Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_006746829.1 THITH_RS15835 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000227685.2:WP_006746829.1
Length = 1254
Score = 1677 bits (4343), Expect = 0.0
Identities = 845/1245 (67%), Positives = 998/1245 (80%), Gaps = 27/1245 (2%)
Query: 6 EQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIA 65
+ ++ L ERIL+LDGGMGTMIQ YRL EAD+RGERFADW DLKGNNDLLVL++P+VI
Sbjct: 5 QPIQQALAERILILDGGMGTMIQEYRLEEADYRGERFADWNSDLKGNNDLLVLTRPDVIQ 64
Query: 66 AIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEK 125
AIH Y EAGADIIETNTFN T IAMADY ME L E+N AA++AR AD WTA+TPEK
Sbjct: 65 AIHGDYLEAGADIIETNTFNGTRIAMADYAMEDLVPELNREAARIAREAADAWTAKTPEK 124
Query: 126 PRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFD 185
PR+VAGVLGPTNRTASISPDVNDP +RN+ FD LVA YRES AL+EGG DL+LIETVFD
Sbjct: 125 PRFVAGVLGPTNRTASISPDVNDPGYRNVDFDTLVANYRESAAALIEGGVDLLLIETVFD 184
Query: 186 TLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGL 245
TLNAKAAVFAV+T F+ G +P+MISGTITDASGRTLSGQTTEAF+NSLRHA L+ GL
Sbjct: 185 TLNAKAAVFAVETLFDETGQRVPVMISGTITDASGRTLSGQTTEAFWNSLRHARPLSIGL 244
Query: 246 NCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLN 305
NCALGP ELR Y++ELSRIA +V+AHPNAGLPN FG+YD + MA +I EWA +GFLN
Sbjct: 245 NCALGPKELRAYIEELSRIANTHVSAHPNAGLPNEFGDYDETPEQMAVEIGEWAASGFLN 304
Query: 306 IVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNV 365
I+GGCCGTTP HI A++ AV+ PR++PEI ACRLSGLEPLNI EDSLFVNVGERTNV
Sbjct: 305 IIGGCCGTTPDHIRAIAAAVQAHPPRRMPEIAPACRLSGLEPLNITEDSLFVNVGERTNV 364
Query: 366 TGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPD 425
TGS +F RLI+EE Y AL+VA+ QVENGAQ+IDINMDEGMLD++AAM RFLNLIAGEPD
Sbjct: 365 TGSKRFARLIREEDYETALEVAKDQVENGAQVIDINMDEGMLDSQAAMQRFLNLIAGEPD 424
Query: 426 IARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAF 485
IARVPIMIDSSKW+++E GLKCIQGKG+VNSIS+KEG + FI A+L+RRYGAAV+VMAF
Sbjct: 425 IARVPIMIDSSKWEILEAGLKCIQGKGVVNSISLKEGEEKFIEQARLVRRYGAAVIVMAF 484
Query: 486 DEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGA 545
DEQGQADT RK+EIC RAY+ILTE +GFP ED+IFDPNIFA+ATGIEEH+NY DFI A
Sbjct: 485 DEQGQADTAERKLEICTRAYQILTERIGFPAEDVIFDPNIFAIATGIEEHDNYGVDFIEA 544
Query: 546 CEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIY 605
IK LPHALISGGVSNVSFSFRGN+PVREAIHAVFLY+AI GMDMGIVNAGQLA+Y
Sbjct: 545 TRAIKERLPHALISGGVSNVSFSFRGNEPVREAIHAVFLYHAIHAGMDMGIVNAGQLAVY 604
Query: 606 DDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEY 665
D++ EL++AVEDV+LNRR D TERLL+LAE+YRGS A + EWRSW V KRLE+
Sbjct: 605 DEIEPELKEAVEDVVLNRRSDATERLLDLAERYRGS--GGAAKKEDLEWRSWPVAKRLEH 662
Query: 666 SLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVM 725
SLVKGI ++ +DTEEAR +A RPI VIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVM
Sbjct: 663 SLVKGIDSYVVEDTEEARLEAERPIHVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVM 722
Query: 726 KQAVAYLEPFIEASKEQ-GKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMV 784
K+AVA+L PFIEA K G+ NG++++ATVKGDVHDIGKNIVGVVLQCNN+E++DLGVMV
