Query 030231
Match_columns 181
No_of_seqs 94 out of 96
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 10:34:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030231.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030231hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13225 DUF4033: Domain of un 95.6 0.0048 1E-07 46.4 0.9 16 166-181 15-30 (86)
2 smart00288 VHS Domain present 44.3 74 0.0016 24.7 5.6 46 63-122 2-47 (133)
3 PHA02611 51 baseplate hub asse 44.2 27 0.00059 31.0 3.5 41 89-131 22-62 (249)
4 PRK15031 5-carboxymethyl-2-hyd 40.4 4.4 9.5E-05 32.2 -1.9 30 92-121 59-88 (126)
5 PF02671 PAH: Paired amphipath 38.2 67 0.0015 20.4 3.8 44 90-135 3-47 (47)
6 COG5442 FlaF Flagellar biosynt 37.5 40 0.00088 26.6 3.1 16 89-104 98-113 (115)
7 COG4840 Uncharacterized protei 35.9 1.7E+02 0.0038 21.4 6.3 56 57-120 11-68 (71)
8 PF00790 VHS: VHS domain; Int 32.9 2.3E+02 0.0049 21.9 6.8 31 62-104 6-36 (140)
9 cd03569 VHS_Hrs_Vps27p VHS dom 29.3 2.8E+02 0.0062 21.9 6.9 49 62-124 5-53 (142)
10 PHA02591 hypothetical protein; 28.7 1E+02 0.0022 23.2 3.9 49 63-120 26-82 (83)
11 PF02654 CobS: Cobalamin-5-pho 26.5 64 0.0014 27.4 2.9 28 89-116 70-97 (235)
12 cd07354 HN_L-delphilin-R1_like 26.3 1.5E+02 0.0033 22.1 4.5 62 61-136 7-68 (80)
13 PF13089 PP_kinase_N: Polyphos 24.2 72 0.0016 24.2 2.5 55 53-121 27-84 (109)
14 PRK00235 cobS cobalamin syntha 23.9 68 0.0015 27.5 2.6 28 89-116 79-106 (249)
15 PF14974 DUF4511: Domain of un 23.9 87 0.0019 24.4 2.9 38 89-126 64-101 (105)
16 cd03561 VHS VHS domain family; 22.9 2.9E+02 0.0063 21.2 5.7 16 89-104 16-31 (133)
17 TIGR00317 cobS cobalamin 5'-ph 22.2 79 0.0017 27.1 2.6 28 89-116 76-103 (241)
18 COG5201 SKP1 SCF ubiquitin lig 22.1 2.2E+02 0.0049 23.5 5.0 48 53-113 82-133 (158)
19 PF04675 DNA_ligase_A_N: DNA l 20.8 1.6E+02 0.0034 23.2 4.0 48 91-138 3-54 (177)
No 1
>PF13225 DUF4033: Domain of unknown function (DUF4033)
Probab=95.59 E-value=0.0048 Score=46.44 Aligned_cols=16 Identities=69% Similarity=1.111 Sum_probs=14.9
Q ss_pred ecCeeeecceEeccCC
Q 030231 166 INGEKQRSGVHIKKCR 181 (181)
Q Consensus 166 vdG~k~~sgV~IeKCR 181 (181)
.||.+++|||||||||
T Consensus 15 ~~~~~~~sgV~i~kCR 30 (86)
T PF13225_consen 15 GNGRGQKSGVHIEKCR 30 (86)
T ss_pred CCCccccceEEEEEeE
Confidence 6899999999999998
No 2
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=44.28 E-value=74 Score=24.69 Aligned_cols=46 Identities=17% Similarity=0.273 Sum_probs=28.6
Q ss_pred HHHHHHHcCCCCCcchhhccccccCCCChhHHHHHHHHHHccCCHHHHHHHHHHHHHhcC
Q 030231 63 ARKMEKFASPAKSKTETKKKRWFDFGYDYESFVDVSKRVMEGRSRQQQQEVVREVLLSML 122 (181)
Q Consensus 63 ~rkm~~~~G~~~~~~~~~~~~~~~~~~gYdglVe~a~~lm~grs~~~q~~~v~rVL~sl~ 122 (181)
-+.+.+++...... ++++.++++|..|..+ +...+++++-+...|-
T Consensus 2 ~~~i~kATs~~l~~------------~dw~~~l~icD~i~~~--~~~~k~a~r~l~krl~ 47 (133)
T smart00288 2 ERLIDKATSPSLLE------------EDWELILEICDLINST--PDGPKDAVRLLKKRLN 47 (133)
