Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_012592503.1 MSIL_RS18005 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000021745.1:WP_012592503.1
Length = 1245
Score = 1483 bits (3838), Expect = 0.0
Identities = 763/1221 (62%), Positives = 922/1221 (75%), Gaps = 15/1221 (1%)
Query: 14 ERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAIHNAYFE 73
+RILVLDG MGTMIQ ++ E FRGERFADWP DL+GNNDLL L++P+ I IH AY +
Sbjct: 20 KRILVLDGAMGTMIQQHKFTEEQFRGERFADWPSDLRGNNDLLSLTQPKAIEQIHRAYID 79
Query: 74 AGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPRYVAGVL 133
AGADII TNTFNST+I+ ADY M+ L E+N +A+L R AD + K R+VAG L
Sbjct: 80 AGADIIATNTFNSTSISQADYGMQELVFELNRESARLCRVAADA-AEKHDGKRRFVAGAL 138
Query: 134 GPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTLNAKAAV 193
GPT+RTASISPDVN+P FR ++FD L AY E+ +AL+EGGADL++IET+FDTLNAKAA+
Sbjct: 139 GPTSRTASISPDVNNPGFRAVSFDELRDAYDEAARALIEGGADLLIIETIFDTLNAKAAL 198
Query: 194 FAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNCALGPDE 253
V+ F LGVE P+MISGTITD SGRTLSGQT AF++SLRHA+ LT GLNCALG E
Sbjct: 199 AGVRDAFAKLGVEAPVMISGTITDLSGRTLSGQTPTAFWHSLRHADPLTIGLNCALGARE 258
Query: 254 LRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIVGGCCGT 313
+R ++ ELSRIA+ V A+PNAGLPN FG YD + MA + E+A +G +N+VGGCCGT
Sbjct: 259 MRAHLAELSRIADTLVCAYPNAGLPNEFGLYDESPEYMASLVGEFADSGLVNVVGGCCGT 318
Query: 314 TPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKR 373
TP HI A+++ +EG+APR++PEI RLSGLEP + + FVNVGERTNVTGSAKF++
Sbjct: 319 TPAHIHAIAKRIEGVAPREIPEIAPLLRLSGLEPFVLAPEIPFVNVGERTNVTGSAKFRK 378
Query: 374 LIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMI 433
LIK+ ++ ALDVAR QV GAQIID+NMDEG+LD+E AMV FLNLIA EPDIARVP+MI
Sbjct: 379 LIKQGDFAAALDVARDQVAAGAQIIDVNMDEGLLDSEKAMVEFLNLIAAEPDIARVPVMI 438
Query: 434 DSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADT 493
DSSK+ VIE GLKC+QGK +VNSISMKEGV+ FI A+ +R YGAAVVVMAFDE+GQADT
Sbjct: 439 DSSKFSVIEAGLKCVQGKSVVNSISMKEGVEKFIADARTVRAYGAAVVVMAFDEKGQADT 498
Query: 494 RARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACEDIKREL 553
RK+EIC +AY+ILT+E GFPPEDIIFDPNIFA+ATGIEEHNNY DFI A +I++
Sbjct: 499 FERKVEICAKAYQILTQEAGFPPEDIIFDPNIFAIATGIEEHNNYGVDFIEATREIRKRF 558
Query: 554 PHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELR 613
P ISGGVSN+SFSFRGN+PVREA+HAVFLY+AI+ GMDMGIVNAGQLA+Y ++ LR
Sbjct: 559 PLVHISGGVSNLSFSFRGNEPVREAMHAVFLYHAIQAGMDMGIVNAGQLAVYAEIEPGLR 618
Query: 614 DAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYSLVKGITE 673
+A EDV+LNRR D TERLL +AE +RG + + WR V KRLE++LV GITE
Sbjct: 619 EACEDVVLNRRPDATERLLAIAEGFRGHGVEKA--ERDLVWREQPVIKRLEHALVNGITE 676
Query: 674 FIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLE 733
F+E D EEAR + RP++VIEGPLM GMNVVGDLFG GKMFLPQVVKSARVMKQAVAYL
Sbjct: 677 FVELDVEEARAASKRPLDVIEGPLMAGMNVVGDLFGAGKMFLPQVVKSARVMKQAVAYLL 736
Query: 734 PFIEASKEQG-----KTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEK 788
