Query 000727
Match_columns 1328
No_of_seqs 47 out of 49
Neff 2.8
Searched_HMMs 46136
Date Mon Apr 1 22:42:26 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000727.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000727hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11277 Med24_N: Mediator com 96.5 0.27 5.7E-06 63.1 22.2 593 31-917 12-629 (990)
2 PRK02866 cyanate hydratase; Va 83.1 2.3 5E-05 44.5 5.7 95 58-157 28-129 (147)
3 TIGR00673 cynS cyanate hydrata 68.1 2.9 6.2E-05 44.1 1.6 94 58-156 31-131 (150)
4 TIGR00380 cobD cobalamin biosy 35.8 17 0.00036 41.8 1.1 48 895-942 199-246 (305)
5 PF03186 CobD_Cbib: CobD/Cbib 30.0 28 0.0006 39.6 1.6 46 898-943 195-244 (295)
6 PF12949 HeH: HeH/LEM domain; 29.6 39 0.00085 28.3 1.9 17 947-963 7-23 (35)
7 PRK08878 adenosylcobinamide-ph 28.7 26 0.00057 40.5 1.1 47 895-942 202-248 (317)
8 COG1270 CbiB Cobalamin biosynt 22.7 41 0.00088 39.4 1.2 46 897-942 201-251 (320)
9 cd00559 Cyanase_C Cyanase C-te 21.0 8.7 0.00019 36.3 -3.6 46 109-155 4-49 (69)
10 PRK07630 CobD/CbiB family prot 20.9 45 0.00097 38.3 1.1 47 895-942 193-239 (312)
11 PRK01209 cobD cobalamin biosyn 20.8 55 0.0012 37.6 1.7 48 895-942 195-246 (312)
12 PF10382 DUF2439: Protein of u 20.4 33 0.00071 32.7 -0.1 14 1023-1036 13-27 (83)
No 1
>PF11277 Med24_N: Mediator complex subunit 24 N-terminal; InterPro: IPR021429 This subunit of the Mediator complex appears to be conserved only from insects to humans. It is essential for correct retinal development in fish. Subunit composition of the mediator contributes to the control of differentiation in the vertebrate CNS as there are divergent functions of the mediator subunits Crsp34/Med27, Trap100/Med24, and Crsp150/Med14 [].
Probab=96.50 E-value=0.27 Score=63.10 Aligned_cols=593 Identities=20% Similarity=0.270 Sum_probs=329.5
Q ss_pred HHHhhCCCcchHHHHHHHHhhcCCCch---hhhHHHHHHhhhccC-CCcchhHHHHHHHHcccchhHHHHhhhhcccccC
Q 000727 31 RCQQRHDSPVMWAVEMTRCLKSGSGSV---VELGEVLVSYLCFQN-NHPSLWKFLDYALTSNLLSPIHILSLLTSRVIPH 106 (1328)
Q Consensus 31 ~AQer~~~PLlWAvevas~l~s~~Gv~---~ELAevLVs~LCf~n-N~Ps~WKfLe~ALssrLvsPLhvLALLSsRVIP~ 106 (1328)
.|=.++-+|..|++-+=..+.. |++ .+||+.|+.+..-+. ..|-+=.||++|+++++|+...+|.-++.--
T Consensus 12 ~aW~ERw~d~~w~i~iK~~~~~--g~~~d~~~LAe~LL~qa~iG~~Pn~LiLSYLk~al~sqlvs~~~vl~~I~k~~--- 86 (990)
T PF11277_consen 12 RAWRERWTDIQWGINIKKIIPR--GVSGDIYNLAECLLQQAFIGPSPNPLILSYLKYALSSQLVSYAAVLEAISKFD--- 86 (990)
T ss_pred HHHHhcCChhhHHHHHHHHccC--CCcccHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHhcchhHHHHHHHHhhcc---
Confidence 3444567889999999888875 443 889999999876654 6677999999999999999999887664321
Q ss_pred CcCchhHHHHHHHHhhhcccccccccccchhhHHHHhHHHHhhhccccCccccccceeehHHHHHHHHHHHHh---hhcc
Q 000727 107 RRSQPQAFRLYLELLSRYALNFHAVASEDCNVKIIESIEACLQLSRTYNVRVVEFGHALVLSFFDLVVRLIDS---LFED 183 (1328)
Q Consensus 107 R~~qPeAYRLYLELL~r~aFs~~~~i~~pn~~kimkSID~~L~LS~~~g~~~~e~G~~vV~F~f~iv~~LiD~---~ldD 183 (1328)
..++|.--.--||++...-= ...|+-| .|-++ +--=+++++.-|+-+ .++.
