Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_027456941.1 K420_RS0104145 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000519045.1:WP_027456941.1
Length = 1219
Score = 1473 bits (3813), Expect = 0.0
Identities = 767/1226 (62%), Positives = 926/1226 (75%), Gaps = 18/1226 (1%)
Query: 4 KVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEV 63
+ +L++ L +R+LVLDG MGTMIQ + L EAD+RG RFAD P DLKGNNDLLVL++P++
Sbjct: 5 RTSELQSLLQQRLLVLDGAMGTMIQRHGLQEADYRGARFADHPHDLKGNNDLLVLTRPDI 64
Query: 64 IAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTP 123
I IH AY EAGADI+ET TFNST ++ ADY++E++ E+N A LAR DE+TA P
Sbjct: 65 IGGIHRAYLEAGADILETCTFNSTAVSQADYKLEAIVYELNKEGAALARRLCDEFTAANP 124
Query: 124 EKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETV 183
+KPR+VAGVLGPT+RTASISPDVNDP +RN+TFD LVA Y E+T LVEGGAD++L+ETV
Sbjct: 125 DKPRFVAGVLGPTSRTASISPDVNDPGYRNVTFDELVANYFEATTGLVEGGADILLVETV 184
Query: 184 FDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTF 243
FDTLNAKAA+FA++ F+ G P+MISGTITDASGRTLSGQT EAF+NSLRH + ++F
Sbjct: 185 FDTLNAKAALFAIEQFFDVAGRRWPVMISGTITDASGRTLSGQTAEAFWNSLRHIQPISF 244
Query: 244 GLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGF 303
GLNCALG ELRQYV+ELSR+ +CYV+AHPNAGLPNAFG YD AD +A +I WA+AG
Sbjct: 245 GLNCALGAKELRQYVEELSRVCDCYVSAHPNAGLPNAFGGYDETADMLADEIESWAKAGI 304
Query: 304 LNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERT 363
+NIVGGCCGT+P+HIAA++R V + PRK P+I A RLSGLEP N G+DSLFVNVGERT
Sbjct: 305 VNIVGGCCGTSPEHIAAIARRVAAVHPRKTPKIEPALRLSGLEPFNCGKDSLFVNVGERT 364
Query: 364 NVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGE 423
NVTGS F R+I E ++ +AL VARQQVENGAQ+IDINMDE MLD+ AAM +FL LIA E
Sbjct: 365 NVTGSRAFARMILEGRFDDALAVARQQVENGAQVIDINMDEAMLDSIAAMDKFLKLIASE 424
Query: 424 PDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVM 483
PDI+RVPIMIDSSKW+VIE GLKCIQGKGIVNSISMKEG F+ AKL RRYGAAV+VM
Sbjct: 425 PDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISMKEGEAKFLEQAKLARRYGAAVIVM 484
Query: 484 AFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFI 543
AFDE+GQADT ARKIEIC +AY++LT +GFP EDIIFDPNIFA+ATGI EH+NYA DFI
Sbjct: 485 AFDEKGQADTYARKIEICGKAYELLT-GMGFPAEDIIFDPNIFAIATGIPEHDNYAVDFI 543
Query: 544 GACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLA 603
+ IK+ LPHA ISGGVSNVSFSFRGNDPVREAIH VFLY+AI+NGM MGIVNAG L
Sbjct: 544 ESVRWIKQNLPHAHISGGVSNVSFSFRGNDPVREAIHTVFLYHAIQNGMTMGIVNAGMLG 603
Query: 604 IYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRL 663
+YDDL ELR VEDV+LNR E L++ A+ + K+ D + WR V KRL
Sbjct: 604 VYDDLEPELRAKVEDVVLNRHPGAGEALVDFAQTVKEGKSKD--SGPDLSWREQSVEKRL 661
Query: 664 EYSLVKGITEFIEQDTEEAR----QQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVV 719
E++L+KGIT+F+ DTEE R + P+ VIEGPLM GMN VGDLFG GKMFLPQVV
Sbjct: 662 EHALIKGITDFVVADTEEVRAKLEAEGKPPLAVIEGPLMAGMNHVGDLFGAGKMFLPQVV 721
Query: 720 KSARVMKQAVAYLEPFIEASKEQG--KTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEI 777
