Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_044411026.1 NA59_RS08555 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000934765.1:WP_044411026.1
Length = 1237
Score = 1585 bits (4103), Expect = 0.0
Identities = 794/1232 (64%), Positives = 965/1232 (78%), Gaps = 11/1232 (0%)
Query: 4 KVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEV 63
++ L+ L ER+LVLDG MGTMIQ L+E DFRGERFAD+ D+KGNND+LV++KP+
Sbjct: 6 RIALLKQLLTERVLVLDGAMGTMIQGLNLSEEDFRGERFADFHMDIKGNNDILVITKPDA 65
Query: 64 IAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTP 123
I IH ++ G DI+ETN+FN+TTIA ADY M+ +IN AA++AR D +
Sbjct: 66 IRDIHLSFLRKGVDILETNSFNATTIAQADYDMQDQVRDINIYAAQVARQACDI-AEQED 124
Query: 124 EKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETV 183
KPR+VAGVLGPTNRTASISPDVNDP FRN FD LV AY ++T AL+EGGAD+ILIET+
Sbjct: 125 GKPRFVAGVLGPTNRTASISPDVNDPGFRNTHFDELVEAYVQATNALLEGGADVILIETI 184
Query: 184 FDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTF 243
FDTLNAKAA+FAVK + LG E+PIMISGTITDASGRTLSGQTTEAFYN++RHA+ L+
Sbjct: 185 FDTLNAKAAIFAVKQVEDTLGEEVPIMISGTITDASGRTLSGQTTEAFYNAIRHAKPLSV 244
Query: 244 GLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGF 303
GLNCALGP+ELR YV+ELSRI E YV+ HPNAGLPN FGEYD + MAK+I+ WA+ G+
Sbjct: 245 GLNCALGPNELRPYVEELSRICETYVSVHPNAGLPNEFGEYDETPEQMAKEIQTWAENGW 304
Query: 304 LNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERT 363
LNI+GGCCGTTP+H+ AM++A + R LP++ VACRLSGLEP+ I + +LFVNVGER
Sbjct: 305 LNIIGGCCGTTPEHVEAMAKAAQAYPQRTLPKVKVACRLSGLEPMTIDDSTLFVNVGERN 364
Query: 364 NVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGE 423
NVTGSA FKRLI E+ Y +A+++A +QV +GAQIID+NMDEGMLDA+A M RFLN++AGE
Sbjct: 365 NVTGSALFKRLIIEDNYEQAVEIAVKQVNDGAQIIDVNMDEGMLDAKACMTRFLNMMAGE 424
Query: 424 PDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVM 483
PD ARVP+MIDSSKW+ IE GLKCIQGKGIVNSIS+KEG + F+ AKL++RYGAA +VM
Sbjct: 425 PDAARVPVMIDSSKWEAIEAGLKCIQGKGIVNSISLKEGEENFLAQAKLIQRYGAATIVM 484
Query: 484 AFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFI 543
AFDE GQADT ARK EIC+R+Y +L GFPPEDIIFDPNIFA+ATGI+EHNNYA DFI
Sbjct: 485 AFDEDGQADTFARKTEICKRSYDLLVAN-GFPPEDIIFDPNIFAIATGIDEHNNYAMDFI 543
Query: 544 GACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLA 603
A E IK LPHALISGGVSNVSFSFRGN+PVREAIH+VFLYYAI+ GMDMGIVNA Q+A
Sbjct: 544 NAVEWIKNHLPHALISGGVSNVSFSFRGNNPVREAIHSVFLYYAIQKGMDMGIVNASQMA 603
Query: 604 IYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRL 663
+YDDL EL+ AVEDV+LN+ D +RLLE+AEK+RG + + + A WR V KRL
Sbjct: 604 VYDDLDPELKQAVEDVVLNKDDGAADRLLEVAEKFRGDGSVQSKESDIA-WRDASVEKRL 662
Query: 664 EYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSAR 723
E+SLVKGIT+FIE DTEEAR P++VIEGPLMDGMNVVGDLFG GKMFLPQVVKSAR
Sbjct: 663 EHSLVKGITDFIEADTEEARTTLGSPLQVIEGPLMDGMNVVGDLFGAGKMFLPQVVKSAR 722
Query: 724 VMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVM 783
VMK+AVAYL+PF+E K G+ GK+V+ATVKGDVHDIGKNIVGVVLQCNN+E++DLGVM
