Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate HSERO_RS21740 HSERO_RS21740 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>FitnessBrowser__HerbieS:HSERO_RS21740
Length = 1247
Score = 1478 bits (3827), Expect = 0.0
Identities = 777/1244 (62%), Positives = 927/1244 (74%), Gaps = 38/1244 (3%)
Query: 8 LRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCD-----LKGNNDLLVLSKPE 62
LR +++RIL+LDG MGTMIQ Y+L E D+RG+RFAD+ +KGNN+LL L++P
Sbjct: 13 LRDLMSQRILILDGAMGTMIQRYKLTEEDYRGQRFADFSVPGKDLFVKGNNELLSLTQPH 72
Query: 63 VIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTART 122
+I IH Y AGAD+IETNTF +T++A DY M L E+N +A+LARA D++ T
Sbjct: 73 IIQEIHEQYLAAGADLIETNTFGATSVAQDDYHMAHLVYEMNVESARLARAACDKYA--T 130
Query: 123 PEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIET 182
P+KPR+VAG LGPT +TASISPDVNDPA RN+TFD LVAAY E T+ALVEGGAD++L+ET
Sbjct: 131 PDKPRFVAGALGPTPKTASISPDVNDPAARNVTFDQLVAAYLEQTRALVEGGADVLLVET 190
Query: 183 VFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALT 242
+FDTLN KAA+FA+ T FE G LPIMISGT+TDASGR LSGQT AF+NS+RHA LT
Sbjct: 191 IFDTLNCKAALFAIDTFFEESGQRLPIMISGTVTDASGRILSGQTVTAFWNSIRHARPLT 250
Query: 243 FGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGE--YDLDADTMAKQIREWAQ 300
GLNCALG +R Y +ELS+IA+ +V +PNAGLPN + +D D + ++E+A+
Sbjct: 251 VGLNCALGAALMRPYAEELSKIADTFVCIYPNAGLPNPMSDTGFDETPDVTSALLKEFAE 310
Query: 301 AGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVG 360
+GF+N+ GGCCGTTP HI A++ V +APRK+PE RLSGLEP I +DSL+VNVG
Sbjct: 311 SGFVNVAGGCCGTTPPHIKAIAETVAKIAPRKVPEPTHEMRLSGLEPFTINDDSLYVNVG 370
Query: 361 ERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLI 420
ERTNVTGS F RLI E+Y EAL VARQQVENGAQIIDINMDE MLD+ AAM RFLNLI
Sbjct: 371 ERTNVTGSKAFARLILNEQYDEALAVARQQVENGAQIIDINMDEAMLDSVAAMTRFLNLI 430
Query: 421 AGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAV 480
A EPDIARVPIMIDSSKW+VIE GLKC+QGK IVNSISMKEG + F+ AKL RRYGAAV
Sbjct: 431 ASEPDIARVPIMIDSSKWEVIEAGLKCVQGKSIVNSISMKEGEEKFLREAKLCRRYGAAV 490
Query: 481 VVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQ 540
+VMAFDE GQADT ARKIEIC RAY++L +++ FPPEDIIFDPNIFAVATGIEEHNNYA
Sbjct: 491 IVMAFDEVGQADTFARKIEICERAYRLLVDKLDFPPEDIIFDPNIFAVATGIEEHNNYAV 550
Query: 541 DFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAG 600
DFI A I + LP+A ISGGVSNVSFSFRGNDP REAIH VFLY+AI+ GM MGIVNAG
Sbjct: 551 DFIEATRWIHQNLPYAKISGGVSNVSFSFRGNDPAREAIHTVFLYHAIKAGMTMGIVNAG 610
Query: 601 QLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVN 660
+ +YDDLPAELR+ VEDV+LNRR+D TER++E A K D EWR+ V
Sbjct: 611 MIGVYDDLPAELRERVEDVVLNRREDATERMIEYAATL---KAGDKKEEATLEWRNLPVA 667
Query: 661 KRLEYSLVKGITEFIEQDTEEARQQAT----RPIEVIEGPLMDGMNVVGDLFGEGKMFLP 716
KRL ++LV GIT++I +DTEE RQQ RPI VIEGPLMDGMNVVGDLFG+GKMFLP
Sbjct: 668 KRLSHALVHGITQWIVEDTEEVRQQIAADGGRPIHVIEGPLMDGMNVVGDLFGQGKMFLP 727
Query: 717 QVVKSARVMKQAVAYLEPFIEASKEQ--------GKTNGKMVIATVKGDVHDIGKNIVGV 768
QVVKSARVMKQAVA+L PFIE K Q K GK+VIATVKGDVHDIGKNIV V
Sbjct: 728 QVVKSARVMKQAVAHLIPFIEEEKRQLEIATGEVAKPKGKIVIATVKGDVHDIGKNIVTV 787
Query: 769 VLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQ---- 824