KSARVMKQAVA+L PFIEA K + + GK+++ATVKGDVHDIGKNIVGVVL CN Y++
Sbjct: 722 KSARVMKQAVAHLLPFIEAEKSRTGLGSKGKILMATVKGDVHDIGKNIVGVVLGCNGYDV 781
Query: 778 VDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATT 837
VDLGVMV + IL+ A E D+IGLSGLITPSL+EM +VA EM+R G PLLIGGATT
Sbjct: 782 VDLGVMVSCDNILKAALEHRVDIIGLSGLITPSLEEMAHVAAEMKRHGMKQPLLIGGATT 841
Query: 838 SKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRK 897
S+AHTA+KI N GP VYV +ASR VGV LLS QRD + A EYETVR +H +
Sbjct: 842 SRAHTAIKIAPNAEGPVVYVPDASRAVGVATKLLSIDQRDAYHAEIAAEYETVRAEHAGR 901
Query: 898 KPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEASIETLRNYIDWTPFFMTWSLA 957
K T V+L+ AR N F ++ + YTP +LG QE+ + L YIDW+PFF +W LA
Sbjct: 902 KGAT-LVSLDDARANRFTWN-ETYTPVKPAQLGRQEITIPLADLVPYIDWSPFFQSWDLA 959
Query: 958 GKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDE 1017
G+YP IL++E VG A++LF DA ML ++ +E L + V GL+ A +DI +Y DE
Sbjct: 960 GRYPAILQNETVGETARQLFHDAQAMLARIVSENWLTAKAVFGLYAAKGENEDIVLYTDE 1019
Query: 1018 TRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAF 1076
+R+ LRQQ ++ G N LADFV G+ DY GAFAVT GL D F
Sbjct: 1020 SRSQEATRWVGLRQQIKQPQGRFNTALADFV-----GEQDYAGAFAVTAGLGIDEHVARF 1074
Query: 1077 EAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPA 1136
EA HDDY+ IM+KALADRLAEA AE+LH +VR +WGYA E L N+ LI E Y+GIRPA
Sbjct: 1075 EAAHDDYSAIMLKALADRLAEAAAEWLHMKVRTEFWGYAAGEKLDNDGLIAEQYKGIRPA 1134
Query: 1137 PGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQ 1196
PGYPACP+HT K +++LL+ GM LTES AM P A+VSG+Y HP S Y+A+ +I
Sbjct: 1135 PGYPACPDHTAKRELFKLLDAPA-IGMGLTESCAMTPAAAVSGFYIGHPASSYFAIPKIG 1193
Query: 1197 RDQVEDYARRKGMSVTEVERWLAPNL 1222
RDQ+ED+A RKGM++ E ERWLAP L
Sbjct: 1194 RDQLEDWAARKGMALKEAERWLAPLL 1219
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: 3610
Number of extensions: 161
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: 1219
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1172
Effective search space: 1382960
Effective search space used: 1382960
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_027456941.1 K420_RS0104145 (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.30459.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 1694.3 0.0 0 1694.1 0.0 1.0 1 lcl|NCBI__GCF_000519045.1:WP_027456941.1 K420_RS0104145 methionine syntha
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000519045.1:WP_027456941.1 K420_RS0104145 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1694.1 0.0 0 0 1 1182 [] 13 1189 .. 13 1189 .. 0.98
Alignments for each domain:
== domain 1 score: 1694.1 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDi 66
l++r+lvlDGamGt++q++ L+ead+rg+ +ad++ +lkGnndlL+lt+P++i ihray+eaGaDi
lcl|NCBI__GCF_000519045.1:WP_027456941.1 13 LQQRLLVLDGAMGTMIQRHGLQEADYRGArFADHPHDLKGNNDLLVLTRPDIIGGIHRAYLEAGADI 79
689**************************************************************** PP
TIGR02082 67 vetntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspd 132
