Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_050464099.1 AKL27_RS17280 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_001189915.1:WP_050464099.1
Length = 1247
Score = 1472 bits (3810), Expect = 0.0
Identities = 773/1244 (62%), Positives = 922/1244 (74%), Gaps = 38/1244 (3%)
Query: 8 LRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCD-----LKGNNDLLVLSKPE 62
LR +++RIL+LDG MGTMIQ Y+L E D+RGERFA + +KGNN+LL L++P
Sbjct: 13 LRDLMSQRILILDGAMGTMIQQYKLTEEDYRGERFAGFSVPGKELFVKGNNELLSLTQPH 72
Query: 63 VIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTART 122
+I IH Y AGAD+IETNTF +T +A DY M L E+N +A+LARA D+++ T
Sbjct: 73 IIQEIHEQYLAAGADLIETNTFGATGVAQDDYHMAHLVYEMNVQSARLARAACDKYS--T 130
Query: 123 PEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIET 182
P+KPR+VAG LGPT +TASISPDVNDPA RN++FD LV Y E T+ALVEGGAD++L+ET
Sbjct: 131 PDKPRFVAGALGPTPKTASISPDVNDPAARNVSFDQLVTTYLEQTRALVEGGADVLLVET 190
Query: 183 VFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALT 242
+FDTLN KAA+FA+ T FE G LPIMISGT+TDASGR LSGQT AF+NS+RHA LT
Sbjct: 191 IFDTLNCKAALFALDTFFEESGKRLPIMISGTVTDASGRILSGQTVPAFWNSIRHARPLT 250
Query: 243 FGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGE--YDLDADTMAKQIREWAQ 300
GLNCALG +R Y +ELS+IA+ +V +PNAGLPN + +D D + ++E+A+
Sbjct: 251 VGLNCALGAALMRPYAEELSKIADTFVCIYPNAGLPNPMSDTGFDETPDVTSALLKEFAE 310
Query: 301 AGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVG 360
+GF+N+ GGCCGTTP HI A++ V +APRK+PE RLSGLEP I + SL+VNVG
Sbjct: 311 SGFVNVAGGCCGTTPPHIKAIAETVASIAPRKVPEGTHEMRLSGLEPFTINDQSLYVNVG 370
Query: 361 ERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLI 420
ERTNVTGS F RLI E+Y EAL VARQQVENGAQIIDINMDE MLD+ AAM RFLNLI
Sbjct: 371 ERTNVTGSKAFARLILNEQYDEALAVARQQVENGAQIIDINMDEAMLDSVAAMTRFLNLI 430
Query: 421 AGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAV 480
A EPDIARVPIMIDSSKW VIE GLKC+QGK IVNSISMKEG + F+H AKL RRYGAAV
Sbjct: 431 ASEPDIARVPIMIDSSKWSVIEAGLKCVQGKSIVNSISMKEGEEKFLHEAKLCRRYGAAV 490
Query: 481 VVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQ 540
+VMAFDE GQADT RK EIC RAY++L ++VGFPPEDIIFDPNIFAVATGIEEHNNYA
Sbjct: 491 IVMAFDEVGQADTFERKTEICERAYRLLVDKVGFPPEDIIFDPNIFAVATGIEEHNNYAV 550
Query: 541 DFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAG 600
DFI A I + LP+A ISGGVSNVSFSFRGNDP REAIH VFLY+AI+ GM MGIVNAG
Sbjct: 551 DFIEATRWIHQNLPYAKISGGVSNVSFSFRGNDPAREAIHTVFLYHAIKAGMTMGIVNAG 610
Query: 601 QLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVN 660
+ +YDDLP EL++ VEDV+LNRR D TER++++A K D EWR V
Sbjct: 611 MIGVYDDLPVELKERVEDVVLNRRPDATERMIDIAATL---KAGDKKEEATLEWRGETVQ 667
Query: 661 KRLEYSLVKGITEFIEQDTEEARQQ----ATRPIEVIEGPLMDGMNVVGDLFGEGKMFLP 716
KRL ++LV GIT++I +DTEEARQQ RPI VIEGPLMDGMN+VGDLFG+GKMFLP
Sbjct: 668 KRLAHALVHGITQWIVEDTEEARQQLLRDGGRPIHVIEGPLMDGMNIVGDLFGQGKMFLP 727
Query: 717 QVVKSARVMKQAVAYLEPFIEASKE--------QGKTNGKMVIATVKGDVHDIGKNIVGV 768
QVVKSARVMKQAVA+L PFIE K K GK+VIATVKGDVHDIGKNIV V
Sbjct: 728 QVVKSARVMKQAVAHLIPFIEEEKRLHEQETGIASKPKGKIVIATVKGDVHDIGKNIVSV 787
