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.1304486.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 FitnessBrowser__Caulo:CCNA_02221
Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Caulo:CCNA_02221
# 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 sfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakv 416
fvniGeRtnv+Gs+kf+kli +++y eal++a+qqve Gaq++D+n+De+llD++++m+++l+l+a+epdia+v
FitnessBrowser__Caulo:CCNA_02221 8 VFVNIGERTNVTGSAKFKKLIVEGNYPEALSVARQQVEAGAQVIDVNMDEGLLDSQQAMVTFLNLMAAEPDIARV 82
69************************************************************************* PP
TIGR02082 417 PlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRa 491
P+m+Dss++ev+eaGLk++qGkaivnsislk+Gee+Fle+a l +yGaavvvmafDe Gqa+t ++k+ei++Ra
FitnessBrowser__Caulo:CCNA_02221 83 PVMIDSSKWEVIEAGLKCVQGKAIVNSISLKEGEEKFLEQATLCLRYGAAVVVMAFDEVGQADTEKRKVEICTRA 157
*************************************************************************** PP
TIGR02082 492 yklltekvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavReal 566
y++l++kvgfppediifDpni+++atGieehd+ya+dfiea+r+ik+ lP+a++sgGvsnvsFs+rgn++vR+a+
FitnessBrowser__Caulo:CCNA_02221 158 YNTLVDKVGFPPEDIIFDPNIFAVATGIEEHDNYAVDFIEATRRIKQMLPYARVSGGVSNVSFSFRGNEPVRRAI 232
*************************************************************************** PP
TIGR02082 567 hsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildrr.....reatekLlelaelykgtkeksskea 636
hsvFLy+ai+aG+Dmgivnag l vyddid+ lre+ved+il+r +te+L+e+a +ykg k + ++
FitnessBrowser__Caulo:CCNA_02221 233 HSVFLYHAINAGMDMGIVNAGDLPVYDDIDPALREAVEDVILNRPqrdpvMTNTERLVEMAPRYKGEKGQ--QQV 305
*******************************************9866666678***************99..667 PP
TIGR02082 637 qeaewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarv 711
++ ewr+ v+eRL++alv+G++e+ie+d+eear +++pl++iegpL+dGm+vvGdLFG+GkmfLPqvvksarv
FitnessBrowser__Caulo:CCNA_02221 306 ANLEWRKGTVNERLTHALVHGITEFIEQDTEEARLAAERPLHVIEGPLMDGMNVVGDLFGAGKMFLPQVVKSARV 380
999************************************************************************ PP
TIGR02082 712 mkkavayLePylekekeed..kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkk 784
mk+ava+L+P++e+eke + k++Gk+++atvkGDvhDiGkniv+vvL+cn+yevvdlGv+vP+++il++akk+k
FitnessBrowser__Caulo:CCNA_02221 381 MKQAVAWLMPFMEAEKEGQerKAAGKVLMATVKGDVHDIGKNIVGVVLQCNNYEVVDLGVMVPADRILDEAKKHK 455
*************99986555999*************************************************** PP
TIGR02082 785 aDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekYk.gevvyvkdaseavkvvdkll 858
D+iglsGLi++sldemv+va emer+g++iPll+GGa++s++h+avki+++Y+ g++ yv das+av vv+ ll
FitnessBrowser__Caulo:CCNA_02221 456 VDMIGLSGLITPSLDEMVFVAAEMERQGFDIPLLIGGATTSRTHTAVKIEPAYRrGPTTYVVDASRAVGVVSGLL 530
*****************************************************6489****************** PP
TIGR02082 859 sekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleasieellkyi 933
se +++ ++++++ey ++re++ + ++ + +s+++ark fa+d++ + +p+p f+Gt+v+e s++el+++i
FitnessBrowser__Caulo:CCNA_02221 531 SEGERDRIIAETRAEYVKVREQYARGQTTKARASIQEARKRAFAIDWK-GYAPPKPAFIGTRVFEPSLAELVPFI 604
************************************************.9************************* PP
TIGR02082 934 DwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddieiytdetvs 1008
Dw ++F +Wel g++p+il+d+++g+ a+ l++da+++ldk+++ek a+gv+G++Paq +gddi++ytdet+
FitnessBrowser__Caulo:CCNA_02221 605 DWSPFFASWELIGRFPQILEDDVVGQAATDLYRDARAMLDKVVEEKWFGAKGVIGFWPAQAQGDDIVLYTDETRV 679
**************************************************************************9 PP
TIGR02082 1009 qetkpiatvrekleqlrqqsdr...ylclaDfiaskesGikDylgallvtaglgaeelakkleakeddydsilvk 1080
e + + t+r+++++ +s++ +++l+Df+a+ G +Dy+g ++vtag g++e+ k++a ddy++i+
FitnessBrowser__Caulo:CCNA_02221 680 AEFSRLHTLRQQMDKGADKSGEakaNVALSDFVAPIGQG-ADYVGGFAVTAGHGEDEIVAKFKAAGDDYNAIMAS 753
9********99999888888878899*********6666.7********************************** PP
TIGR02082 1081 aladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdhtekatlleLleaer.iGlk 1154
aladrlaea+ae+lh + R elwgya++e+ d+e l+ e+Y+Girpa+GYpa+Pdhtek tl++Ll+ae +Gl+
FitnessBrowser__Caulo:CCNA_02221 754 ALADRLAEAFAEWLHYKARVELWGYAADEDADVERLIAEKYQGIRPAPGYPAQPDHTEKGTLFKLLDAEAaTGLQ 828
**********************************************************************9**** PP
TIGR02082 1155 lteslalaPeasvsglyfahpeakYfav 1182
ltes+a++P a+vsgl+f+h +a+Yf v
FitnessBrowser__Caulo:CCNA_02221 829 LTESYAMTPGAAVSGLFFSHRQAHYFGV 856
**************************86 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 26.83
//
[ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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