T Consensus 87 ~f~k~~c~~~ll~~l~~~~~------~~sC~gk-------------------~EE~i-L~~Alls~v~WLL~~~~~~l~~ 140 (990)
T PF11277_consen 87 DFSKPHCINALLELLESIID------GLSCRGK-------------------AEECI-LCRALLSLVHWLLQCYEYSLEK 140 (990)
T ss_pred ccchhHHHHHHHHHHHHhcC------CcccCCc-------------------chHHH-HHHHHHHHHHHHHHHHHHHHHH
Confidence 13445555555555543111 1122211 22222 222244444444433 2221
Q ss_pred cCCCCCCCCCCcccccCCCCcccccchhHHHHhhhhhHHHHHHHHHHhhhhhHHHHHHHHhhcCCchhhhHHHHHHHHhh
Q 000727 184 MGLQVGPLDQQSMEIDSIGNFCVGNNEHFEQIRRKNSLLVIEVLNKLMDSSKAMVLLRLIHFNMPESFNGLLQRLQFLEA 263 (1328)
Q Consensus 184 ~GL~~~~~e~qdMeiD~~g~~~~k~~E~~EqLrk~NT~mAiEvi~~~l~nK~ts~iLrLv~~Nmpe~w~~f~QRLq~lea 263 (1328)
. +++. +-..++.+. .-+..+++++++++++...+|++++.|=||-|+...|+.+-+++
T Consensus 141 ~---------~e~~--------~~~~~~e~~-----l~~~~~~L~~i~~s~f~~aLL~Iak~ee~e~w~~v~q~~~~l~~ 198 (990)
T PF11277_consen 141 L---------RENN--------ELSAEQEEI-----LEKCCQRLEKILESTFLRALLYIAKLEEPESWNEVEQKCAKLKN 198 (990)
T ss_pred H---------hhcC--------CCcchHHHH-----HHHHHHHHHHHHcCchHHHHHHHhhhccHhHHHHHHHHHHHHHH
Confidence 1 1110 101234443 34678999999999999999999999999999999999999987
Q ss_pred hhhh------hhhhhhhHHHHHHHhhhccccccccccccccceeeeecccCCCCCccccCcCCcccccchhhhHhhhccC
Q 000727 264 NKLE------SSKLKTVSQLLARLCDNVRNVPSYDYKLNKHRFIGMLIDTKSLRPMRSCNSESSWSSCWLSFDIFMENSM 337 (1328)
Q Consensus 264 ~~la------~~~~k~~~~~l~~L~~~i~~V~~~~yk~~~~~~~~~l~~~~s~~s~~g~~~Gas~Sa~WlPfDiymEdaM 337 (1328)
.... ..++...-+.+..+..++=.-.. .+..+..+.+ .++ =..+| ++|-.|
T Consensus 199 ~l~~~~~~~~~~tL~~~l~kl~sl~~~~~~m~~----v~~~~~~e~~---~~s------------VqaLI----~vE~ll 255 (990)
T PF11277_consen 199 SLSNSGFVKSNVTLRDQLEKLASLEKSIPSMKP----VNSEQLSETI---FPS------------VQALI----AVEVLL 255 (990)
T ss_pred HhcccccccCchHHHHHHHHHHHHHhcCccccC----CCcccCCCCC---cch------------HHHHH----HHHHHH
Confidence 4444 11122233333333333221111 1111110000 000 01233 334332
Q ss_pred CCCccCcchhHHHHHHHHHHHHHHhhcchHHHHHHHHHHHhhhhhhcCCCCCCCCCcccchhhhhhhhhhHHHHHHHHHh
