Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_015817782.1 TERTU_RS09440 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000023025.1:WP_015817782.1
Length = 1229
Score = 1553 bits (4022), Expect = 0.0
Identities = 796/1224 (65%), Positives = 961/1224 (78%), Gaps = 13/1224 (1%)
Query: 8 LRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAI 67
L+ LN+RIL+LDG MGTMIQ ++L E D+RGERFA DL GNND+L L++P++IA I
Sbjct: 12 LQEALNQRILILDGAMGTMIQRHKLQENDYRGERFASHHQDLIGNNDILSLTRPDIIAGI 71
Query: 68 HNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPR 127
H Y EAGADIIETNTFN+T ++ +DY +S++ E+N A+A LAR AD + TPEKPR
Sbjct: 72 HREYLEAGADIIETNTFNATRLSQSDYDTQSIAFELNKASATLAREAADAYA--TPEKPR 129
Query: 128 YVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTL 187
+VAG+LGPT+RTASISPDVNDP RN+TFD LV Y E+T L+EGGAD+++IET+FDTL
Sbjct: 130 FVAGILGPTSRTASISPDVNDPGARNVTFDQLVENYTEATHGLIEGGADILMIETIFDTL 189
Query: 188 NAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNC 247
NAKAAVFAV + F+ALG +LPIMISGTITDASGRTLSGQTTEAFYNSL HAE L+ GLNC
Sbjct: 190 NAKAAVFAVSSVFDALGYKLPIMISGTITDASGRTLSGQTTEAFYNSLAHAEPLSIGLNC 249
Query: 248 ALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIV 307
ALG EL YV+EL+R+A C V+AHPNAGLPN FGEYD A MA+ + ++A+ G+LN+V
Sbjct: 250 ALGASELEPYVKELARVANCRVSAHPNAGLPNEFGEYDQSAAEMAEIVIKFAENGYLNVV 309
Query: 308 GGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTG 367
GGCCGTTP HIAA++ AV L PR++ PV+CRL+GLEP NI DSLFVNVGER NVTG
Sbjct: 310 GGCCGTTPAHIAAIADAVASLPPREINPPPVSCRLAGLEPFNITADSLFVNVGERCNVTG 369
Query: 368 SAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIA 427
SA+FKRLI EE Y+ ALDVA+QQV +GAQIIDINMDEGMLDAEAA+VRFLNLIAGEP+IA
Sbjct: 370 SARFKRLILEEDYATALDVAQQQVTDGAQIIDINMDEGMLDAEAAIVRFLNLIAGEPEIA 429
Query: 428 RVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDE 487
RVPIM+DSSKW+VIE GLKCIQGK IVNSIS+KEG F+ A+L RRYGAAV+VMAFDE
Sbjct: 430 RVPIMVDSSKWEVIEAGLKCIQGKPIVNSISLKEGEAEFVEKARLCRRYGAAVIVMAFDE 489
Query: 488 QGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACE 547
QGQADT+ARKIEIC R+Y+ILTEE+GFPPEDIIFDPNIFAVATGI+EHNNYA DFI A
Sbjct: 490 QGQADTQARKIEICSRSYRILTEELGFPPEDIIFDPNIFAVATGIDEHNNYAVDFIEATR 549
Query: 548 DIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDD 607
I++ LPHA +SGGVSNVSFSFRGN+PVREAIH+VFLY+AIR GM+MGIVNAGQLAIYDD
Sbjct: 550 WIRQNLPHAGVSGGVSNVSFSFRGNNPVREAIHSVFLYHAIRAGMNMGIVNAGQLAIYDD 609
Query: 608 LPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYSL 667
LP ELR VE VI N D TE LL +AEKYRG + + + EWR+ +VNKRLE++L
Sbjct: 610 LPEELRTRVEAVISNTSADATEALLSIAEKYRGDGSQQQSK-EDLEWRTADVNKRLEHAL 668
Query: 668 VKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQ 727
VKGIT +IE DTEEAR Q++RP++VIEGPLMDGMNVVG+LFG GKMFLPQVVKSARVMKQ
Sbjct: 669 VKGITSYIEADTEEARLQSSRPLDVIEGPLMDGMNVVGELFGSGKMFLPQVVKSARVMKQ 728
Query: 728 AVAYLEPFIEASKEQG-KTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPA 786
AVA+L+P+IEA K +G ++NGK+++ATVKGDVHDIGKNIVGVVLQCNN+E+VDLGVMVP
