Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_011319793.1 AVA_RS15430 methionine synthase
Query= metacyc::G18NG-11090-MONOMER
(1221 letters)
>NCBI__GCF_000204075.1:WP_011319793.1
Length = 1178
Score = 994 bits (2571), Expect = 0.0
Identities = 550/1229 (44%), Positives = 764/1229 (62%), Gaps = 67/1229 (5%)
Query: 5 VTSPAHNNAHSSEFLDALANHVLIGDGAMGTQLQGFDLDVEKDF--LDLEGCNEILNDTR 62
+T P HS EF V++ DGAMGT LQ +L E DF + EGCNE L T+
Sbjct: 1 MTHPFLKRLHSPEF------PVIVFDGAMGTNLQTQNLTAE-DFGGVQYEGCNEYLVHTK 53
Query: 63 PDVLRQIHRAYFEAGADLVETNTFGCNLPNLADYDIADRCRELAYKGTAVAREVADEMGP 122
P+ + ++HR + GAD++ET+TFG LA+YD+AD+ L K +A+ VA E
Sbjct: 54 PEAVAKVHRDFLAVGADVIETDTFGATSIVLAEYDLADQTYYLNKKAAELAKSVAAEFST 113
Query: 123 GRNGMRRFVVGSLGPGTKLPSLGHAPYADLRGHYKEAALGIIDGGGDAFLIETAQDLLQV 182
RFV GS+GP TKLP+LGH + L+ + E A ++DGG D L+ET QD+LQ+
Sbjct: 114 PDKP--RFVAGSIGPTTKLPTLGHIDFDTLKTAFAEQAEALLDGGVDLLLVETCQDVLQI 171
Query: 183 KAAVHGVQDAMAELDTFLPIICHVTVETTGTMLMGSEIGAALTALQPLGIDMIGLNCATG 242
KAA++G+++ A+ +P++ VT+E+ GTML+GSEI A LT L+P ID++GLNCATG
Sbjct: 172 KAALNGIEEVFAKRGERIPLMVSVTMESMGTMLVGSEINAVLTILEPFPIDILGLNCATG 231
Query: 243 PDEMSEHLRYLSKHADIPVSVMPNAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMV 302
PD M H++YL++H+ VS +PNAGLP A Y L +L AL FV + G+ ++
Sbjct: 232 PDLMKPHIKYLAEHSPFVVSCIPNAGLPENVGGQAHYRLTPMELRMALMHFVEDLGVQVI 291
Query: 303 GGCCGTTPEHIRAVRDAVVGVPEQETSTLTKIPAGPVEQASREVEKEDSVASLYTSVPLS 362
GGCCGT PEHI+ + + A ++ R+ E + AS+Y++
Sbjct: 292 GGCCGTRPEHIQQLAEI----------------AKDLKPKVRQPSLEPAAASIYSTQTYE 335
Query: 363 QETGISMIGERTNSNGSKAFREAMLSGDWEKCVDIAKQQTRDGAHMLDLCVDYVGRDGTA 422
Q+ ++GER N++GSK R+ + + DW+ V +A+ Q ++GAH+LD+ VDYVGRDG
Sbjct: 336 QDNSFLIVGERLNASGSKKCRDLLNAEDWDGLVSMARSQVKEGAHILDVNVDYVGRDGVR 395
Query: 423 DMATLAALLATSSTLPIMIDSTEPEVIRTGLEHLGGRSIVNSVNFEDGDGPESRYQRIMK 482
DM L + + + TLP+M+DSTE E + GL+ GG+ ++NS N+EDG E R+ ++++
Sbjct: 396 DMHELVSRIVNNVTLPLMLDSTEWEKMEAGLKVAGGKCLLNSTNYEDG---EPRFLKVLE 452
Query: 483 LVKQHGAAVVALTIDEEGQARTAEHKVRIAKRLIDDITGSYGLDIKDIVVDCLTFPISTG 542
L K++GA VV TIDEEG ARTAE K +IA+R YG+ +I D L PISTG
Sbjct: 453 LAKKYGAGVVIGTIDEEGMARTAEKKFQIAQRAYRQAV-EYGIPPTEIFFDTLALPISTG 511
Query: 543 QEETRRDGIETIEAIRELKKLYPEIHTTLGLSNISFGLNPAARQVLNSVFLNECIEAGLD 602
EE R +G TIE+I +++ P H LG+SNISFGL+PA+R VLNSVFL+E AG+D
Sbjct: 512 IEEDRENGKATIESISRIRQQLPGCHVILGVSNISFGLSPASRMVLNSVFLHEATAAGMD 571
Query: 603 SAIAHSSKILPMNRIDDRQREVALDMVYDRRTED-----YDPLQEFMQLFEGVSAADAKD 657
+AI +SKILP+++I+DR +EV ++YD+R D YDPL E +LFEGV+ K
Sbjct: 572 AAIVSASKILPLSKIEDRHQEVCRQLIYDQRQFDGDVCIYDPLTELTKLFEGVTTKRNKG 631
Query: 658 ARAEQLAAMPLFERLAQRIIDGDKNGLEDDLEAGMKEKSPIAIINEDLLNGMKTVGELFG 717
++P+ ERL + IIDG++ GLE L +++ P+ IIN LL+GMK VGELFG
Sbjct: 632 VD----ESLPIEERLKRHIIDGERIGLEAQLTKALEQYPPLEIINTFLLDGMKVVGELFG 687
Query: 718 SGQMQLPFVLQSAETMKTAVAYLEPFMEEEAEATGSAQAEGKGKIVVATVKGDVHDIGKN 777
SGQMQLPFVLQSAETMK AVAYLEPFME+ + KGK+++ATVKGDVHDIGKN
Sbjct: 688 SGQMQLPFVLQSAETMKAAVAYLEPFMEKSESGNNA-----KGKVIIATVKGDVHDIGKN 742