Q 000727 338 DGKQLPVTSAIIVLTRIITTLRVLNRASWQETFLALWLSALRLVQRERDPPEGPLPHLEARLGILLSIVPLAIANVLAEQ 417 (1328)
Q Consensus 338 DG~ql~~tSaIEiL~~liKtlq~vN~asW~etFlaLWiaaLRLVQReRdp~EGPiPhldsRLCmLLsI~pLaia~il~Ee 417 (1328)
+.++-++-+.+-...+|.+.+=++.+-|.=+|=|.+=-.- |..||. -|.+.| +.+=|=|=.||++=
T Consensus 256 -----Npt~dtq~lVeqL~mlqrlk~~~~~~ly~EIirACfl~L~---e~~~ts---~E~~w~---AFtFlKlPqIl~~L 321 (990)
T PF11277_consen 256 -----NPTSDTQQLVEQLMMLQRLKGIPNPRLYCEIIRACFLGLI---ESPETS---EELKWC---AFTFLKLPQILKQL 321 (990)
T ss_pred -----ccCccHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHhhhc---cCCCCC---cchhhh---hhhhhhHHHHHHHH
Confidence 4577888888888999999999999999999988765332 233444 578888 44333333444432
Q ss_pred hhhhhhhccCCCCCCCcccCCCCCCcchhhhhhhhhhhhhhhhcccccccccCchhhhhHHHHHHHHHhhhhhccccCCC
Q 000727 418 ANIQLSTLQGSKTSGSIETGCGHGMEEKSLASKKEGLVSSLQALGNFSALLCPPASVACEANNAAAKAASFISVSKNMKD 497 (1328)
Q Consensus 418 ~~~~l~~~~~~~~~g~~~~~~~k~~~~~~~~~~R~gLisSLQvLG~y~gLL~PP~~vv~aANqAA~KAa~FiSg~~~~~g 497 (1328)
-... ++.+. + + +.. .-..+++.++..|=++..||
T Consensus 322 ~~~~----~~~~~--~-----d--~~~----~~~~dl~~Afe~Ll~~~pLL----------------------------- 355 (990)
T PF11277_consen 322 HALS----RGDKP--Q-----D--KIA----EYSEDLVEAFELLLQLTPLL----------------------------- 355 (990)
T ss_pred HHhc----cCCCc--c-----c--ccc----cccHHHHHHHHHHHccchhh-----------------------------
Confidence 2210 00000 0 0 011 44678899999999999986
Q ss_pred CcccCCCCCCccccccchhHHHHHHHhhhcccccc--ceeecccccccccccccCCCCCCCccchhccCCCCchhhhhhh
Q 000727 498 GICSGSPSETLLNSGGNMRHLIVEACIARNLIDTS--AYYWPGYVSASVIAVNEFSPVQKSPWSMFMEGAPLNGSLVNLL 575 (1328)
Q Consensus 498 ~~~~~~~~d~~~n~~GNmrHLIVEaCIaRnLlDtS--~Y~WpGyv~~~~~~~~~s~p~q~spWs~fM~GspL~~~L~naL 575 (1328)
+..| +||.-|.--.+.|-|-..|||+-+ .++ . +.-+ +.+++
T Consensus 356 -----D~~D--~kc~Cn~v~~LL~e~~K~~lise~~~k~l-----~----~kR~----~~~~~----------------- 398 (990)
T PF11277_consen 356 -----DKMD--QKCNCNCVECLLNELVKLGLISESQVKNL-----L----AKRE----EMSPG----------------- 398 (990)
