Query 032056
Match_columns 148
No_of_seqs 105 out of 340
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 09:00:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032056.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032056hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04398 DUF538: Protein of un 100.0 6.5E-49 1.4E-53 291.0 6.4 110 27-138 1-110 (110)
2 cd03697 EFTU_II EFTU_II: Elong 54.9 26 0.00056 24.0 4.1 39 80-120 15-57 (87)
3 cd02410 archeal_CPSF_KH The ar 50.1 18 0.0004 28.3 3.0 38 26-69 52-91 (145)
4 PF15284 PAGK: Phage-encoded v 48.8 5.1 0.00011 27.1 -0.2 18 2-19 4-21 (61)
5 cd03694 GTPBP_II Domain II of 46.5 35 0.00075 23.4 3.7 38 80-119 15-58 (87)
6 PF08710 nsp9: nsp9 replicase; 44.5 69 0.0015 24.1 5.2 36 44-79 49-85 (111)
7 PF10262 Rdx: Rdx family; Int 39.4 46 0.001 22.3 3.3 12 54-65 41-52 (76)
8 PRK15016 isochorismate synthas 38.3 30 0.00066 30.9 2.9 56 4-63 290-347 (391)
9 PF06691 DUF1189: Protein of u 38.1 1.2E+02 0.0025 24.7 6.1 76 43-137 63-138 (250)
10 PRK09967 putative outer membra 36.2 68 0.0015 24.8 4.2 31 46-78 34-64 (160)
11 PF05963 Cytomega_US3: Cytomeg 32.8 72 0.0016 26.1 4.0 50 44-99 26-75 (187)
12 PRK12442 translation initiatio 32.3 95 0.0021 22.4 4.1 53 55-123 19-71 (87)
13 PRK03467 hypothetical protein; 31.4 1.4E+02 0.0029 23.3 5.2 45 56-103 28-88 (144)
14 PRK13488 chemoreceptor glutami 30.4 91 0.002 24.3 4.1 36 26-64 110-151 (157)
15 PF14263 DUF4354: Domain of un 30.1 55 0.0012 25.0 2.7 31 60-90 63-97 (124)
16 PRK06923 isochorismate synthas 29.9 54 0.0012 29.4 3.1 56 5-63 292-348 (399)
17 PF11153 DUF2931: Protein of u 29.6 1.9E+02 0.0041 23.0 6.0 105 1-111 1-108 (216)
18 cd03695 CysN_NodQ_II CysN_NodQ 29.4 88 0.0019 21.1 3.5 38 82-121 17-56 (81)
19 cd03693 EF1_alpha_II EF1_alpha 28.7 1.3E+02 0.0028 20.6 4.3 38 80-119 19-58 (91)
20 COG1254 AcyP Acylphosphatases 28.4 68 0.0015 23.0 2.9 21 45-65 31-51 (92)
21 PF03975 CheD: CheD chemotacti 28.2 65 0.0014 23.4 2.8 35 27-64 68-108 (114)
22 COG1169 MenF Isochorismate syn 28.1 65 0.0014 29.3 3.3 58 4-64 321-379 (423)
23 PF11092 Alveol-reg_P311: Neur 27.8 32 0.0007 23.7 1.0 44 33-77 21-66 (68)
24 cd04089 eRF3_II eRF3_II: domai 27.0 1.6E+02 0.0035 19.6 4.5 34 80-115 14-49 (82)
25 cd03698 eRF3_II_like eRF3_II_l 26.5 89 0.0019 21.0 3.1 35 79-115 14-50 (83)
26 PF08300 HCV_NS5a_1a: Hepatiti 25.9 46 0.00099 22.6 1.5 17 80-97 27-43 (62)
27 PF12103 Lipl32: Surface lipop 25.6 1.4E+02 0.003 24.2 4.4 34 76-109 4-41 (182)
28 TIGR00543 isochor_syn isochori 25.2 76 0.0016 27.7 3.1 56 5-63 254-310 (351)
29 PF07172 GRP: Glycine rich pro 24.9 38 0.00082 24.4 1.0 10 3-12 4-13 (95)
30 KOG2455 Delta-1-pyrroline-5-ca 24.7 42 0.0009 31.3 1.4 16 27-42 241-256 (561)
31 PF02402 Lysis_col: Lysis prot 23.3 37 0.0008 21.7 0.6 18 84-101 29-46 (46)
32 cd03676 Nudix_hydrolase_3 Memb 22.0 67 0.0015 24.5 2.0 60 38-102 27-98 (180)
33 smart00540 LEM in nuclear memb 21.9 57 0.0012 20.5 1.3 16 27-42 10-25 (44)
34 PRK15321 putative type III sec 21.8 55 0.0012 24.5 1.4 30 15-44 29-58 (120)
35 smart00110 C1Q Complement comp 21.5 2.2E+02 0.0047 21.3 4.6 38 50-91 37-74 (135)
36 PRK11657 dsbG disulfide isomer 21.5 2.4E+02 0.0053 23.1 5.3 49 23-71 21-72 (251)
37 PRK09738 small toxic polypepti 21.1 42 0.00092 22.0 0.6 27 57-89 22-48 (52)
38 PRK15012 menaquinone-specific 20.8 1.2E+02 0.0026 27.4 3.5 54 8-65 335-389 (431)
39 PRK09759 small toxic polypepti 20.6 41 0.00088 21.9 0.4 27 57-89 20-46 (50)
No 1
>PF04398 DUF538: Protein of unknown function, DUF538; InterPro: IPR007493 This family consists of several plant proteins of unknown function.; PDB: 1YDU_A.
Probab=100.00 E-value=6.5e-49 Score=290.99 Aligned_cols=110 Identities=38% Similarity=0.784 Sum_probs=84.2
Q ss_pred cHHHHHhhCCCCCCCCCCCceeEEEecCCcEEEEEeCCeeEEEeCCCceEEEecceEEEEEcccccccccceEEEEEEee
Q 032056 27 LAHAELTNYGFPIGLLPVSVQSHTLNQTSGEFFVHLGGACRLTLPPDNYLATYSNKIRGKIEQGRIAELDGIRVRAFFKW 106 (148)
Q Consensus 27 tayelL~~~glP~GLLP~~V~~y~l~~~tG~f~v~l~~~C~~~f~~~~~~v~Y~~~ItG~i~~g~i~~L~GVk~K~lf~W 106 (148)
||||+|++||||+||||++|++|+||++||+|||+|+++|+|+|+ +|+|+|+++|||+|++|+|++|+|||+|++|+|
T Consensus 1 tayelL~~~glP~GLLP~~v~~y~l~~~tG~f~v~l~~~C~~~~~--~~~v~Y~~~ItG~i~~g~i~~L~GVk~k~l~~W 78 (110)
T PF04398_consen 1 TAYELLEEYGLPRGLLPLGVTEYGLNRDTGFFWVKLKSPCEFRFE--GYLVSYDSEITGYIEKGKIKNLTGVKVKELFLW 78 (110)
T ss_dssp --HHHHHHHS-TT-TTTSSS-EEEE-TTT-SEEEE-SS-EEEEST--TSEEEE-SEEEEEE-SS-EEEEES-EEE-SSSE
T ss_pred CHHHhHHHcCCCCCcCCCCceEEEEecCCcEEEEEecCCEEEEEE--EEEEEEcCeEEEEECCCcCccccCEEEEEEEEE
Confidence 799999999999999999999999999999999999999999996 389999999999999999999999999999999
Q ss_pred eeeEEEEEeCCeEEEEEceeeeeeecCCccCC
Q 032056 107 WAITGIRSSGDNLVFEVGMVTAKYPSKNFDES 138 (148)
Q Consensus 107 v~V~eI~v~~~~i~F~vg~~s~sFP~s~F~~~ 138 (148)
++|+||.+++++|+|++|+++++||+++|++|
T Consensus 79 ~~v~~i~~~~~~i~F~~g~~s~sfp~~~F~~s 110 (110)
T PF04398_consen 79 VPVTEISVDGDKIYFKVGGISKSFPVSAFEES 110 (110)
T ss_dssp ES---BEE-SSSEE-TTSSSS----TTTTSS-
T ss_pred eeEEEEEEcCCEEEEEEeeEeccCCHHHhccC
Confidence 99999999999999999999999999999985
No 2
>cd03697 EFTU_II EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven a-helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Either non-catalytic domain is composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: in a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA, and in an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher
Probab=54.86 E-value=26 Score=23.96 Aligned_cols=39 Identities=28% Similarity=0.315 Sum_probs=26.6
Q ss_pred cceEEEEEcccccccccceEEEEE----EeeeeeEEEEEeCCeEE
Q 032056 80 SNKIRGKIEQGRIAELDGIRVRAF----FKWWAITGIRSSGDNLV 120 (148)
Q Consensus 80 ~~~ItG~i~~g~i~~L~GVk~K~l----f~Wv~V~eI~v~~~~i~ 120 (148)
.+.++|+|+.|+|+ .|-++..+ .....|..|.+....+.
