Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate YP_001328535.1 Smed_2870 B12-dependent methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000017145.1:YP_001328535.1
Length = 1257
Score = 1474 bits (3815), Expect = 0.0
Identities = 761/1227 (62%), Positives = 912/1227 (74%), Gaps = 11/1227 (0%)
Query: 7 QLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAA 66
QL ERIL++DG MGT IQ E FRGERF C +GNNDLL L++P+ I
Sbjct: 23 QLAQAAAERILIMDGAMGTEIQQLGFVEDHFRGERFGACNCHQQGNNDLLTLTQPKAIEE 82
Query: 67 IHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKP 126
IH Y AGADI+ETNTF+ST IA ADY ME + ++N A+LAR A A +
Sbjct: 83 IHYHYAIAGADILETNTFSSTRIAQADYGMEDMVYDLNRDGARLARRAARRAEAEDGRR- 141
Query: 127 RYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDT 186
R+VAG LGPTNRTASISPDVN+P +R ++FD L AY E + L++GGAD+ILIET+FDT
Sbjct: 142 RFVAGALGPTNRTASISPDVNNPGYRAVSFDDLRLAYSEQVRGLIDGGADIILIETIFDT 201
Query: 187 LNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLN 246
LNAKAA+FA + F V LPIMISGTITD SGRTLSGQT AF+ S+RHA T GLN
Sbjct: 202 LNAKAAIFATQEVFAEKAVHLPIMISGTITDLSGRTLSGQTPTAFWYSVRHASPFTIGLN 261
Query: 247 CALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNI 306
CALG + +R ++ ELS IA+ V A+PNAGLPN FG+YD + MA QI +A+ G +N+
Sbjct: 262 CALGANAMRAHIDELSAIADTLVCAYPNAGLPNEFGQYDESPEQMAAQIEGFARDGLVNV 321
Query: 307 VGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVT 366
VGGCCG+TP HI A++ AV PR++PE RLSGLEP + ++ FVNVGERTNVT
Sbjct: 322 VGGCCGSTPAHIRAIAEAVAKYPPRRVPETERLMRLSGLEPFTLTDEIPFVNVGERTNVT 381
Query: 367 GSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDI 426
GSAKF++LI Y+ AL+VAR QV NGAQIID+NMDEG++D++ MV FLNL+A EPDI
Sbjct: 382 GSAKFRKLITAGDYAAALEVARDQVANGAQIIDVNMDEGLIDSKQVMVEFLNLVASEPDI 441
Query: 427 ARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFD 486
ARVP+MIDSSKW+VIE GLKC+QGK +VNSIS+KEG +AF++HA+L+R YGAAVVVMAFD
Sbjct: 442 ARVPVMIDSSKWEVIEAGLKCVQGKALVNSISLKEGEEAFLYHARLVRAYGAAVVVMAFD 501
Query: 487 EQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGAC 546
E+GQADT+ RK+EICRRAY++LTEEVGFPPEDIIFDPNIFAVATGIEEH+NY DFI A
Sbjct: 502 EKGQADTKTRKVEICRRAYRLLTEEVGFPPEDIIFDPNIFAVATGIEEHDNYGVDFIEAT 561
Query: 547 EDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYD 606
+I LPH ISGGVSN+SFSFRGN+PVREA+HAVFLY+AI+ GMDMGIVNAGQLA+YD
Sbjct: 562 HEIVAALPHVHISGGVSNLSFSFRGNEPVREAMHAVFLYHAIQAGMDMGIVNAGQLAVYD 621
Query: 607 DLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYS 666
+ AELR+A EDV+LNRR DGTERLLE+AE+YRG + + WR W V KRLE++
Sbjct: 622 AIDAELREACEDVVLNRRSDGTERLLEIAERYRG-QGGSQGREKDLAWREWPVEKRLEHA 680
Query: 667 LVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMK 726
LV GITEFIE DTEEAR A RP+ VIEGPLM GMNVVGDLFG GKMFLPQVVKSARVMK
Sbjct: 681 LVYGITEFIEADTEEARLSAERPLHVIEGPLMAGMNVVGDLFGSGKMFLPQVVKSARVMK 740
Query: 727 QAVAYLEPFIEASK------EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
QAVA L P +EA K E ++ GK+++ATVKGDVHDIGKNIVGVVL CNNYEI+DL