T ss_pred -----HHHh--hhcCCcHHHHHHHHHHHcCcccHHHHHHH-----H----HHhh----hhhhh-----------------
Confidence 2233 478889999999999999999865 211 0 0000 00111
Q ss_pred hcCCCCcHHHHHHHHHHHccCChhhhhhHhHHhcccccccccchhhHHHHHHHHhcCCCCCCCCCCCcccccccchhHHH
Q 000727 576 FSTPASSLAEIEKLYHIALTGSAEERSAAAKILCGASLARGWNIQEHVVRFVVKLLSPPIPPGYTGPRSHLVDHMPMLTA 655 (1328)
Q Consensus 576 v~tPAsSlaElEKly~iA~~GS~eEk~aAA~ILCGASL~RGWnIQEH~v~~vvkLLSpp~P~~~sG~~s~li~~~pmLna 655 (1328)
+++.- |+.. +.-.--||. -|-++-=|+|.|+ +||+-...-+++ ||.=
T Consensus 399 -------------l~~~~-n~~~--qp~~~lIlR----------AE~tl~~IlKtl~----ad~~k~~e~ll~---vL~~ 445 (990)
T PF11277_consen 399 -------------LQKLE-NTNQ--QPNPKLILR----------AEPTLTGILKTLD----ADYSKSQEGLLG---VLCQ 445 (990)
T ss_pred -------------hhhcc-cCCC--CCCcceEEe----------cccHHHHHHHHhc----cccccchHHHHH---HHHh
Confidence 11000 1111 000001111 2556677788877 555533322221 3333
Q ss_pred HHhcCCcccce-eeecccCcchhhhhhhhhhhhhhcCCCCCCCCCCCCCCCCchhhhHHHHHHHHHHhhhcCCCcchhhc
Q 000727 656 IFFGASSVDTV-HILSLHGLVPDVVASLMPLCEVFGSLVPTSSSKSSTGDEPSVYMVFSCAFLFLVRLWKFYRSPHELCL 734 (1328)
Q Consensus 656 ~l~GissvD~v-hIlSlhGlvP~~Aa~LMPiCEvFGS~~P~~~~~~~~gee~S~~~VFS~AFl~LlRLWkF~~PPlE~~l 734 (1328)
++.| +|.|.| -...--|=.+.+|..|.=+=|.--.+ |.-.-+ ...+-...|=.-|+.|-|.=+-|-
T Consensus 446 mlsG-~SfdlilAaAa~~GkLk~FaskLIk~Ne~~K~~-~~e~~K----~a~~Ra~LFDiSFLMLc~i~q~YG------- 512 (990)
T PF11277_consen 446 MLSG-KSFDLILAAAAVTGKLKSFASKLIKCNEFSKQI-SGEGSK----SAQTRALLFDISFLMLCSIVQTYG------- 512 (990)
T ss_pred hccC-CcHHHHHHHHHHcccHHHHHHHHHhhccccccC-Cccccc----cchhHHHHHhhHHHHHHHHHHHcC-------
Confidence 3332 344432 12233577777777777766654331 111111 123445788888998877665542
Q ss_pred cCCcccCcCChhHHHHhccccccccccchhhhcccCCCCCcccCCCCeeeccCchhhHHHhhchh----hHHhhhccccC
Q 000727 735 SGGTLAGELTLEYLLLLHNSHIASRTSAAQSERNSNLDQLDTVSDDPIYIDHFPKLRAWYCQNKT----CIASTLSGLCS 810 (1328)
Q Consensus 735 ~~~~vgs~ltleyLLllrN~~~~~~~~~~~~~~~~~~~~~~~~s~~Pv~iDSFPKLr~WY~Q~qa----CiAStlSgl~~ 810 (1328)
+|.-+. -|+ || =..-|+++.-- +. |.-..+.
