Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_012466960.1 CLIM_RS10375 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000020465.1:WP_012466960.1
Length = 1228
Score = 1437 bits (3720), Expect = 0.0
Identities = 727/1222 (59%), Positives = 916/1222 (74%), Gaps = 8/1222 (0%)
Query: 12 LNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAIHNAY 71
L +RILVLDG MGTMIQ ++L EAD+RGERFA L GNND+LVL++P++I AIH +
Sbjct: 9 LEQRILVLDGAMGTMIQRHKLQEADYRGERFASHDHPLIGNNDMLVLTQPDIIYAIHCDF 68
Query: 72 FEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPRYVAG 131
EAG+DIIETNTFN+ I+ DY L E+N AA+LAR AD ++A+TP+KPR+VAG
Sbjct: 69 LEAGSDIIETNTFNANPISQGDYNAVELVRELNLEAARLARKAADAYSAKTPDKPRFVAG 128
Query: 132 VLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTLNAKA 191
+GPTN+T S+SPDVN+P +R +TF +V Y + L+EGG DL+LIETVFDTLN KA
Sbjct: 129 SIGPTNKTLSLSPDVNNPGYRAVTFREVVDNYIVQLEGLMEGGVDLLLIETVFDTLNCKA 188
Query: 192 AVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHA-EALTFGLNCALG 250
A+FAV+ F A+G +P+M+SGT+ DASGRTLSGQTTEAF+ S+ H + ++ GLNCALG
Sbjct: 189 ALFAVEEYFNAIGRRVPVMVSGTVVDASGRTLSGQTTEAFWISIAHMPDLISVGLNCALG 248
Query: 251 PDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIVGGC 310
++R +++ LS IAE YV+ +PNAGLPN FGEYD MA QI +A++GF+NIVGGC
Sbjct: 249 SKQMRPFIEALSGIAESYVSVYPNAGLPNEFGEYDDSPAYMAAQIAGFAESGFVNIVGGC 308
Query: 311 CGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTGSAK 370
CGTTPQHI A++ AV L PR+ PE +LSGLEPL + + + F+NVGERTNVTGS K
Sbjct: 309 CGTTPQHIKAIADAVSSLKPRRKPEPKHELQLSGLEPLMVNQTTGFINVGERTNVTGSRK 368
Query: 371 FKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIARVP 430
F RLIKE Y EAL +ARQQVE+GAQ+ID+N+DEGMLD+E M FLNLIA EP+I+RVP
Sbjct: 369 FARLIKEGNYDEALSIARQQVESGAQVIDVNVDEGMLDSEKVMKEFLNLIASEPEISRVP 428
Query: 431 IMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDEQGQ 490
+MIDSS+W VIE+GL+C+QGK IVNSIS+KEG D F A + +YGAA VVMAFDEQGQ
Sbjct: 429 VMIDSSRWSVIEEGLQCVQGKSIVNSISLKEGEDPFRERALKILQYGAAAVVMAFDEQGQ 488
Query: 491 ADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACEDIK 550
AD+ R+ EIC RAY ILT EVGFPPEDIIFDPN+ VATGI+EHNNYA DFI + I+
Sbjct: 489 ADSLERRKEICGRAYDILTREVGFPPEDIIFDPNVLTVATGIDEHNNYALDFIESVRWIR 548
Query: 551 RELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDDLPA 610
LP+A +SGG+SNVSFSFRGN+PVREA+HA FLY+AIR G+DMGIVNAGQLAIY+D+
Sbjct: 549 ENLPYAKVSGGISNVSFSFRGNEPVREAMHAAFLYHAIRAGLDMGIVNAGQLAIYEDIEP 608
Query: 611 ELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYSLVKG 670
L + VEDV+ NRR D TERL+ AE R + + A+ AEWR+ V +RL ++LVKG
Sbjct: 609 TLLELVEDVLFNRRPDATERLVSHAETIR--EGGEKIEAKAAEWRNAPVEERLRHALVKG 666
Query: 671 ITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVA 730
I E+I+ DTEEARQ P++VIEGPLMDGMN +GDLF EGKMFLPQVVKSARVMK++VA
Sbjct: 667 IVEYIDVDTEEARQLYPSPLQVIEGPLMDGMNTIGDLFAEGKMFLPQVVKSARVMKRSVA 726
Query: 731 YLEPFIEASKEQGKTN---GKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAE 787
