Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate 7026140 Shewana3_3282 B12-dependent methionine synthase (RefSeq)
Query= CharProtDB::CH_090726
(1227 letters)
>FitnessBrowser__ANA3:7026140
Length = 1244
Score = 1624 bits (4206), Expect = 0.0
Identities = 819/1238 (66%), Positives = 974/1238 (78%), Gaps = 14/1238 (1%)
Query: 2 SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
S + +R QL++RIL+LDG MGTMIQ Y+L E D+RGERF DW D+KGNNDLLVL++P
Sbjct: 9 SQTLADIRNQLSKRILILDGAMGTMIQGYKLEEEDYRGERFKDWHTDVKGNNDLLVLTQP 68
Query: 62 EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
+I IH Y +AGADIIETNTFN+TTIAMADY M+SLSAEIN A+LAR DE
Sbjct: 69 HIIKQIHIDYLKAGADIIETNTFNATTIAMADYDMQSLSAEINREGARLAREACDEIEQA 128
Query: 122 TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
T KPRYVAGVLGPTNRT SISPDVNDP +RNI FD LV AY EST+AL+EGGAD+I++E
Sbjct: 129 TG-KPRYVAGVLGPTNRTCSISPDVNDPGYRNIHFDELVTAYCESTRALIEGGADIIMVE 187
Query: 182 TVFDTLNAKAAVFAVKTEFEAL-----GVELPIMISGTITDASGRTLSGQTTEAFYNSLR 236
T+FDTLNAKAA+FA++T F+ L LP+MISGTITDASGRTL+GQTTEAFYNSLR
Sbjct: 188 TIFDTLNAKAALFAIETVFDELFGPNSPARLPVMISGTITDASGRTLTGQTTEAFYNSLR 247
Query: 237 HAEALTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIR 296
H + L+ GLNCALGP ELR YV+ELSRIAECYV+AHPNAGLPN FG YD + MA I+
Sbjct: 248 HIKPLSIGLNCALGPKELRPYVEELSRIAECYVSAHPNAGLPNEFGGYDETPEDMASVIQ 307
Query: 297 EWAQAGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLF 356
EWA+ G LNI+GGCCG+TP+HI + AVE APR LPEIPVACRLSGLEPL I +LF
Sbjct: 308 EWAREGMLNIIGGCCGSTPEHIKVIREAVEPFAPRVLPEIPVACRLSGLEPLTIDAQTLF 367
Query: 357 VNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRF 416
VNVGERTNVTGSAKF +LIKE K+ +ALDVAR+QVE+GAQIIDINMDEGMLD M +F
Sbjct: 368 VNVGERTNVTGSAKFLKLIKEGKFEQALDVAREQVESGAQIIDINMDEGMLDGVEVMHKF 427
Query: 417 LNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRY 476
LNLIA EPDI+RVPIMIDSSKW+VIE GLKCIQGKGIVNSIS+KEG + FI A L++RY
Sbjct: 428 LNLIASEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISLKEGEEKFIEQATLVKRY 487
Query: 477 GAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHN 536
GAA ++MAFDEQGQADT+ARK+EIC RAY++L ++VGFPPEDIIFDPNIFA+ATGI+EH+
Sbjct: 488 GAAAIIMAFDEQGQADTKARKVEICTRAYRVLVDKVGFPPEDIIFDPNIFAIATGIDEHD 547
Query: 537 NYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGI 596
NYA DFI A ++IK LPHA+ISGGVSNVSFSFRGN+PVREAIHAVFLY+AI+ GMDMGI
Sbjct: 548 NYAVDFIEAIKEIKATLPHAMISGGVSNVSFSFRGNNPVREAIHAVFLYHAIKVGMDMGI 607
Query: 597 VNAGQLAIYDDLPAELRDAVEDVILN-----RRDDGTERLLELAEKYRGSKTDDTANAQQ 651
VNAGQLAIYDD+ EL+D VE+V+LN + TE+LLE+AEK+RG + +A +
Sbjct: 608 VNAGQLAIYDDIDPELKDKVENVVLNLHCPVEDSNNTEQLLEIAEKFRGDGS-SSAKKED 666
Query: 652 AEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEG 711
EWRSW VN+RL ++LVKGITEFI++DTE ARQ A+RP++VIEGPLMDGMN+VGDLFG G
Sbjct: 667 LEWRSWPVNQRLAHALVKGITEFIDEDTEAARQLASRPLDVIEGPLMDGMNIVGDLFGSG 726
Query: 712 KMFLPQVVKSARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQ 771
