Query 001828
Match_columns 1008
No_of_seqs 42 out of 44
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 10:17:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001828.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001828hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00380 cobD cobalamin biosy 42.4 11 0.00024 41.7 0.9 48 565-612 199-246 (305)
2 PF12949 HeH: HeH/LEM domain; 36.5 25 0.00054 28.4 1.8 17 617-633 7-23 (35)
3 PF03186 CobD_Cbib: CobD/Cbib 36.1 18 0.0004 39.4 1.4 47 567-613 194-244 (295)
4 PRK08878 adenosylcobinamide-ph 34.6 17 0.00038 40.3 0.9 47 565-612 202-248 (317)
5 PRK01209 cobD cobalamin biosyn 27.7 34 0.00075 37.6 1.8 48 565-612 195-246 (312)
6 COG1270 CbiB Cobalamin biosynt 27.3 28 0.00062 39.3 1.1 46 567-612 201-251 (320)
7 PF10382 DUF2439: Protein of u 26.7 20 0.00044 32.8 -0.2 14 694-707 13-27 (83)
8 PRK07630 CobD/CbiB family prot 26.6 31 0.00067 38.1 1.1 47 565-612 193-239 (312)
9 PF10755 DUF2585: Protein of u 24.1 36 0.00078 35.6 1.0 35 536-570 73-107 (165)
10 PRK00944 hypothetical protein; 23.3 38 0.00083 36.1 1.1 16 535-550 101-116 (195)
11 PF14210 DUF4322: Domain of un 22.3 63 0.0014 29.6 2.1 21 481-501 4-25 (66)
12 PRK02925 glucuronate isomerase 22.2 71 0.0015 37.9 3.0 121 236-361 231-364 (466)
No 1
>TIGR00380 cobD cobalamin biosynthesis protein CobD. This protein is involved in cobalamin (vitamin B12) biosynthesis and porphyrin biosynthesis. It converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group. It is part of the cob operon.
Probab=42.40 E-value=11 Score=41.72 Aligned_cols=48 Identities=19% Similarity=0.392 Sum_probs=32.3
Q ss_pred hhhhhhhhhhcchhHHHHHHHhhhhhccccccccccCCCCCCCcccch
Q 001828 565 ATGLKELSDCLPATLATVVSYFSAEVTRGLWKPAFMNGTDWPSPATNL 612 (1008)
Q Consensus 565 ~TGLrDL~DFLPASlatIvSYFSAEVTRGiWKpv~MNGtDWPSPAAnL 612 (1008)
+.-+.|+.+|+||-|.++.--+.+-=.++-||-..=.+.+||||.+-.
T Consensus 199 aarlddiln~iPaRLtal~~~~~~~~~~~a~~~~~r~~~~~~spNsG~ 246 (305)
T TIGR00380 199 AARLDDILNYIPSRLTVFMLLFLSGKPKGAFAIVLRDAPKDPSPNSGW 246 (305)
T ss_pred HHHHHHHHccHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCcCCCccH
Confidence 345889999999999886432332111345555566788999998765
No 2
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=36.47 E-value=25 Score=28.42 Aligned_cols=17 Identities=35% Similarity=0.745 Sum_probs=12.6
Q ss_pred HHHHHHHHhhCCCcccc
Q 001828 617 QQIKKILAATGVDVPTV 633 (1008)
Q Consensus 617 ~eIK~ILAatGVdvP~~ 633 (1008)
.|+|+||.+.||++|+-
T Consensus 7 ~~Lk~iL~~~~I~~ps~ 23 (35)
T PF12949_consen 7 AQLKRILDEHGIEFPSN 23 (35)
T ss_dssp HHHHHHHHHHT---SSS
T ss_pred HHHHHHHHHcCCCCCCC
Confidence 58999999999999984
No 3
>PF03186 CobD_Cbib: CobD/Cbib protein; InterPro: IPR004485 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 CbiB protein, which is involved in cobalamin biosynthesis and porphyrin biosynthesis. It converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group. It is part of the cob operon [].; GO: 0009236 cobalamin biosynthetic process, 0016021 integral to membrane
Probab=36.08 E-value=18 Score=39.39 Aligned_cols=47 Identities=21% Similarity=0.353 Sum_probs=38.1
Q ss_pred hhhhhhhhcchhHHHHHHHhhhhhcc----ccccccccCCCCCCCcccchh
Q 001828 567 GLKELSDCLPATLATVVSYFSAEVTR----GLWKPAFMNGTDWPSPATNLS 613 (1008)
Q Consensus 567 GLrDL~DFLPASlatIvSYFSAEVTR----GiWKpv~MNGtDWPSPAAnL~ 613 (1008)
-|.|+++|+||-|.+..--+.+=..+ +-|+...=.+..||||.+-..