T Consensus 513 ------sevvls-----e~~------------------------------~S--fFe~Wv~~~m~e~~~~~-sP~~~~~- 547 (990)
T PF11277_consen 513 ------SEVVLS-----ENG------------------------------DS--FFEKWVRECMPEEGKSK-SPDQPLA- 547 (990)
T ss_pred ------CcEEEC-----CCC------------------------------Cc--HHHHHHHHhcccccCCC-Chhhhhh-
Confidence 322111 000 11 13456654210 00 0001111
Q ss_pred CCchhHHHHHHHHHHHhhhcCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCchh-HHhhhhhhHHHHHHhhhccCCC
Q 000727 811 GNPVHQVANKILSMIYSKMTKTGASSSNSSTPPSGSASESPACTGEDAYQRPMLPAW-EVLEAIPFVLEAILSACAYGRL 889 (1328)
Q Consensus 811 g~pvhqv~~~lL~mm~~K~~k~g~ss~~~ss~sSss~~gSs~~~~dD~~~rp~lPAW-eiLEAvPfVlea~LTACaHGrL 889 (1328)
.|=...+|.+++.+ |+ + + ..+|.---| ||--.+|.|+-=+|.|=-+|-+
T Consensus 548 -~~d~~~vd~ll~~l----~~-------------~----------~--~~k~~~~kW~eiC~~iP~~i~eiL~AwE~g~l 597 (990)
T PF11277_consen 548 -LCDPAKVDSLLAQL----NS-------------S----------Q--EFKLSQVKWHEICLNIPGAIKEILNAWENGTL 597 (990)
T ss_pred -ccCchhHHHHHHHh----cC-------------c----------c--ccCcccCcHHHHHHhhHHHHHHHHHHHHhCcc
Confidence 12334667777663 22 1 2 244433445 7889999999999999999999
Q ss_pred Cchhh---hhhhhhhhhcch-hhHHHHHHhhh
Q 000727 890 SSRDL---ITGLRELVDFLP-ASIATIISYFS 917 (1328)
Q Consensus 890 S~RdL---~TGLrdL~DFLP-ASlatIvSYfS 917 (1328)
|.-|+ +.++||=+-+|| .--|-+.+|..
T Consensus 598 s~~~Vk~ild~ik~~~~~l~VCa~awLcay~~ 629 (990)
T PF11277_consen 598 SIEEVKRILDNIKGKMCCLSVCAAAWLCAYMR 629 (990)
T ss_pred cHHHHHHHHHHhhcccccHHHHHHHHHHHHHH
Confidence 99885 788888777777 33445666654
No 2
>PRK02866 cyanate hydratase; Validated
Probab=83.14 E-value=2.3 Score=44.54 Aligned_cols=95 Identities=20% Similarity=0.282 Sum_probs=66.9
Q ss_pred hhhHHHHHHhhhccCCCcchhHHHHHHHHcccchhHHHHhhhhcccccCCc-------CchhHHHHHHHHhhhccccccc
Q 000727 58 VELGEVLVSYLCFQNNHPSLWKFLDYALTSNLLSPIHILSLLTSRVIPHRR-------SQPQAFRLYLELLSRYALNFHA 130 (1328)
Q Consensus 58 ~ELAevLVs~LCf~nN~Ps~WKfLe~ALssrLvsPLhvLALLSsRVIP~R~-------~qPeAYRLYLELL~r~aFs~~~ 130 (1328)
.+++++-+..+|.+.|.++. ---++++.-|=.|=-..+.|+ ..|.|- .-|..||+| |.+..|+-+++.
T Consensus 28 iG~S~v~vaaa~lGQ~~ls~--e~A~kla~~LgL~~~~~~~l~--~~P~rg~~~~~~ptdP~iYR~y-E~v~vYG~~~K~ 102 (147)
T PRK02866 28 IGLSEVWVTAALLGQMTLPA--EEAEKVAELLGLDEDAVALLQ--EVPYRGSLPPAVPTDPLIYRFY-EMVQVYGTTLKA 102 (147)
T ss_pred hCCCHHHHHHHHhCCCCCCH--HHHHHHHHHhCCCHHHHHHHh--cCCcCCCCCCCCCCCcHHHHHH-HHHHHhhHHHHH
Confidence 34668888899999888871 111222222322333555565 478885 468899999 999999999999
Q ss_pred ccccchhhHHHHhHHHHhhhccccCcc
Q 000727 131 VASEDCNVKIIESIEACLQLSRTYNVR 157 (1328)
Q Consensus 131 ~i~~pn~~kimkSID~~L~LS~~~g~~ 157 (1328)
.|+..-=|-||..||=-+.+-+.-+-.