Sbjct: 729 AVAWLQPYIEAEKSEGTRSNGKILMATVKGDVHDIGKNIVGVVLQCNNFEVVDLGVMVPG 788
Query: 787 EKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKI 846
EKIL TAK D+IGLSGLITPSLDEMV VA+EME QG +PL+IGGATTSKAHTAVKI
Sbjct: 789 EKILETAKREGCDIIGLSGLITPSLDEMVAVAREMETQGIDLPLMIGGATTSKAHTAVKI 848
Query: 847 E-QNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVT 905
+ Q + VYV +ASR VGV LLS R DF+A + EYET+R + + + P
Sbjct: 849 DPQFHLNQAVYVPDASRAVGVATRLLSKDLRPDFIAALKTEYETIRERRANRTSKRPATP 908
Query: 906 LEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAGKYPRIL 964
A +W+ YTPP G Q E + L YIDWTPFF+TW L GK+P IL
Sbjct: 909 YAEAVKLRKPLNWENYTPPKPQFTGTQVWEDYPLTELVEYIDWTPFFITWDLVGKFPAIL 968
Query: 965 EDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVG-DDIEIYRDETRTHVI 1023
D+VVG A L++DA +L + K L + ++G + AN V DDI + + I
Sbjct: 969 TDKVVGEAATSLYQDARALLQDIVDGKLLQAKAILGFWEANTVDHDDIVLTHN---AEPI 1025
Query: 1024 NVSHHLRQQTEKTGFANY--CLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHD 1081
HH+RQQ K + LADF+AP+ SG D++G F+VT G+ D LA +++A+ D
Sbjct: 1026 ATLHHIRQQVIKNDNDKHLLSLADFIAPQESGVTDFVGGFSVTAGIGADELAASYQAKGD 1085
Query: 1082 DYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPA 1141
DYN IMVKALADRLAEAFAE+LHERVRK +WGY E L +ELIRE Y+GIRPAPGYPA
Sbjct: 1086 DYNAIMVKALADRLAEAFAEHLHERVRKEFWGYDSAEALDKDELIREKYRGIRPAPGYPA 1145
Query: 1142 CPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVE 1201
CP+HTEKAT+++LL+ ++ G+ LTE +AM+P ASVSGWYFSHP+S+Y+ V +I RDQVE
Sbjct: 1146 CPDHTEKATLFKLLQADR-IGVSLTEHYAMFPAASVSGWYFSHPESQYFNVGKISRDQVE 1204
Query: 1202 DYARRKGMSVTEVERWLAPNLGYD 1225
A RKG+SV+++E+WL L YD
Sbjct: 1205 SLAERKGLSVSDMEKWLQSVLAYD 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: 3632
Number of extensions: 137
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: 1229
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1182
Effective search space: 1394760
Effective search space used: 1394760
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_015817782.1 TERTU_RS09440 (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.2374.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 1756.3 0.0 0 1756.2 0.0 1.0 1 lcl|NCBI__GCF_000023025.1:WP_015817782.1 TERTU_RS09440 methionine synthas
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023025.1:WP_015817782.1 TERTU_RS09440 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1756.2 0.0 0 0 1 1182 [] 16 1195 .. 16 1195 .. 0.98
Alignments for each domain:
== domain 1 score: 1756.2 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDi 66
ln+ril+lDGamGt++q+++L+e+d+rge +a ++++l Gnnd+L+lt+P++ia ihr+y+eaGaDi
lcl|NCBI__GCF_000023025.1:WP_015817782.1 16 LNQRILILDGAMGTMIQRHKLQENDYRGErFASHHQDLIGNNDILSLTRPDIIAGIHREYLEAGADI 82
68***************************************************************** PP
TIGR02082 67 vetntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdv 133