Sbjct: 741 QAVAVLLPHMEAEKRANGGGEARESAGKILMATVKGDVHDIGKNIVGVVLACNNYEIIDL 800
Query: 781 GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
GVMV + +IL A+E D+IGLSGLITPSLDEM +VA E+ER+GF +PLLIGGATTS+
Sbjct: 801 GVMVSSARILEVAREQKVDIIGLSGLITPSLDEMAHVASELEREGFDLPLLIGGATTSRV 860
Query: 841 HTAVKIEQNYS-GPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKP 899
HTAVKI YS G TVYV +ASR VGVV++LLS RD + R EY V H R +
Sbjct: 861 HTAVKINPRYSLGQTVYVTDASRAVGVVSSLLSPEVRDGYKETIRAEYLKVAEAHARNEA 920
Query: 900 RTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYIDWTPFFMTWSLAG 958
+ L AR N DW+A+ P V LG + + + L YIDWTPFF TW + G
Sbjct: 921 EKRRLPLSQARANAVKIDWEAHRPKVPSFLGTRVFDGWDLAELARYIDWTPFFQTWEMKG 980
Query: 959 KYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDET 1018
YPRIL+DE G A++LF+DA ML ++ AEK P+ VVG +PA VGDD+ ++ DET
Sbjct: 981 VYPRILDDEHQGAAARQLFEDAQAMLAQIVAEKWFAPKAVVGFWPAGSVGDDVRLFTDET 1040
Query: 1019 RTHVINVSHHLRQQ-TEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFE 1077
R + LRQQ ++ G N LADFVAP SGK DY GAF VT G+EE A+A+ FE
Sbjct: 1041 RKGELATLFTLRQQLVKRDGRPNVALADFVAPAESGKRDYAGAFVVTAGIEEVAIAERFE 1100
Query: 1078 AQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAP 1137
+DDY+ IMVKALADR AEAFAE +HE VRK WGYA +E + +ELI E Y GIRPAP
Sbjct: 1101 RANDDYSSIMVKALADRFAEAFAERMHEYVRKELWGYAADEAFTPQELIGEPYAGIRPAP 1160
Query: 1138 GYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQR 1197
GYPA P+HTEK T++ LL E G+KLTES+AMWPG+SVSG Y HPDS Y+ VA+I+R
Sbjct: 1161 GYPAQPDHTEKETLFRLLNAEAAIGVKLTESYAMWPGSSVSGLYIGHPDSYYFGVAKIER 1220
Query: 1198 DQVEDYARRKGMSVTEVERWLAPNLGY 1224
DQVEDYA RK MSV EVERWL+P L Y
Sbjct: 1221 DQVEDYAERKQMSVREVERWLSPVLNY 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: 3732
Number of extensions: 154
Number of successful extensions: 8
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: 1257
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1209
Effective search space: 1425411
Effective search space used: 1425411
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 YP_001328535.1 Smed_2870 (B12-dependent 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.8305.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 1734.2 0.0 0 1733.9 0.0 1.0 1 lcl|NCBI__GCF_000017145.1:YP_001328535.1 Smed_2870 B12-dependent methioni
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017145.1:YP_001328535.1 Smed_2870 B12-dependent methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1733.9 0.0 0 0 2 1182 .] 29 1215 .. 28 1215 .. 0.99
Alignments for each domain:
== domain 1 score: 1733.9 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67
+ril++DGamGt++q+ e++Frge + ++++++GnndlL+lt+P +i++ih +y aGaDi+
lcl|NCBI__GCF_000017145.1:YP_001328535.1 29 AERILIMDGAMGTEIQQLGFVEDHFRGErFGACNCHQQGNNDLLTLTQPKAIEEIHYHYAIAGADIL 95
589*************************9************************************** PP
TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134
etntF+st ia+adY++ed +y+ln+ +a+lar++a + + ++RfvaG+lGPtn++a++spdv+
lcl|NCBI__GCF_000017145.1:YP_001328535.1 96 ETNTFSSTRIAQADYGMEDMVYDLNRDGARLARRAARRAEAEDGRRRFVAGALGPTNRTASISPDVN 162
****************************************9999*********************** PP
TIGR02082 135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201
+p++r v +d+l+ aY+eqv+gl+dGG+D++Liet+fDtlnakaa+fa++evf+ek ++lPi+isg+
lcl|NCBI__GCF_000017145.1:YP_001328535.1 163 NPGYRAVSFDDLRLAYSEQVRGLIDGGADIILIETIFDTLNAKAAIFATQEVFAEKAVHLPIMISGT 229
******************************************************************* PP
TIGR02082 202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268
i+d sGrtLsGqt af s++ha +++GLnCalGa+ +r ++ els++a++lv ++PnaGLPn++
lcl|NCBI__GCF_000017145.1:YP_001328535.1 230 ITDLSGRTLSGQTPTAFWYSVRHASPFTIGLNCALGANAMRAHIDELSAIADTLVCAYPNAGLPNEF 296
******************************************************************* PP
TIGR02082 269 geYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgleal 335
g+Yd+ pe++a++++ fa++gl+n+vGGCCG+tP+hiraiaeav++ pr+++e+e ++lsgle++
lcl|NCBI__GCF_000017145.1:YP_001328535.1 297 GQYDESPEQMAAQIEGFARDGLVNVVGGCCGSTPAHIRAIAEAVAKYPPRRVPETERLMRLSGLEPF 363
******************************************************************* PP
TIGR02082 336 kiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkk 402
++++e fvn+GeRtnv+Gs+kfrkli+a+dy +al++a++qv +Gaqi+D+n+De+l D+++ m++
lcl|NCBI__GCF_000017145.1:YP_001328535.1 364 TLTDEIPFVNVGERTNVTGSAKFRKLITAGDYAAALEVARDQVANGAQIIDVNMDEGLIDSKQVMVE 430
******************************************************************* PP
TIGR02082 403 llsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvv 469
+l+l+asepdia+vP+m+Dss++ev+eaGLk++qGka+vnsislk+Gee+Fl +a+l++ yGaavvv
lcl|NCBI__GCF_000017145.1:YP_001328535.1 431 FLNLVASEPDIARVPVMIDSSKWEVIEAGLKCVQGKALVNSISLKEGEEAFLYHARLVRAYGAAVVV 497
******************************************************************* PP
TIGR02082 470 mafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieairei 536
mafDe+Gqa+t+ +k+ei++Ray+llte+vgfppediifDpni+++atGieehd+y++dfiea++ei
lcl|NCBI__GCF_000017145.1:YP_001328535.1 498 MAFDEKGQADTKTRKVEICRRAYRLLTEEVGFPPEDIIFDPNIFAVATGIEEHDNYGVDFIEATHEI 564
******************************************************************* PP
TIGR02082 537 keelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevv 603
lP+++isgGvsn+sFs+rgn++vRea+h+vFLy+ai+aG+Dmgivnag+lavyd id+elre++
lcl|NCBI__GCF_000017145.1:YP_001328535.1 565 VAALPHVHISGGVSNLSFSFRGNEPVREAMHAVFLYHAIQAGMDMGIVNAGQLAVYDAIDAELREAC 631
******************************************************************* PP
TIGR02082 604 edlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleear 670
ed++l+rr++ te+Lle+ae+y+g+ ++ + ++ +wr++pve+RLe+alv G++e+ie+d+eear
lcl|NCBI__GCF_000017145.1:YP_001328535.1 632 EDVVLNRRSDGTERLLEIAERYRGQGGSQGR-EKDLAWREWPVEKRLEHALVYGITEFIEADTEEAR 697