+L P+IE K Q K + ++++ATVKGDVHDIGKNIV VVL CNNYE++D+GVM+P +
Sbjct: 727 WLIPYIEEEKAQQKNSKPAARVLLATVKGDVHDIGKNIVSVVLSCNNYEVIDIGVMMPCD 786
Query: 788 KILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIE 847
+IL + AD++GLSGLITPSLDEMV+VA+EMER G IPLLIGGATTSK HTAVKI
Sbjct: 787 RILDAVEREKADILGLSGLITPSLDEMVHVAREMERLGMKIPLLIGGATTSKMHTAVKIA 846
Query: 848 QNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLE 907
YSGP V V +ASR+V VV++LL+ DD++AR + + T+R H + +++E
Sbjct: 847 PVYSGPVVQVLDASRSVPVVSSLLNPMLCDDYLARLKADQATMRQSHESRSREKKYLSIE 906
Query: 908 AARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAGKYPRILED 966
AR N W T + G+ E ++ LR YIDWTPFF+TW L G+YP I +
Sbjct: 907 DARKNRPDLQWDETTVRTPLKTGITLFEDVTVSALRPYIDWTPFFLTWELHGRYPEIFGN 966
Query: 967 EVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVINVS 1026
G EA++LF DAN++LD + EK L +GV G+FPAN GDD+ IY D+ R+ +
Sbjct: 967 AKFGSEARQLFDDANELLDTIDREKLLGLKGVAGIFPANSSGDDVVIYTDDNRSSALMQV 1026
Query: 1027 HHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYNK 1085
H LRQQ EK G N LADF+AP+ SG DYIGAFAVT GL + + F + DDY +
Sbjct: 1027 HTLRQQQEKQEGEPNLALADFIAPEESGIRDYIGAFAVTAGLGIEKTLNRFSLEQDDYRR 1086
Query: 1086 IMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEH 1145
I+ +ALADRLAEAFAE LHE+VR+ WGYAP E L +EEL+ E Y+GIRPAPGYPACP+H
Sbjct: 1087 ILTQALADRLAEAFAEMLHEKVRRELWGYAPAEILGSEELLSEKYRGIRPAPGYPACPDH 1146
Query: 1146 TEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYAR 1205
TEKA ++ LL E +TG+ LTE++AM P ASVSG+YF+HP+++Y+ + +I RDQVEDYA
Sbjct: 1147 TEKAELFTLLNAETNTGITLTETYAMNPAASVSGFYFAHPEARYFVLGKIGRDQVEDYAL 1206
Query: 1206 RKGMSVTEVERWLAPNLGYDAD 1227
RKGMSV E E+WLAP L YD +
Sbjct: 1207 RKGMSVQETEKWLAPALNYDPE 1228
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: 3457
Number of extensions: 113
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: 1228
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1181
Effective search space: 1393580
Effective search space used: 1393580
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 WP_012466960.1 CLIM_RS10375 (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.32713.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 1722.4 0.0 0 1722.2 0.0 1.0 1 lcl|NCBI__GCF_000020465.1:WP_012466960.1 CLIM_RS10375 methionine synthase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020465.1:WP_012466960.1 CLIM_RS10375 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1722.2 0.0 0 0 1 1180 [. 9 1191 .. 9 1193 .. 0.99
Alignments for each domain:
== domain 1 score: 1722.2 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDi 66
l++rilvlDGamGt++q+++L+ead+rge +a + l Gnnd+L+lt+P++i+aih +++eaG+Di
lcl|NCBI__GCF_000020465.1:WP_012466960.1 9 LEQRILVLDGAMGTMIQRHKLQEADYRGErFASHDHPLIGNNDMLVLTQPDIIYAIHCDFLEAGSDI 75
589**************************************************************** PP
TIGR02082 67 vetntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspd 132