Query: 778 LVDIILSNNGYDVVNLGIKQPLSAMLEAAEEHKADVIGMSGLLVKSTVVMKENLEEMNNA 837
LVDIILSNNGY V+NLGIKQP+ ++EA +HKAD I MSGLLVKST MKENLE N
Sbjct: 743 LVDIILSNNGYKVINLGIKQPVENIIEAYNQHKADCIAMSGLLVKSTAFMKENLEVFNEK 802
Query: 838 GASNYPVILGGAALTRTYVENDLNEVYTGEVYYARDAFEGLRLMDEVMAEKRGEGLDP-- 895
G N PVILGGAALT +V D Y G+V Y +DAF L MD++M K D
Sbjct: 803 GI-NVPVILGGAALTPKFVHKDCQNTYKGKVIYGKDAFSDLHFMDKLMPAKATGKWDNFL 861
Query: 896 ---NSPEAIEQAKKKAERKARNERSRKIAAERKANAAPVIVPERSDVSTDTPTAAPPFWG 952
+ E E ++ N +S + PV V+ D P PPFWG
Sbjct: 862 GFLDEVETEETEPTNSQSPVPNSQS---PVPSPQSPVPVDTRRSEAVAVDIPRPTPPFWG 918
Query: 953 TRIVK--GLPLAEFLGNLDERALFMGQWGLKSTRGNEGPSYEDLVETEGRPRLRYWLDRL 1010
T++++ + L E ++D +AL GQW + + Y+ + + P L W R+
Sbjct: 919 TQLLQPSDISLEEIFWHMDLQALVAGQWQFRKPKEQSKEEYQAFLNEQVYPILETWKQRI 978
Query: 1011 KSEGILDHVALVYGYFPAVAEGDDVVILESPDPHAAERMRFSFPRQQRGRFLCIADFIRP 1070
+E +L H ++YGYFP +EG+ + + +S P+A E +F FPRQ+ R LCIADF P
Sbjct: 979 IAENLL-HPQVIYGYFPCQSEGNTLYVYDSNSPNAKEITQFEFPRQKSSRRLCIADFFAP 1037
Query: 1071 REQAVKDGQVDVMPFQLVTMGNPIADFANELFAANEYREYLEVHGIGVQLTEALAEYWHS 1130
++ G +DV P Q VT+G+ +FA +LFA N+Y +YL HG+ VQ+ EALAE+ H+
Sbjct: 1038 KD----SGIIDVFPMQAVTVGDIATEFAQKLFANNQYTDYLYFHGLAVQVAEALAEWTHA 1093
Query: 1131 RVRSELKLNDGGSVADFDPEDKTKFFDLDYRGARFSFGYGSCPDLEDRAKLVELLEPGRI 1190
R+R EL G A+ +P++ Y+G+R+SFGY +CP+++D+ K ++LLE RI
Sbjct: 1094 RIRREL-----GFGAE-EPDNIRDILAQRYQGSRYSFGYPACPNIQDQFKQLDLLETSRI 1147
Query: 1191 GVELSEELQLHPEQSTDAFVLYHPEAKYF 1219
+ + E QL+PEQST A + YHP AKYF
Sbjct: 1148 NLYMDESEQLYPEQSTTAIITYHPVAKYF 1176
Lambda K H
0.316 0.135 0.386
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: 3198
Number of extensions: 157
Number of successful extensions: 17
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: 1221
Length of database: 1178
Length adjustment: 47
Effective length of query: 1174
Effective length of database: 1131
Effective search space: 1327794
Effective search space used: 1327794
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 (21.6 bits)
S2: 59 (27.3 bits)
Align candidate WP_011319793.1 AVA_RS15430 (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.27660.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 1584.3 0.0 0 1584.1 0.0 1.0 1 lcl|NCBI__GCF_000204075.1:WP_011319793.1 AVA_RS15430 methionine synthase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204075.1:WP_011319793.1 AVA_RS15430 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1584.1 0.0 0 0 4 1181 .. 15 1177 .. 12 1178 .] 0.96
Alignments for each domain:
== domain 1 score: 1584.1 bits; conditional E-value: 0
TIGR02082 4 rilvlDGamGtqlqsanLteadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDivetn 70
+++v+DGamGt+lq++nLt++dF g +++G+n++L++tkPe++a++hr+++ GaD++et+
lcl|NCBI__GCF_000204075.1:WP_011319793.1 15 PVIVFDGAMGTNLQTQNLTAEDFGG------VQYEGCNEYLVHTKPEAVAKVHRDFLAVGADVIETD 75
69***********************......59********************************** PP