T Consensus 15 G~vv~G~v~~G~v~--~gd~v~~~p~~~~~~~~V~si~~~~~~~~ 57 (87)
T cd03697 15 GTVVTGRIERGTIK--VGDEVEIVGFGETLKTTVTGIEMFRKTLD 57 (87)
T ss_pred EEEEEEEECCCCCc--cCCEEEEeCCCCCceEEEEEEEECCcCCC
Confidence 35799999999998 45555443 45677888887543333
No 3
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=50.12 E-value=18 Score=28.30 Aligned_cols=38 Identities=11% Similarity=0.216 Sum_probs=30.5
Q ss_pred ccHHHHHhhCCCCCCCCC--CCceeEEEecCCcEEEEEeCCeeEEE
Q 032056 26 TLAHAELTNYGFPIGLLP--VSVQSHTLNQTSGEFFVHLGGACRLT 69 (148)
Q Consensus 26 ~tayelL~~~glP~GLLP--~~V~~y~l~~~tG~f~v~l~~~C~~~ 69 (148)
..|.++..+ +.| .++++.-+|++||.++++..++=-+.
T Consensus 52 e~A~~~I~~------ivP~ea~i~di~Fd~~tGEV~IeaeKPG~Vi 91 (145)
T cd02410 52 EEAIKIILE------IVPEEAGITDIYFDDDTGEVIIEAEKPGLVI 91 (145)
T ss_pred HHHHHHHHH------hCCCccCceeeEecCCCcEEEEEEcCCeEEE
Confidence 467777766 567 68999999999999999999885543
No 4
>PF15284 PAGK: Phage-encoded virulence factor
Probab=48.84 E-value=5.1 Score=27.14 Aligned_cols=18 Identities=22% Similarity=0.180 Sum_probs=10.4
Q ss_pred chhHHHHHHHHHHhhccC
Q 032056 2 LKSPLLLSILLVLIPLSS 19 (148)
Q Consensus 2 ~~~~~~~~~l~~~~~~~~ 19 (148)
+++++|.++|+++....+
T Consensus 4 ~ksifL~l~~~LsA~~FS 21 (61)
T PF15284_consen 4 FKSIFLALVFILSAAGFS 21 (61)
T ss_pred HHHHHHHHHHHHHHhhhh
Confidence 367777666665444433
No 5
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=46.53 E-value=35 Score=23.39 Aligned_cols=38 Identities=16% Similarity=0.218 Sum_probs=26.5
Q ss_pred cceEEEEEcccccccccceEEEEE------EeeeeeEEEEEeCCeE
Q 032056 80 SNKIRGKIEQGRIAELDGIRVRAF------FKWWAITGIRSSGDNL 119 (148)
Q Consensus 80 ~~~ItG~i~~g~i~~L~GVk~K~l------f~Wv~V~eI~v~~~~i 119 (148)
.+.|+|+++.|.++ .|-++..+ +....|..|.++...+
T Consensus 15 GtVv~G~v~~G~v~--~g~~v~~~P~~~g~~~~~~V~sI~~~~~~~ 58 (87)
T cd03694 15 GTVVGGTVSKGVIR--LGDTLLLGPDQDGSFRPVTVKSIHRNRSPV 58 (87)
T ss_pred ceEEEEEEecCEEe--CCCEEEECCCCCCCEeEEEEEEEEECCeEC
Confidence 57899999999998 45454433 2567888888753333
No 6
>PF08710 nsp9: nsp9 replicase; InterPro: IPR014822 Nsp9 is a single-stranded RNA-binding viral protein likely to be involved in RNA synthesis []. The structure comprises of a single beta barrel []. ; GO: 0003723 RNA binding, 0019079 viral genome replication, 0019034 viral replication complex; PDB: 2J97_A 2J98_A 3EE7_B 1QZ8_A 1UW7_A.
Probab=44.51 E-value=69 Score=24.11 Aligned_cols=36 Identities=11% Similarity=0.300 Sum_probs=21.1
Q ss_pred CCceeEEEecCCcEEEEEeCCeeEEEeCC-CceEEEe
Q 032056 44 VSVQSHTLNQTSGEFFVHLGGACRLTLPP-DNYLATY 79 (148)
Q Consensus 44 ~~V~~y~l~~~tG~f~v~l~~~C~~~f~~-~~~~v~Y 79 (148)
.+.+--....++|...+.|+-+|.|..+. ++-++.|
T Consensus 49 ~~Lk~vk~~~d~G~v~ieLePPckF~v~~~~g~~vkY 85 (111)
T PF08710_consen 49 DNLKYVKWEKDDGKVVIELEPPCKFAVDVPKGPEVKY 85 (111)
T ss_dssp S-EEEEEEE-TTSEEEEEB---EEEEEEETTSEEEEE
T ss_pred CCceEEEEEccCCEEEEecCCCcEEEEEcCCCcEEEE
Confidence 34444556667899999999999987752 2445555
No 7
>PF10262 Rdx: Rdx family; InterPro: IPR011893 This entry represents the Rdx family of selenoproteins, which includes mammalian selenoproteins SelW, SelV, SelT and SelH, bacterial SelW-like proteins and cysteine-containing proteins of unknown function in all three domains of life. Mammalian Rdx12 and its fish selenoprotein orthologues are also members of this family []. These proteins possess a thioredoxin-like fold and a conserved CXXC or CxxU (U is selenocysteine) motif near the N terminus, suggesting a redox function. Rdx proteins can use catalytic cysteine (or selenocysteine) to form transient mixed disulphides with substrate proteins. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins. Selenoprotein W (SelW) plays an important role in protection of neurons from oxidative stress during neuronal development [], []. Selenoprotein T (SelT) is conserved from plants to humans. SelT is localized to the endoplasmic reticulum through a hydrophobic domain. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [, ]. The function of SelT is unknown, although it may have a role in PACAP signaling during PC12 cell differentiation [, ]. Selenoprotein H (SelH) protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways [].; GO: 0008430 selenium binding, 0045454 cell redox homeostasis; PDB: 2OJL_B 2FA8_A 2P0G_C 2NPB_A 3DEX_C 2OKA_A 2OBK_G.