Query: 769 VLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMER----Q 824
VLQCNN+E+V++GVMVP +IL AKE NAD+IGLSGLITPSL+EM VAKEM+R
Sbjct: 788 VLQCNNFEVVNMGVMVPCSQILAKAKEENADIIGLSGLITPSLEEMAYVAKEMQRDPYFS 847
Query: 825 GFTIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTR 884
G +PLLIGGATTS+AHTAVKI NY GP VYV +ASR V V +LL+ Q+D +VA
Sbjct: 848 GLKMPLLIGGATTSRAHTAVKIAPNYDGPVVYVPDASRAVAVAQSLLTPEQKDQYVADIN 907
Query: 885 KEYETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEASIETLRNY 944
+Y +R QH KK P V++ AARDN A ++ P R + V+ + TL NY
Sbjct: 908 ADYVRIREQHANKK-AVPLVSIAAARDNKTALEFAPLKPKFIGRRVFKNVD--LATLSNY 964
Query: 945 IDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPA 1004
IDW PFF TW LAG YP IL DEVVG A ++F++A +L K+ + L G+V L PA
Sbjct: 965 IDWGPFFQTWDLAGPYPAILTDEVVGEAASKVFEEAQALLKKIIDGRWLTANGIVSLLPA 1024
Query: 1005 NRV-GDDIEIYRDETRTHVINVSHHLRQQTEK---TGFA--NYCLADFVAPKLSGKADYI 1058
N V DDIEIY D+TRT V + +RQQT K G A N CL+DF+APK SG ADYI
Sbjct: 1025 NTVHDDDIEIYTDDTRTKVALTYYGVRQQTVKPVIDGVARPNQCLSDFIAPKQSGIADYI 1084
Query: 1059 GAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNE 1118
G FAVT GL + FE HDDY+ IM+KALADRLAEAFAEYLHERVRK WGYAP E
Sbjct: 1085 GMFAVTSGLGIEKYEKRFEDAHDDYSSIMLKALADRLAEAFAEYLHERVRKDLWGYAPQE 1144
Query: 1119 NLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVS 1178
LS+ ELI+E Y GIRPA GYPACPEHT K +E+++ ++ GM +TES+AM+PGASVS
Sbjct: 1145 QLSSAELIKEKYVGIRPAAGYPACPEHTVKKEAFEVMQCDE-IGMMVTESYAMFPGASVS 1203
Query: 1179 GWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNL 1222
G+YF+HP+SKY+ V +I DQV D A R+G+ +VERWLAPNL
Sbjct: 1204 GFYFAHPESKYFVVGKIGDDQVSDMAERRGVPKEDVERWLAPNL 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: 3663
Number of extensions: 162
Number of successful extensions: 13
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: 1247
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1199
Effective search space: 1413621
Effective search space used: 1413621
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_050464099.1 AKL27_RS17280 (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.7706.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 1696.2 0.1 0 1696.0 0.1 1.0 1 lcl|NCBI__GCF_001189915.1:WP_050464099.1 AKL27_RS17280 methionine synthas
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001189915.1:WP_050464099.1 AKL27_RS17280 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1696.0 0.1 0 0 2 1182 .] 18 1217 .. 17 1217 .. 0.96
Alignments for each domain:
== domain 1 score: 1696.0 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlare.....lkGnndlLnltkPeviaaihrayfea 62
++ril+lDGamGt++q+++Lte+d+rge +a + +kGnn+lL+lt+P +i++ih++y+ a
lcl|NCBI__GCF_001189915.1:WP_050464099.1 18 SQRILILDGAMGTMIQQYKLTEEDYRGErFAGFSVPgkelfVKGNNELLSLTQPHIIQEIHEQYLAA 84
79**************************888765432223379************************ PP
TIGR02082 63 GaDivetntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatl 129
GaD++etntF++t +a+ dY++++++ye+n ++a+lar+++d+++ tp+k+RfvaG+lGPt k+a++