T ss_pred hhHHHHHcCcCCCC------------cCHHHHHHHHHHHhCC--CccHHHHHHHHHHHHc
Confidence 34566677654433 7899999999999755 3444445544444443
No 3
>PHA02611 51 baseplate hub assembly protein; Provisional
Probab=44.22 E-value=27 Score=31.02 Aligned_cols=41 Identities=37% Similarity=0.615 Sum_probs=32.6
Q ss_pred CChhHHHHHHHHHHccCCHHHHHHHHHHHHHhcCCCChHHHHH
Q 030231 89 YDYESFVDVSKRVMEGRSRQQQQEVVREVLLSMLPPGAPAQFR 131 (181)
Q Consensus 89 ~gYdglVe~a~~lm~grs~~~q~~~v~rVL~sl~Pp~~p~~fr 131 (181)
.+|-+|+ +|+.-|.|+++.+|++++-.++..++|. ++...+
T Consensus 22 kEy~~Ll-lar~~me~~~~~Eq~eii~eli~~~~~e-l~k~e~ 62 (249)
T PHA02611 22 KDYRDFL-LVRNDMEGRSPEEQQEILDELLDEYFPE-YPKTEQ 62 (249)
T ss_pred HHHHHHH-hhhhhhcCCChhhHHHHHHHHHHHHhcc-CChHHH
Confidence 5688886 4666789999999999999999999864 554433
No 4
>PRK15031 5-carboxymethyl-2-hydroxymuconate delta-isomerase; Provisional
Probab=40.44 E-value=4.4 Score=32.17 Aligned_cols=30 Identities=27% Similarity=0.390 Sum_probs=25.7
Q ss_pred hHHHHHHHHHHccCCHHHHHHHHHHHHHhc
Q 030231 92 ESFVDVSKRVMEGRSRQQQQEVVREVLLSM 121 (181)
Q Consensus 92 dglVe~a~~lm~grs~~~q~~~v~rVL~sl 121 (181)
++||.+..+||.|||.++.++....++..|
T Consensus 59 ~~Fihv~l~i~~GRs~e~k~~l~~~l~~~l 88 (126)
T PRK15031 59 YAFVHMTLKIGAGRSLESRQEVGEMLFALI 88 (126)
T ss_pred CcEEEEEeeecCCCCHHHHHHHHHHHHHHH
Confidence 389999999999999999998887776655
No 5
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=38.18 E-value=67 Score=20.38 Aligned_cols=44 Identities=25% Similarity=0.427 Sum_probs=28.7
Q ss_pred ChhHHHHHHHHHHc-cCCHHHHHHHHHHHHHhcCCCChHHHHHHhcC
Q 030231 90 DYESFVDVSKRVME-GRSRQQQQEVVREVLLSMLPPGAPAQFRKLFP 135 (181)
Q Consensus 90 gYdglVe~a~~lm~-grs~~~q~~~v~rVL~sl~Pp~~p~~fr~lf~ 135 (181)
-|+.|+++-+...+ ..|..+-.+.|...|..- |-+..-|+.++|
T Consensus 3 ~Y~~FL~il~~y~~~~~~~~~v~~~v~~Ll~~h--pdLl~~F~~FlP 47 (47)
T PF02671_consen 3 VYNEFLKILNDYKKGRISRSEVIEEVSELLRGH--PDLLEEFNRFLP 47 (47)
T ss_dssp HHHHHHHHHHHHHCTCSCHHHHHHHHHHHTTT---HHHHHHHHHHSS
T ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHccC--HHHHHHHHhhCc
Confidence 49999999999986 566777665554444332 345566666664
No 6
>COG5442 FlaF Flagellar biosynthesis regulator FlaF [Cell motility and secretion]
Probab=37.49 E-value=40 Score=26.61 Aligned_cols=16 Identities=13% Similarity=0.669 Sum_probs=14.7
Q ss_pred CChhHHHHHHHHHHcc
Q 030231 89 YDYESFVDVSKRVMEG 104 (181)
Q Consensus 89 ~gYdglVe~a~~lm~g 104 (181)
.+|+||||+.+-+|+|
T Consensus 98 ~nfeglIeit~iIrdG 113 (115)
T COG5442 98 NNFEGLIEITQIIRDG 113 (115)
T ss_pred ccchhHHHHHHHHHhh
Confidence 5899999999999987
No 7
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.91 E-value=1.7e+02 Score=21.36 Aligned_cols=56 Identities=14% Similarity=0.151 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHcCCCCCcchhhccccccCCCChhHHHHHHHHHHc--cCCHHHHHHHHHHHHHh
Q 030231 57 AFMTLFARKMEKFASPAKSKTETKKKRWFDFGYDYESFVDVSKRVME--GRSRQQQQEVVREVLLS 120 (181)
Q Consensus 57 ~~i~lF~rkm~~~~G~~~~~~~~~~~~~~~~~~gYdglVe~a~~lm~--grs~~~q~~~v~rVL~s 120 (181)