**************************99666.67789****************************** PP
TIGR02082 671 kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed......k 731
+++pl++iegpL++Gm+vvGdLFGsGkmfLPqvvksarvmk+ava+L P++e+ek ++ +
lcl|NCBI__GCF_000017145.1:YP_001328535.1 698 LSAERPLHVIEGPLMAGMNVVGDLFGSGKMFLPQVVKSARVMKQAVAVLLPHMEAEKRANgggearE 764
*********************************************************9999999999 PP
TIGR02082 732 skGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksl 798
s+Gki++atvkGDvhDiGkniv+vvL+cn+ye++dlGv+v ++ile+a+++k D+iglsGLi++sl
lcl|NCBI__GCF_000017145.1:YP_001328535.1 765 SAGKILMATVKGDVHDIGKNIVGVVLACNNYEIIDLGVMVSSARILEVAREQKVDIIGLSGLITPSL 831
******************************************************************* PP
TIGR02082 799 demvevaeemerrgvkiPlllGGaalskahvavkiaekYk.gevvyvkdaseavkvvdkllsekkka 864
dem++va e+er+g+++Pll+GGa++s+ h+avki+++Y+ g++vyv+das+av vv++lls + ++
lcl|NCBI__GCF_000017145.1:YP_001328535.1 832 DEMAHVASELEREGFDLPLLIGGATTSRVHTAVKINPRYSlGQTVYVTDASRAVGVVSSLLSPEVRD 898
***************************************978************************* PP
TIGR02082 865 eelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieell 930
+ e i++ey ++ e + +++ +++ l++++ar + +++d++ + ++ +p flGt+v++ ++el
lcl|NCBI__GCF_000017145.1:YP_001328535.1 899 GYKETIRAEYLKVAEAHARNEAEKRRLPLSQARANAVKIDWE-AHRPKVPSFLGTRVFDGWdLAELA 964
******************************************.9999******************** PP
TIGR02082 931 kyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgd 997
yiDw+++F +We++g yp+il+de +g+ ar+lf+da+++l +++aek +++vvG++Pa svgd
lcl|NCBI__GCF_000017145.1:YP_001328535.1 965 RYIDWTPFFQTWEMKGVYPRILDDEHQGAAARQLFEDAQAMLAQIVAEKWFAPKAVVGFWPAGSVGD 1031
******************************************************************* PP
TIGR02082 998 dieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeel 1063
d+ ++tdet++ ++at+ + ++ql + +r +++laDf+a+ esG++Dy ga++vtag+++ ++
lcl|NCBI__GCF_000017145.1:YP_001328535.1 1032 DVRLFTDETRK---GELATLFTLRQQLVKRDGRpNVALADFVAPAESGKRDYAGAFVVTAGIEEVAI 1095
*********95...55566665567777777776********************************* PP
TIGR02082 1064 akkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGY 1130
a+++e +ddy+si+vkaladr+aea+ae +he vRkelwgya++e+ ++l+ e Y Girpa+GY
lcl|NCBI__GCF_000017145.1:YP_001328535.1 1096 AERFERANDDYSSIMVKALADRFAEAFAERMHEYVRKELWGYAADEAFTPQELIGEPYAGIRPAPGY 1162
******************************************************************* PP
TIGR02082 1131 pacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
pa+Pdhtek tl++Ll+ae iG+kltes+a++P +svsgly+ hp++ Yf v
lcl|NCBI__GCF_000017145.1:YP_001328535.1 1163 PAQPDHTEKETLFRLLNAEAaIGVKLTESYAMWPGSSVSGLYIGHPDSYYFGV 1215
***************************************************76 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1257 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: 13.57
//
[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