Probab=39.41 E-value=46 Score=22.33 Aligned_cols=12 Identities=33% Similarity=0.684 Sum_probs=9.6
Q ss_pred CCcEEEEEeCCe
Q 032056 54 TSGEFFVHLGGA 65 (148)
Q Consensus 54 ~tG~f~v~l~~~ 65 (148)
.+|.|+|++++.
T Consensus 41 ~~G~FEV~v~g~ 52 (76)
T PF10262_consen 41 STGAFEVTVNGE 52 (76)
T ss_dssp STT-EEEEETTE
T ss_pred cCCEEEEEEccE
Confidence 589999999976
No 8
>PRK15016 isochorismate synthase EntC; Provisional
Probab=38.34 E-value=30 Score=30.92 Aligned_cols=56 Identities=23% Similarity=0.300 Sum_probs=36.3
Q ss_pred hHHHHHHHHHHhhccCCCCCCCccHHHHHhhC-CCCCCCCCCCceeE-EEecCCcEEEEEeC
Q 032056 4 SPLLLSILLVLIPLSSSDPNPPTLAHAELTNY-GFPIGLLPVSVQSH-TLNQTSGEFFVHLG 63 (148)
Q Consensus 4 ~~~~~~~l~~~~~~~~~~~~~~~tayelL~~~-glP~GLLP~~V~~y-~l~~~tG~f~v~l~ 63 (148)
+.+-++..++.+|+..- .|+..|+++++++ ++|||..= |..+| +.+ .+|.+.|.+.
T Consensus 290 ~~l~l~~aLhPtpAV~G--~Pk~~A~~~I~~~E~~~RG~Ya-G~vGw~d~~-G~ge~~V~IR 347 (391)
T PRK15016 290 NALTLACLLHPTPALSG--FPHQAAKQVIAELEPFDRELFG-GIVGWCDSE-GNGEWVVTIR 347 (391)
T ss_pred CHHHHHHhcCCCCccCc--hhHHHHHHHHHHhCCCCCCceE-EEEEEEeCC-CCEEEEEEee
Confidence 34445555666664443 4778999999999 88999874 33344 333 4577777665
No 9
>PF06691 DUF1189: Protein of unknown function (DUF1189); InterPro: IPR009574 This family consists of several hypothetical bacterial proteins of around 260 residues in length. The function of this family is unknown.
Probab=38.15 E-value=1.2e+02 Score=24.73 Aligned_cols=76 Identities=12% Similarity=0.291 Sum_probs=50.9
Q ss_pred CCCceeEEEecCCcEEEEEeCCeeEEEeCCCceEEEecceEEEEEcccccccccceEEEEEEeeeeeEEEEEeCCeEEEE
Q 032056 43 PVSVQSHTLNQTSGEFFVHLGGACRLTLPPDNYLATYSNKIRGKIEQGRIAELDGIRVRAFFKWWAITGIRSSGDNLVFE 122 (148)
Q Consensus 43 P~~V~~y~l~~~tG~f~v~l~~~C~~~f~~~~~~v~Y~~~ItG~i~~g~i~~L~GVk~K~lf~Wv~V~eI~v~~~~i~F~ 122 (148)
.+++-+|++. +|.+....+.+ +.++.++..+-||++ |.+...-+++- -++|....|++++.
T Consensus 63 ~~~iP~F~I~--nG~L~~~~~~~--i~~~~~~~~i~~D~~--~~~~~~dl~~~-------------~~~i~~lkd~iv~~ 123 (250)
T PF06691_consen 63 ENDIPDFTIE--NGKLTSDQSEP--IIYQTNNFIIIFDPT--GKVTEDDLSDY-------------KNAIAFLKDEIVIK 123 (250)
T ss_pred HhhCCCeEEE--CCcEecCCCCc--eEecCCcEEEEECCC--CCcchhhhcCC-------------cceEEEecceEEEE
Confidence 3455569885 69998766666 455567788889984 55554433221 12456668999998
Q ss_pred EceeeeeeecCCccC
Q 032056 123 VGMVTAKYPSKNFDE 137 (148)
Q Consensus 123 vg~~s~sFP~s~F~~ 137 (148)
.++.++++|-+.+..
T Consensus 124 ~~g~~~s~~Ys~~~~ 138 (250)
T PF06691_consen 124 DNGQTQSISYSDLND 138 (250)
T ss_pred eCCeeEEeehhhccc
Confidence 877788888887653
No 10
>PRK09967 putative outer membrane lipoprotein; Provisional
Probab=36.18 E-value=68 Score=24.84 Aligned_cols=31 Identities=19% Similarity=0.348 Sum_probs=20.8
Q ss_pred ceeEEEecCCcEEEEEeCCeeEEEeCCCceEEE
Q 032056 46 VQSHTLNQTSGEFFVHLGGACRLTLPPDNYLAT 78 (148)
Q Consensus 46 V~~y~l~~~tG~f~v~l~~~C~~~f~~~~~~v~ 78 (148)
+.++++.+++|.+.+.+...-.|.+ +++.+.
T Consensus 34 ~~~~g~~~~~~~~~i~l~~~v~F~~--~sa~L~ 64 (160)
T PRK09967 34 MQSYGFTESAGDWSLGLSDAILFAK--NDYKLL 64 (160)
T ss_pred HHhcCceecCCceEEEcCCceeeCC--CccccC
Confidence 3466666678888888887766555 455443
No 11
>PF05963 Cytomega_US3: Cytomegalovirus US3 protein; InterPro: IPR009237 US3 of human cytomegalovirus is an endoplasmic reticulum resident transmembrane glycoprotein that binds to major histocompatibility complex class I molecules and prevents their departure. The endoplasmic reticulum retention signal of the US3 protein is contained in the luminal domain of the protein [].; PDB: 1IM3_L.
Probab=32.82 E-value=72 Score=26.06 Aligned_cols=50 Identities=12% Similarity=0.278 Sum_probs=21.8
Q ss_pred CCceeEEEecCCcEEEEEeCCeeEEEeCCCceEEEecceEEEEEcccccccccceE
Q 032056 44 VSVQSHTLNQTSGEFFVHLGGACRLTLPPDNYLATYSNKIRGKIEQGRIAELDGIR 99 (148)
Q Consensus 44 ~~V~~y~l~~~tG~f~v~l~~~C~~~f~~~~~~v~Y~~~ItG~i~~g~i~~L~GVk 99 (148)
..+++ .+-..--.|+|. ...|. ++++ ++...-+|+|++.+--.-+.-++.