+.|.-.+.||.-.-++--+.++-.. ..|+.|-|+=+.+++ .+||.+.|+++. -|.+
T Consensus 11 fmi~eI~~KLnmvN~gvl~~e~~d~-------~~~edLtdiy~mvkkkenfSpsEmqaiA~-eL~r 68 (71)
T COG4840 11 FMIEEIREKLNMVNVGVLDPEKYDN-------ANYEDLTDIYDMVKKKENFSPSEMQAIAD-ELGR 68 (71)
T ss_pred HHHHHHHHHHhhhhhhccCHHhccc-------ccHHHHHHHHHHHHHhccCCHHHHHHHHH-HHHH
Confidence 3556677888776554322211111 679999999999985 899999996653 3443
No 8
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=32.88 E-value=2.3e+02 Score=21.94 Aligned_cols=31 Identities=13% Similarity=0.228 Sum_probs=19.4
Q ss_pred HHHHHHHHcCCCCCcchhhccccccCCCChhHHHHHHHHHHcc
Q 030231 62 FARKMEKFASPAKSKTETKKKRWFDFGYDYESFVDVSKRVMEG 104 (181)
Q Consensus 62 F~rkm~~~~G~~~~~~~~~~~~~~~~~~gYdglVe~a~~lm~g 104 (181)
|...+.+++...... +|++.++++|..+..+
T Consensus 6 ~~~li~kATs~~~~~------------~Dw~~~l~icD~i~~~ 36 (140)
T PF00790_consen 6 ITELIEKATSESLPS------------PDWSLILEICDLINSS 36 (140)
T ss_dssp HHHHHHHHT-TTSSS--------------HHHHHHHHHHHHTS
T ss_pred HHHHHHHHhCcCCCC------------CCHHHHHHHHHHHHcC
Confidence 445666777655433 6888888888888765
No 9
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=29.35 E-value=2.8e+02 Score=21.86 Aligned_cols=49 Identities=18% Similarity=0.235 Sum_probs=29.9
Q ss_pred HHHHHHHHcCCCCCcchhhccccccCCCChhHHHHHHHHHHccCCHHHHHHHHHHHHHhcCCC
Q 030231 62 FARKMEKFASPAKSKTETKKKRWFDFGYDYESFVDVSKRVMEGRSRQQQQEVVREVLLSMLPP 124 (181)
Q Consensus 62 F~rkm~~~~G~~~~~~~~~~~~~~~~~~gYdglVe~a~~lm~grs~~~q~~~v~rVL~sl~Pp 124 (181)
|-..+.+++-..... ++++..+|+|..|.... ..++++++-+-..|.-+
T Consensus 5 ~~~~I~kATs~~l~~------------~dw~~ileicD~In~~~--~~~k~a~ral~krl~~~ 53 (142)
T cd03569 5 FDELIEKATSELLGE------------PDLASILEICDMIRSKD--VQPKYAMRALKKRLLSK 53 (142)
T ss_pred HHHHHHHHcCcccCc------------cCHHHHHHHHHHHhCCC--CCHHHHHHHHHHHHcCC
Confidence 445666776644322 78999999999997532 24555555555554443
No 10
>PHA02591 hypothetical protein; Provisional
Probab=28.66 E-value=1e+02 Score=23.23 Aligned_cols=49 Identities=20% Similarity=0.358 Sum_probs=31.8
Q ss_pred HHHHHHHcCCCCCcchhhccccccCCCChhHHHHHHHHHH-ccCCHHHH-------HHHHHHHHHh
Q 030231 63 ARKMEKFASPAKSKTETKKKRWFDFGYDYESFVDVSKRVM-EGRSRQQQ-------QEVVREVLLS 120 (181)
Q Consensus 63 ~rkm~~~~G~~~~~~~~~~~~~~~~~~gYdglVe~a~~lm-~grs~~~q-------~~~v~rVL~s 120 (181)
-+||.+.+-..... .+- ..=|.++.+|+.|. +|.|..+. +++|++.|.|
T Consensus 26 ~~~m~k~vqv~~~r-------yfi--~~~dd~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 26 EKKMQKVVQVGQTR-------YFV--ESEDDLISVTHELARKGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred hHhHHHhheeCCEE-------EEE--eccchHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 36787776432211 111 46689999999997 59998773 4566666654
No 11