KMFLPQVVKSARVMK+AVAYL PFIE K +G++NG++++ TVKGDVHDIGKNIVGVVL
Sbjct: 727 KMFLPQVVKSARVMKKAVAYLNPFIEQEKVEGQSNGRILMVTVKGDVHDIGKNIVGVVLA 786
Query: 772 CNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLL 831
CN +E+ DLGVMV E+IL KE N D+IG+SGLITPSLDEMV+ K R+G TIP +
Sbjct: 787 CNGFEVFDLGVMVSVERILEAVKEHNIDIIGMSGLITPSLDEMVHNVKTFHREGLTIPAI 846
Query: 832 IGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVR 891
IGGAT SK HTAVKI +Y +Y+ +ASR V +V+ L+S+ R + T EYE +R
Sbjct: 847 IGGATCSKIHTAVKIAPHYPHGAIYIADASRAVPMVSKLVSNETRQATIDETYAEYEEMR 906
Query: 892 IQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEV-EASIETLRNYIDWTPF 950
I+ + R V+LEAAR+N DW YTP + LG Q + + L + IDWTPF
Sbjct: 907 IKRLSQTKRKEIVSLEAARENRCQHDWANYTPFKPNVLGRQVFDDYPLTDLVDRIDWTPF 966
Query: 951 FMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVG-D 1009
F W L G YP IL D+VVGVEAQ+LF D ML K+ EK L +GV+GLFPAN VG D
Sbjct: 967 FRAWELHGHYPEILTDKVVGVEAQKLFADGQAMLKKIIDEKWLTAKGVIGLFPANTVGFD 1026
Query: 1010 DIEIYRDETRTHVINVSHHLRQQTEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEE 1069
DIE+Y DETRT V +HHLR Q E+ G N+CLADFVAPK SG ADY+G FAVT G
Sbjct: 1027 DIELYTDETRTEVEMTTHHLRMQLERVGNDNFCLADFVAPKDSGVADYMGGFAVTAGHGI 1086
Query: 1070 DALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIREN 1129
D FEA HDDYN IM+K LADRLAEAFAE +HERVRK +WGYA +E L NE LIRE
Sbjct: 1087 DEHIARFEANHDDYNAIMLKCLADRLAEAFAERMHERVRKEFWGYAADEQLDNEALIREK 1146
Query: 1130 YQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKY 1189
Y+GIRPAPGYPACP+HTEK +W+LL+ + + +TES+AM+P A+VSGWYF+HP S+Y
Sbjct: 1147 YKGIRPAPGYPACPDHTEKGLLWDLLKPNETIDLNITESYAMFPTAAVSGWYFAHPKSRY 1206
Query: 1190 YAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYDAD 1227
+ V I RDQVEDYA+RKGM+V E E+WLAP L YD +
Sbjct: 1207 FGVTNIGRDQVEDYAKRKGMTVAETEKWLAPVLDYDPE 1244
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: 3805
Number of extensions: 150
Number of successful extensions: 7
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: 1244
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1196
Effective search space: 1410084
Effective search space used: 1410084
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: 59 (27.3 bits)
Align candidate 7026140 Shewana3_3282 (B12-dependent methionine synthase (RefSeq))
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.7424.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 1770.9 0.0 0 1770.7 0.0 1.0 1 lcl|FitnessBrowser__ANA3:7026140 Shewana3_3282 B12-dependent meth
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026140 Shewana3_3282 B12-dependent methionine synthase (RefSeq)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1770.7 0.0 0 0 1 1182 [] 19 1209 .. 19 1209 .. 0.98
Alignments for each domain:
== domain 1 score: 1770.7 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntFns 74
l+kril+lDGamGt++q ++L+e+d+rge ++d+++++kGnndlL+lt+P +i++ih +y++aGaDi+etntFn+