T Consensus 103 ~i~E~FGDGIMSAIdf~~~v~k~~dp~ 129 (147)
T PRK02866 103 LIHEKFGDGIMSAIDFKLDVDKVEDPK 129 (147)
T ss_pred HHHHHhCCceeeeeeeceeeeeccCCC
Confidence 998877799999999777776654443
No 3
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=68.09 E-value=2.9 Score=44.05 Aligned_cols=94 Identities=21% Similarity=0.302 Sum_probs=64.3
Q ss_pred hhhHHHHHHhhhccCCCcchhHHHHHHHHcccchhHHHHhhhhcccccCCc-------CchhHHHHHHHHhhhccccccc
Q 000727 58 VELGEVLVSYLCFQNNHPSLWKFLDYALTSNLLSPIHILSLLTSRVIPHRR-------SQPQAFRLYLELLSRYALNFHA 130 (1328)
Q Consensus 58 ~ELAevLVs~LCf~nN~Ps~WKfLe~ALssrLvsPLhvLALLSsRVIP~R~-------~qPeAYRLYLELL~r~aFs~~~ 130 (1328)
.++.++-+..+|.+.+.++- ---++++.-|=.|-=....|. ..|.|- .-|.-||+| |.+..|+-+++.
T Consensus 31 iG~sevwvaaa~lGQ~~ls~--e~A~kla~lLgL~~e~~~~l~--~~P~rg~~~~~~ptdP~iYR~y-E~v~vYG~~~K~ 105 (150)
T TIGR00673 31 LGLAEVFVAAALYGQAAAPA--DEARLVGAKLDLDEDSILELQ--MAPLRGCIDPVIPTDPTMYRFY-EMLQVYGTTLKA 105 (150)
T ss_pred HCCCHHHHHHHHhCCCCCCH--HHHHHHHHHhCcCHHHHHHHh--cCCCCCCCCCCCCCCchHHHHH-HHHHHhhHHHHH
Confidence 45667788888888877761 111112222222223344443 578885 578899999 999999999999
Q ss_pred ccccchhhHHHHhHHHHhhhccccCc
Q 000727 131 VASEDCNVKIIESIEACLQLSRTYNV 156 (1328)
Q Consensus 131 ~i~~pn~~kimkSID~~L~LS~~~g~ 156 (1328)
.|+..-=|-||..||=-+.+.+.-+-
T Consensus 106 ~i~E~FGDGIMSAIdF~~~v~k~~dp 131 (150)
T TIGR00673 106 VVHEKFGDGIMSAIDFKLDVEKVADP 131 (150)
T ss_pred HHHHHhCcceeeeeeeceeeeeecCC
Confidence 99877779999999977777665443
No 4
>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=35.83 E-value=17 Score=41.82 Aligned_cols=48 Identities=17% Similarity=0.407 Sum_probs=32.5
Q ss_pred hhhhhhhhhcchhhHHHHHHhhhhhhccccccccccCCCCCCCCCCCc
Q 000727 895 ITGLRELVDFLPASIATIISYFSAEISRGIWKAVPMNGTDWPSPAPML 942 (1328)
Q Consensus 895 ~TGLrdL~DFLPASlatIvSYfSAEvTRGiWKpv~MNGtDWPSPaanL 942 (1328)
+.-+.|+.+|+||-|.++.--+.+-=.++-|+-..=.+.+||||.+-.
T Consensus 199 aarlddiln~iPaRLtal~~~~~~~~~~~a~~~~~r~~~~~~spNsG~ 246 (305)
T TIGR00380 199 AARLDDILNYIPSRLTVFMLLFLSGKPKGAFAIVLRDAPKDPSPNSGW 246 (305)
T ss_pred HHHHHHHHccHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCcCCCccH
Confidence 345889999999999986432332111345666666788999998765
No 5
>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=29.97 E-value=28 Score=39.57 Aligned_cols=46 Identities=24% Similarity=0.488 Sum_probs=35.6
Q ss_pred hhhhhhcchhhHHHHHHhhhhhhcc----ccccccccCCCCCCCCCCCcc
Q 000727 898 LRELVDFLPASIATIISYFSAEISR----GIWKAVPMNGTDWPSPAPMLP 943 (1328)
Q Consensus 898 LrdL~DFLPASlatIvSYfSAEvTR----GiWKpv~MNGtDWPSPaanL~ 943 (1328)
|.|+++|+||-|.+..--+.+=..+ +-|+...=.|..||||.+-..