VLQCNN+E+V++GVMVP +IL AKE AD+IGLSGLITPSL+EM VAKEM+R
Sbjct: 788 VLQCNNFEVVNMGVMVPCAEILAKAKEEKADIIGLSGLITPSLEEMAYVAKEMQRDPYFA 847
Query: 825 GFTIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTR 884
G +PL+IGGATTS+AHTAVKI NY GP VYV +ASR V V +LL+D Q+ +VA
Sbjct: 848 GLKMPLMIGGATTSRAHTAVKIAPNYEGPVVYVPDASRAVSVAQSLLADEQKTQYVAELN 907
Query: 885 KEYETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEASIETLRNY 944
+YE +R QH KK P ++L AAR N D+ P R + V+ + L NY
Sbjct: 908 ADYERIREQHASKK-AAPMLSLAAARANKTKLDFAPVKPKFIGRRLFKNVDLGL--LANY 964
Query: 945 IDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPA 1004
IDW PFF TW LAG YP IL DEVVG A ++F++A ML K+ + L GV+ L PA
Sbjct: 965 IDWGPFFQTWDLAGPYPAILTDEVVGEAATKVFQEAQAMLKKIIDGRWLTANGVISLLPA 1024
Query: 1005 NRVG-DDIEIYRDETRTHVINVSHHLRQQTEK---TGFA--NYCLADFVAPKLSGKADYI 1058
N V DDIEIY D++R+ V + LRQQTEK G A N CL+DF+APK SG DYI
Sbjct: 1025 NTVNDDDIEIYTDDSRSQVAFTYYGLRQQTEKPVVDGVARPNQCLSDFIAPKESGVQDYI 1084
Query: 1059 GAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNE 1118
G FAVT GL + FE HDDY+ IM+KALADRLAEAFAEYLHERVRK WGYA +E
Sbjct: 1085 GMFAVTAGLGIEKYEKRFEDAHDDYSSIMLKALADRLAEAFAEYLHERVRKDLWGYAADE 1144
Query: 1119 NLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVS 1178
NLS+ +LI+E Y GIRPAPGYPACPEHT KA ++ ++ ++ GM+LTES+AM+PGASVS
Sbjct: 1145 NLSSTDLIKEKYLGIRPAPGYPACPEHTVKADVFRTMQCDE-IGMQLTESYAMFPGASVS 1203
Query: 1179 GWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNL 1222
G+YF+HP SKY+ V +I DQV D A R+ + E+ERWLAPNL
Sbjct: 1204 GFYFAHPQSKYFVVGKIGEDQVVDMAERRHVPKEELERWLAPNL 1247
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: 3653
Number of extensions: 156
Number of successful extensions: 12
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: 1247
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1199
Effective search space: 1413621
Effective search space used: 1413621
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 HSERO_RS21740 HSERO_RS21740 (methionine synthase)
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.20748.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 1723.1 0.1 0 1722.9 0.1 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS21740 HSERO_RS21740 methionine synthas
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS21740 HSERO_RS21740 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1722.9 0.1 0 0 2 1182 .] 18 1217 .. 17 1217 .. 0.97
Alignments for each domain:
== domain 1 score: 1722.9 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlare.....lkGnndlLnltkPeviaaihrayfe 61
++ril+lDGamGt++q+++Lte+d+rg+ +ad + +kGnn+lL+lt+P +i++ih++y+
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 18 SQRILILDGAMGTMIQRYKLTEEDYRGQrFADFSVPgkdlfVKGNNELLSLTQPHIIQEIHEQYLA 83
79**************************999987643333379*********************** PP
TIGR02082 62 aGaDivetntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnkla 127
aGaD++etntF++t++a+ dY++++++ye+n ++a+lar+++d++ tp+k+RfvaG+lGPt k+a
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 84 AGADLIETNTFGATSVAQDDYHMAHLVYEMNVESARLARAACDKYA-TPDKPRFVAGALGPTPKTA 148