Sbjct: 723 KKAVAHLIPFIEAEKSGCGENNGRILMATVKGDVHDIGKNIVGVVLQCNNFEVIDLGVMV 782
Query: 785 PAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAV 844
PA+KIL TA+E N D+IGLSGLITPSL+EM +VA EM+RQGF PLLIGGATTS+AHTAV
Sbjct: 783 PAQKILETAREKNVDVIGLSGLITPSLEEMAHVAAEMQRQGFDTPLLIGGATTSRAHTAV 842
Query: 845 KIEQNY-SGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPP 903
KIE NY +GP V+V++ASR VGV +L+S + + +TR EY +R +K R
Sbjct: 843 KIEPNYGAGPVVWVKDASRAVGVAQSLISPELKGPYAEKTRAEYAQLRESLAGRKQRIHW 902
Query: 904 VTLEAARDNDFAFDWQAY-------------TPPVAHRL---GVQEV-----EASIETLR 942
+ LE AR N DW++Y PP RL G V + + +
Sbjct: 903 LGLEQARANRPQIDWESYRPVRPRALDPDFPLPPGVTRLQPYGPDSVLLRFDDFDVREVA 962
Query: 943 NYIDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLF 1002
+IDWTPFF +W L YPRIL+DEVVG EA++LF DA ML+++ E + RGVVGLF
Sbjct: 963 RFIDWTPFFHSWQLHAAYPRILDDEVVGAEARKLFDDAQKMLERMIDEGWVRLRGVVGLF 1022
Query: 1003 PANRVG-DDIEIYRDETRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGA 1060
PAN V DDIE+YRDE R+ VI HHLRQQ +K G ++ LADFVAP+ +G D++GA
Sbjct: 1023 PANSVEFDDIEVYRDEARSEVITRLHHLRQQAQKRRGTPSHSLADFVAPRETGVPDWMGA 1082
Query: 1061 FAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENL 1120
FAV+ G E DA A AFE HDDY+ I+VK+LADRLAEAFAE +H+RVR+ +WGYAP+E+L
Sbjct: 1083 FAVSAGGEVDARAKAFEDAHDDYHAILVKSLADRLAEAFAEAMHQRVRREFWGYAPDEDL 1142
Query: 1121 SNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGW 1180
N++LI+E Y GIRPAPGYPACPEHTEK +WEL++ +H GM LTES+AM P ++VSGW
Sbjct: 1143 GNDDLIQERYTGIRPAPGYPACPEHTEKGLLWELIDPVEHAGMTLTESYAMLPVSAVSGW 1202
Query: 1181 YFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYD 1225
Y +HP S+Y+ + +I RDQVEDYARRKG S+ E ERWLAPNLGYD
Sbjct: 1203 YMAHPQSRYFGLGKINRDQVEDYARRKGWSMDEAERWLAPNLGYD 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: 4024
Number of extensions: 177
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: 1254
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1206
Effective search space: 1421874
Effective search space used: 1421874
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_006746829.1 THITH_RS15835 (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.12845.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 1775.0 0.0 0 1774.7 0.0 1.0 1 lcl|NCBI__GCF_000227685.2:WP_006746829.1 THITH_RS15835 methionine synthas
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000227685.2:WP_006746829.1 THITH_RS15835 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1774.7 0.0 0 0 2 1181 .. 12 1213 .. 11 1214 .. 0.97
Alignments for each domain:
== domain 1 score: 1774.7 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67
+ril+lDG+mGt++q ++L+ead+rge +ad++++lkGnndlL+lt+P+vi+aih +y+eaGaDi+
lcl|NCBI__GCF_000227685.2:WP_006746829.1 12 AERILILDGGMGTMIQEYRLEEADYRGErFADWNSDLKGNNDLLVLTRPDVIQAIHGDYLEAGADII 78
68***************************************************************** PP
TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdv 133