+etntFn+t ++++dYd+++ a elnk++a+lare+ad + tpek+RfvaG lGPt+++a++spdv
lcl|NCBI__GCF_000023025.1:WP_015817782.1 83 IETNTFNATRLSQSDYDTQSIAFELNKASATLAREAADAYA-TPEKPRFVAGILGPTSRTASISPDV 148
*****************************************.************************* PP
TIGR02082 134 erpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisg 200
++p+ rnvt+d+lv+ Y+e+++gl++GG+D+l+iet+fDtlnakaa+fav +vf++ g +lPi+isg
lcl|NCBI__GCF_000023025.1:WP_015817782.1 149 NDPGARNVTFDQLVENYTEATHGLIEGGADILMIETIFDTLNAKAAVFAVSSVFDALGYKLPIMISG 215
******************************************************************* PP
TIGR02082 201 vivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPna 267
+i+d+sGrtLsGqt+eaf++sl hae l++GLnCalGa el+++vkel++ a++ vs++PnaGLPn+
lcl|NCBI__GCF_000023025.1:WP_015817782.1 216 TITDASGRTLSGQTTEAFYNSLAHAEPLSIGLNCALGASELEPYVKELARVANCRVSAHPNAGLPNE 282
******************************************************************* PP
TIGR02082 268 lgeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglea 334
+geYd+ + e+a+++ +fae+g+ln+vGGCCGttP+hi+aia+av+ + pr+ + + +++l+gle+
lcl|NCBI__GCF_000023025.1:WP_015817782.1 283 FGEYDQSAAEMAEIVIKFAENGYLNVVGGCCGTTPAHIAAIADAVASLPPREINPPPVSCRLAGLEP 349
******************************************************************* PP
TIGR02082 335 lkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmk 401
++i+ +s fvn+GeR+nv+Gs++f++li +edy al++a+qqv++Gaqi+Din+De++lD+ea+++
lcl|NCBI__GCF_000023025.1:WP_015817782.1 350 FNITADSLFVNVGERCNVTGSARFKRLILEEDYATALDVAQQQVTDGAQIIDINMDEGMLDAEAAIV 416
******************************************************************* PP
TIGR02082 402 kllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavv 468
++l+l+a+ep+ia+vP+m+Dss++ev+eaGLk+iqGk ivnsislk+Ge++F+eka+l ++yGaav+
lcl|NCBI__GCF_000023025.1:WP_015817782.1 417 RFLNLIAGEPEIARVPIMVDSSKWEVIEAGLKCIQGKPIVNSISLKEGEAEFVEKARLCRRYGAAVI 483
******************************************************************* PP
TIGR02082 469 vmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaire 535
vmafDe+Gqa+t+++kiei++R y++lte++gfppediifDpni+++atGi+eh++ya+dfiea+r+
lcl|NCBI__GCF_000023025.1:WP_015817782.1 484 VMAFDEQGQADTQARKIEICSRSYRILTEELGFPPEDIIFDPNIFAVATGIDEHNNYAVDFIEATRW 550
******************************************************************* PP
TIGR02082 536 ikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrev 602
i+++lP+a +sgGvsnvsFs+rgn++vRea+hsvFLy+ai+aG++mgivnag+la+ydd+++elr
lcl|NCBI__GCF_000023025.1:WP_015817782.1 551 IRQNLPHAGVSGGVSNVSFSFRGNNPVREAIHSVFLYHAIRAGMNMGIVNAGQLAIYDDLPEELRTR 617
******************************************************************* PP
TIGR02082 603 vedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleea 669
ve +i + + +ate Ll +ae+y+g ++ +++++ ewr +v++RLe+alvkG++++ie+d+eea
lcl|NCBI__GCF_000023025.1:WP_015817782.1 618 VEAVISNTSADATEALLSIAEKYRGDGSQ-QQSKEDLEWRTADVNKRLEHALVKGITSYIEADTEEA 683