lcl|FitnessBrowser__ANA3:7026140 19 LSKRILILDGAMGTMIQGYKLEEEDYRGErFKDWHTDVKGNNDLLVLTQPHIIKQIHIDYLKAGADIIETNTFNA 93
579************************************************************************ PP
TIGR02082 75 teialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdverpefrnvtydelvda 149
t+ia+adYd++++++e+n+++a+lare++de+++ + k+R+vaG+lGPtn++ ++spdv++p++rn+++delv a
lcl|FitnessBrowser__ANA3:7026140 94 TTIAMADYDMQSLSAEINREGARLAREACDEIEQATGKPRYVAGVLGPTNRTCSISPDVNDPGYRNIHFDELVTA 168
*************************************************************************** PP
TIGR02082 150 YkeqvkglldGGvDllLietvfDtlnakaalfaveevfee.....kgrelPilisgvivdksGrtLsGqtleafl 219
Y e++++l++GG+D++++et+fDtlnakaalfa+e+vf+e ++lP++isg+i+d+sGrtL+Gqt+eaf+
lcl|FitnessBrowser__ANA3:7026140 169 YCESTRALIEGGADIIMVETIFDTLNAKAALFAIETVFDElfgpnSPARLPVMISGTITDASGRTLTGQTTEAFY 243
**************************************97222224689************************** PP
TIGR02082 220 aslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalkefaeegllniv 294
+sl+h + l++GLnCalG++elr++v+els++ae++vs++PnaGLPn++g Yd+tpe +a++++e+a+eg+lni+
lcl|FitnessBrowser__ANA3:7026140 244 NSLRHIKPLSIGLNCALGPKELRPYVEELSRIAECYVSAHPNAGLPNEFGGYDETPEDMASVIQEWAREGMLNII 318
*************************************************************************** PP
TIGR02082 295 GGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyee 369
GGCCG+tPehi+ i eav+ +pr +e++ +++lsgle+l+i+ ++ fvn+GeRtnv+Gs+kf klik++++e+
lcl|FitnessBrowser__ANA3:7026140 319 GGCCGSTPEHIKVIREAVEPFAPRVLPEIPVACRLSGLEPLTIDAQTLFVNVGERTNVTGSAKFLKLIKEGKFEQ 393
*************************************************************************** PP
TIGR02082 370 alkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsi 444
al++a++qve+Gaqi+Din+De++lDg++ m+k+l+l+asepdi++vP+m+Dss++ev+eaGLk+iqGk+ivnsi
lcl|FitnessBrowser__ANA3:7026140 394 ALDVAREQVESGAQIIDINMDEGMLDGVEVMHKFLNLIASEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSI 468
*************************************************************************** PP
TIGR02082 445 slkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGi 519
slk+Gee+F+e+a l+k+yGaa+++mafDe+Gqa+t+++k+ei++Ray++l++kvgfppediifDpni++iatGi
lcl|FitnessBrowser__ANA3:7026140 469 SLKEGEEKFIEQATLVKRYGAAAIIMAFDEQGQADTKARKVEICTRAYRVLVDKVGFPPEDIIFDPNIFAIATGI 543
*************************************************************************** PP
TIGR02082 520 eehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavydd 594
+ehd+ya+dfieai+eik +lP+a isgGvsnvsFs+rgn++vRea+h+vFLy+aik+G+Dmgivnag+la+ydd
lcl|FitnessBrowser__ANA3:7026140 544 DEHDNYAVDFIEAIKEIKATLPHAMISGGVSNVSFSFRGNNPVREAIHAVFLYHAIKVGMDMGIVNAGQLAIYDD 618
*************************************************************************** PP
TIGR02082 595 idkelrevvedlildrr.....reatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregiee 664
id+el+++ve+++l+ + +++te+Lle+ae+++g ++s ++++ ewr++pv++RL++alvkG++e+i+e