>PF02654 CobS: Cobalamin-5-phosphate synthase; InterPro: IPR003805 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents the CobS protein, a cobalamin-5-phosphate synthase that catyalzes the reactions: Adenosylcobinamide-GDP + alpha-ribazole-5'-P = adenosylcobalamin-5'-phosphate + GMP Adenosylcobinamide-GDP + alpha-ribazole = adenosylcobalamin + GMP The protein product from these catalyses is associated with a large complex of proteins and is induced by cobinamide. CobS is involved in part III of cobalamin biosynthesis, one of the late steps in adenosylcobalamin synthesis that, together with CobU, CobT, and CobC proteins, defines the nucleotide loop assembly pathway [, ].; GO: 0008818 cobalamin 5'-phosphate synthase activity, 0009236 cobalamin biosynthetic process
Probab=26.51 E-value=64 Score=27.40 Aligned_cols=28 Identities=18% Similarity=0.570 Sum_probs=24.2
Q ss_pred CChhHHHHHHHHHHccCCHHHHHHHHHH
Q 030231 89 YDYESFVDVSKRVMEGRSRQQQQEVVRE 116 (181)
Q Consensus 89 ~gYdglVe~a~~lm~grs~~~q~~~v~r 116 (181)
--+|||.|.+..++.++++++-.|+.++
T Consensus 70 lHlDGlaD~~Dgl~s~~~~er~LeIMKD 97 (235)
T PF02654_consen 70 LHLDGLADTADGLFSGRDRERRLEIMKD 97 (235)
T ss_pred hhHHHHHHHHHHhcCCCCHHHHHHHHhC
Confidence 4599999999999999999998877653
No 12
>cd07354 HN_L-delphilin-R1_like First harmonin_N_like domain (repeat 1) of L-delphilin, and related domains. This subgroup contains the first of two harmonin_N_like domains of an alternatively spliced longer variant of mouse delphilin (L-delphilin, isoform 1), and related domains. Delphilin is a scaffold protein which binds the glutamate receptor delta-2 (GRID2) subunit and the monocarboxylate transporter 2 at the cerebellar parallel fiber-Purkinje cell synapses. The N-terminus of L-delphilin contains this harmonin_N_like domain preceded by a postsynaptic density-95/discs-large/ZO-1 (PDZ) protein-binding domain, PDZ1. L-delphilin, in common with the shorter C-terminal isoforms (S-delphilin/delphilin alpha and delphilin beta) has a second harmonin_N_like domain (not belonging to this subgroup) and a second PDZ domain, PDZ2. This first harmonin_N_like domain is a putative protein-binding module based on its sequence similarity to the harmonin N-domain.
Probab=26.30 E-value=1.5e+02 Score=22.12 Aligned_cols=62 Identities=15% Similarity=0.127 Sum_probs=36.1
Q ss_pred HHHHHHHHHcCCCCCcchhhccccccCCCChhHHHHHHHHHHccCCHHHHHHHHHHHHHhcCCCChHHHHHHhcCC
Q 030231 61 LFARKMEKFASPAKSKTETKKKRWFDFGYDYESFVDVSKRVMEGRSRQQQQEVVREVLLSMLPPGAPAQFRKLFPP 136 (181)
Q Consensus 61 lF~rkm~~~~G~~~~~~~~~~~~~~~~~~gYdglVe~a~~lm~grs~~~q~~~v~rVL~sl~Pp~~p~~fr~lf~P 136 (181)
=|+.|+...+|.++.. =|-++++-++..+-++.+.--.+...+|..=-=.-+..-+|.++|.
T Consensus 7 eF~~Kvd~iL~~dp~~--------------Ke~l~~aLk~Ya~~k~vd~l~~aL~~~L~~e~~~~Lld~IR~fIP~ 68 (80)
T cd07354 7 EFSRKVDAILGDDPVK--------------KEQVFAALKQYAADKNVDCLVWALCGLLQTEAHKKLLDEIRIFIPK 68 (80)
T ss_pred HHHHHHHHHhcCCHHH--------------HHHHHHHHHHHHHHcCHHHHHHHHHHHhCcHHHHHHHHHhHhcCCc
Confidence 3899999999988744 2456666666655555544433333333311112355677777764
No 13
>PF13089 PP_kinase_N: Polyphosphate kinase N-terminal domain; PDB: 2O8R_A 1XDP_A 1XDO_B.