lcl|NCBI__GCF_001189915.1:WP_050464099.1 85 GADLIETNTFGATGVAQDDYHMAHLVYEMNVQSARLARAACDKYS-TPDKPRFVAGALGPTPKTASI 150
*********************************************.********************* PP
TIGR02082 130 spdverpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPi 196
spdv++p+ rnv +d+lv Y eq+++l++GG+D+lL+et+fDtln kaalfa+ + fee g++lPi
lcl|NCBI__GCF_001189915.1:WP_050464099.1 151 SPDVNDPAARNVSFDQLVTTYLEQTRALVEGGADVLLVETIFDTLNCKAALFALDTFFEESGKRLPI 217
******************************************************************* PP
TIGR02082 197 lisgvivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaG 263
+isg+++d+sGr+LsGqt+ af +s++ha l++GLnCalGa+++r++ +els++a+++v ++PnaG
lcl|NCBI__GCF_001189915.1:WP_050464099.1 218 MISGTVTDASGRILSGQTVPAFWNSIRHARPLTVGLNCALGAALMRPYAEELSKIADTFVCIYPNAG 284
******************************************************************* PP
TIGR02082 264 LPnalg..eYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksv 328
LPn ++ +d+tp+ + + lkefae g++n+ GGCCGttP hi+aiae v+ i+prk++e ++++
lcl|NCBI__GCF_001189915.1:WP_050464099.1 285 LPNPMSdtGFDETPDVTSALLKEFAESGFVNVAGGCCGTTPPHIKAIAETVASIAPRKVPEGTHEMR 351
****99778********************************************************** PP
TIGR02082 329 lsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllD 395
lsgle+++i+++s +vn+GeRtnv+Gsk f++li +e+y+eal +a+qqve+Gaqi+Din+De++lD
lcl|NCBI__GCF_001189915.1:WP_050464099.1 352 LSGLEPFTINDQSLYVNVGERTNVTGSKAFARLILNEQYDEALAVARQQVENGAQIIDINMDEAMLD 418
******************************************************************* PP
TIGR02082 396 geadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklike 462
++a+m+++l+l+asepdia+vP+m+Dss++ v+eaGLk++qGk+ivnsis+k+Gee+Fl++akl ++
lcl|NCBI__GCF_001189915.1:WP_050464099.1 419 SVAAMTRFLNLIASEPDIARVPIMIDSSKWSVIEAGLKCVQGKSIVNSISMKEGEEKFLHEAKLCRR 485
******************************************************************* PP
TIGR02082 463 yGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidf 529
yGaav+vmafDe Gqa+t ++k ei++Ray+ll++kvgfppediifDpni+++atGieeh++ya+df
lcl|NCBI__GCF_001189915.1:WP_050464099.1 486 YGAAVIVMAFDEVGQADTFERKTEICERAYRLLVDKVGFPPEDIIFDPNIFAVATGIEEHNNYAVDF 552
******************************************************************* PP
TIGR02082 530 ieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddid 596
iea+r+i+++lP+akisgGvsnvsFs+rgnd++Rea+h+vFLy+aikaG+ mgivnag++ vydd++
lcl|NCBI__GCF_001189915.1:WP_050464099.1 553 IEATRWIHQNLPYAKISGGVSNVSFSFRGNDPAREAIHTVFLYHAIKAGMTMGIVNAGMIGVYDDLP 619
******************************************************************* PP
TIGR02082 597 kelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregie 663
el+e ved++l+rr++ate++ ++a + k + ke+++ ewr+ v++RL++alv+G+++ i
lcl|NCBI__GCF_001189915.1:WP_050464099.1 620 VELKERVEDVVLNRRPDATERMIDIAATLKAGDK---KEEATLEWRGETVQKRLAHALVHGITQWIV 683
****************************665544...5889************************** PP
TIGR02082 664 edleearkkl....kapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePyleke 726