lcl|FitnessBrowser__ANA3:7026140 619 IDPELKDKVENVVLNLHcpvedSNNTEQLLEIAEKFRGDGSSS-AKKEDLEWRSWPVNQRLAHALVKGITEFIDE 692
***************888887799***************9995.558899************************* PP
TIGR02082 665 dleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGkivla 739
d+e+ar+ +++pl++iegpL+dGm++vGdLFGsGkmfLPqvvksarvmkkavayL+P++e+ek e +s+G+i++
lcl|FitnessBrowser__ANA3:7026140 693 DTEAARQLASRPLDVIEGPLMDGMNIVGDLFGSGKMFLPQVVKSARVMKKAVAYLNPFIEQEKVEGQSNGRILMV 767
*************************************************************************** PP
TIGR02082 740 tvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvk 814
tvkGDvhDiGkniv+vvL+cng+ev dlGv+v ve+ilea k+++ D+ig+sGLi++sldemv++++ ++r+g++
lcl|FitnessBrowser__ANA3:7026140 768 TVKGDVHDIGKNIVGVVLACNGFEVFDLGVMVSVERILEAVKEHNIDIIGMSGLITPSLDEMVHNVKTFHREGLT 842
*************************************************************************** PP
TIGR02082 815 iPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkekli 889
iP ++GGa+ sk h+avkia++Y +y das+av +v+kl+s++++++ ++++ +eyee+r k ++ ++++
lcl|FitnessBrowser__ANA3:7026140 843 IPAIIGGATCSKIHTAVKIAPHYPHGAIYIADASRAVPMVSKLVSNETRQATIDETYAEYEEMRIKRLSQTKRKE 917
*************************************************************************** PP
TIGR02082 890 alsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdelegleark 963
+s++aar+++ + d+ ++++ +p+ lG++v++++ + +l++ iDw+++F +Wel+g+yp+il+d+++g+ea+k
lcl|FitnessBrowser__ANA3:7026140 918 IVSLEAARENRCQHDWA-NYTPFKPNVLGRQVFDDYpLTDLVDRIDWTPFFRAWELHGHYPEILTDKVVGVEAQK 991
*****************.9******************************************************** PP
TIGR02082 964 lfkdakelldklsaekllrargvvGlfPaqsvg.ddieiytdetvsqetkpiatvrekleqlrqqsdrylclaDf 1037
lf+d +++l+k++ ek l+a+gv+GlfPa++vg ddie+ytdet+ t++ t+++ + ql++ + + claDf
lcl|FitnessBrowser__ANA3:7026140 992 LFADGQAMLKKIIDEKWLTAKGVIGLFPANTVGfDDIELYTDETR---TEVEMTTHHLRMQLERVGNDNFCLADF 1063
******************************98769*********9...55555555556666666666******* PP
TIGR02082 1038 iaskesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenld 1112
+a+k+sG +Dy+g ++vtag g++e ++ea++ddy++i++k ladrlaea+ae +hervRke+wgya++e+ld
lcl|FitnessBrowser__ANA3:7026140 1064 VAPKDSGVADYMGGFAVTAGHGIDEHIARFEANHDDYNAIMLKCLADRLAEAFAERMHERVRKEFWGYAADEQLD 1138
*************************************************************************** PP
TIGR02082 1113 kedllkerYrGirpafGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
+e l++e+Y+Girpa+GYpacPdhtek l++Ll++++ i l++tes+a+ P+a+vsg+yfahp+++Yf v
lcl|FitnessBrowser__ANA3:7026140 1139 NEALIREKYKGIRPAPGYPACPDHTEKGLLWDLLKPNEtIDLNITESYAMFPTAAVSGWYFAHPKSRYFGV 1209
***********************************9887******************************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1244 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: 0.08u 0.03s 00:00:00.11 Elapsed: 00:00:00.11
# Mc/sec: 12.91
//
[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