T Consensus 194 rldd~ln~iPaRLtal~~~l~~~~~~~~~~~a~~~~~r~~~~~~SpNsg~~ 244 (295)
T PF03186_consen 194 RLDDLLNWIPARLTALLIALAAPFLGLDWKGALRAWRRDARKHPSPNSGWP 244 (295)
T ss_pred HHHHHhCcHHHHHHHHHHHHHHccccccHHHHHHHHHhhhcCCCCCCcccH
Confidence 37899999999999888777776664 667788888999999976543
No 4
>PRK08878 adenosylcobinamide-phosphate synthase; Provisional
Probab=34.60 E-value=17 Score=40.33 Aligned_cols=47 Identities=15% Similarity=0.367 Sum_probs=32.8
Q ss_pred hhhhhhhhhhcchhHHHHHHHhhhhhccccccccccCCCCCCCcccch
Q 001828 565 ATGLKELSDCLPATLATVVSYFSAEVTRGLWKPAFMNGTDWPSPATNL 612 (1008)
Q Consensus 565 ~TGLrDL~DFLPASlatIvSYFSAEVTRGiWKpv~MNGtDWPSPAAnL 612 (1008)
+.-+.|+.||+||-|.+..--..+- .++-||-..=.+..||||.+-.
T Consensus 202 aArlddiLnwiPARLtal~~~l~~~-~~~a~~~~~rd~~~~~SpNsG~ 248 (317)
T PRK08878 202 AVRILAILDFIPLRLFALLILLGKN-AGHTFQGLLQQSKSWPLPGPAW 248 (317)
T ss_pred HHHHHHHHccHHHHHHHHHHHHHhh-HHHHHHHHHHhcccCCCCCchH
Confidence 4458899999999998765444332 2445555555788999998754
No 5
>PRK01209 cobD cobalamin biosynthesis protein; Provisional
Probab=27.65 E-value=34 Score=37.63 Aligned_cols=48 Identities=21% Similarity=0.286 Sum_probs=34.3
Q ss_pred hhhhhhhhhhcchhHHHHHHHhhhhhcccccc----ccccCCCCCCCcccch
Q 001828 565 ATGLKELSDCLPATLATVVSYFSAEVTRGLWK----PAFMNGTDWPSPATNL 612 (1008)
Q Consensus 565 ~TGLrDL~DFLPASlatIvSYFSAEVTRGiWK----pv~MNGtDWPSPAAnL 612 (1008)
+.-+.|+.||+||-|.++.=-..|=..+|=+| -..=.+.+||||.+-.