*************************9999.6678999****************************** PP
TIGR02082 670 rkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.kskGk 735
r + ++pl++iegpL+dGm+vvG+LFGsGkmfLPqvvksarvmk+ava+L+Py+e+ek+e +s+Gk
lcl|NCBI__GCF_000023025.1:WP_015817782.1 684 RLQSSRPLDVIEGPLMDGMNVVGELFGSGKMFLPQVVKSARVMKQAVAWLQPYIEAEKSEGtRSNGK 750
**********************************************************997589*** PP
TIGR02082 736 ivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemv 802
i++atvkGDvhDiGkniv+vvL+cn++evvdlGv+vP ekile+ak++ D+iglsGLi++sldemv
lcl|NCBI__GCF_000023025.1:WP_015817782.1 751 ILMATVKGDVHDIGKNIVGVVLQCNNFEVVDLGVMVPGEKILETAKREGCDIIGLSGLITPSLDEMV 817
******************************************************************* PP
TIGR02082 803 evaeemerrgvkiPlllGGaalskahvavkiaekYk.gevvyvkdaseavkvvdkllsekkkaeele 868
va+eme++g+++Pl++GGa++skah+avki+++++ + vyv das+av v+ +lls++ + ++++
lcl|NCBI__GCF_000023025.1:WP_015817782.1 818 AVAREMETQGIDLPLMIGGATTSKAHTAVKIDPQFHlNQAVYVPDASRAVGVATRLLSKDLRPDFIA 884
**********************************984689*************************** PP
TIGR02082 869 kikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiD 934
++k+eye+ire+ ++ +k+ a + ++a k + l+++ ++++p+p+f Gt+v e++ + el++yiD
lcl|NCBI__GCF_000023025.1:WP_015817782.1 885 ALKTEYETIRERRANRTSKRPATPYAEAVKLRKPLNWE-NYTPPKPQFTGTQVWEDYpLTELVEYID 950
*************************************9.**************************** PP
TIGR02082 935 wkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddiei 1001
w+++F++W+l gk+p il+d+++g+ a+ l++da++ll+ ++ kll+a++++G++ a++v+ d +
lcl|NCBI__GCF_000023025.1:WP_015817782.1 951 WTPFFITWDLVGKFPAILTDKVVGEAATSLYQDARALLQDIVDGKLLQAKAILGFWEANTVDHDDIV 1017
***********************************************************88655555 PP
TIGR02082 1002 ytdetvsqetkpiatvrek.leqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakk 1066
+t+ +++piat+++ ++ +++++d+ l+laDfia++esG +D++g + vtag+ga+ela
lcl|NCBI__GCF_000023025.1:WP_015817782.1 1018 LTH-----NAEPIATLHHIrQQVIKNDNDKhLLSLADFIAPQESGVTDFVGGFSVTAGIGADELAAS 1079
552.....5679999876515667777787789********************************** PP
TIGR02082 1067 leakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpac 1133
++ak ddy++i+vkaladrlaea+ae+lhervRke+wgy + e+ldk++l++e+YrGirpa+GYpac
lcl|NCBI__GCF_000023025.1:WP_015817782.1 1080 YQAKGDDYNAIMVKALADRLAEAFAEHLHERVRKEFWGYDSAEALDKDELIREKYRGIRPAPGYPAC 1146
******************************************************************* PP
TIGR02082 1134 PdhtekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfav 1182
Pdhtekatl++Ll+a+riG+ lte +a+ P+asvsg+yf+hpe++Yf+v
lcl|NCBI__GCF_000023025.1:WP_015817782.1 1147 PDHTEKATLFKLLQADRIGVSLTEHYAMFPAASVSGWYFSHPESQYFNV 1195
***********************************************98 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1229 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: 0.07u 0.04s 00:00:00.11 Elapsed: 00:00:00.10
# Mc/sec: 13.58
//
[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