T Consensus 26 ~~~~~-~~~a~~~~ftV~-~n~C~--ie~G--klf~~G~I~GN~t~~~fv~~~v~~ 75 (187)
T PF05963_consen 26 PEITE-QLTARRAHFTVE-QNRCY--IEGG--KLFMTGRISGNFTKSHFVQVGVVG 75 (187)
T ss_dssp --------------EEEE-EEEEE--ESSS--EEEEEEEEEE--S-EEEEESSS-E
T ss_pred HHHHh-hhccCCceEEEE-eeeEE--EECC--EEEEEEEEeeeeeeEEEEEEeeee
Confidence 44555 443322356666 45784 5433 577888999999866555555555
No 12
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=32.28 E-value=95 Score=22.38 Aligned_cols=53 Identities=21% Similarity=0.192 Sum_probs=35.5
Q ss_pred CcEEEEEeCCeeEEEeCCCceEEEecceEEEEEcccccccccceEEEEEEeeeeeEEEEEeCCeEEEEE
Q 032056 55 SGEFFVHLGGACRLTLPPDNYLATYSNKIRGKIEQGRIAELDGIRVRAFFKWWAITGIRSSGDNLVFEV 123 (148)
Q Consensus 55 tG~f~v~l~~~C~~~f~~~~~~v~Y~~~ItG~i~~g~i~~L~GVk~K~lf~Wv~V~eI~v~~~~i~F~v 123 (148)
++.|+|.|...+++. ..|+|.+...+|+=+.|=+|++- +|- -+-+-+.|.|.-
T Consensus 19 ~~~frV~LenG~~vl-----------a~isGKmR~~rIrIl~GD~V~VE-~sp----YDltkGRIiyR~ 71 (87)
T PRK12442 19 DSRFRVTLENGVEVG-----------AYASGRMRKHRIRILAGDRVTLE-LSP----YDLTKGRINFRH 71 (87)
T ss_pred CCEEEEEeCCCCEEE-----------EEeccceeeeeEEecCCCEEEEE-ECc----ccCCceeEEEEe
Confidence 467777766544321 56889999999999999888876 341 122346777744
No 13
>PRK03467 hypothetical protein; Provisional
Probab=31.43 E-value=1.4e+02 Score=23.27 Aligned_cols=45 Identities=13% Similarity=0.361 Sum_probs=32.2
Q ss_pred cEEEEEeCCeeEEEeCCCceEEEe--------------cceEEEEEcc--cccccccceEEEEE
Q 032056 56 GEFFVHLGGACRLTLPPDNYLATY--------------SNKIRGKIEQ--GRIAELDGIRVRAF 103 (148)
Q Consensus 56 G~f~v~l~~~C~~~f~~~~~~v~Y--------------~~~ItG~i~~--g~i~~L~GVk~K~l 103 (148)
+.+|.- +|.+.|++++..+.+ +..|.|+|.. ..+.+++||+.+-.
T Consensus 28 ~~~w~A---~cFY~fd~~~~~l~~~S~~~TrH~~~~~~np~VAgTI~~~~~~v~~I~GvQ~~G~ 88 (144)
T PRK03467 28 GELWCA---NCFYVFDAQKVAFYLLTEEKTRHGQMMGPNAQVAGTVNGQPKTVALIRGVQFKGE 88 (144)
T ss_pred CCcceE---EEEEEEcCCCeEEEEEcCCCCHHHHHHhhCCCEEEEEcCCCcchhhceEEEEEEE
Confidence 556654 777777666665555 6789999864 46889999998875
No 14
>PRK13488 chemoreceptor glutamine deamidase CheD; Provisional
Probab=30.44 E-value=91 Score=24.33 Aligned_cols=36 Identities=19% Similarity=0.287 Sum_probs=26.6
Q ss_pred ccHHHHHhhCCCCC------CCCCCCceeEEEecCCcEEEEEeCC
Q 032056 26 TLAHAELTNYGFPI------GLLPVSVQSHTLNQTSGEFFVHLGG 64 (148)
Q Consensus 26 ~tayelL~~~glP~------GLLP~~V~~y~l~~~tG~f~v~l~~ 64 (148)
..|.++|+++|+|. |--+. .-.++.+||.+||+-.+
T Consensus 110 ~~a~~~L~~~gi~i~a~dvGG~~gR---~i~f~~~tG~v~vk~~~ 151 (157)
T PRK13488 110 ESAKETLKKLGIRIVAEDVGGDYGR---TVKFDLKTGKVIVRKAN 151 (157)
T ss_pred HHHHHHHHHCCCcEEEEEcCCCCCc---EEEEECCCCEEEEEEcC
Confidence 37899999999995 33332 34578889999998544
No 15
>PF14263 DUF4354: Domain of unknown function (DUF4354); PDB: 3NRF_B 3SB3_A.
Probab=30.11 E-value=55 Score=25.01 Aligned_cols=31 Identities=19% Similarity=0.440 Sum_probs=17.7
Q ss_pred EEeCCeeEEEeCCCceEEEecc---eEE-EEEccc
Q 032056 60 VHLGGACRLTLPPDNYLATYSN---KIR-GKIEQG 90 (148)
Q Consensus 60 v~l~~~C~~~f~~~~~~v~Y~~---~It-G~i~~g 90 (148)
+.|++-|-.-+...++.+.-++ +.+ |.+.+|
T Consensus 63 idLsk~Cf~a~~~~gk~f~ldTVd~~L~~g~lK~g 97 (124)
T PF14263_consen 63 IDLSKMCFKAYSPDGKEFKLDTVDEELTSGTLKPG 97 (124)
T ss_dssp EE-TT-EEEEEETTS-EEEEEEE-GGGG-SEE-TT
T ss_pred cccccchhhhccccCCEEEecccchhhhhccccCC
Confidence 5677889888887777777654 333 444444
No 16
>PRK06923 isochorismate synthase DhbC; Validated
Probab=29.87 E-value=54 Score=29.38 Aligned_cols=56 Identities=20% Similarity=0.272 Sum_probs=36.5
Q ss_pred HHHHHHHHHHhhccCCCCCCCccHHHHHhhC-CCCCCCCCCCceeEEEecCCcEEEEEeC
Q 032056 5 PLLLSILLVLIPLSSSDPNPPTLAHAELTNY-GFPIGLLPVSVQSHTLNQTSGEFFVHLG 63 (148)
Q Consensus 5 ~~~~~~l~~~~~~~~~~~~~~~tayelL~~~-glP~GLLP~~V~~y~l~~~tG~f~v~l~ 63 (148)
.+=++..++.+|+..- .|+..|+++++++ ++|||..= |..+|-=...+|.+.|.+.
T Consensus 292 ~ldl~~aLhPTpAV~G--~Pk~~A~~~I~~lE~~~RG~Ya-G~vGw~d~~G~ge~~V~IR 348 (399)
T PRK06923 292 SLELAIALHPTPAVCG--TPTEEAREAIQQIEPFDREFFT-GMLGWSDLNGDGEWIVTIR 348 (399)
T ss_pred HHHHHHHcCCCcccCC--ccHHHHHHHHHHhcCCCCCceE-EEEEEEecCCCEEEEEEee
Confidence 3445566676665443 4777999999988 88999884 4444532234577777554
No 17
>PF11153 DUF2931: Protein of unknown function (DUF2931); InterPro: IPR021326 Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed. Currently, there is no known function.
