss_pred CCccccccCC
Confidence 6788999874
No 27
>cd08493 PBP2_DppA_like The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of an ATP-binding cassette (ABC)-type dipeptide import system. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their li
Probab=21.11 E-value=66 Score=28.46 Aligned_cols=24 Identities=17% Similarity=0.376 Sum_probs=21.7
Q ss_pred eecCCCCccCHHHHHHHHHHHHHh
Q 031297 10 LKFQDSEELQSHDLADAVKQMKEK 33 (162)
Q Consensus 10 l~Fpd~~~L~a~dL~~~l~~M~~~ 33 (162)
++|.|++.|+++|+..+++.+..+
T Consensus 69 ~~wsDG~pvTA~Dv~~~~~~~~~~ 92 (482)
T cd08493 69 VKFHDGRPFNADDVVFSFNRWLDP 92 (482)
T ss_pred CCccCCCCCcHHHhHhhHHHhhCC
Confidence 789999999999999999988654
No 28
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=20.46 E-value=93 Score=28.81 Aligned_cols=27 Identities=19% Similarity=0.462 Sum_probs=23.0
Q ss_pred eecCCCCccCHHHHHHHHHHHHHhCcc
Q 031297 10 LKFQDSEELQSHDLADAVKQMKEKHRF 36 (162)
Q Consensus 10 l~Fpd~~~L~a~dL~~~l~~M~~~krY 36 (162)
++|.|++.|+|+|+..+++.+.....|
T Consensus 188 v~FhDG~plTA~DVv~s~~rl~~~~~~ 214 (552)
T PRK13626 188 IHFHHGRELEMEDVIASLKRLNTLPLY 214 (552)
T ss_pred CEeCCCCCCcHHHHHHHHHHHhhCccc
Confidence 689999999999999999998764433
No 29
>TIGR02294 nickel_nikA nickel ABC transporter, periplasmic nickel-binding protein. Members of this family are periplasmic nickel-binding proteins of nickel ABC transporters. Nickel is bound specifically, albeit weakly, through water molecules positioned in the binding site. The amino acids whose side chains line the binding site include Tyr-44, Met-49, Trp-122, Arg-159, Trp-420, and Tyr-424 (numbering based on the precursor sequence of E. coli NikA) with the Arg contributing a hydrogen bond indirectly through a water molecule. Sequences that exactly (or mostly) have the same binding site residues score above the trusted (or noise) cutoffs to this model. Most appear to be lipoproteins.
Probab=20.23 E-value=84 Score=28.12 Aligned_cols=25 Identities=12% Similarity=0.329 Sum_probs=22.4
Q ss_pred eecCCCCccCHHHHHHHHHHHHHhC
Q 031297 10 LKFQDSEELQSHDLADAVKQMKEKH 34 (162)
Q Consensus 10 l~Fpd~~~L~a~dL~~~l~~M~~~k 34 (162)
++|.|++.|+++|+..+++.+...+
T Consensus 73 ~kfsDG~pvTA~Dv~~s~~~~~~~~ 97 (500)
T TIGR02294 73 VKFSDGTPFDAEAVKKNFDAVLQNS 97 (500)
T ss_pred CCcCCCCCCCHHHHHHHHHHHhcCC
Confidence 6899999999999999999887654
No 30
>cd08495 PBP2_NikA_DppA_OppA_like_8 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=20.17 E-value=74 Score=28.19 Aligned_cols=24 Identities=17% Similarity=0.367 Sum_probs=21.8
Q ss_pred eecCCCCccCHHHHHHHHHHHHHh
Q 031297 10 LKFQDSEELQSHDLADAVKQMKEK 33 (162)
Q Consensus 10 l~Fpd~~~L~a~dL~~~l~~M~~~ 33 (162)
++|.|++.|+++|+..++++|...
T Consensus 72 ~~wsdG~pvTA~Dv~~s~~~~~~~ 95 (482)
T cd08495 72 VKFHDGTPFDADAVVWNLDRMLDP 95 (482)
T ss_pred CCcCCCcCCCHHHHHHHHHHhcCC
Confidence 789999999999999999998654
No 31
>cd08491 PBP2_NikA_DppA_OppA_like_12 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most
Probab=20.13 E-value=85 Score=27.87 Aligned_cols=25 Identities=16% Similarity=0.348 Sum_probs=22.3
Q ss_pred eecCCCCccCHHHHHHHHHHHHHhC
Q 031297 10 LKFQDSEELQSHDLADAVKQMKEKH 34 (162)
Q Consensus 10 l~Fpd~~~L~a~dL~~~l~~M~~~k 34 (162)
++|.|++.+|++|+.-+++.+...+
T Consensus 69 v~fsDG~pvTA~DV~fs~~r~~~~~ 93 (473)
T cd08491 69 VKFHDGTPFDAEAVAFSIERSMNGK 93 (473)
T ss_pred CEecCCCccCHHHHHHHHHHHhCCC
Confidence 6899999999999999999987543
Done!