P+++ K + T GK+++ATVKGDVHDIGKNIVGVVL CNNYEI+DLGVMVPA K
Sbjct: 737 PYMDEEKRKNGGSERSTAGKILMATVKGDVHDIGKNIVGVVLACNNYEIIDLGVMVPAAK 796
Query: 789 ILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIEQ 848
IL A+ D IGLSGLITPSLDEM VA EMER+GF +PLLIGGATTS+ HTAVKI
Sbjct: 797 ILSVARAEKVDAIGLSGLITPSLDEMCYVAAEMEREGFDLPLLIGGATTSRVHTAVKIHP 856
Query: 849 NYS-GPTVYVQNASRTVGVVAALLSDTQRDDFVART-RKEYETVRIQHGRKKPRTPPVTL 906
NY+ G TVYV +ASR VGVV +LL ++ RD A T R EYE V H R + + +
Sbjct: 857 NYTRGQTVYVNDASRAVGVVQSLLGESARD--AAETFRAEYEKVAAAHRRGEAEKLRLPI 914
Query: 907 EAARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYIDWTPFFMTWSLAGKYPRILE 965
AR N DW Y PP G + + + L YIDWTPFF TW L G+YP IL+
Sbjct: 915 GKARANALKIDWDDYAPPRPTFTGSRVFRSYDVAELIPYIDWTPFFQTWELRGRYPAILD 974
Query: 966 DEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVINV 1025
D G A+ LF DA ML ++ E L+P+ V+G +PAN VGDDI +Y E+R+ +
Sbjct: 975 DPKQGEAARSLFDDAQAMLKRMVEEHWLDPKAVIGFWPANSVGDDIALYTGESRSEKLAA 1034
Query: 1026 SHHLRQQ-TEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYN 1084
H LRQQ T + G N L+DF+AP GK DYIGAF VT G +E +AD F +DDY
Sbjct: 1035 FHTLRQQLTRRDGKPNIALSDFIAP-AGGKPDYIGAFVVTAGAQEGKIADRFAKANDDYG 1093
Query: 1085 KIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPE 1144
I+VKALADR+AEA AE +HERVR+ +W YAP+E +S ++ +RE Y+GIRPAPGYPA P+
Sbjct: 1094 SILVKALADRIAEALAERMHERVRREFWAYAPDEAISEDDRLREEYRGIRPAPGYPAQPD 1153
Query: 1145 HTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYA 1204
HTEKAT++ELL EK G+ LTESFAMWPGASVSG YF+HP + Y+ VA+I+RDQVEDYA
Sbjct: 1154 HTEKATLFELLAAEKRIGVSLTESFAMWPGASVSGLYFAHPQAHYFGVAKIERDQVEDYA 1213
Query: 1205 RRKGMSVTEVERWLAPNLGYD 1225
RKGMSV E+ERWLAP L YD
Sbjct: 1214 LRKGMSVAEMERWLAPILNYD 1234
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: 3661
Number of extensions: 133
Number of successful extensions: 8
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: 1245
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1197
Effective search space: 1411263
Effective search space used: 1411263
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_012592503.1 MSIL_RS18005 (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.13083.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 1727.5 0.0 0 1727.3 0.0 1.0 1 lcl|NCBI__GCF_000021745.1:WP_012592503.1 MSIL_RS18005 methionine synthase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021745.1:WP_012592503.1 MSIL_RS18005 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1727.3 0.0 0 0 2 1182 .] 19 1201 .. 18 1201 .. 0.98
Alignments for each domain:
== domain 1 score: 1727.3 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67
+krilvlDGamGt++q+++ te++Frge +ad++++l+GnndlL+lt+P +i++ihray +aGaDi+
lcl|NCBI__GCF_000021745.1:WP_012592503.1 19 RKRILVLDGAMGTMIQQHKFTEEQFRGErFADWPSDLRGNNDLLSLTQPKAIEQIHRAYIDAGADII 85
79***************************************************************** PP
TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134