Probab=24.19 E-value=72 Score=24.25 Aligned_cols=55 Identities=15% Similarity=0.399 Sum_probs=29.9
Q ss_pred hHHHH-HHHHHHHHHHHHcCCCCCcchhhccccccCCCChhHHHHHHHHH--HccCCHHHHHHHHHHHHHhc
Q 030231 53 FFEKA-FMTLFARKMEKFASPAKSKTETKKKRWFDFGYDYESFVDVSKRV--MEGRSRQQQQEVVREVLLSM 121 (181)
Q Consensus 53 ~lDk~-~i~lF~rkm~~~~G~~~~~~~~~~~~~~~~~~gYdglVe~a~~l--m~grs~~~q~~~v~rVL~sl 121 (181)
.++|+ |++.|+..|-|+.-.... |-...++..... -.|.+|.+|-+.+.+..+.+
T Consensus 27 llERl~Fl~I~ssNlDEFFmVRVA--------------~Lk~~~~~g~~~~~~~g~tP~eqL~~I~~~v~~l 84 (109)
T PF13089_consen 27 LLERLKFLAIFSSNLDEFFMVRVA--------------GLKRQIEAGVKKRDPDGLTPQEQLDAIRKRVHEL 84 (109)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCCCH--------------HHHHHCCHHHCC---S---HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhhhhcchhHHHHHHHH--------------HHHHHHHhccCCCCcCCCCHHHHHHHHHHHHHHH
Confidence 37777 999999999988644321 122222222221 13667777776666655554
No 14
>PRK00235 cobS cobalamin synthase; Reviewed
Probab=23.95 E-value=68 Score=27.55 Aligned_cols=28 Identities=18% Similarity=0.497 Sum_probs=24.4
Q ss_pred CChhHHHHHHHHHHccCCHHHHHHHHHH
Q 030231 89 YDYESFVDVSKRVMEGRSRQQQQEVVRE 116 (181)
Q Consensus 89 ~gYdglVe~a~~lm~grs~~~q~~~v~r 116 (181)
--.|||.|.+..++.++++++-.|+.++
T Consensus 79 lHlDGlaD~~Dgl~s~~~~er~LeIMKD 106 (249)
T PRK00235 79 LHLDGLADTADGLGGGRDRERRLEIMKD 106 (249)
T ss_pred hhhhhhHHHHHHhccCCCHHHHHHHHhc
Confidence 3589999999999999999998888754
No 15
>PF14974 DUF4511: Domain of unknown function (DUF4511)
Probab=23.91 E-value=87 Score=24.43 Aligned_cols=38 Identities=11% Similarity=0.129 Sum_probs=25.6
Q ss_pred CChhHHHHHHHHHHccCCHHHHHHHHHHHHHhcCCCCh
Q 030231 89 YDYESFVDVSKRVMEGRSRQQQQEVVREVLLSMLPPGA 126 (181)
Q Consensus 89 ~gYdglVe~a~~lm~grs~~~q~~~v~rVL~sl~Pp~~ 126 (181)
.|+||+++-++.++.--.-+..-+....-|+|+|=|.+
T Consensus 64 ~~~eG~~~f~~~i~~~e~~D~eva~l~~~iRs~~lPp~ 101 (105)
T PF14974_consen 64 ESREGVMQFAQLIRELEKDDPEVARLHSQIRSLFLPPM 101 (105)
T ss_pred CCcchHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCC
Confidence 57999999999998753444444455666677664433
No 16
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=22.90 E-value=2.9e+02 Score=21.18 Aligned_cols=16 Identities=6% Similarity=0.048 Sum_probs=13.0
Q ss_pred CChhHHHHHHHHHHcc
Q 030231 89 YDYESFVDVSKRVMEG 104 (181)
Q Consensus 89 ~gYdglVe~a~~lm~g 104 (181)
+|++..+++|..|..+
T Consensus 16 ~D~~~il~icd~I~~~ 31 (133)
T cd03561 16 PDWALNLELCDLINLK 31 (133)
T ss_pred ccHHHHHHHHHHHhCC
Confidence 6888999988888754
No 17
>TIGR00317 cobS cobalamin 5'-phosphate synthase/cobalamin synthase. cobS is involved with cobalamin biosynthesis in part III of colbalmin biosynthesis. The enzyme catyalzes the reactions adenosylcobinamide-GDP + alpha-ribazole-5'-P = adenosylcobalamin-5'-phosphate + GMP and adenosylcobinamide-GDP + alpha-ribazole = adenosylcobalamin + GMP. The protein product is associated with a large complex of proteins and is induced by cobinamide.