etntFn+t ia+adY +ed++ eln++aa++are+ad +t +tpek+RfvaG+lGPtn++a++spdv
lcl|NCBI__GCF_000227685.2:WP_006746829.1 79 ETNTFNGTRIAMADYAMEDLVPELNREAARIAREAADAWTaKTPEKPRFVAGVLGPTNRTASISPDV 145
******************************************************************* PP
TIGR02082 134 erpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisg 200
++p++rnv++d+lv+ Y+e++ +l++GGvDllLietvfDtlnakaa+fave++f+e g+++P++isg
lcl|NCBI__GCF_000227685.2:WP_006746829.1 146 NDPGYRNVDFDTLVANYRESAAALIEGGVDLLLIETVFDTLNAKAAVFAVETLFDETGQRVPVMISG 212
******************************************************************* PP
TIGR02082 201 vivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPna 267
+i+d+sGrtLsGqt+eaf +sl+ha l++GLnCalG++elr +++els++a++ vs++PnaGLPn+
lcl|NCBI__GCF_000227685.2:WP_006746829.1 213 TITDASGRTLSGQTTEAFWNSLRHARPLSIGLNCALGPKELRAYIEELSRIANTHVSAHPNAGLPNE 279
******************************************************************* PP
TIGR02082 268 lgeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglea 334
+g+Yd+tpe++a ++ e+a+ g+lni+GGCCGttP+hiraia+av+ pr+++e+ ++++lsgle+
lcl|NCBI__GCF_000227685.2:WP_006746829.1 280 FGDYDETPEQMAVEIGEWAASGFLNIIGGCCGTTPDHIRAIAAAVQAHPPRRMPEIAPACRLSGLEP 346
******************************************************************* PP
TIGR02082 335 lkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmk 401
l+i+++s fvn+GeRtnv+Gsk+f++li++edye al++ak+qve+Gaq++Din+De++lD++a+m+
lcl|NCBI__GCF_000227685.2:WP_006746829.1 347 LNITEDSLFVNVGERTNVTGSKRFARLIREEDYETALEVAKDQVENGAQVIDINMDEGMLDSQAAMQ 413
******************************************************************* PP
TIGR02082 402 kllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavv 468
++l+l+a+epdia+vP+m+Dss++e+leaGLk+iqGk++vnsislk+Gee+F+e+a+l+++yGaav+
lcl|NCBI__GCF_000227685.2:WP_006746829.1 414 RFLNLIAGEPDIARVPIMIDSSKWEILEAGLKCIQGKGVVNSISLKEGEEKFIEQARLVRRYGAAVI 480
******************************************************************* PP
TIGR02082 469 vmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaire 535
vmafDe+Gqa+ta++k+ei++Ray++lte++gfp+ed+ifDpni++iatGieehd+y++dfiea+r
lcl|NCBI__GCF_000227685.2:WP_006746829.1 481 VMAFDEQGQADTAERKLEICTRAYQILTERIGFPAEDVIFDPNIFAIATGIEEHDNYGVDFIEATRA 547
******************************************************************* PP
TIGR02082 536 ikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrev 602
ike+lP+a isgGvsnvsFs+rgn++vRea+h+vFLy+ai+aG+Dmgivnag+lavyd+i++el+e+
lcl|NCBI__GCF_000227685.2:WP_006746829.1 548 IKERLPHALISGGVSNVSFSFRGNEPVREAIHAVFLYHAIHAGMDMGIVNAGQLAVYDEIEPELKEA 614
******************************************************************* PP
TIGR02082 603 vedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleea 669
ved++l+rr++ate+Ll+lae+y+g + ++++ ewr++pv +RLe++lvkG+ +++ ed+eea
lcl|NCBI__GCF_000227685.2:WP_006746829.1 615 VEDVVLNRRSDATERLLDLAERYRGSGGA--AKKEDLEWRSWPVAKRLEHSLVKGIDSYVVEDTEEA 679
***************************99..556889****************************** PP
TIGR02082 670 rkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.kskGk 735