Sbjct: 723 VMKRAVAYLQPFLEEEKASGQAKGKIVMATVKGDVHDIGKNIVGVVLQCNNFEVIDLGVM 782
Query: 784 VPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTA 843
VPAEKIL TA A++IGLSGLITPSL+EMV+VAKEM+R+G +IPLLIGGATTSKAHTA
Sbjct: 783 VPAEKILDTALREGANVIGLSGLITPSLEEMVHVAKEMQRRGMSIPLLIGGATTSKAHTA 842
Query: 844 VKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPP 903
VKIE Y P VYV++ASR VGV +L+S+ + DF A+ R+EY +R + + +
Sbjct: 843 VKIEPQYDHPVVYVKDASRAVGVAQSLISNDLKADFAAKIREEYVQLREERKARAKQVKR 902
Query: 904 VTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYIDWTPFFMTWSLAGKYPR 962
L AR+N DW YTPP LG + + + L IDW+PFF +W L G YPR
Sbjct: 903 TPLNKARENPIPIDWSDYTPPKPSFLGKKVFDTIDLADLVPRIDWSPFFQSWDLHGLYPR 962
Query: 963 ILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHV 1022
IL+D++VG EA+++F DA ML K+ EK L R V+G +PAN V DDIE+Y DETRT
Sbjct: 963 ILDDKIVGEEAKKVFADAQAMLQKIIDEKWLTARAVIGFYPANAVDDDIELYTDETRTTP 1022
Query: 1023 INVSHHLRQQTE-KTGFANYCLADFVAPK-LSGKA-----DYIGAFAVTGGLEEDALADA 1075
+ H+LRQQ E K G N CL+D++APK L + DYIGAFAVT G+ D
Sbjct: 1023 LCRLHNLRQQAEKKAGQYNQCLSDYIAPKNLKDQPGLVINDYIGAFAVTAGIGIDEHIAR 1082
Query: 1076 FEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRP 1135
FEA+HDDY+ IM+KALADRLAEA AE++HE VRK +WGYA +ENL+NEELI+E YQGIRP
Sbjct: 1083 FEAEHDDYHSIMIKALADRLAEALAEHMHELVRKEFWGYAKDENLTNEELIKEKYQGIRP 1142
Query: 1136 APGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQI 1195
APGYPA PEHTEK T+W+LL+ ++ G++LT S+AM P A+VSGWY++HP SKY+ V I
Sbjct: 1143 APGYPANPEHTEKGTLWDLLKPDEEIGLELTSSYAMTPTAAVSGWYYAHPQSKYFGVGSI 1202
Query: 1196 QRDQVEDYARRKGMSVTEVERWLAPNLGYDAD 1227
RDQ EDYA RKG ++ E E+WLAPNLGYD +
Sbjct: 1203 GRDQAEDYAHRKGWTIAEAEKWLAPNLGYDPE 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: 3754
Number of extensions: 139
Number of successful extensions: 9
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: 1237
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1190
Effective search space: 1404200
Effective search space used: 1404200
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_044411026.1 NA59_RS08555 (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.32422.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 1763.5 0.8 0 1763.3 0.8 1.0 1 lcl|NCBI__GCF_000934765.1:WP_044411026.1 NA59_RS08555 methionine synthase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000934765.1:WP_044411026.1 NA59_RS08555 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1763.3 0.8 0 0 2 1182 .] 15 1199 .. 14 1199 .. 0.99
Alignments for each domain:
== domain 1 score: 1763.3 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67
+r+lvlDGamGt++q nL e+dFrge +ad +++ kGnnd+L++tkP++i++ih +++ G Di+
lcl|NCBI__GCF_000934765.1:WP_044411026.1 15 TERVLVLDGAMGTMIQGLNLSEEDFRGErFADFHMDIKGNNDILVITKPDAIRDIHLSFLRKGVDIL 81
68***************************************************************** PP
TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134
