Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate Synpcc7942_1372 Synpcc7942_1372 methionine synthase (B12-dependent)
Query= metacyc::G18NG-11090-MONOMER
(1221 letters)
>FitnessBrowser__SynE:Synpcc7942_1372
Length = 1190
Score = 998 bits (2580), Expect = 0.0
Identities = 561/1223 (45%), Positives = 765/1223 (62%), Gaps = 54/1223 (4%)
Query: 16 SEFLDALANH---VLIGDGAMGTQLQGFDLDVEKDF--LDLEGCNEILNDTRPDVLRQIH 70
S FLD L + VL+ DG MGT LQ +L E DF + EGCNE L T+P+ + +H
Sbjct: 3 SLFLDRLHSPERPVLVFDGGMGTTLQFQNLTAE-DFGGPETEGCNEWLIRTKPEAIATVH 61
Query: 71 RAYFEAGADLVETNTFGCNLPNLADYDIADRCRELAYKGTAVAREVADEMGPGRNGMRRF 130
R + EAGAD++ET+TFG LA+Y + D L + +A+ +A E RF
Sbjct: 62 RQFLEAGADVIETDTFGATSIVLAEYGLEDHAYALNVEAAKLAKAIAAEFSTPEKP--RF 119
Query: 131 VVGSLGPGTKLPSLGHAPYADLRGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQ 190
V GS+GP TKLP+LGH Y +++ + E A G+ +GG D F++ET QD+LQ+KAA++G+
Sbjct: 120 VAGSMGPTTKLPTLGHIGYDEMKASFAEQARGLWEGGVDLFIVETCQDVLQIKAALNGIA 179
Query: 191 DAMAELDTFLPIICHVTVETTGTMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHL 250
+ +E P++ VT+ETTGTML+GS++ A L L+P ID++GLNCATGPD M EH+
Sbjct: 180 EIFSEKGDRRPLMVSVTMETTGTMLVGSDVAAMLAILEPYPIDILGLNCATGPDRMVEHI 239
Query: 251 RYLSKHADIPVSVMPNAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTP 310
+YLS+H+ +S +PNAG+P A Y L +L AL FV + G+ ++GGCCGT P
Sbjct: 240 KYLSEHSPFVISCIPNAGIPENVGGHAHYRLTPMELRMALHRFVEDLGVQVIGGCCGTKP 299
Query: 311 EHIRAVRDAVVGVPEQETSTLTKIPAGPVEQASREVEKE-----DSVASLYTSVPLSQET 365
EHI + E +T + PV + +++ S AS+Y + P Q+
Sbjct: 300 EHIAQL---------AEVATQLQAKDRPVRRDRDHQQRQPFNYVPSAASIYGTTPYIQDN 350
Query: 366 GISMIGERTNSNGSKAFREAMLSGDWEKCVDIAKQQTRDGAHMLDLCVDYVGRDGTADMA 425
+IGER N++GSK RE + DW+ V IA+ Q ++GAH+LD+ VDYVGRDG DM
Sbjct: 351 SFLIIGERLNASGSKKVRELLNEEDWDGLVAIARSQVKEGAHVLDVNVDYVGRDGERDMG 410
Query: 426 TLAALLATSSTLPIMIDSTEPEVIRTGLEHLGGRSIVNSVNFEDGDGPESRYQRIMKLVK 485
L + L T+ LP+M+DSTE + + GL+ GG+ I+NS N+EDGD R+ ++++L K
Sbjct: 411 ELVSRLVTNVNLPLMLDSTEWQKMEAGLKKAGGKCILNSTNYEDGD---ERFFKVLELAK 467
Query: 486 QHGAAVVALTIDEEGQARTAEHKVRIAKRLIDDITGSYGLDIKDIVVDCLTFPISTGQEE 545
Q+GA +V TIDEEG ARTAE K IA+R D +G+ +I D L PISTG EE
Sbjct: 468 QYGAGIVVGTIDEEGMARTAEKKFAIAQRAYRDAL-EFGIPAHEIFYDPLALPISTGIEE 526
Query: 546 TRRDGIETIEAIRELKKLYPEIHTTLGLSNISFGLNPAARQVLNSVFLNECIEAGLDSAI 605
R +G ETIE+IR +++ P +H LG+SNISFGLNPAAR VLNSVFL++ EAG+D AI
Sbjct: 527 DRGNGRETIESIRLIRENLPGVHILLGVSNISFGLNPAARIVLNSVFLHDACEAGMDGAI 586
Query: 606 AHSSKILPMNRIDDRQREVALDMVYDRRTED-----YDPLQEFMQLFEGVSAADAKDARA 660
++KILP+++ID++ +V D++ DRR + YDPL E LFEGVSA +A+ A
Sbjct: 587 VSAAKILPLSKIDEKPLQVCRDLIGDRRRFENGICVYDPLTELTTLFEGVSAKEAR-ASG 645
Query: 661 EQLAAMPLFERLAQRIIDGDKNGLEDDLEAGMKEKSPIAIINEDLLNGMKTVGELFGSGQ 720
LA +PL ERL Q IIDG++ GL+ L +++ P+ IIN LL+GMK VG+LFGSGQ
Sbjct: 646 PSLADLPLEERLKQHIIDGERIGLDQALATALEQYPPLEIINTFLLDGMKVVGDLFGSGQ 705
Query: 721 MQLPFVLQSAETMKTAVAYLEPFMEEEAEATGSAQAEGKGKIVVATVKGDVHDIGKNLVD 780
MQLPFVLQSAETMK+AVAYLEPFM++E GKG ++ATVKGDVHDIGKNLVD