Probab=29.60 E-value=1.9e+02 Score=23.04 Aligned_cols=105 Identities=17% Similarity=0.200 Sum_probs=47.9
Q ss_pred CchhHHHHHHHHHHhhccCCCCCCCccHHHHHhhCCCCCCCCCCCceeEEEecCCcEEEEEeC--CeeEEEeCC-CceEE
Q 032056 1 MLKSPLLLSILLVLIPLSSSDPNPPTLAHAELTNYGFPIGLLPVSVQSHTLNQTSGEFFVHLG--GACRLTLPP-DNYLA 77 (148)
Q Consensus 1 ~~~~~~~~~~l~~~~~~~~~~~~~~~tayelL~~~glP~GLLP~~V~~y~l~~~tG~f~v~l~--~~C~~~f~~-~~~~v 77 (148)
|-+.++|+++| ++++-++....+..+-++---...-|+++ |..|+.-.+..++|..+.... ..|- ..+. .+..-
T Consensus 1 mk~i~~l~l~l-ll~~C~~~~~~~~~~~~~W~~~~~~P~~y-pv~V~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 77 (216)
T PF11153_consen 1 MKKILLLLLLL-LLTGCSTNPNEPLQPYFEWRFGVAAPKHY-PVWVTYAYFVDGDGDWYRFPTGDSTCM-DPERISGSVG 77 (216)
T ss_pred ChHHHHHHHHH-HHHhhcCCCccCCCCCCccEEEEecCCCC-EEEEEEEEEEeCCCcEEEEecccccee-ecccCCCccC
Confidence 43444444333 33443333333222333333444557764 666665545446677744333 3332 1111 12223
Q ss_pred EecceEEEEEcccccccccceEEEEEEeeeeeEE
Q 032056 78 TYSNKIRGKIEQGRIAELDGIRVRAFFKWWAITG 111 (148)
Q Consensus 78 ~Y~~~ItG~i~~g~i~~L~GVk~K~lf~Wv~V~e 111 (148)
.|+.. +| ..|.-.+-..+-.+..+.|+++.|
T Consensus 78 ~W~~~-~~--~~~~~~~~~~lP~~i~i~W~S~~e 108 (216)
T PF11153_consen 78 GWGGF-GG--GSGYFNKGKPLPDSIYICWDSYAE 108 (216)
T ss_pred CcCcc-cc--cccccCCCCCCCCEEEEEEEEccc
Confidence 44444 22 222233444455678889998765
No 18
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=29.44 E-value=88 Score=21.15 Aligned_cols=38 Identities=24% Similarity=0.170 Sum_probs=25.1
Q ss_pred eEEEEEcccccccccceEEEEEE--eeeeeEEEEEeCCeEEE
Q 032056 82 KIRGKIEQGRIAELDGIRVRAFF--KWWAITGIRSSGDNLVF 121 (148)
Q Consensus 82 ~ItG~i~~g~i~~L~GVk~K~lf--~Wv~V~eI~v~~~~i~F 121 (148)
-|+|+|+.|+|+ .|-++..+= ....|..|.+++..+..
T Consensus 17 ~v~Gkv~~G~v~--~Gd~v~~~P~~~~~~V~si~~~~~~~~~ 56 (81)
T cd03695 17 GYAGTIASGSIR--VGDEVVVLPSGKTSRVKSIETFDGELDE 56 (81)
T ss_pred EEEEEEccceEE--CCCEEEEcCCCCeEEEEEEEECCcEeCE
Confidence 499999999998 454443322 34567888776555544
No 19
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=28.71 E-value=1.3e+02 Score=20.65 Aligned_cols=38 Identities=16% Similarity=0.163 Sum_probs=23.2
Q ss_pred cceEEEEEcccccccccceEEEEE--EeeeeeEEEEEeCCeE
Q 032056 80 SNKIRGKIEQGRIAELDGIRVRAF--FKWWAITGIRSSGDNL 119 (148)
Q Consensus 80 ~~~ItG~i~~g~i~~L~GVk~K~l--f~Wv~V~eI~v~~~~i 119 (148)
.+.|+|+|+.|.|+. |-++..+ =....|..|.++.+.+
T Consensus 19 g~vv~G~v~~G~i~~--gd~v~i~P~~~~~~V~sI~~~~~~~ 58 (91)
T cd03693 19 GTVPVGRVETGVLKP--GMVVTFAPAGVTGEVKSVEMHHEPL 58 (91)
T ss_pred eEEEEEEEecceeec--CCEEEECCCCcEEEEEEEEECCcCc
Confidence 468899999999884 3333221 1346677777643333
No 20
>COG1254 AcyP Acylphosphatases [Energy production and conversion]
Probab=28.40 E-value=68 Score=22.98 Aligned_cols=21 Identities=14% Similarity=0.183 Sum_probs=18.6
Q ss_pred CceeEEEecCCcEEEEEeCCe
Q 032056 45 SVQSHTLNQTSGEFFVHLGGA 65 (148)
Q Consensus 45 ~V~~y~l~~~tG~f~v~l~~~ 65 (148)
|+++|-.|.+||.+++...++
T Consensus 31 gl~G~V~N~~DGsVeiva~G~ 51 (92)
T COG1254 31 GLTGWVKNLDDGSVEIVAEGP 51 (92)
T ss_pred CCEEEEEECCCCeEEEEEEcC
Confidence 688999999999999988765
No 21
>PF03975 CheD: CheD chemotactic sensory transduction; InterPro: IPR005659 CheD deamidates glutamine residues to glutamate on methyl-accepting chemotaxis receptors (MCPs). CheD-mediated MCP deamidation is required for productive communication of the conformational signals of the chemoreceptors to the cheA kinase []. CheC is a CheY-P phosphatase (CheY controls flagellar rotation and is activated by phosphorylation). The activity of CheC is enhanced by its interaction with CheD, forming a CheC-CheD heterodimer. It is suggested that CheC exerts its effect on MCP methylation in Bacillus subtilis by controlling the binding of CheD to the MCPs [].; GO: 0050568 protein-glutamine glutaminase activity, 0006935 chemotaxis; PDB: 2F9Z_D.
Probab=28.17 E-value=65 Score=23.44 Aligned_cols=35 Identities=29% Similarity=0.461 Sum_probs=22.3
Q ss_pred cHHHHHhhCCCCC------CCCCCCceeEEEecCCcEEEEEeCC
Q 032056 27 LAHAELTNYGFPI------GLLPVSVQSHTLNQTSGEFFVHLGG 64 (148)
Q Consensus 27 tayelL~~~glP~------GLLP~~V~~y~l~~~tG~f~v~l~~ 64 (148)
.|.++|+++|+|. |-.+ ..-.++..||.+||+.-+
T Consensus 68 ~a~~~L~~~gi~I~a~dvGG~~~---R~v~f~~~tG~v~vk~~~ 108 (114)
T PF03975_consen 68 AARELLAEEGIPIVAEDVGGNFG---RKVRFDPATGEVWVKRIG 108 (114)
T ss_dssp HHHHHHHHTT--EEEEEE-SSS----EEEEEETTTTEEEEE---
T ss_pred HHHHHHHHCCCcEEEeeCCCCCC---cEEEEEcCCCEEEEEECC
Confidence 6889999999994 3333 234578889999997543
No 22
>COG1169 MenF Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=28.06 E-value=65 Score=29.31 Aligned_cols=58 Identities=22% Similarity=0.196 Sum_probs=41.6
Q ss_pred hHHHHHHHHHHhhccCCCCCCCccHHHHHhhCC-CCCCCCCCCceeEEEecCCcEEEEEeCC
Q 032056 4 SPLLLSILLVLIPLSSSDPNPPTLAHAELTNYG-FPIGLLPVSVQSHTLNQTSGEFFVHLGG 64 (148)
Q Consensus 4 ~~~~~~~l~~~~~~~~~~~~~~~tayelL~~~g-lP~GLLP~~V~~y~l~~~tG~f~v~l~~ 64 (148)
+++-++..|+.||+..-- |..-|.++++++- |.||+.---|-=++. +++|.|-|.+..