etn Fn+t+ia+adYd++d+++++n aa++ar+++d +++ k+RfvaG+lGPtn++a++spdv+
lcl|NCBI__GCF_000934765.1:WP_044411026.1 82 ETNSFNATTIAQADYDMQDQVRDINIYAAQVARQACDIAEQEDGKPRFVAGVLGPTNRTASISPDVN 148
******************************************************************* PP
TIGR02082 135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201
+p+frn+++delv+aY++++++ll+GG+D++Liet+fDtlnakaa+fav++v + g+e+Pi+isg+
lcl|NCBI__GCF_000934765.1:WP_044411026.1 149 DPGFRNTHFDELVEAYVQATNALLEGGADVILIETIFDTLNAKAAIFAVKQVEDTLGEEVPIMISGT 215
******************************************************************* PP
TIGR02082 202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268
i+d+sGrtLsGqt+eaf+++++ha+ l++GLnCalG++elr++v+els++ e++vsv+PnaGLPn++
lcl|NCBI__GCF_000934765.1:WP_044411026.1 216 ITDASGRTLSGQTTEAFYNAIRHAKPLSVGLNCALGPNELRPYVEELSRICETYVSVHPNAGLPNEF 282
******************************************************************* PP
TIGR02082 269 geYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgleal 335
geYd+tpe++ak+++ +ae+g lni+GGCCGttPeh+ a+a+a++ +r ++++ +++lsgle++
lcl|NCBI__GCF_000934765.1:WP_044411026.1 283 GEYDETPEQMAKEIQTWAENGWLNIIGGCCGTTPEHVEAMAKAAQAYPQRTLPKVKVACRLSGLEPM 349
******************************************************************* PP
TIGR02082 336 kiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkk 402
+i++ + fvn+GeR nv+Gs+ f++li++++ye+a++ia +qv++Gaqi+D+n+De++lD++a m++
lcl|NCBI__GCF_000934765.1:WP_044411026.1 350 TIDDSTLFVNVGERNNVTGSALFKRLIIEDNYEQAVEIAVKQVNDGAQIIDVNMDEGMLDAKACMTR 416
******************************************************************* PP
TIGR02082 403 llsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvv 469
+l+++a+epd a+vP+m+Dss++e +eaGLk+iqGk+ivnsislk+Gee+Fl +akli++yGaa +v
lcl|NCBI__GCF_000934765.1:WP_044411026.1 417 FLNMMAGEPDAARVPVMIDSSKWEAIEAGLKCIQGKGIVNSISLKEGEENFLAQAKLIQRYGAATIV 483
******************************************************************* PP
TIGR02082 470 mafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieairei 536
mafDe+Gqa+t ++k ei+kR y+ll++ gfppediifDpni++iatGi+eh++ya+dfi+a+++i
lcl|NCBI__GCF_000934765.1:WP_044411026.1 484 MAFDEDGQADTFARKTEICKRSYDLLVA-NGFPPEDIIFDPNIFAIATGIDEHNNYAMDFINAVEWI 549
***************************9.8************************************* PP
TIGR02082 537 keelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevv 603
k++lP+a isgGvsnvsFs+rgn++vRea+hsvFLy+ai+ G+Dmgivna+++avydd+d+el+++v
lcl|NCBI__GCF_000934765.1:WP_044411026.1 550 KNHLPHALISGGVSNVSFSFRGNNPVREAIHSVFLYYAIQKGMDMGIVNASQMAVYDDLDPELKQAV 616
******************************************************************* PP
TIGR02082 604 edlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleear 670
ed++l++++ a ++Lle+ae+++g + +sk + +wr+ +ve+RLe++lvkG++++ie+d+eear
lcl|NCBI__GCF_000934765.1:WP_044411026.1 617 EDVVLNKDDGAADRLLEVAEKFRGDGSVQSK-ESDIAWRDASVEKRLEHSLVKGITDFIEADTEEAR 682