Sbjct: 706 MQLPFVLQSAETMKSAVAYLEPFMDKE-----ETNDSGKGTFLIATVKGDVHDIGKNLVD 760
Query: 781 IILSNNGYDVVNLGIKQPLSAMLEAAEEHKADVIGMSGLLVKSTVVMKENLEEMNNAGAS 840
IIL+NNGY VVN+GIKQP+ +++A + AD I MSGLLVKST MKENL N G S
Sbjct: 761 IILTNNGYKVVNIGIKQPVENIIQAYRDCNADCIAMSGLLVKSTAFMKENLATFNEEGIS 820
Query: 841 NYPVILGGAALTRTYVENDLNEVYTGEVYYARDAFEGLRLMDEVMAEKRGEGLDPNSPEA 900
PVILGGAALT +V D + Y G+V Y +DAF L MD++MA K + D
Sbjct: 821 -VPVILGGAALTPKFVYEDCQQTYKGQVIYGKDAFADLHFMDQLMAAKSKDQWDDQLGFL 879
Query: 901 IEQAKKKAERKARNERSRKIAAERKANAAPVIVPERSD-VSTDTPTAAPPFWGTRIV--K 957
EQ + +E + R++ A VI ERS+ V+ D PPFWG++I+
Sbjct: 880 DEQGQPLQVAAIASEAAEP-TESRESVAEVVIDLERSEAVAVDIDRPTPPFWGSKILGPD 938
Query: 958 GLPLAEFLGNLDERALFMGQWGLKSTRGNEGPSYEDLVETEGRPRLRYWLDRLKSEGILD 1017
+P AE LD +ALF+GQW + + Y+ + + P L+ W R+ +E +L+
Sbjct: 939 EIPFAEVFSYLDRQALFVGQWQFRKPKEQSREEYDAFIAEKVEPILQQWTTRILAEDLLE 998
Query: 1018 HVALVYGYFPAVAEGDDVVILESPDPHAAERMRFSFPRQQRGRFLCIADFIRPREQAVKD 1077
+VYGYFP VA G+ + + + P+ RF FPRQ+ R LCIADF P E ++
Sbjct: 999 -PQVVYGYFPCVAVGNSLQLFD-PNDRDRPTARFDFPRQRSLRRLCIADFFAPEELGIQ- 1055
Query: 1078 GQVDVMPFQLVTMGNPIADFANELFAANEYREYLEVHGIGVQLTEALAEYWHSRVRSELK 1137
DV P Q VT+G+ +FA +LFA ++Y +YL HG+ VQL EALAE+ H+R+R EL
Sbjct: 1056 ---DVFPMQAVTVGHKATEFAAQLFAGDQYSDYLYFHGLAVQLAEALAEWTHARIRREL- 1111
Query: 1138 LNDGGSVADFDPEDKTKFFDLDYRGARFSFGYGSCPDLEDRAKLVELLEPGRIGVELSEE 1197
+PE Y+G+R+SFGY +CP++ D +ELLE RIG+ + E
Sbjct: 1112 -----GYGSLEPESLRDILAQRYQGSRYSFGYPACPNVADSRIQLELLEADRIGMSMDES 1166
Query: 1198 LQLHPEQSTDAFVLYHPEAKYFN 1220
QL+PEQST A V YHP AKYF+
Sbjct: 1167 EQLYPEQSTTAIVAYHPAAKYFS 1189
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: 3401
Number of extensions: 173
Number of successful extensions: 16
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: 1190
Length adjustment: 47
Effective length of query: 1174
Effective length of database: 1143
Effective search space: 1341882
Effective search space used: 1341882
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 Synpcc7942_1372 Synpcc7942_1372 (methionine synthase (B12-dependent))
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.4435.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 1521.6 0.0 0 1521.4 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_1372 Synpcc7942_1372 methionine synth
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1372 Synpcc7942_1372 methionine synthase (B12-dependent)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1521.4 0.0 0 0 2 1181 .. 13 1189 .. 12 1190 .] 0.97
Alignments for each domain:
== domain 1 score: 1521.4 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDive 68
++++lv+DG+mGt+lq +nLt++dF g e +G+n+ L tkPe+ia++hr+++eaGaD++e
lcl|FitnessBrowser__SynE:Synpcc7942_1372 13 ERPVLVFDGGMGTTLQFQNLTAEDFGGP------ETEGCNEWLIRTKPEAIATVHRQFLEAGADVIE 73
689************************5......99******************************* PP
TIGR02082 69 tntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdver 135
t+tF++t+i+la+Y+led+ay+ln +aakla+++a+ef+ tpek+RfvaGs+GPt+kl+tl+