+et tFnst +++adY+le+ +yelnk++a+lar+ +deft +p+k+RfvaG+lGPt+++a++spd
lcl|NCBI__GCF_000519045.1:WP_027456941.1 80 LETCTFNSTAVSQADYKLEAIVYELNKEGAALARRLCDEFTaANPDKPRFVAGVLGPTSRTASISPD 146
*****************************************9************************* PP
TIGR02082 133 verpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilis 199
v++p++rnvt+delv+ Y e+++gl++GG+D+lL+etvfDtlnakaalfa+e+ f+ +gr+ P++is
lcl|NCBI__GCF_000519045.1:WP_027456941.1 147 VNDPGYRNVTFDELVANYFEATTGLVEGGADILLVETVFDTLNAKAALFAIEQFFDVAGRRWPVMIS 213
******************************************************************* PP
TIGR02082 200 gvivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPn 266
g+i+d+sGrtLsGqt eaf +sl+h + +++GLnCalGa+elr++v+els+ +++vs++PnaGLPn
lcl|NCBI__GCF_000519045.1:WP_027456941.1 214 GTITDASGRTLSGQTAEAFWNSLRHIQPISFGLNCALGAKELRQYVEELSRVCDCYVSAHPNAGLPN 280
******************************************************************* PP
TIGR02082 267 algeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgle 333
a+g Yd+t+++la +++++a++g +nivGGCCGt Pehi+aia+ v+ ++prk++++e++++lsgle
lcl|NCBI__GCF_000519045.1:WP_027456941.1 281 AFGGYDETADMLADEIESWAKAGIVNIVGGCCGTSPEHIAAIARRVAAVHPRKTPKIEPALRLSGLE 347
******************************************************************* PP
TIGR02082 334 alkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadm 400
+++ +++s fvn+GeRtnv+Gs+ f+++i ++ +++al +a+qqve+Gaq++Din+De++lD+ a+m
lcl|NCBI__GCF_000519045.1:WP_027456941.1 348 PFNCGKDSLFVNVGERTNVTGSRAFARMILEGRFDDALAVARQQVENGAQVIDINMDEAMLDSIAAM 414
******************************************************************* PP
TIGR02082 401 kkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaav 467
k+l+l+asepdi++vP+m+Dss++ev+eaGLk+iqGk+ivnsis+k+Ge++Fle+akl+++yGaav
lcl|NCBI__GCF_000519045.1:WP_027456941.1 415 DKFLKLIASEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISMKEGEAKFLEQAKLARRYGAAV 481
******************************************************************* PP
TIGR02082 468 vvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieair 534
+vmafDe+Gqa+t+++kiei+ +ay+llt +gfp+ediifDpni++iatGi ehd+ya+dfie++r
lcl|NCBI__GCF_000519045.1:WP_027456941.1 482 IVMAFDEKGQADTYARKIEICGKAYELLTG-MGFPAEDIIFDPNIFAIATGIPEHDNYAVDFIESVR 547
*****************************9.************************************ PP
TIGR02082 535 eikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelre 601
+ik++lP+a+isgGvsnvsFs+rgnd+vRea+h+vFLy+ai++G+ mgivnag+l vydd+++elr
lcl|NCBI__GCF_000519045.1:WP_027456941.1 548 WIKQNLPHAHISGGVSNVSFSFRGNDPVREAIHTVFLYHAIQNGMTMGIVNAGMLGVYDDLEPELRA 614
******************************************************************* PP
TIGR02082 602 vvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedlee 668
+ved++l+r++ a e L+++a++ k+ k+k+s wr+++ve+RLe+al+kG+++++ +d+ee
lcl|NCBI__GCF_000519045.1:WP_027456941.1 615 KVEDVVLNRHPGAGEALVDFAQTVKEGKSKDS--GPDLSWREQSVEKRLEHALIKGITDFVVADTEE 679