+etntFn+++i+++dY+ ++++eln +aa+lar++ad ++ +tp+k+RfvaGs+GPtnk+ +lspd
lcl|NCBI__GCF_000020465.1:WP_012466960.1 76 IETNTFNANPISQGDYNAVELVRELNLEAARLARKAADAYSaKTPDKPRFVAGSIGPTNKTLSLSPD 142
*****************************************9************************* PP
TIGR02082 133 verpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilis 199
v++p++r vt+ e+vd Y +q +gl++GGvDllLietvfDtln kaalfavee f++ gr++P+++s
lcl|NCBI__GCF_000020465.1:WP_012466960.1 143 VNNPGYRAVTFREVVDNYIVQLEGLMEGGVDLLLIETVFDTLNCKAALFAVEEYFNAIGRRVPVMVS 209
******************************************************************* PP
TIGR02082 200 gvivdksGrtLsGqtleaflasleha.eililGLnCalGadelrefvkelsetaealvsviPnaGLP 265
g++vd+sGrtLsGqt+eaf +s+ h+ +++++GLnCalG++++r+f+++ls +ae +vsv+PnaGLP
lcl|NCBI__GCF_000020465.1:WP_012466960.1 210 GTVVDASGRTLSGQTTEAFWISIAHMpDLISVGLNCALGSKQMRPFIEALSGIAESYVSVYPNAGLP 276
************************9835789************************************ PP
TIGR02082 266 nalgeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgl 332
n++geYd p +a++++ fae g++nivGGCCGttP+hi+aia+av +kpr+++e ++++ lsgl
lcl|NCBI__GCF_000020465.1:WP_012466960.1 277 NEFGEYDDSPAYMAAQIAGFAESGFVNIVGGCCGTTPQHIKAIADAVSSLKPRRKPEPKHELQLSGL 343
******************************************************************* PP
TIGR02082 333 ealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgead 399
e+l ++q + f+n+GeRtnv+Gs+kf++lik+++y+eal+ia+qqve+Gaq++D+nvDe++lD+e+
lcl|NCBI__GCF_000020465.1:WP_012466960.1 344 EPLMVNQTTGFINVGERTNVTGSRKFARLIKEGNYDEALSIARQQVESGAQVIDVNVDEGMLDSEKV 410
******************************************************************* PP
TIGR02082 400 mkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaa 466
mk++l+l+asep+i++vP+m+Dss++ v+e GL+++qGk+ivnsislk+Ge+ F e+a +i +yGaa
lcl|NCBI__GCF_000020465.1:WP_012466960.1 411 MKEFLNLIASEPEISRVPVMIDSSRWSVIEEGLQCVQGKSIVNSISLKEGEDPFRERALKILQYGAA 477
******************************************************************* PP
TIGR02082 467 vvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieai 533
+vvmafDe+Gqa+ +++ ei+ Ray++lt +vgfppediifDpn+lt+atGi+eh++ya+dfie++
lcl|NCBI__GCF_000020465.1:WP_012466960.1 478 AVVMAFDEQGQADSLERRKEICGRAYDILTREVGFPPEDIIFDPNVLTVATGIDEHNNYALDFIESV 544
******************************************************************* PP
TIGR02082 534 reikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelr 600
r+i+e+lP+ak+sgG+snvsFs+rgn++vRea+h+ FLy+ai+aGlDmgivnag+la+y+di++ l+
lcl|NCBI__GCF_000020465.1:WP_012466960.1 545 RWIRENLPYAKVSGGISNVSFSFRGNEPVREAMHAAFLYHAIRAGLDMGIVNAGQLAIYEDIEPTLL 611
******************************************************************* PP
TIGR02082 601 evvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedle 667
e+ved++++rr++ate+L+ ae+ ++ ek ea+ aewrn pveeRL++alvkG+ e+i+ d+e
lcl|NCBI__GCF_000020465.1:WP_012466960.1 612 ELVEDVLFNRRPDATERLVSHAETIREGGEK--IEAKAAEWRNAPVEERLRHALVKGIVEYIDVDTE 676