lcl|FitnessBrowser__SynE:Synpcc7942_1372 74 TDTFGATSIVLAEYGLEDHAYALNVEAAKLAKAIAAEFS-TPEKPRFVAGSMGPTTKLPTLG----- 134
***************************************.**********************..... PP
TIGR02082 136 pefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvi 202
++ yde+++++ eq++gl +GGvDl+++et++D+l++kaal+++ e+f+ekg+++P+++s v+
lcl|FitnessBrowser__SynE:Synpcc7942_1372 135 ----HIGYDEMKASFAEQARGLWEGGVDLFIVETCQDVLQIKAALNGIAEIFSEKGDRRPLMVS-VT 196
....************************************************************.** PP
TIGR02082 203 vdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalg 269
++++G++L+G++++a+la+le+++i+ilGLnCa+G+d + e++k+lse++++++s+iPnaG+P+++g
lcl|FitnessBrowser__SynE:Synpcc7942_1372 197 METTGTMLVGSDVAAMLAILEPYPIDILGLNCATGPDRMVEHIKYLSEHSPFVISCIPNAGIPENVG 263
******************************************************************9 PP
TIGR02082 270 ...eYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqe........... 322
+Y+ltp+el +al+ f+e+++++++GGCCGt+Pehi+++ae++ +++ ++r+
lcl|FitnessBrowser__SynE:Synpcc7942_1372 264 ghaHYRLTPMELRMALHRFVEDLGVQVIGGCCGTKPEHIAQLAEVATQLQAKDRPVrrdrdhqqrqp 330
999*********************************************9987665433444444455 PP
TIGR02082 323 .leeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDin 388
+ +s++s++ + ++ q++sf++iGeR+n++Gskk+r+l+++ed++ ++ ia++qv+eGa++lD+n
lcl|FitnessBrowser__SynE:Synpcc7942_1372 331 fNYVPSAASIYGTTPYIQDNSFLIIGERLNASGSKKVRELLNEEDWDGLVAIARSQVKEGAHVLDVN 397
567899************************************************************* PP
TIGR02082 389 vDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFle 455
vD+v++Dge+dm +l+s+l+++ + ++PlmlDs+e++++eaGLk+++Gk+i+ns++++dG+erF++
lcl|FitnessBrowser__SynE:Synpcc7942_1372 398 VDYVGRDGERDMGELVSRLVTN--V-NLPLMLDSTEWQKMEAGLKKAGGKCILNSTNYEDGDERFFK 461
**********************..6.99*************************************** PP
TIGR02082 456 kaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieeh 522
++l+k+yGa++vv ++DeeG+arta+kk+ ia+Ray+++ e +g+p+++i++Dp++l+i+tGiee+
lcl|FitnessBrowser__SynE:Synpcc7942_1372 462 VLELAKQYGAGIVVGTIDEEGMARTAEKKFAIAQRAYRDALE-FGIPAHEIFYDPLALPISTGIEED 527
*****************************************9.************************ PP
TIGR02082 523 dryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagkl 589
+ ++ ++ie+ir i+e+lP ++i++Gvsn+sF+l+ +a+R +l+svFL++a +aG+D +iv+a+k+
lcl|FitnessBrowser__SynE:Synpcc7942_1372 528 RGNGRETIESIRLIRENLPGVHILLGVSNISFGLN--PAARIVLNSVFLHDACEAGMDGAIVSAAKI 592
***********************************..****************************** PP
TIGR02082 590 avyddidkelrevvedlildrr.....reatekLlelaelykgtkeksskeaqeaewrnlpveeRLe 651
+++ +id+ ++v+ dli drr + +++L+el++l++g+++k ++ a +++lp+eeRL+
lcl|FitnessBrowser__SynE:Synpcc7942_1372 593 LPLSKIDEKPLQVCRDLIGDRRrfengICVYDPLTELTTLFEGVSAK-EARASGPSLADLPLEERLK 658
**********************77776789*****************.55588899*********** PP
TIGR02082 652 ralvkGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavay 718