TIGR02082 71 tFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdverpe 137
tF++t+i+la+Ydl+d++y+lnkkaa+la+ va+ef+ tp+k+RfvaGs+GPt+kl+tl+
lcl|NCBI__GCF_000204075.1:WP_011319793.1 76 TFGATSIVLAEYDLADQTYYLNKKAAELAKSVAAEFS-TPDKPRFVAGSIGPTTKLPTLG------- 134
*************************************.**********************....... PP
TIGR02082 138 frnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivd 204
++++d+l+ a+ eq+++lldGGvDllL+et++D+l++kaal+++eevf+++g+++P+++s v+++
lcl|NCBI__GCF_000204075.1:WP_011319793.1 135 --HIDFDTLKTAFAEQAEALLDGGVDLLLVETCQDVLQIKAALNGIEEVFAKRGERIPLMVS-VTME 198
..************************************************************.**** PP
TIGR02082 205 ksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalg.. 269
++G++L+G++++a+l++le+ +i+ilGLnCa+G+d++++++k+l+e+++++vs+iPnaGLP+++g
lcl|NCBI__GCF_000204075.1:WP_011319793.1 199 SMGTMLVGSEINAVLTILEPFPIDILGLNCATGPDLMKPHIKYLAEHSPFVVSCIPNAGLPENVGgq 265
****************************************************************999 PP
TIGR02082 270 .eYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgleal 335
+Y+ltp+el +al++f+e+++++++GGCCGt+Pehi+++ae++kd+kp+ rq + e+ ++s+++++
lcl|NCBI__GCF_000204075.1:WP_011319793.1 266 aHYRLTPMELRMALMHFVEDLGVQVIGGCCGTRPEHIQQLAEIAKDLKPKVRQPSLEPAAASIYSTQ 332
9****************************************************************** PP
TIGR02082 336 kiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkk 402
+++q++sf+++GeR+n++Gskk+r+l++aed++ ++++a++qv+eGa+ilD+nvD+v++Dg++dm++
lcl|NCBI__GCF_000204075.1:WP_011319793.1 333 TYEQDNSFLIVGERLNASGSKKCRDLLNAEDWDGLVSMARSQVKEGAHILDVNVDYVGRDGVRDMHE 399
******************************************************************* PP
TIGR02082 403 llsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvv 469
l+s+++++ + ++PlmlDs+e+e++eaGLkv++Gk+++ns++++dGe rFl+ ++l+k+yGa+vv+
lcl|NCBI__GCF_000204075.1:WP_011319793.1 400 LVSRIVNN--V-TLPLMLDSTEWEKMEAGLKVAGGKCLLNSTNYEDGEPRFLKVLELAKKYGAGVVI 463
********..6.******************************************************* PP
TIGR02082 470 mafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieairei 536
++DeeG+arta+kk++ia+Ray++++e +g+pp++i+fD+++l+i+tGiee++++++++ie+i +i
lcl|NCBI__GCF_000204075.1:WP_011319793.1 464 GTIDEEGMARTAEKKFQIAQRAYRQAVE-YGIPPTEIFFDTLALPISTGIEEDRENGKATIESISRI 529
***************************9.************************************** PP
TIGR02082 537 keelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevv 603
+++lP +++ +Gvsn+sF+l +a R +l+svFL+ea aG+D++iv+a+k++++ +i++ +ev+
lcl|NCBI__GCF_000204075.1:WP_011319793.1 530 RQQLPGCHVILGVSNISFGLS--PASRMVLNSVFLHEATAAGMDAAIVSASKILPLSKIEDRHQEVC 594
*********************..******************************************** PP
TIGR02082 604 edlildrr.....reatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieed 665
+li+d+r + +++L+el++l++g+++k++k + +lp+eeRL+r++++Ger g+e++
lcl|NCBI__GCF_000204075.1:WP_011319793.1 595 RQLIYDQRqfdgdVCIYDPLTELTKLFEGVTTKRNK----GVDESLPIEERLKRHIIDGERIGLEAQ 657