r ++++p+++iegpL+dGm+vvGdLFG+GkmfLPqvvksarvmkkava+L+P++e+ek+ +++G+
lcl|NCBI__GCF_000227685.2:WP_006746829.1 680 RLEAERPIHVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKKAVAHLIPFIEAEKSGCgENNGR 746
**********************************************************875599*** PP
TIGR02082 736 ivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemv 802
i++atvkGDvhDiGkniv+vvL+cn++ev+dlGv+vP++kile+a++k+ DviglsGLi++sl+em+
lcl|NCBI__GCF_000227685.2:WP_006746829.1 747 ILMATVKGDVHDIGKNIVGVVLQCNNFEVIDLGVMVPAQKILETAREKNVDVIGLSGLITPSLEEMA 813
******************************************************************* PP
TIGR02082 803 evaeemerrgvkiPlllGGaalskahvavkiaekY.kgevvyvkdaseavkvvdkllsekkkaeele 868
+va em+r+g+++Pll+GGa++s+ah+avki+++Y g+vv+vkdas+av v+++l+s + k +++e
lcl|NCBI__GCF_000227685.2:WP_006746829.1 814 HVAAEMQRQGFDTPLLIGGATTSRAHTAVKIEPNYgAGPVVWVKDASRAVGVAQSLISPELKGPYAE 880
***********************************5589**************************** PP
TIGR02082 869 kikeeyeeirekfgekkeklialsekaarkevfaldrse....................dlevpapk 915
k+++ey ++re+ +k++++ l +++ar ++ ++d+++ l++ p
lcl|NCBI__GCF_000227685.2:WP_006746829.1 881 KTRAEYAQLRESLAGRKQRIHWLGLEQARANRPQIDWESyrpvrpraldpdfplppgvtRLQPYGPD 947
**************************************99999999885555554433222222222 PP
TIGR02082 916 flGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekll 981
+ +++ + e+ +iDw+++F +W+l+ yp+il+de++g+earklf+da+++l++++ e+ +
lcl|NCBI__GCF_000227685.2:WP_006746829.1 948 SVL-LRFDDFdVREVARFIDWTPFFHSWQLHAAYPRILDDEVVGAEARKLFDDAQKMLERMIDEGWV 1013
222.23455579******************************************************* PP
TIGR02082 982 rargvvGlfPaqsvg.ddieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGik 1046
r rgvvGlfPa+sv+ ddie+y+de++ ++i+ +++ ++q+++ ++ +laDf+a++e+G
lcl|NCBI__GCF_000227685.2:WP_006746829.1 1014 RLRGVVGLFPANSVEfDDIEVYRDEAR---SEVITRLHHLRQQAQKRRGTpSHSLADFVAPRETGVP 1077
************8755**********9...55555555556777777776899************** PP
TIGR02082 1047 DylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldk 1113
D++ga++v+ag ++++ ak++e+ +ddy++ilvk+ladrlaea+ae +h+rvR+e+wgya +e+l +
lcl|NCBI__GCF_000227685.2:WP_006746829.1 1078 DWMGAFAVSAGGEVDARAKAFEDAHDDYHAILVKSLADRLAEAFAEAMHQRVRREFWGYAPDEDLGN 1144
******************************************************************* PP
TIGR02082 1114 edllkerYrGirpafGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakY 1179
+dl++erY Girpa+GYpacP+htek l+eL+++ + G++ltes+a+ P ++vsg+y+ahp+++Y
lcl|NCBI__GCF_000227685.2:WP_006746829.1 1145 DDLIQERYTGIRPAPGYPACPEHTEKGLLWELIDPVEhAGMTLTESYAMLPVSAVSGWYMAHPQSRY 1211
*********************************97555***************************** PP
TIGR02082 1180 fa 1181
f
lcl|NCBI__GCF_000227685.2:WP_006746829.1 1212 FG 1213
*5 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1254 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 0.04s 00:00:00.15 Elapsed: 00:00:00.15
# Mc/sec: 9.61
//
[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