T Consensus 195 ldd~ln~iPaRLtal~~~l~~~~~~~~~~~a~~~~~r~~~~~~SpNsg~~ 244 (295)
T PF03186_consen 195 LDDLLNWIPARLTALLIALAAPFLGLDWKGALRAWRRDARKHPSPNSGWP 244 (295)
T ss_pred HHHHhCcHHHHHHHHHHHHHHccccccHHHHHHHHHhhhcCCCCCCcccH
Confidence 7899999999888877777776664 567777778899999966543
No 6
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=29.59 E-value=39 Score=28.31 Aligned_cols=17 Identities=29% Similarity=0.604 Sum_probs=12.6
Q ss_pred HHHHHHHHHhCccCCCC
Q 000727 947 SEIKEILAAVGVSVPCC 963 (1328)
Q Consensus 947 ~~iK~ILAa~GV~vP~~ 963 (1328)
.|+|+||.+.||++|+-
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 58999999999999985
No 7
>PRK08878 adenosylcobinamide-phosphate synthase; Provisional
Probab=28.73 E-value=26 Score=40.48 Aligned_cols=47 Identities=15% Similarity=0.496 Sum_probs=32.7
Q ss_pred hhhhhhhhhcchhhHHHHHHhhhhhhccccccccccCCCCCCCCCCCc
Q 000727 895 ITGLRELVDFLPASIATIISYFSAEISRGIWKAVPMNGTDWPSPAPML 942 (1328)
Q Consensus 895 ~TGLrdL~DFLPASlatIvSYfSAEvTRGiWKpv~MNGtDWPSPaanL 942 (1328)
+.-+.|+.||+||-|.+..=-..+- .++-||-..=.+..||||.+-.
T Consensus 202 aArlddiLnwiPARLtal~~~l~~~-~~~a~~~~~rd~~~~~SpNsG~ 248 (317)
T PRK08878 202 AVRILAILDFIPLRLFALLILLGKN-AGHTFQGLLQQSKSWPLPGPAW 248 (317)
T ss_pred HHHHHHHHccHHHHHHHHHHHHHhh-HHHHHHHHHHhcccCCCCCchH
Confidence 3457899999999998765444332 2445665555789999998754
No 8
>COG1270 CbiB Cobalamin biosynthesis protein CobD/CbiB [Coenzyme metabolism]
Probab=22.65 E-value=41 Score=39.42 Aligned_cols=46 Identities=17% Similarity=0.376 Sum_probs=35.6
Q ss_pred hhhhhhhcchhhHHHHHHh-----hhhhhccccccccccCCCCCCCCCCCc
Q 000727 897 GLRELVDFLPASIATIISY-----FSAEISRGIWKAVPMNGTDWPSPAPML 942 (1328)
Q Consensus 897 GLrdL~DFLPASlatIvSY-----fSAEvTRGiWKpv~MNGtDWPSPaanL 942 (1328)
-+.|+++|+||-|.++.=- .+..-+|..||-+-=....||||.+--
T Consensus 201 rlDD~lN~iPARLt~~l~~~~~~~~~~~~~~~a~~~~~rda~~~~SpNsg~ 251 (320)
T COG1270 201 RLDDLLNYIPARLTALLLALASLVLGGGPTRQALRIWRRDARKHPSPNAGW 251 (320)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhhccCcHHHHHHHHHHHhccCCCCCCcc
Confidence 3789999999998754322 235667888998888888999998754
No 9
>cd00559 Cyanase_C Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the toxicity of environmental cyanate and to use cyanate as a source of nitrogen for growth. This enzyme is a homodecamer, formed by five dimers. Each monomer is composed of two domains, an N-terminal helix-turn-helix and this structurally unique C-terminal domain.