T Consensus 195 aarlddilnwiPaRLtal~~~l~a~~~~g~~~~a~~~~~~~~~~~~spn~g~ 246 (312)
T PRK01209 195 AARLDDVLNYIPARLTALLLALAAPLLGGDPRGALRIWRRDARKHPSPNAGW 246 (312)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHhccCCHHHHHHHHHHhhcCCcCCCchH
Confidence 56689999999999987765555444444333 3345789999998764
No 6
>COG1270 CbiB Cobalamin biosynthesis protein CobD/CbiB [Coenzyme metabolism]
Probab=27.34 E-value=28 Score=39.25 Aligned_cols=46 Identities=22% Similarity=0.311 Sum_probs=35.3
Q ss_pred hhhhhhhhcchhHHHHHHH-----hhhhhccccccccccCCCCCCCcccch
Q 001828 567 GLKELSDCLPATLATVVSY-----FSAEVTRGLWKPAFMNGTDWPSPATNL 612 (1008)
Q Consensus 567 GLrDL~DFLPASlatIvSY-----FSAEVTRGiWKpv~MNGtDWPSPAAnL 612 (1008)
-+.|+++|+||-|.++.-- .+.+-+|..||-+-=....||||.+--
T Consensus 201 rlDD~lN~iPARLt~~l~~~~~~~~~~~~~~~a~~~~~rda~~~~SpNsg~ 251 (320)
T COG1270 201 RLDDLLNYIPARLTALLLALASLVLGGGPTRQALRIWRRDARKHPSPNAGW 251 (320)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhhccCcHHHHHHHHHHHhccCCCCCCcc
Confidence 3789999999998754322 234667888988888888999998754
No 7
>PF10382 DUF2439: Protein of unknown function (DUF2439); InterPro: IPR018838 This domain is found at the N-terminal of proteins implicated in telomere maintenance in Saccharomyces cerevisiae (Baker's yeast) [] and in meiotic chromosome segregation in Schizosaccharomyces pombe (Fission yeast) [].
Probab=26.67 E-value=20 Score=32.81 Aligned_cols=14 Identities=43% Similarity=1.035 Sum_probs=10.8
Q ss_pred Hhhhhcccc-eEEEE
Q 001828 694 AQKVKRWND-FLVFS 707 (1008)
Q Consensus 694 ~QKVkRW~d-fiVfS 707 (1008)
+||.|+||| |+.|.
T Consensus 13 ~kK~K~W~DG~l~~~ 27 (83)
T PF10382_consen 13 TKKRKKWHDGFLKYH 27 (83)
T ss_pred cccceeeECCEEEEE
Confidence 699999999 55444
No 8
>PRK07630 CobD/CbiB family protein; Provisional
Probab=26.55 E-value=31 Score=38.07 Aligned_cols=47 Identities=15% Similarity=0.153 Sum_probs=34.2
Q ss_pred hhhhhhhhhhcchhHHHHHHHhhhhhccccccccccCCCCCCCcccch
Q 001828 565 ATGLKELSDCLPATLATVVSYFSAEVTRGLWKPAFMNGTDWPSPATNL 612 (1008)
Q Consensus 565 ~TGLrDL~DFLPASlatIvSYFSAEVTRGiWKpv~MNGtDWPSPAAnL 612 (1008)
+.-|.|+.||+||-|.++.=-..+... +.|+...=.+.+||||.+..
T Consensus 193 aarldd~lnwiPaRL~al~~al~g~~~-~a~~~~~~~~~~~~spn~g~ 239 (312)
T PRK07630 193 AQRAFFVIDWVPARLTALGFAIVGNFE-DAIYAWRNQARQWPDENDGI 239 (312)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHcCHH-HHHHHHHHhhccCCCCCchH
Confidence 556889999999999887655555432 34454455688999998876
No 9
>PF10755 DUF2585: Protein of unknown function (DUF2585); InterPro: IPR019691 This family is conserved in Proteobacteria. The function is not known, but it is thought to be a transmembrane protein. ; GO: 0005886 plasma membrane
Probab=24.10 E-value=36 Score=35.56 Aligned_cols=35 Identities=23% Similarity=0.455 Sum_probs=22.3
Q ss_pred hhHHhhhhhhHHHHHHhhhccCCCChhhhhhhhhh