ed+eear++l +p+++iegpL+dGm++vGdLFG+GkmfLPqvvksarvmk+ava+L+P++e+e
lcl|NCBI__GCF_001189915.1:WP_050464099.1 684 EDTEEARQQLlrdgGRPIHVIEGPLMDGMNIVGDLFGQGKMFLPQVVKSARVMKQAVAHLIPFIEEE 750
*******776232268*************************************************** PP
TIGR02082 727 keed........kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkka 785
k + k kGkiv+atvkGDvhDiGkniv+vvL+cn++evv++Gv+vP+ +il +ak+++a
lcl|NCBI__GCF_001189915.1:WP_050464099.1 751 KRLHeqetgiasKPKGKIVIATVKGDVHDIGKNIVSVVLQCNNFEVVNMGVMVPCSQILAKAKEENA 817
97556789999999***************************************************** PP
TIGR02082 786 DviglsGLivksldemvevaeemer....rgvkiPlllGGaalskahvavkiaekYkgevvyvkdas 848
D+iglsGLi++sl+em++va+em+r g+k+Pll+GGa++s+ah+avkia++Y+g+vvyv das
lcl|NCBI__GCF_001189915.1:WP_050464099.1 818 DIIGLSGLITPSLEEMAYVAKEMQRdpyfSGLKMPLLIGGATTSRAHTAVKIAPNYDGPVVYVPDAS 884
************************944445899********************************** PP
TIGR02082 849 eavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapk 915
+av v+++ll+ ++k+++++ i+++y ire++ + k+ + +s++aar+++ al+ + +pk
lcl|NCBI__GCF_001189915.1:WP_050464099.1 885 RAVAVAQSLLTPEQKDQYVADINADYVRIREQHAN-KKAVPLVSIAAARDNKTALEFA----PLKPK 946
*********************************98.77899**********9999888....99*** PP
TIGR02082 916 flGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekll 981
f+G++v++++ +++l +yiDw ++F +W+l+g yp il+de++g+ a k+f++a++ll+k++ + l
lcl|NCBI__GCF_001189915.1:WP_050464099.1 947 FIGRRVFKNVdLATLSNYIDWGPFFQTWDLAGPYPAILTDEVVGEAASKVFEEAQALLKKIIDGRWL 1013
******************************************************************* PP
TIGR02082 982 rargvvGlfPaqsv.gddieiytdetvsqetkpiatvrekleqlrqqsdr....ylclaDfiaskes 1043
+a+g+v l Pa++v +ddieiytd+t+++ + + vr+++ ++ + ++cl+Dfia+k+s
lcl|NCBI__GCF_001189915.1:WP_050464099.1 1014 TANGIVSLLPANTVhDDDIEIYTDDTRTKVALTYYGVRQQTVKPVID--GvarpNQCLSDFIAPKQS 1078
************762578*******9955444444444333222222..24458************* PP
TIGR02082 1044 GikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeen 1110
Gi+Dy+g+++vt glg+e++ k++e+ +ddy+si++kaladrlaea+ae+lhervRk+lwgya +e+
lcl|NCBI__GCF_001189915.1:WP_050464099.1 1079 GIADYIGMFAVTSGLGIEKYEKRFEDAHDDYSSIMLKALADRLAEAFAEYLHERVRKDLWGYAPQEQ 1145
******************************************************************* PP
TIGR02082 1111 ldkedllkerYrGirpafGYpacPdhtekatlleLleaeriGlklteslalaPeasvsglyfahpea 1177
l+ ++l+ke+Y Girpa GYpacP+ht k++ +e+++ ++iG+ +tes+a+ P asvsg+yfahpe+
lcl|NCBI__GCF_001189915.1:WP_050464099.1 1146 LSSAELIKEKYVGIRPAAGYPACPEHTVKKEAFEVMQCDEIGMMVTESYAMFPGASVSGFYFAHPES 1212
******************************************************************* PP
TIGR02082 1178 kYfav 1182
kYf v
lcl|NCBI__GCF_001189915.1:WP_050464099.1 1213 KYFVV 1217
***76 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1247 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: 0.12u 0.03s 00:00:00.15 Elapsed: 00:00:00.15
# Mc/sec: 9.74
//
[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