**********************************************.******************* PP
TIGR02082 128 tlspdverpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgre 193
++spdv++p+ rnvt+d+lv+aY eq+++l++GG+D+lL+et+fDtln kaalfa+ + fee g++
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 149 SISPDVNDPAARNVTFDQLVAAYLEQTRALVEGGADVLLVETIFDTLNCKAALFAIDTFFEESGQR 214
****************************************************************** PP
TIGR02082 194 lPilisgvivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsvi 259
lPi+isg+++d+sGr+LsGqt+ af +s++ha l++GLnCalGa+++r++ +els++a+++v ++
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 215 LPIMISGTVTDASGRILSGQTVTAFWNSIRHARPLTVGLNCALGAALMRPYAEELSKIADTFVCIY 280
****************************************************************** PP
TIGR02082 260 PnaGLPnalg..eYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqel 323
PnaGLPn ++ +d+tp+ + + lkefae g++n+ GGCCGttP hi+aiae v++i+prk++e
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 281 PNAGLPNPMSdtGFDETPDVTSALLKEFAESGFVNVAGGCCGTTPPHIKAIAETVAKIAPRKVPEP 346
********99778***************************************************** PP
TIGR02082 324 eeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinv 389
++++lsgle+++i+++s +vn+GeRtnv+Gsk f++li +e+y+eal +a+qqve+Gaqi+Din+
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 347 THEMRLSGLEPFTINDDSLYVNVGERTNVTGSKAFARLILNEQYDEALAVARQQVENGAQIIDINM 412
****************************************************************** PP
TIGR02082 390 DevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFle 455
De++lD++a+m+++l+l+asepdia+vP+m+Dss++ev+eaGLk++qGk+ivnsis+k+Gee+Fl+
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 413 DEAMLDSVAAMTRFLNLIASEPDIARVPIMIDSSKWEVIEAGLKCVQGKSIVNSISMKEGEEKFLR 478
****************************************************************** PP
TIGR02082 456 kaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGiee 521
+akl ++yGaav+vmafDe Gqa+t ++kiei++Ray+ll++k++fppediifDpni+++atGiee
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 479 EAKLCRRYGAAVIVMAFDEVGQADTFARKIEICERAYRLLVDKLDFPPEDIIFDPNIFAVATGIEE 544
****************************************************************** PP
TIGR02082 522 hdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnag 587
h++ya+dfiea+r+i+++lP+akisgGvsnvsFs+rgnd++Rea+h+vFLy+aikaG+ mgivnag
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 545 HNNYAVDFIEATRWIHQNLPYAKISGGVSNVSFSFRGNDPAREAIHTVFLYHAIKAGMTMGIVNAG 610
****************************************************************** PP
TIGR02082 588 klavyddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLera 653
++ vydd+++elre ved++l+rr++ate++ e+a + k + ke+++ ewrnlpv +RL++a
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 611 MIGVYDDLPAELRERVEDVVLNRREDATERMIEYAATLKAGDK---KEEATLEWRNLPVAKRLSHA 673
*************************************665544...5889**************** PP
TIGR02082 654 lvkGeregieedleearkklk....apleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkka 715
lv+G+++ i ed+ee r++ +p+++iegpL+dGm+vvGdLFG+GkmfLPqvvksarvmk+a