Q 001828 536 AWDILEATPFVLDAALAACAHGRLSPRELATGLKE 570 (1008)
Q Consensus 536 AWdiLEAvPfVldaaLTACaHGrLS~RdL~TGLrD 570 (1008)
+|||+|..|||+|--=++-.-..-.---.....-|
T Consensus 73 ~WEi~ENsp~II~rYR~~Tia~~Y~GDSV~NSv~D 107 (165)
T PF10755_consen 73 AWEIVENSPFIIERYRAATIALDYFGDSVLNSVSD 107 (165)
T ss_pred hhhhhhCCHHHHHHHHHhhhcccccchHHHHHHHH
Confidence 89999999999996554443333333334444444
No 10
>PRK00944 hypothetical protein; Provisional
Probab=23.35 E-value=38 Score=36.13 Aligned_cols=16 Identities=31% Similarity=0.972 Sum_probs=14.2
Q ss_pred chhHHhhhhhhHHHHH
Q 001828 535 PAWDILEATPFVLDAA 550 (1008)
Q Consensus 535 PAWdiLEAvPfVldaa 550 (1008)
.||||+|..|||+|-=
T Consensus 101 ~aWEi~ENsp~II~RY 116 (195)
T PRK00944 101 SAWELLENSPLIIERY 116 (195)
T ss_pred hhhHhhcCCHHHHHHH
Confidence 5899999999999853
No 11
>PF14210 DUF4322: Domain of unknown function (DUF4322)
Probab=22.32 E-value=63 Score=29.57 Aligned_cols=21 Identities=29% Similarity=0.469 Sum_probs=18.1
Q ss_pred cccCCChHHHHHHHHHHHH-HH
Q 001828 481 GLVHGTSVHLIVDALLTKM-FR 501 (1008)
Q Consensus 481 gl~~g~pVhqv~d~lLnmm-fr 501 (1008)
++-|-|-++||..+||+|+ |+
T Consensus 4 ~~phqnn~qQIgyKLlSml~Fk 25 (66)
T PF14210_consen 4 DLPHQNNIQQIGYKLLSMLNFK 25 (66)
T ss_pred CCCchhHHHHHHHHHHHHHccc
Confidence 4568889999999999999 64
No 12
>PRK02925 glucuronate isomerase; Reviewed
Probab=22.20 E-value=71 Score=37.92 Aligned_cols=121 Identities=21% Similarity=0.250 Sum_probs=81.3
Q ss_pred CCCCChhhhhhhhcCCCCcHHHHHHHHHHHhcCCc---hh--hhhhhh--hhcccccccccchhhHH--HH----HHHHh
Q 001828 236 GSPLTPSLTNALVVTPASSLAEIEKVYEIAVNGSD---DE--KICAAT--VLCGASLVRGWSVQENT--IL----FIIKL 302 (1008)
Q Consensus 236 GspLt~~L~naLv~tPAsSlAElEKly~iA~~GS~---eE--k~aAA~--ILCGASL~RGWniQEH~--v~----~vvkL 302 (1008)
|..++.--...+..+| -+-.|+|++|+-|++|.+ +| |-.++. -||..+.-+||-.|=|. ++ -+.+-
T Consensus 231 Gc~~sDHgl~~~~~~~-~~~~e~~~if~k~~~g~~lt~~E~~~f~~~~l~~la~~y~e~gwvmQlH~Ga~Rn~n~~~~~~ 309 (466)
T PRK02925 231 GCRSSDHGLDTVVTAE-LSEAEADAIFAKALAGGTLTEEEIAQFRTAMLTELARMYAEDGWVMQLHIGALRNNNTRMFKK 309 (466)
T ss_pred CCEEhhcCCCccCCCC-CCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHCCCeEEeecccccCCCHHHHHH
Confidence 4555544444455566 456899999999998865 33 332332 36888999999999998 54 56677
Q ss_pred cCCCCCCCCCCCcccccchhhHHHHHHhcCCcccceeeeecccchhhhHhhhhhhhhhh
Q 001828 303 LSPPVPADYSGSESHLIGYAALLNTLLVGISSVDCIQIFSLHGWVPLLAAALMPICEVF 361 (1008)
Q Consensus 303 LSppvP~~~sg~~s~li~~~pmLn~ll~GissvD~v~I~SLhGlvP~lAa~LMPiCEvF 361 (1008)
|-|=.--|..|.... +-=|+.+|.-+..=|.++..=||-|=|.--..|-|++=.|
T Consensus 310 lG~DtG~Dsi~d~~~----a~~L~~lL~~l~~~~~LpktIly~Lnp~~n~~lat~~g~F 364 (466)
T PRK02925 310 LGPDTGFDSIGDTPI----AEALSPLLDALGNENDLPKTILYTLNPTDNEELATMAGNF 364 (466)
T ss_pred hCCCCCcCCCCchhH----HHHHHHHHHhcccCCCCCeEEEEecCcccHHHHHHHHccc
Confidence 777777776666553 4445555555677777776566777775455666777777
Done!