Probab=22.25 E-value=79 Score=27.09 Aligned_cols=28 Identities=11% Similarity=0.330 Sum_probs=24.3
Q ss_pred CChhHHHHHHHHHHccCCHHHHHHHHHH
Q 030231 89 YDYESFVDVSKRVMEGRSRQQQQEVVRE 116 (181)
Q Consensus 89 ~gYdglVe~a~~lm~grs~~~q~~~v~r 116 (181)
=-.|||.|.+..++-++++++-.|+.++
T Consensus 76 lHlDGLaD~~Dgl~s~~~~er~L~IMKD 103 (241)
T TIGR00317 76 HHLDGLADFGDGLFAPGSKERKLEAMKD 103 (241)
T ss_pred chhhhhHHHhhHhccCCCHHHHHHHHHc
Confidence 3489999999999999999998887754
No 18
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=22.06 E-value=2.2e+02 Score=23.53 Aligned_cols=48 Identities=17% Similarity=0.422 Sum_probs=35.9
Q ss_pred hHHHHHHHHHHHHHHHHcCCCCCcchhhccccccCCCChhHHHHHHHHH----HccCCHHHHHHH
Q 030231 53 FFEKAFMTLFARKMEKFASPAKSKTETKKKRWFDFGYDYESFVDVSKRV----MEGRSRQQQQEV 113 (181)
Q Consensus 53 ~lDk~~i~lF~rkm~~~~G~~~~~~~~~~~~~~~~~~gYdglVe~a~~l----m~grs~~~q~~~ 113 (181)
.-|+.||.+=...|-+..-..+- =+|.-|.|++-.+ |+|+||++.++.
T Consensus 82 ~wdr~Fm~vDqemL~eI~laaNY-------------L~ikpLLd~gCKivaemirgkSpeeir~t 133 (158)
T COG5201 82 FWDRFFMEVDQEMLLEICLAANY-------------LEIKPLLDLGCKIVAEMIRGKSPEEIRET 133 (158)
T ss_pred HHHHHHHHhhHHHHHHHHHhhcc-------------ccchHHHHHHHHHHHHHHccCCHHHHHHH
Confidence 35899999988888777655443 2688888887655 589999987754
No 19
>PF04675 DNA_ligase_A_N: DNA ligase N terminus; InterPro: IPR012308 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I (P18858 from SWISSPROT), and in Saccharomyces cerevisiae (Baker's yeast) (P04819 from SWISSPROT), this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In Vaccinia virus (P16272 from SWISSPROT) this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation []. ; GO: 0003677 DNA binding, 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 2CFM_A 3RR5_A 2HIX_A 2HIV_A 3L2P_A 1X9N_A 4EQ5_A 3GDE_A.
Probab=20.85 E-value=1.6e+02 Score=23.19 Aligned_cols=48 Identities=15% Similarity=0.255 Sum_probs=34.8
Q ss_pred hhHHHHHHHHHHccCCHHHHHHHHHHHHHhcCCC----ChHHHHHHhcCCch
Q 030231 91 YESFVDVSKRVMEGRSRQQQQEVVREVLLSMLPP----GAPAQFRKLFPPTK 138 (181)
Q Consensus 91 YdglVe~a~~lm~grs~~~q~~~v~rVL~sl~Pp----~~p~~fr~lf~P~~ 138 (181)
|..|.++..+|..-.+..+-.+++.+-|.+..+. -+-.+++.++|+..
T Consensus 3 F~~l~~l~~~l~~~~~~~~k~~~l~~~~~~~~~~~~~~~~~~~~~~l~P~~d 54 (177)
T PF04675_consen 3 FSDLCELFEKLESTSSRLEKIAILSNFFRSWREEDLGPDLYLLLRLLFPEYD 54 (177)
T ss_dssp HHHHHHHHHHHHT---HHHHHHHHHHHHHTSHCCGHHCHHHHHHTHSSTTTC
T ss_pred HHHHHHHHHHHHhccCHHHHHHHHHHHHHHcccchhhhHHHHHhcccccchh
Confidence 6778888888888777777788888888888665 45567788888643
Done!