**************************99777.66779****************************** PP
TIGR02082 671 kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGkiv 737
+l +pl++iegpL+dGm+vvGdLFG+GkmfLPqvvksarvmk+avayL+P+le+ek++ ++kGkiv
lcl|NCBI__GCF_000934765.1:WP_044411026.1 683 TTLGSPLQVIEGPLMDGMNVVGDLFGAGKMFLPQVVKSARVMKRAVAYLQPFLEEEKASGQAKGKIV 749
******************************************************************* PP
TIGR02082 738 latvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvev 804
+atvkGDvhDiGkniv+vvL+cn++ev+dlGv+vP+ekil++a ++ a+viglsGLi++sl+emv+v
lcl|NCBI__GCF_000934765.1:WP_044411026.1 750 MATVKGDVHDIGKNIVGVVLQCNNFEVIDLGVMVPAEKILDTALREGANVIGLSGLITPSLEEMVHV 816
******************************************************************* PP
TIGR02082 805 aeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekik 871
a+em+rrg++iPll+GGa++skah+avki+++Y+ +vvyvkdas+av v+++l+s++ ka++++ki+
lcl|NCBI__GCF_000934765.1:WP_044411026.1 817 AKEMQRRGMSIPLLIGGATTSKAHTAVKIEPQYDHPVVYVKDASRAVGVAQSLISNDLKADFAAKIR 883
******************************************************************* PP
TIGR02082 872 eeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwka 937
eey ++re+ + + ++++ ++++ar++ + +d+s d+++p+p flG+kv++++ +++l++ iDw +
lcl|NCBI__GCF_000934765.1:WP_044411026.1 884 EEYVQLREERKARAKQVKRTPLNKARENPIPIDWS-DYTPPKPSFLGKKVFDTIdLADLVPRIDWSP 949
***********************************.******************************* PP
TIGR02082 938 lFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddieiytd 1004
+F +W+l+g yp+il+d+++g+ea+k+f+da+++l+k++ ek l+ar+v+G++Pa+ v+ddie+ytd
lcl|NCBI__GCF_000934765.1:WP_044411026.1 950 FFQSWDLHGLYPRILDDKIVGEEAKKVFADAQAMLQKIIDEKWLTARAVIGFYPANAVDDDIELYTD 1016
******************************************************************* PP
TIGR02082 1005 etvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskes......GikDylgallvtaglgaeela 1064
et+ t+p+ +++ ++q++++ ++ ++cl+D+ia+k+ i+Dy+ga++vtag+g++e
lcl|NCBI__GCF_000934765.1:WP_044411026.1 1017 ETR---TTPLCRLHNLRQQAEKKAGQyNQCLSDYIAPKNLkdqpglVINDYIGAFAVTAGIGIDEHI 1080
*99...88999999999999999999899*********54445533589****************** PP
TIGR02082 1065 kkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYp 1131
++ea++ddy+si++kaladrlaealae++he vRke+wgya++enl +e+l+ke+Y+Girpa+GYp
lcl|NCBI__GCF_000934765.1:WP_044411026.1 1081 ARFEAEHDDYHSIMIKALADRLAEALAEHMHELVRKEFWGYAKDENLTNEELIKEKYQGIRPAPGYP 1147
******************************************************************* PP
TIGR02082 1132 acPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
a P+htek tl++Ll++++ iGl+lt s+a++P+a+vsg+y+ahp++kYf v
lcl|NCBI__GCF_000934765.1:WP_044411026.1 1148 ANPEHTEKGTLWDLLKPDEeIGLELTSSYAMTPTAAVSGWYYAHPQSKYFGV 1199
****************9988******************************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1237 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: 00:00:00.10
# Mc/sec: 13.56
//
[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