tntFnst+i++adY++++++ eln+++a+l r +ad +++ k+RfvaG+lGPt+++a++spdv+
lcl|NCBI__GCF_000021745.1:WP_012592503.1 86 ATNTFNSTSISQADYGMQELVFELNRESARLCRVAADAAEKHDGKRRFVAGALGPTSRTASISPDVN 152
****************************************999************************ PP
TIGR02082 135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201
+p+fr v +del+daY e++++l++GG+Dll+iet+fDtlnakaal +v+++f++ g+e P++isg+
lcl|NCBI__GCF_000021745.1:WP_012592503.1 153 NPGFRAVSFDELRDAYDEAARALIEGGADLLIIETIFDTLNAKAALAGVRDAFAKLGVEAPVMISGT 219
******************************************************************* PP
TIGR02082 202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268
i+d sGrtLsGqt af +sl+ha+ l++GLnCalGa e+r ++ els++a++lv ++PnaGLPn++
lcl|NCBI__GCF_000021745.1:WP_012592503.1 220 ITDLSGRTLSGQTPTAFWHSLRHADPLTIGLNCALGAREMRAHLAELSRIADTLVCAYPNAGLPNEF 286
******************************************************************* PP
TIGR02082 269 geYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgleal 335
g Yd+ pe +a+ + efa gl+n+vGGCCGttP+hi+aia+ +++++pr+ +e+ + ++lsgle++
lcl|NCBI__GCF_000021745.1:WP_012592503.1 287 GLYDESPEYMASLVGEFADSGLVNVVGGCCGTTPAHIHAIAKRIEGVAPREIPEIAPLLRLSGLEPF 353
******************************************************************* PP
TIGR02082 336 kiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkk 402
+a+e fvn+GeRtnv+Gs+kfrklik++d+ +al++a++qv Gaqi+D+n+De+llD+e++m++
lcl|NCBI__GCF_000021745.1:WP_012592503.1 354 VLAPEIPFVNVGERTNVTGSAKFRKLIKQGDFAAALDVARDQVAAGAQIIDVNMDEGLLDSEKAMVE 420
******************************************************************* PP
TIGR02082 403 llsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvv 469
+l+l+a+epdia+vP+m+Dss+f v+eaGLk++qGk++vnsis+k+G+e+F+ a+ ++ yGaavvv
lcl|NCBI__GCF_000021745.1:WP_012592503.1 421 FLNLIAAEPDIARVPVMIDSSKFSVIEAGLKCVQGKSVVNSISMKEGVEKFIADARTVRAYGAAVVV 487
******************************************************************* PP
TIGR02082 470 mafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieairei 536
mafDe+Gqa+t ++k+ei+ +ay++lt+++gfppediifDpni++iatGieeh++y++dfiea+rei
lcl|NCBI__GCF_000021745.1:WP_012592503.1 488 MAFDEKGQADTFERKVEICAKAYQILTQEAGFPPEDIIFDPNIFAIATGIEEHNNYGVDFIEATREI 554
******************************************************************* PP
TIGR02082 537 keelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevv 603
++++P ++isgGvsn+sFs+rgn++vRea+h+vFLy+ai+aG+Dmgivnag+lavy++i++ lre++
lcl|NCBI__GCF_000021745.1:WP_012592503.1 555 RKRFPLVHISGGVSNLSFSFRGNEPVREAMHAVFLYHAIQAGMDMGIVNAGQLAVYAEIEPGLREAC 621
******************************************************************* PP
TIGR02082 604 edlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleear 670
ed++l+rr++ate+Ll +ae ++g + k ++ wr++pv +RLe+alv+G++e++e d+eear
lcl|NCBI__GCF_000021745.1:WP_012592503.1 622 EDVVLNRRPDATERLLAIAEGFRGHGVE--KAERDLVWREQPVIKRLEHALVNGITEFVELDVEEAR 686
