Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate CCNA_02221 CCNA_02221 methionine synthase I metH
Query= CharProtDB::CH_090726 (1227 letters) >FitnessBrowser__Caulo:CCNA_02221 Length = 899 Score = 1084 bits (2803), Expect = 0.0 Identities = 566/885 (63%), Positives = 667/885 (75%), Gaps = 17/885 (1%) Query: 355 LFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMV 414 +FVN+GERTNVTGSAKFK+LI E Y EAL VARQQVE GAQ+ID+NMDEG+LD++ AMV Sbjct: 8 VFVNIGERTNVTGSAKFKKLIVEGNYPEALSVARQQVEAGAQVIDVNMDEGLLDSQQAMV 67 Query: 415 RFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLR 474 FLNL+A EPDIARVP+MIDSSKW+VIE GLKC+QGK IVNSIS+KEG + F+ A L Sbjct: 68 TFLNLMAAEPDIARVPVMIDSSKWEVIEAGLKCVQGKAIVNSISLKEGEEKFLEQATLCL 127 Query: 475 RYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEE 534 RYGAAVVVMAFDE GQADT RK+EIC RAY L ++VGFPPEDIIFDPNIFAVATGIEE Sbjct: 128 RYGAAVVVMAFDEVGQADTEKRKVEICTRAYNTLVDKVGFPPEDIIFDPNIFAVATGIEE 187 Query: 535 HNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDM 594 H+NYA DFI A IK+ LP+A +SGGVSNVSFSFRGN+PVR AIH+VFLY+AI GMDM Sbjct: 188 HDNYAVDFIEATRRIKQMLPYARVSGGVSNVSFSFRGNEPVRRAIHSVFLYHAINAGMDM 247 Query: 595 GIVNAGQLAIYDDLPAELRDAVEDVILNR--RD---DGTERLLELAEKYRGSKTDDTANA 649 GIVNAG L +YDD+ LR+AVEDVILNR RD TERL+E+A +Y+G K Sbjct: 248 GIVNAGDLPVYDDIDPALREAVEDVILNRPQRDPVMTNTERLVEMAPRYKGEKGQQ--QV 305 Query: 650 QQAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFG 709 EWR VN+RL ++LV GITEFIEQDTEEAR A RP+ VIEGPLMDGMNVVGDLFG Sbjct: 306 ANLEWRKGTVNERLTHALVHGITEFIEQDTEEARLAAERPLHVIEGPLMDGMNVVGDLFG 365 Query: 710 EGKMFLPQVVKSARVMKQAVAYLEPFIEASKE--QGKTNGKMVIATVKGDVHDIGKNIVG 767 GKMFLPQVVKSARVMKQAVA+L PF+EA KE + K GK+++ATVKGDVHDIGKNIVG Sbjct: 366 AGKMFLPQVVKSARVMKQAVAWLMPFMEAEKEGQERKAAGKVLMATVKGDVHDIGKNIVG 425 Query: 768 VVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFT 827 VVLQCNNYE+VDLGVMVPA++IL AK+ D+IGLSGLITPSLDEMV VA EMERQGF Sbjct: 426 VVLQCNNYEVVDLGVMVPADRILDEAKKHKVDMIGLSGLITPSLDEMVFVAAEMERQGFD 485 Query: 828 IPLLIGGATTSKAHTAVKIEQNY-SGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKE 886 IPLLIGGATTS+ HTAVKIE Y GPT YV +ASR VGVV+ LLS+ +RD +A TR E Sbjct: 486 IPLLIGGATTSRTHTAVKIEPAYRRGPTTYVVDASRAVGVVSGLLSEGERDRIIAETRAE 545 Query: 887 YETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEASIETLRNYID 946 Y VR Q+ R + +++ AR FA DW+ Y PP +G + E S+ L +ID Sbjct: 546 YVKVREQYARGQTTKARASIQEARKRAFAIDWKGYAPPKPAFIGTRVFEPSLAELVPFID 605 Query: 947 WTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANR 1006 W+PFF +W L G++P+ILED+VVG A L++DA MLDK+ EK +GV+G +PA Sbjct: 606 WSPFFASWELIGRFPQILEDDVVGQAATDLYRDARAMLDKVVEEKWFGAKGVIGFWPAQA 665 Query: 1007 VGDDIEIYRDETRTHVINVSHHLRQQTEK------TGFANYCLADFVAPKLSGKADYIGA 1060 GDDI +Y DETR + H LRQQ +K AN L+DFVAP G ADY+G Sbjct: 666 QGDDIVLYTDETRVAEFSRLHTLRQQMDKGADKSGEAKANVALSDFVAPIGQG-ADYVGG 724 Query: 1061 FAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENL 1120 FAVT G ED + F+A DDYN IM ALADRLAEAFAE+LH + R WGYA +E+ Sbjct: 725 FAVTAGHGEDEIVAKFKAAGDDYNAIMASALADRLAEAFAEWLHYKARVELWGYAADEDA 784 Query: 1121 SNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGW 1180 E LI E YQGIRPAPGYPA P+HTEK T+++LL+ E TG++LTES+AM PGA+VSG Sbjct: 785 DVERLIAEKYQGIRPAPGYPAQPDHTEKGTLFKLLDAEAATGLQLTESYAMTPGAAVSGL 844 Query: 1181 YFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYD 1225 +FSH + Y+ V +I DQVEDYARRKG + ERWL+P L YD Sbjct: 845 FFSHRQAHYFGVGKIDADQVEDYARRKGWDMETAERWLSPILNYD 889 Lambda K H 0.318 0.134 0.391 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 2687 Number of extensions: 101 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 1227 Length of database: 899 Length adjustment: 45 Effective length of query: 1182 Effective length of database: 854 Effective search space: 1009428 Effective search space used: 1009428 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 58 (26.9 bits)
Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate CCNA_02222 CCNA_02222 5-methyltetrahydrofolate--homocysteine methyltransferase homocysteine-binding subunit
Query= CharProtDB::CH_090726 (1227 letters) >FitnessBrowser__Caulo:CCNA_02222 Length = 358 Score = 375 bits (963), Expect = e-108 Identities = 182/350 (52%), Positives = 243/350 (69%), Gaps = 1/350 (0%) Query: 2 SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61 +++V L+A ERIL+LDG G M Q L EAD+R ERFA + +KGNND+L L++P Sbjct: 8 ANRVAALKAAAKERILILDGSWGVMFQKKGLTEADYRAERFAAYNGQMKGNNDILCLTRP 67 Query: 62 EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSA-EINFAAAKLARACADEWTA 120 +++A +H+AYF AGADI ETNTF+ TTIA ADY + +IN AK+ R+ AD W A Sbjct: 68 DLVAELHDAYFSAGADISETNTFSGTTIAQADYHLGEQDVWDINLEGAKIGRSVADRWNA 127 Query: 121 RTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILI 180 + P++P+++AG +GP N S+S DVNDP R +TFD + AYR+ AL +GG DL LI Sbjct: 128 QNPDRPKFIAGSMGPLNVMLSMSSDVNDPGARKVTFDQVYEAYRQQVDALYQGGVDLFLI 187 Query: 181 ETVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEA 240 ET+ DTLN KAA+ A+ + ELPI ISGTITD SGRTLSGQT EAF+NS++HA+ Sbjct: 188 ETITDTLNCKAAIKAILDWRDEGHEELPIWISGTITDRSGRTLSGQTAEAFWNSVKHAKP 247 Query: 241 LTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQ 300 G NCALG D +R ++ E++RIA+ V A+PNAGLPNA G+YD + + EWA+ Sbjct: 248 FAVGFNCALGADLMRPHIAEMARIADTLVAAYPNAGLPNAMGQYDEEPHETGHALHEWAK 307 Query: 301 AGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNI 350 G +NI+GGCCGTTP HI ++ V G+ PR++PE P A RL+GLEP + Sbjct: 308 DGLVNILGGCCGTTPDHIRHVADEVRGVTPRQIPERPKAMRLAGLEPFEL 357 Lambda K H 0.318 0.134 0.391 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1056 Number of extensions: 36 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 1227 Length of database: 358 Length adjustment: 38 Effective length of query: 1189 Effective length of database: 320 Effective search space: 380480 Effective search space used: 380480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
Align candidate CCNA_02221 CCNA_02221 (methionine synthase I metH)
to HMM TIGR02082 (metH: methionine synthase (EC 2.1.1.13))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR02082.hmm # target sequence database: /tmp/gapView.5762.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02082 [M=1182] Accession: TIGR02082 Description: metH: methionine synthase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1216.9 0.1 0 1216.6 0.1 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_02221 CCNA_02221 methionine synthase I Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_02221 CCNA_02221 methionine synthase I metH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1216.6 0.1 0 0 342 1182 .] 8 856 .. 3 856 .. 0.98 Alignments for each domain: == domain 1 score: 1216.6 bits; conditional E-value: 0 TIGR02082 342 sfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepd 412 fvniGeRtnv+Gs+kf+kli +++y eal++a+qqve Gaq++D+n+De+llD++++m+++l+l+a+epd lcl|FitnessBrowser__Caulo:CCNA_02221 8 VFVNIGERTNVTGSAKFKKLIVEGNYPEALSVARQQVEAGAQVIDVNMDEGLLDSQQAMVTFLNLMAAEPD 78 69********************************************************************* PP TIGR02082 413 iakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadk 483 ia+vP+m+Dss++ev+eaGLk++qGkaivnsislk+Gee+Fle+a l +yGaavvvmafDe Gqa+t ++ lcl|FitnessBrowser__Caulo:CCNA_02221 79 IARVPVMIDSSKWEVIEAGLKCVQGKAIVNSISLKEGEEKFLEQATLCLRYGAAVVVMAFDEVGQADTEKR 149 *********************************************************************** PP TIGR02082 484 kieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsnvsF 554 