***********************999888844..57789**************************** PP
TIGR02082 669 ar....kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed. 730
r + k+pl++iegpL++Gm+ vGdLFG+GkmfLPqvvksarvmk+ava+L P++e+ek+ +
lcl|NCBI__GCF_000519045.1:WP_027456941.1 680 VRakleAEGKPPLAVIEGPLMAGMNHVGDLFGAGKMFLPQVVKSARVMKQAVAHLLPFIEAEKSRTg 746
99544445678****************************************************9998 PP
TIGR02082 731 .kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivk 796
skGki++atvkGDvhDiGkniv+vvL+cngy+vvdlGv+v +++il+aa +++ D+iglsGLi++
lcl|NCBI__GCF_000519045.1:WP_027456941.1 747 lGSKGKILMATVKGDVHDIGKNIVGVVLGCNGYDVVDLGVMVSCDNILKAALEHRVDIIGLSGLITP 813
889**************************************************************** PP
TIGR02082 797 sldemvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkk 863
sl+em++va em+r+g+k Pll+GGa++s+ah+a kia++ +g+vvyv das+av v+ klls +++
lcl|NCBI__GCF_000519045.1:WP_027456941.1 814 SLEEMAHVAAEMKRHGMKQPLLIGGATTSRAHTAIKIAPNAEGPVVYVPDASRAVGVATKLLSIDQR 880
******************************************************************* PP
TIGR02082 864 aeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleasieell 930
+++ ++i +eye++r ++ ++ + +s+++ar ++f ++e +++++p +lG++++ +++l+
lcl|NCBI__GCF_000519045.1:WP_027456941.1 881 DAYHAEIAAEYETVRAEHAG-RKGATLVSLDDARANRF--TWNETYTPVKPAQLGRQEITIPLADLV 944
******************98.6678899******8876..57888********************** PP
TIGR02082 931 kyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgd 997
+yiDw ++F +W+l+g+yp il++e++g+ ar+lf+da+++l ++++e+ l+a++v+Gl+ a+ +++
lcl|NCBI__GCF_000519045.1:WP_027456941.1 945 PYIDWSPFFQSWDLAGRYPAILQNETVGETARQLFHDAQAMLARIVSENWLTAKAVFGLYAAKGENE 1011
******************************************************************* PP
TIGR02082 998 dieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeel 1063
di++ytde++sqe++ + ++q++q ++r +++laDf+ G++Dy ga++vtaglg++e
lcl|NCBI__GCF_000519045.1:WP_027456941.1 1012 DIVLYTDESRSQEATRWVGL---RQQIKQPQGRfNTALADFV-----GEQDYAGAFAVTAGLGIDEH 1070
**********9988877766...5899999999899*****9.....569***************** PP
TIGR02082 1064 akkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGY 1130
++ea +ddy++i++kaladrlaea ae+lh +vR e+wgya+ e+ld++ l+ e+Y+Girpa+GY
lcl|NCBI__GCF_000519045.1:WP_027456941.1 1071 VARFEAAHDDYSAIMLKALADRLAEAAAEWLHMKVRTEFWGYAAGEKLDNDGLIAEQYKGIRPAPGY 1137
******************************************************************* PP
TIGR02082 1131 pacPdhtekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfav 1182
pacPdht k++l++Ll+a iG+ ltes+a++P+a+vsg+y+ hp++ Yfa+
lcl|NCBI__GCF_000519045.1:WP_027456941.1 1138 PACPDHTAKRELFKLLDAPAIGMGLTESCAMTPAAAVSGFYIGHPASSYFAI 1189
**************************************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1219 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: 0.10u 0.05s 00:00:00.15 Elapsed: 00:00:00.15
# Mc/sec: 9.47
//
[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