T Consensus 321 ~~l~l~~~LHPTPAV~G~--P~~~A~~~Ir~~E~fdRG~Yag~vGw~D~-~GngEf~VaIRs 379 (423)
T COG1169 321 TALDLAKALHPTPAVGGL--PREAALQFIREHEPFDRGWYAGPVGWCDS-EGNGEFVVAIRS 379 (423)
T ss_pred CHHHHHHHhCCCccccCC--chHHHHHHHHHhCCCCcchhccceeeecc-CCCeEEEEEEEE
Confidence 467788889988866644 5569999999995 999998533322322 357888887653
No 23
>PF11092 Alveol-reg_P311: Neuronal protein 3.1 (p311); InterPro: IPR024417 Neuronal protein 3.1, also known as P311, is found in neurone and muscle cells []. It contains a conserved PEST (Pro, Glu, Ser, and Thr) motif, which is involved in protein-protein interactions, as well as in targeting proteins for degradation by the ubiquitin/proteasome system. In addition to a potential role in neural function, P311 may be involved in regulating glioma motility [] and could have some function in myo-fibroblast transformation and prevention of fibrosis []. It has also been identified as a potential regulator of alveolar generation [].
Probab=27.75 E-value=32 Score=23.68 Aligned_cols=44 Identities=23% Similarity=0.294 Sum_probs=29.3
Q ss_pred hhCCCCCCCCC--CCceeEEEecCCcEEEEEeCCeeEEEeCCCceEE
Q 032056 33 TNYGFPIGLLP--VSVQSHTLNQTSGEFFVHLGGACRLTLPPDNYLA 77 (148)
Q Consensus 33 ~~~glP~GLLP--~~V~~y~l~~~tG~f~v~l~~~C~~~f~~~~~~v 77 (148)
.+=+||+|=|| +.|..=.-+ +|..=.+...+.-+++...++|+-
T Consensus 21 ~egrlpkg~LPVpKEVNRKK~~-e~~aAsltP~gs~~~~sp~isYlh 66 (68)
T PF11092_consen 21 MEGRLPKGRLPVPKEVNRKKMD-ETEAASLTPLGSDELRSPRISYLH 66 (68)
T ss_pred cccccccCCcCCchhhcccccc-cccceeccCCCCCCccCCcceeee
Confidence 35689999998 777766555 455555555566666666666643
No 24
>cd04089 eRF3_II eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-li
Probab=27.01 E-value=1.6e+02 Score=19.64 Aligned_cols=34 Identities=21% Similarity=0.313 Sum_probs=21.6
Q ss_pred cceEEEEEcccccccccceEEEEE--EeeeeeEEEEEe
Q 032056 80 SNKIRGKIEQGRIAELDGIRVRAF--FKWWAITGIRSS 115 (148)
Q Consensus 80 ~~~ItG~i~~g~i~~L~GVk~K~l--f~Wv~V~eI~v~ 115 (148)
.+.++|+|+.|.|+. |-++..+ =....|..|.++
T Consensus 14 g~vv~G~v~~G~i~~--G~~v~i~P~~~~~~V~si~~~ 49 (82)
T cd04089 14 GTVVLGKVESGTIKK--GDKLLVMPNKTQVEVLSIYNE 49 (82)
T ss_pred CEEEEEEEeeeEEec--CCEEEEeCCCcEEEEEEEEEC
Confidence 568999999999883 4333221 134567777764
No 25
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=26.54 E-value=89 Score=20.98 Aligned_cols=35 Identities=20% Similarity=0.263 Sum_probs=21.1
Q ss_pred ecceEEEEEcccccccccceEEEEE--EeeeeeEEEEEe
Q 032056 79 YSNKIRGKIEQGRIAELDGIRVRAF--FKWWAITGIRSS 115 (148)
Q Consensus 79 Y~~~ItG~i~~g~i~~L~GVk~K~l--f~Wv~V~eI~v~ 115 (148)
-++.++|+|+.|.|+. |-++..+ =....|.+|.+.
T Consensus 14 ~g~vv~G~v~~G~i~~--Gd~v~i~P~~~~~~V~si~~~ 50 (83)
T cd03698 14 GGTVVSGKVESGSIQK--GDTLLVMPSKESVEVKSIYVD 50 (83)
T ss_pred CCcEEEEEEeeeEEeC--CCEEEEeCCCcEEEEEEEEEC
Confidence 3568899999998884 4333221 123456666654
No 26
>PF08300 HCV_NS5a_1a: Hepatitis C virus non-structural 5a zinc finger domain; InterPro: IPR013192 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in the non-structural 5a protein (NS5a) in Hepatitis C virus. The molecular function of NS5a is uncertain, but it is phosphorylated when expressed in mammalian cells. It is thought to interact with the dsRNA dependent (interferon inducible) kinase PKR, P19525 from SWISSPROT [, ]. This region corresponds to the N-terminal zinc binding domain (1a) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003968 RNA-directed RNA polymerase activity, 0004252 serine-type endopeptidase activity, 0008270 zinc ion binding, 0017111 nucleoside-triphosphatase activity, 0006355 regulation of transcription, DNA-dependent, 0006915 apoptosis, 0030683 evasion by virus of host immune response, 0005789 endoplasmic reticulum membrane, 0016021 integral to membrane; PDB: 1ZH1_B 3FQM_A 3FQQ_B.
Probab=25.91 E-value=46 Score=22.64 Aligned_cols=17 Identities=24% Similarity=0.575 Sum_probs=12.7
Q ss_pred cceEEEEEcccccccccc
Q 032056 80 SNKIRGKIEQGRIAELDG 97 (148)
Q Consensus 80 ~~~ItG~i~~g~i~~L~G 97 (148)
..+|+|.|+.|+|+ +.|
T Consensus 27 Ga~ItGhVknG~mr-i~g 43 (62)
T PF08300_consen 27 GAVITGHVKNGSMR-IYG 43 (62)
T ss_dssp S-EEEEEEETTEEE-EE-
T ss_pred CCEEeEEEeCCeEE-Eec
Confidence 57899999999998 444
No 27
>PF12103 Lipl32: Surface lipoprotein of Spirochaetales order; InterPro: IPR021962 Lipl32 is an outer membrane surface lipoprotein of Leptospira like bacteria. ; PDB: 2ZZ8_A 2WFK_D 3FRL_B.
Probab=25.63 E-value=1.4e+02 Score=24.23 Aligned_cols=34 Identities=21% Similarity=0.500 Sum_probs=24.6
Q ss_pred EEEecceEE--EEEccccc--ccccceEEEEEEeeeee
Q 032056 76 LATYSNKIR--GKIEQGRI--AELDGIRVRAFFKWWAI 109 (148)
Q Consensus 76 ~v~Y~~~It--G~i~~g~i--~~L~GVk~K~lf~Wv~V 109 (148)
.+-|...|+ |++++|.- ....|=++.-|++|+|.