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 674 LVHGITQWIVEDTEEVRQQIAadggRPIHVIEGPLMDGMNVVGDLFGQGKMFLPQVVKSARVMKQA 739
*****************876433338**************************************** PP
TIGR02082 716 vayLePylekekeed........kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPv 773
va+L+P++e+ek + k kGkiv+atvkGDvhDiGkniv vvL+cn++evv++Gv+vP+
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 740 VAHLIPFIEEEKRQLeiatgevaKPKGKIVIATVKGDVHDIGKNIVTVVLQCNNFEVVNMGVMVPC 805
************8878999**999****************************************** PP
TIGR02082 774 ekileaakkkkaDviglsGLivksldemvevaeemerr....gvkiPlllGGaalskahvavkiae 835
++il +ak++kaD+iglsGLi++sl+em++va+em+r g+k+Pl++GGa++s+ah+avkia+
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 806 AEILAKAKEEKADIIGLSGLITPSLEEMAYVAKEMQRDpyfaGLKMPLMIGGATTSRAHTAVKIAP 871
************************************954444899********************* PP
TIGR02082 836 kYkgevvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevf 901
+Y+g+vvyv das+av+v+++ll +++k++++++++++ye ire++ + k+ ls++aar ++
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 872 NYEGPVVYVPDASRAVSVAQSLLADEQKTQYVAELNADYERIREQHAS-KKAAPMLSLAAARANKT 936
**********************************************98.677899*******9998 PP
TIGR02082 902 aldrsedlevpapkflGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfk 966
+ld +++pkf+G++ ++++ + l +yiDw ++F +W+l+g yp il+de++g+ a+k+f+
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 937 KLDFA----PVKPKFIGRRLFKNVdLGLLANYIDWGPFFQTWDLAGPYPAILTDEVVGEAATKVFQ 998
88877....9******************************************************** PP
TIGR02082 967 dakelldklsaekllrargvvGlfPaqsvg.ddieiytdetvsqetkpiatvrekleqlrqqsdr. 1030
+a+++l+k++ + l+a+gv+ l Pa++v+ ddieiytd+++sq + + +r+++e++ +
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 999 EAQAMLKKIIDGRWLTANGVISLLPANTVNdDDIEIYTDDSRSQVAFTYYGLRQQTEKPVVDGVAr 1064
***************************876268*********888888888877777766654435 PP
TIGR02082 1031 .ylclaDfiaskesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellh 1095
++cl+Dfia+kesG +Dy+g+++vtaglg+e++ k++e+ +ddy+si++kaladrlaea+ae+lh
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 1065 pNQCLSDFIAPKESGVQDYIGMFAVTAGLGIEKYEKRFEDAHDDYSSIMLKALADRLAEAFAEYLH 1130
8***************************************************************** PP
TIGR02082 1096 ervRkelwgyaeeenldkedllkerYrGirpafGYpacPdhtekatlleLleaeriGlklteslal 1161
ervRk+lwgya++enl+ +dl+ke+Y Girpa+GYpacP+ht ka +++ ++ ++iG++ltes+a+
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 1131 ERVRKDLWGYAADENLSSTDLIKEKYLGIRPAPGYPACPEHTVKADVFRTMQCDEIGMQLTESYAM 1196
****************************************************************** PP
TIGR02082 1162 aPeasvsglyfahpeakYfav 1182
P asvsg+yfahp++kYf v
lcl|FitnessBrowser__HerbieS:HSERO_RS21740 1197 FPGASVSGFYFAHPQSKYFVV 1217
*******************76 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1247 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: 0.12u 0.04s 00:00:00.16 Elapsed: 00:00:00.15
# Mc/sec: 9.25
//
[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