+++++Ger g++++l a+ ++++pleii++ LldGmkvvGdLFGsG+m+LP+v++sa++mk avay
lcl|FitnessBrowser__SynE:Synpcc7942_1372 659 QHIIDGERIGLDQALATAL-EQYPPLEIINTFLLDGMKVVGDLFGSGQMQLPFVLQSAETMKSAVAY 724
*******************.999******************************************** PP
TIGR02082 719 LePylekekeedkskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkka 785
LeP+++ke+++d+ kG++++atvkGDvhDiGkn+vd++L++ngy+vv++G+k+Pve+i++a+++ +a
lcl|FitnessBrowser__SynE:Synpcc7942_1372 725 LEPFMDKEETNDSGKGTFLIATVKGDVHDIGKNLVDIILTNNGYKVVNIGIKQPVENIIQAYRDCNA 791
******************************************************************* PP
TIGR02082 786 DviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavk 852
D+i++sGL+vks+++m+e++ ++++g+++P++lGGaal++++v +++++Ykg+v+y+kda+++++
lcl|FitnessBrowser__SynE:Synpcc7942_1372 792 DCIAMSGLLVKSTAFMKENLATFNEEGISVPVILGGAALTPKFVYEDCQQTYKGQVIYGKDAFADLH 858
******************************************************************* PP
TIGR02082 853 vvdkllsekkk...aeelekikeeyeeirekfgekkeklialsekaarkevfaldrse....dlevp 912
++d+l+ +k+k +++l+ + e+ + ++ + ++ + s+++ + v++l+rse d+++p
lcl|FitnessBrowser__SynE:Synpcc7942_1372 859 FMDQLMAAKSKdqwDDQLGFLDEQGQPLQVAAIASEAAEPTESRESVAEVVIDLERSEavavDIDRP 925
*********99555556667788888899999999999999999999999********99999**** PP
TIGR02082 913 apkflGtkvleas...ieellkyiDwkalFv.qWelrgkypkilkdeleglearklfkdakelldkl 975
+p+f+G+k+l +e+++y+D +alFv qW++r+ ++ ++++e+ + a+k+ ++++++ ++
lcl|FitnessBrowser__SynE:Synpcc7942_1372 926 TPPFWGSKILGPDeipFAEVFSYLDRQALFVgQWQFRKPKE-QSREEYDAFIAEKVEPILQQWTTRI 991
**********7555579************************.9************************ PP
TIGR02082 976 saekllrargvvGlfPaqsvgddieiytdetvsqetkpiatvrekleqlrqqsdrylclaDfiaske 1042
ae+ll++++v+G+fP+ vg+ +++++++ + + ++ ++++++rq s r+lc+aDf+a+ e
lcl|FitnessBrowser__SynE:Synpcc7942_1372 992 LAEDLLEPQVVYGYFPCVAVGNSLQLFDPNDR------DRPT-ARFDFPRQRSLRRLCIADFFAPEE 1051
****************************8777......2222.4689******************** PP
TIGR02082 1043 sGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeee 1109
Gi+D++++++vt+g +a+e+a +l+a +++ d++++++la++laealae++h r+R+el y++ e
lcl|FitnessBrowser__SynE:Synpcc7942_1372 1052 LGIQDVFPMQAVTVGHKATEFAAQLFAGDQYSDYLYFHGLAVQLAEALAEWTHARIRRELG-YGSLE 1117
***********************************************************96.669** PP
TIGR02082 1110 nldkedllkerYrGirpafGYpacPdhtekatlleLleaeriGlklteslalaPeasvsglyfahpe 1176
+++ +d+l +rY+G+r++fGYpacP++ + + +leLlea+riG+ ++es++l+Pe+s+++++ +hp+
lcl|FitnessBrowser__SynE:Synpcc7942_1372 1118 PESLRDILAQRYQGSRYSFGYPACPNVADSRIQLELLEADRIGMSMDESEQLYPEQSTTAIVAYHPA 1184
******************************************************************* PP
TIGR02082 1177 akYfa 1181
akYf+
lcl|FitnessBrowser__SynE:Synpcc7942_1372 1185 AKYFS 1189
****8 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1190 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: 0.13u 0.03s 00:00:00.16 Elapsed: 00:00:00.15
# Mc/sec: 9.08
//
[ok]
This GapMind analysis is from Apr 09 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