T Consensus 4 ~~PY~~~~~Y~GYv~~g~~pD~~~~gK~~yYlYvWvPa 41 (182)
T PF12103_consen 4 KVPYTDVINYFGYVDPGNEPDEVVDGKKAYYLYVWVPA 41 (182)
T ss_dssp EEE-SEEEEEEEEE-TTS--SEEETTEEEEEEEEEESS
T ss_pred ecccccceeeeEeecCCCCCcccccCceeEEEEEEeeh
Confidence 456777776 99999987 45688889999999974
No 28
>TIGR00543 isochor_syn isochorismate synthases. This enzyme interconverts chorismate and isochorismate. In E. coli, different loci encode isochorismate synthases for the pathways of menaquinone biosynthesis and enterobactin biosynthesis (via salicilate) and fail to complement each other. Among isochorismate synthases, the N-terminal domain is poorly conserved.
Probab=25.18 E-value=76 Score=27.70 Aligned_cols=56 Identities=23% Similarity=0.153 Sum_probs=33.2
Q ss_pred HHHHHHHHHHhhccCCCCCCCccHHHHHhhC-CCCCCCCCCCceeEEEecCCcEEEEEeC
Q 032056 5 PLLLSILLVLIPLSSSDPNPPTLAHAELTNY-GFPIGLLPVSVQSHTLNQTSGEFFVHLG 63 (148)
Q Consensus 5 ~~~~~~l~~~~~~~~~~~~~~~tayelL~~~-glP~GLLP~~V~~y~l~~~tG~f~v~l~ 63 (148)
.+=++-.++.+|+..- .|+..|.++++++ ++|||+-= |..+|-=...+|.|.|-+.
T Consensus 254 ~~~ll~~lhPtpAV~G--~Pk~~A~~~I~~~E~~~Rg~Ya-G~vG~i~~~g~~ef~V~IR 310 (351)
T TIGR00543 254 LLDLLKQLHPTPAVGG--LPREEALDFIREHEPFDRGLYA-APLGWLDGEGNGEFAVGIR 310 (351)
T ss_pred HHHHHHHhCCCcccCc--ccHHHHHHHHHHhcCCCCccEE-EEEEEEeCCCCeEEEEEee
Confidence 3444555565554443 4778999999998 89999863 2222311123356666554
No 29
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=24.95 E-value=38 Score=24.43 Aligned_cols=10 Identities=60% Similarity=0.790 Sum_probs=4.2
Q ss_pred hhHHHHHHHH
Q 032056 3 KSPLLLSILL 12 (148)
Q Consensus 3 ~~~~~~~~l~ 12 (148)
|.++|+.++|
T Consensus 4 K~~llL~l~L 13 (95)
T PF07172_consen 4 KAFLLLGLLL 13 (95)
T ss_pred hHHHHHHHHH
Confidence 4444444433
No 30
>KOG2455 consensus Delta-1-pyrroline-5-carboxylate dehydrogenase [Amino acid transport and metabolism]
Probab=24.71 E-value=42 Score=31.27 Aligned_cols=16 Identities=25% Similarity=0.497 Sum_probs=14.3
Q ss_pred cHHHHHhhCCCCCCCC
Q 032056 27 LAHAELTNYGFPIGLL 42 (148)
Q Consensus 27 tayelL~~~glP~GLL 42 (148)
-+|++|+|-|||.|++
T Consensus 241 ii~~il~EAGlP~Gvi 256 (561)
T KOG2455|consen 241 IIYRILREAGLPPGVI 256 (561)
T ss_pred HHHHHHHHcCCCccce
Confidence 4689999999999986
No 31
>PF02402 Lysis_col: Lysis protein; InterPro: IPR003059 The DNA sequence of the entire colicin E2 operon has been determined []. The operon comprises the colicin activity gene (ceaB), the colicin immunity gene (ceiB) and the lysis gene (celB), which is essential for colicin release from producing cells []. A putative LexA binding site is located upstream from ceaB, and a rho-independent terminator structure is located downstream from celB []. Comparison of the amino acid sequences of colicin E2 and cloacin DF13 reveal extensive similarity. These colicins have different modes of action and recognise different cell surface receptors; the two major regions of heterology at the C terminus, and in the C-terminal end of the central region are thought to correspond to the catalytic and receptor-recognition domains, respectively []. Sequence similarities between colicins E2, A and E1 [] are less striking. The colicin E2 (pyocin) immunity protein does not share similarity with either the colicin E3 or cloacin DF13 [] immunity proteins. By contrast, the lysis proteins of the ColE2, ColE1 and CloDF13 plasmids are almost identical except in the N-terminal regions, which themselves are similar to lipoprotein signal peptides []. Processing of the ColE2 prolysis protein to the mature form is prevented by globomycin, a specific inhibitor of the lipoprotein signal peptidase []. The mature ColE2 lysis protein is located in the cell envelope [].; GO: 0009405 pathogenesis, 0019835 cytolysis, 0019867 outer membrane
Probab=23.35 E-value=37 Score=21.73 Aligned_cols=18 Identities=28% Similarity=0.551 Sum_probs=14.2
Q ss_pred EEEEcccccccccceEEE
Q 032056 84 RGKIEQGRIAELDGIRVR 101 (148)
Q Consensus 84 tG~i~~g~i~~L~GVk~K 101 (148)
.|.+++-+.++|+||+++
T Consensus 29 GGtVaPSSss~lTGv~~q 46 (46)
T PF02402_consen 29 GGTVAPSSSSELTGVAVQ 46 (46)
T ss_pred CceECCCccceeeeeecC
Confidence 378888888888888763
No 32
>cd03676 Nudix_hydrolase_3 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belong to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate spe
Probab=22.02 E-value=67 Score=24.53 Aligned_cols=60 Identities=17% Similarity=0.283 Sum_probs=40.2
Q ss_pred CCCCCCCCce--eEEEecC-CcEEEEEeCCeeEEEeCCCceEEEecceEEEEEccc---------ccccccceEEEE
Q 032056 38 PIGLLPVSVQ--SHTLNQT-SGEFFVHLGGACRLTLPPDNYLATYSNKIRGKIEQG---------RIAELDGIRVRA 102 (148)
Q Consensus 38 P~GLLP~~V~--~y~l~~~-tG~f~v~l~~~C~~~f~~~~~~v~Y~~~ItG~i~~g---------~i~~L~GVk~K~ 102 (148)
+.|+.-..|. .|..|.+ .|.+++...+.....+. ++ +|..+.|.++.| .+..=.|+..+.