*******988777789*****************666....66779********************** PP
TIGR02082 666 leearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedks 732
l +a+ ++++pleii++ LldGmkvvG+LFGsG+m+LP+v++sa++mk+avayLeP++ek+++ +++
lcl|NCBI__GCF_000204075.1:WP_011319793.1 658 LTKAL-EQYPPLEIINTFLLDGMKVVGELFGSGQMQLPFVLQSAETMKAAVAYLEPFMEKSESGNNA 723
*****.999********************************************************** PP
TIGR02082 733 kGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksld 799
kGk+++atvkGDvhDiGkn+vd++Ls+ngy+v++lG+k+Pve+i+ea++++kaD+i++sGL+vks++
lcl|NCBI__GCF_000204075.1:WP_011319793.1 724 KGKVIIATVKGDVHDIGKNLVDIILSNNGYKVINLGIKQPVENIIEAYNQHKADCIAMSGLLVKSTA 790
******************************************************************* PP
TIGR02082 800 emvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkk... 863
+m+e++e+++++g+++P++lGGaal++++v+++++++Ykg+v+y+kda+++++++dkl+++k+
lcl|NCBI__GCF_000204075.1:WP_011319793.1 791 FMKENLEVFNEKGINVPVILGGAALTPKFVHKDCQNTYKGKVIYGKDAFSDLHFMDKLMPAKATgkw 857
**************************************************************98777 PP
TIGR02082 864 ...aeelekikeeyeeirekfgekkeklialsekaarkevfaldrse....dlevpapkflGtkvle 923
+l+++++e+ e ++ + + + ++ + +++ rse d+ +p+p+f+Gt+ l+
lcl|NCBI__GCF_000204075.1:WP_011319793.1 858 dnfLGFLDEVETEETEPTNSQSPVPNSQSPVPSPQSP-VPVDTRRSEavavDIPRPTPPFWGTQLLQ 923
5553333444444444333333333333333333332.33455555567678889************ PP
TIGR02082 924 as...ieellkyiDwkalFv.qWelrgkypkilkdeleglearklfkdakelldklsaekllrargv 986
s +ee++ ++D++al qW++r+ ++ ++k+e++ +++++++++++ ++++++ae+ll+++++
lcl|NCBI__GCF_000204075.1:WP_011319793.1 924 PSdisLEEIFWHMDLQALVAgQWQFRKPKE-QSKEEYQAFLNEQVYPILETWKQRIIAENLLHPQVI 989
988899************************.9*********************************** PP
TIGR02082 987 vGlfPaqsvgddieiytdetvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgall 1053
+G+fP+qs+g+++ +y+ +p a ++++e++rq+s r+lc+aDf+a+k+sGi D++++++
lcl|NCBI__GCF_000204075.1:WP_011319793.1 990 YGYFPCQSEGNTLYVYDS------NSPNAKEITQFEFPRQKSSRRLCIADFFAPKDSGIIDVFPMQA 1050
*****************3......45677777889******************************** PP
TIGR02082 1054 vtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllker 1120
vt+g +a+e+a+kl+a+++++d++++++la+++aealae++h r+R+el ++ +ee+++++d+l +r
lcl|NCBI__GCF_000204075.1:WP_011319793.1 1051 VTVGDIATEFAQKLFANNQYTDYLYFHGLAVQVAEALAEWTHARIRRELGFG-AEEPDNIRDILAQR 1116
**************************************************99.899*********** PP
TIGR02082 1121 YrGirpafGYpacPdhtekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfa 1181
Y+G+r++fGYpacP+ +++ ++l+Lle+ ri l+++es++l+Pe+s+++++ +hp akYf+
lcl|NCBI__GCF_000204075.1:WP_011319793.1 1117 YQGSRYSFGYPACPNIQDQFKQLDLLETSRINLYMDESEQLYPEQSTTAIITYHPVAKYFT 1177
************************************************************7 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1178 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 0.04s 00:00:00.16 Elapsed: 00:00:00.14
# Mc/sec: 9.39
//
[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