**************************99999..889******************************* PP
TIGR02082 668 earkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed...k 731
ear+ + +pl++iegpL+dGm+++GdLF +GkmfLPqvvksarvmk++va+L+Py+e+ek+++ k
lcl|NCBI__GCF_000020465.1:WP_012466960.1 677 EARQLYPSPLQVIEGPLMDGMNTIGDLFAEGKMFLPQVVKSARVMKRSVAWLIPYIEEEKAQQknsK 743
************************************************************9886556 PP
TIGR02082 732 skGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksl 798
+ +++latvkGDvhDiGkniv+vvLscn+yev+d+Gv++P+++il+a +++kaD++glsGLi++sl
lcl|NCBI__GCF_000020465.1:WP_012466960.1 744 PAARVLLATVKGDVHDIGKNIVSVVLSCNNYEVIDIGVMMPCDRILDAVEREKADILGLSGLITPSL 810
679**************************************************************** PP
TIGR02082 799 demvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkae 865
demv+va+emer g+kiPll+GGa++sk h+avkia+ Y+g+vv v das++v vv++ll+ ++
lcl|NCBI__GCF_000020465.1:WP_012466960.1 811 DEMVHVAREMERLGMKIPLLIGGATTSKMHTAVKIAPVYSGPVVQVLDASRSVPVVSSLLNPMLCDD 877
******************************************************************* PP
TIGR02082 866 elekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellk 931
+l+++k+++ ++r++++++ +++++ls+++ark++ +l++ +++v +p + G+ +e++ + l++
lcl|NCBI__GCF_000020465.1:WP_012466960.1 878 YLARLKADQATMRQSHESRSREKKYLSIEDARKNRPDLQWD-ETTVRTPLKTGITLFEDVtVSALRP 943
****************************************9.99999******************** PP
TIGR02082 932 yiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgdd 998
yiDw+++F++Wel+g+yp+i+ + + g ear+lf+da+elld++ ekll +gv G+fPa+s gdd
lcl|NCBI__GCF_000020465.1:WP_012466960.1 944 YIDWTPFFLTWELHGRYPEIFGNAKFGSEARQLFDDANELLDTIDREKLLGLKGVAGIFPANSSGDD 1010
******************************************************************* PP
TIGR02082 999 ieiytdetvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvtaglgaeelak 1065
++iytd+ +s + ++ t+r ++q +q+ + +l+laDfia+ esGi+Dy+ga++vtaglg+e+ +
lcl|NCBI__GCF_000020465.1:WP_012466960.1 1011 VVIYTDDNRSSALMQVHTLR--QQQEKQEGEPNLALADFIAPEESGIRDYIGAFAVTAGLGIEKTLN 1075
*********99999988886..7777777788*********************************** PP
TIGR02082 1066 kleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpa 1132
++ ++ddy il +aladrlaea+ae+lhe+vR+elwgya e l e+ll e+YrGirpa+GYpa
lcl|NCBI__GCF_000020465.1:WP_012466960.1 1076 RFSLEQDDYRRILTQALADRLAEAFAEMLHEKVRRELWGYAPAEILGSEELLSEKYRGIRPAPGYPA 1142
******************************************************************* PP
TIGR02082 1133 cPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYf 1180
cPdhteka+l+ Ll+ae+ +G++lte +a++P+asvsg+yfahpea+Yf
lcl|NCBI__GCF_000020465.1:WP_012466960.1 1143 CPDHTEKAELFTLLNAETnTGITLTETYAMNPAASVSGFYFAHPEARYF 1191
************************************************* PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1228 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: 0.11u 0.06s 00:00:00.17 Elapsed: 00:00:00.16
# Mc/sec: 8.72
//
[ok]
This GapMind analysis is from Apr 10 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