T Consensus 27 ~~g~~h~~v~~~~~~~~~~~~~~l~lqrRs~~K~~~P--g~---wd~~~~G~v~~gE~~~~aA~REl~EE~Gl~~~~ 98 (180)
T cd03676 27 LFGLVTYGVHLNGYVRDEDGGLRIWIPRRSPTKATWP--GM---LDNLVAGGLGHGEGPEETLVKECDEEAGLPEDL 98 (180)
T ss_pred cCCceEEEEEEEEEEEcCCCCeEEEEEeccCCCCCCC--Cc---eeeecccCCCCCCCHHHHHHHHHHHHhCCCHHH
Confidence 4566655555 5666643 49999999988776664 33 888999999977 233334776654
No 33
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=21.90 E-value=57 Score=20.48 Aligned_cols=16 Identities=44% Similarity=0.748 Sum_probs=12.4
Q ss_pred cHHHHHhhCCCCCCCC
Q 032056 27 LAHAELTNYGFPIGLL 42 (148)
Q Consensus 27 tayelL~~~glP~GLL 42 (148)
-..+.|.+||+|.|=+
T Consensus 10 eL~~~L~~~G~~~gPI 25 (44)
T smart00540 10 ELRAELKQYGLPPGPI 25 (44)
T ss_pred HHHHHHHHcCCCCCCc
Confidence 4567899999999843
No 34
>PRK15321 putative type III secretion system effector protein OrgC; Provisional
Probab=21.81 E-value=55 Score=24.52 Aligned_cols=30 Identities=17% Similarity=0.100 Sum_probs=22.5
Q ss_pred hhccCCCCCCCccHHHHHhhCCCCCCCCCC
Q 032056 15 IPLSSSDPNPPTLAHAELTNYGFPIGLLPV 44 (148)
Q Consensus 15 ~~~~~~~~~~~~tayelL~~~glP~GLLP~ 44 (148)
+|...+++..++++|.+|.++|=|.|==|.
T Consensus 29 LP~la~S~~~KD~I~q~m~~F~dp~~G~pA 58 (120)
T PRK15321 29 LPESASSETLKDSIYQEMNAFKDPNSGDSA 58 (120)
T ss_pred CCcccCcHHHHHHHHHHHHHhCCCCCCCcc
Confidence 344455556678999999999999886554
No 35
>smart00110 C1Q Complement component C1q domain. Globular domain found in many collagens and eponymously in complement C1q. When part of full length proteins these domains form a 'bouquet' due to the multimerization of heterotrimers. The C1q fold is similar to that of tumour necrosis factor.
Probab=21.54 E-value=2.2e+02 Score=21.32 Aligned_cols=38 Identities=8% Similarity=0.226 Sum_probs=26.3
Q ss_pred EEecCCcEEEEEeCCeeEEEeCCCceEEEecceEEEEEcccc
Q 032056 50 TLNQTSGEFFVHLGGACRLTLPPDNYLATYSNKIRGKIEQGR 91 (148)
Q Consensus 50 ~l~~~tG~f~v~l~~~C~~~f~~~~~~v~Y~~~ItG~i~~g~ 91 (148)
.+|++||.|....++...|.|- . ..++.++.-.|.++.
T Consensus 37 ~yd~~TG~Ftcpv~GvY~F~f~---~-~~~~~~~~v~L~~N~ 74 (135)
T smart00110 37 HYDPRTGKFTCPVPGVYYFSYH---V-ESKGRNVKVSLMKNG 74 (135)
T ss_pred CccCCCCEEECeeceEEEEEEE---E-EEcCCEEEEEEEECC
Confidence 3678899999999999998883 1 223445555555443
No 36
>PRK11657 dsbG disulfide isomerase/thiol-disulfide oxidase; Provisional
Probab=21.46 E-value=2.4e+02 Score=23.15 Aligned_cols=49 Identities=10% Similarity=0.066 Sum_probs=36.0
Q ss_pred CCCccHHHHHhhCCCCC-CC--CCCCceeEEEecCCcEEEEEeCCeeEEEeC
Q 032056 23 NPPTLAHAELTNYGFPI-GL--LPVSVQSHTLNQTSGEFFVHLGGACRLTLP 71 (148)
Q Consensus 23 ~~~~tayelL~~~glP~-GL--LP~~V~~y~l~~~tG~f~v~l~~~C~~~f~ 71 (148)
++.+.+.+-|++.|+.. .. -|.++.++-.....+.-.+|......|-+.
T Consensus 21 ~~~p~~~~~l~~~g~~v~~~~~~p~~l~g~~~~~~~~~~i~Y~t~dg~y~i~ 72 (251)
T PRK11657 21 EELPAPVKALEKQGITIIKTFDAPGGLKGYAAKYQDMGVTIYLTPDGKHAIS 72 (251)
T ss_pred hcccHHHHHHHhCCCEEEEeecCCCCceEEEEEeCCCceEEEEcCCCCEEEE
Confidence 45678889999999987 44 478899888776544447787777777663
No 37
>PRK09738 small toxic polypeptide; Provisional
Probab=21.07 E-value=42 Score=21.97 Aligned_cols=27 Identities=7% Similarity=0.185 Sum_probs=18.7
Q ss_pred EEEEEeCCeeEEEeCCCceEEEecceEEEEEcc
Q 032056 57 EFFVHLGGACRLTLPPDNYLATYSNKIRGKIEQ 89 (148)
Q Consensus 57 ~f~v~l~~~C~~~f~~~~~~v~Y~~~ItG~i~~ 89 (148)
+.|+.-++-||++++.++ ++|.+++.+
T Consensus 22 f~~l~r~sLCEl~i~~g~------~evaA~LAy 48 (52)
T PRK09738 22 FTYLTRKSLCELRYRDGD------REVAAFMAY 48 (52)
T ss_pred HHHHccCCceEEEEecCC------EEEEEEEee
Confidence 446666788999998654 566666654
No 38
>PRK15012 menaquinone-specific isochorismate synthase; Provisional
Probab=20.78 E-value=1.2e+02 Score=27.37 Aligned_cols=54 Identities=19% Similarity=0.105 Sum_probs=35.6
Q ss_pred HHHHHHHhhccCCCCCCCccHHHHHhhC-CCCCCCCCCCceeEEEecCCcEEEEEeCCe
Q 032056 8 LSILLVLIPLSSSDPNPPTLAHAELTNY-GFPIGLLPVSVQSHTLNQTSGEFFVHLGGA 65 (148)
Q Consensus 8 ~~~l~~~~~~~~~~~~~~~tayelL~~~-glP~GLLP~~V~~y~l~~~tG~f~v~l~~~ 65 (148)
++-.++.||+..- .|+..|.++++++ +++||.-= |..+|- +.++|.|.|-+...
T Consensus 335 ~l~~LhPtpAV~G--~Pk~~A~~~I~~~E~~~RG~Ya-G~vG~i-~~~~~ef~V~IRsa 389 (431)
T PRK15012 335 CLHQLQPTAAVAG--LPRDLARQFIARHEPFTREWYA-GSAGYL-SLQQSEFCVSLRSA 389 (431)
T ss_pred HHHHhCCCCcccC--CCHHHHHHHHHHhCCCCCccEE-EEEEEE-ECCCCEEEEEccEE
Confidence 3444555554443 4778999999999 89999873 233342 44568888877643
No 39
>PRK09759 small toxic polypeptide; Provisional
Probab=20.56 E-value=41 Score=21.86 Aligned_cols=27 Identities=7% Similarity=0.153 Sum_probs=18.2
Q ss_pred EEEEEeCCeeEEEeCCCceEEEecceEEEEEcc
Q 032056 57 EFFVHLGGACRLTLPPDNYLATYSNKIRGKIEQ 89 (148)
Q Consensus 57 ~f~v~l~~~C~~~f~~~~~~v~Y~~~ItG~i~~ 89 (148)
+.|+.-++-||++++.++ ++|.+++.+
T Consensus 20 f~~l~r~sLCEl~i~~g~------~evaA~Lay 46 (50)
T PRK09759 20 FTWMIRDSLCELHIKQGS------YELAAFLAC 46 (50)
T ss_pred HHHHhCCCceEEEEecCC------EEEEEEEee
Confidence 345666788999997554 566666554
Done!