**************************99..888999******************************* PP
TIGR02082 671 kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.....ks 732
k+pl++iegpL++Gm+vvGdLFG+GkmfLPqvvksarvmk+avayL Py+++ek ++ ++
lcl|NCBI__GCF_000021745.1:WP_012592503.1 687 AASKRPLDVIEGPLMAGMNVVGDLFGAGKMFLPQVVKSARVMKQAVAYLLPYMDEEKRKNggserST 753
*********************************************************999999999* PP
TIGR02082 733 kGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksld 799
+Gki++atvkGDvhDiGkniv+vvL+cn+ye++dlGv+vP++kil +a+ +k D iglsGLi++sld
lcl|NCBI__GCF_000021745.1:WP_012592503.1 754 AGKILMATVKGDVHDIGKNIVGVVLACNNYEIIDLGVMVPAAKILSVARAEKVDAIGLSGLITPSLD 820
******************************************************************* PP
TIGR02082 800 emvevaeemerrgvkiPlllGGaalskahvavkiaekYk.gevvyvkdaseavkvvdkllsekkkae 865
em +va emer+g+++Pll+GGa++s+ h+avki+++Y g++vyv+das+av vv++ll e ++++
lcl|NCBI__GCF_000021745.1:WP_012592503.1 821 EMCYVAAEMEREGFDLPLLIGGATTSRVHTAVKIHPNYTrGQTVYVNDASRAVGVVQSLLGESARDA 887
**************************************548**********************8665 PP
TIGR02082 866 elekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellk 931
+e ++eye++ +++ + ++ l++ +ar + +++d+ d+ +p p+f G++v++++ ++el++
lcl|NCBI__GCF_000021745.1:WP_012592503.1 888 -AETFRAEYEKVAAAHRRGEAEKLRLPIGKARANALKIDWD-DYAPPRPTFTGSRVFRSYdVAELIP 952
.59*************************************9.************************* PP
TIGR02082 932 yiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgdd 998
yiDw+++F +Welrg+yp il+d+++g+ ar lf+da+++l+++++e+ l +++v+G++Pa+svgdd
lcl|NCBI__GCF_000021745.1:WP_012592503.1 953 YIDWTPFFQTWELRGRYPAILDDPKQGEAARSLFDDAQAMLKRMVEEHWLDPKAVIGFWPANSVGDD 1019
******************************************************************* PP
TIGR02082 999 ieiytdetvsqetkpiatvrekleq.lrqqsdrylclaDfiaskesGikDylgallvtaglgaeela 1064
i++yt+e++s +++a++++ ++q +r++ + +++l+Dfia+ + G+ Dy+ga++vtag ++ ++a
lcl|NCBI__GCF_000021745.1:WP_012592503.1 1020 IALYTGESRS---EKLAAFHTLRQQlTRRDGKPNIALSDFIAP-AGGKPDYIGAFVVTAGAQEGKIA 1082
*****99995...45555555445505555555**********.88********************* PP
TIGR02082 1065 kkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYp 1131
+++ + +ddy+silvkaladr+aealae +hervR+e+w+ya +e+ + +d l+e+YrGirpa+GYp
lcl|NCBI__GCF_000021745.1:WP_012592503.1 1083 DRFAKANDDYGSILVKALADRIAEALAERMHERVRREFWAYAPDEAISEDDRLREEYRGIRPAPGYP 1149
******************************************************************* PP
TIGR02082 1132 acPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
a+Pdhtekatl+eLl ae+ iG+ ltes+a++P asvsglyfahp+a+Yf v
lcl|NCBI__GCF_000021745.1:WP_012592503.1 1150 AQPDHTEKATLFELLAAEKrIGVSLTESFAMWPGASVSGLYFAHPQAHYFGV 1201
******************99******************************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1245 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 0.04s 00:00:00.12 Elapsed: 00:00:00.11
# Mc/sec: 13.01
//
[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