Probab=21.01 E-value=8.7 Score=36.28 Aligned_cols=46 Identities=22% Similarity=0.468 Sum_probs=37.6
Q ss_pred CchhHHHHHHHHhhhcccccccccccchhhHHHHhHHHHhhhccccC
Q 000727 109 SQPQAFRLYLELLSRYALNFHAVASEDCNVKIIESIEACLQLSRTYN 155 (1328)
Q Consensus 109 ~qPeAYRLYLELL~r~aFs~~~~i~~pn~~kimkSID~~L~LS~~~g 155 (1328)
.-|.-|||| |.+..|+-+++..++..-=|-||..||=-+.+-+.-+
T Consensus 4 tDP~iYRly-E~v~vYG~~~K~li~E~FGDGIMSAIdF~~~v~k~~d 49 (69)
T cd00559 4 TDPLIYRFY-EIVQVYGPTLKALIHEKFGDGIMSAIDFKLDVDKVED 49 (69)
T ss_pred CCceeeehH-HHHHHhhHHHHHHHHHHcCCceeeeEEeeeeEEeccC
Confidence 468999999 8899999999998887777889999987766655443
No 10
>PRK07630 CobD/CbiB family protein; Provisional
Probab=20.92 E-value=45 Score=38.30 Aligned_cols=47 Identities=13% Similarity=0.205 Sum_probs=34.1
Q ss_pred hhhhhhhhhcchhhHHHHHHhhhhhhccccccccccCCCCCCCCCCCc
Q 000727 895 ITGLRELVDFLPASIATIISYFSAEISRGIWKAVPMNGTDWPSPAPML 942 (1328)
Q Consensus 895 ~TGLrdL~DFLPASlatIvSYfSAEvTRGiWKpv~MNGtDWPSPaanL 942 (1328)
+.-|.|+.||+||-|.++.=-..+... +.|+...=.+.+||||.+..
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 456889999999999887655555432 34455455688999998875
No 11
>PRK01209 cobD cobalamin biosynthesis protein; Provisional
Probab=20.76 E-value=55 Score=37.56 Aligned_cols=48 Identities=17% Similarity=0.369 Sum_probs=34.0
Q ss_pred hhhhhhhhhcchhhHHHHHHhhhhhhcccc----ccccccCCCCCCCCCCCc
Q 000727 895 ITGLRELVDFLPASIATIISYFSAEISRGI----WKAVPMNGTDWPSPAPML 942 (1328)
Q Consensus 895 ~TGLrdL~DFLPASlatIvSYfSAEvTRGi----WKpv~MNGtDWPSPaanL 942 (1328)
+.-+.|+.||+||-|.++.=-..|=+.+|= |+...=.+.+||||.+-.
T Consensus 195 aarlddilnwiPaRLtal~~~l~a~~~~g~~~~a~~~~~~~~~~~~spn~g~ 246 (312)
T PRK01209 195 AARLDDVLNYIPARLTALLLALAAPLLGGDPRGALRIWRRDARKHPSPNAGW 246 (312)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHhccCCHHHHHHHHHHhhcCCcCCCchH
Confidence 456899999999998877655554444443 333445789999998764
No 12
>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=20.42 E-value=33 Score=32.71 Aligned_cols=14 Identities=36% Similarity=0.961 Sum_probs=10.7
Q ss_pred Hhhhhcccc-eEEEe
Q 000727 1023 AQKVRRWHD-FIVVS 1036 (1328)
Q Consensus 1023 ~QKVrRWhd-fiV~S 1036 (1328)
+||.|+||| |+.|.
T Consensus 13 ~kK~K~W~DG~l~~~ 27 (83)
T PF10382_consen 13 TKKRKKWHDGFLKYH 27 (83)
T ss_pred cccceeeECCEEEEE
Confidence 699999999 44443
Done!