k+ei++Ray++l++kvgfppediifDpni+++atGieehd+ya+dfiea+r+ik+ lP+a++sgGvsnvsF lcl|FitnessBrowser__Caulo:CCNA_02221 150 KVEICTRAYNTLVDKVGFPPEDIIFDPNIFAVATGIEEHDNYAVDFIEATRRIKQMLPYARVSGGVSNVSF 220 *********************************************************************** PP TIGR02082 555 slrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildrr.....reatekLle 620 s+rgn++vR+a+hsvFLy+ai+aG+Dmgivnag l vyddid+ lre+ved+il+r +te+L+e lcl|FitnessBrowser__Caulo:CCNA_02221 221 SFRGNEPVRRAIHSVFLYHAINAGMDMGIVNAGDLPVYDDIDPALREAVEDVILNRPqrdpvMTNTERLVE 291 *******************************************************9866666678****** PP TIGR02082 621 laelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldGmkvv 691 +a +ykg k + ++ ++ ewr+ v+eRL++alv+G++e+ie+d+eear +++pl++iegpL+dGm+vv lcl|FitnessBrowser__Caulo:CCNA_02221 292 MAPRYKGEKGQ--QQVANLEWRKGTVNERLTHALVHGITEFIEQDTEEARLAAERPLHVIEGPLMDGMNVV 360 *********99..667999**************************************************** PP TIGR02082 692 GdLFGsGkmfLPqvvksarvmkkavayLePylekekeed..kskGkivlatvkGDvhDiGknivdvvLscn 760 GdLFG+GkmfLPqvvksarvmk+ava+L+P++e+eke + k++Gk+++atvkGDvhDiGkniv+vvL+cn lcl|FitnessBrowser__Caulo:CCNA_02221 361 GDLFGAGKMFLPQVVKSARVMKQAVAWLMPFMEAEKEGQerKAAGKVLMATVKGDVHDIGKNIVGVVLQCN 431 *********************************99986555999*************************** PP TIGR02082 761 gyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvav 831 +yevvdlGv+vP+++il++akk+k D+iglsGLi++sldemv+va emer+g++iPll+GGa++s++h+av lcl|FitnessBrowser__Caulo:CCNA_02221 432 NYEVVDLGVMVPADRILDEAKKHKVDMIGLSGLITPSLDEMVFVAAEMERQGFDIPLLIGGATTSRTHTAV 502 *********************************************************************** PP TIGR02082 832 kiaekYk.gevvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevf 901 ki+++Y+ g++ yv das+av vv+ llse +++ ++++++ey ++re++ + ++ + +s+++ark f lcl|FitnessBrowser__Caulo:CCNA_02221 503 KIEPAYRrGPTTYVVDASRAVGVVSGLLSEGERDRIIAETRAEYVKVREQYARGQTTKARASIQEARKRAF 573 ******6489************************************************************* PP TIGR02082 902 aldrsedlevpapkflGtkvleasieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakell 972 a+d++ + +p+p f+Gt+v+e s++el+++iDw ++F +Wel g++p+il+d+++g+ a+ l++da+++l lcl|FitnessBrowser__Caulo:CCNA_02221 574 AIDWK-GYAPPKPAFIGTRVFEPSLAELVPFIDWSPFFASWELIGRFPQILEDDVVGQAATDLYRDARAML 643 *****.9**************************************************************** PP TIGR02082 973 dklsaekllrargvvGlfPaqsvgddieiytdetvsqetkpiatvrekleqlrqqsdr...ylclaDfias 1040 dk+++ek a+gv+G++Paq +gddi++ytdet+ e + + t+r+++++ +s++ +++l+Df+a+ lcl|FitnessBrowser__Caulo:CCNA_02221 644 DKVVEEKWFGAKGVIGFWPAQAQGDDIVLYTDETRVAEFSRLHTLRQQMDKGADKSGEakaNVALSDFVAP 714 ***********************************99********99999888888878899********* PP TIGR02082 1041 kesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenl 1111 G +Dy+g ++vtag g++e+ k++a ddy++i+ aladrlaea+ae+lh + R elwgya++e+ lcl|FitnessBrowser__Caulo:CCNA_02221 715 IGQG-ADYVGGFAVTAGHGEDEIVAKFKAAGDDYNAIMASALADRLAEAFAEWLHYKARVELWGYAADEDA 784 6666.7***************************************************************** PP TIGR02082 1112 dkedllkerYrGirpafGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfa 1181 d+e l+ e+Y+Girpa+GYpa+Pdhtek tl++Ll+ae +Gl+ltes+a++P a+vsgl+f+h +a+Yf lcl|FitnessBrowser__Caulo:CCNA_02221 785 DVERLIAEKYQGIRPAPGYPAQPDHTEKGTLFKLLDAEAaTGLQLTESYAMTPGAAVSGLFFSHRQAHYFG 855 ***************************************9******************************8 PP TIGR02082 1182 v 1182 v lcl|FitnessBrowser__Caulo:CCNA_02221 856 V 856 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1182 nodes) Target sequences: 1 (899 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.08 # Mc/sec: 11.82 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory