Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_013450377.1 CALNI_RS01215 methionine synthase
Query= metacyc::G18NG-11090-MONOMER
(1221 letters)
>NCBI__GCF_000183405.1:WP_013450377.1
Length = 1126
Score = 874 bits (2258), Expect = 0.0
Identities = 502/1209 (41%), Positives = 720/1209 (59%), Gaps = 89/1209 (7%)
Query: 17 EFLDALANHVLIGDGAMGTQLQGFDLDVEKDFLDLEGCNEILNDTRPDVLRQIHRAYFEA 76
+F+ + V++ DGAMGT +Q + + + + GCNE LN P ++ +IH + EA
Sbjct: 3 DFVKFAKDRVILFDGAMGTNIQKYSIS-DATWQGKNGCNEYLNIVAPHIIEEIHGNFLEA 61
Query: 77 GADLVETNTFGCNLPNLADYDIADRCRELAYKGTAVAREVADEMGPGRNGMRRFVVGSLG 136
GAD++ETN+FG L++Y + D E+ + +AR VAD+ G RFV GS+G
Sbjct: 62 GADVLETNSFGGTRLVLSEYGLEDAVYEINLQAARIARRVADKYG-------RFVAGSVG 114
Query: 137 PGTKLPSLGHAPYADLRGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQDAMAEL 196
PGTKL SLGH Y DL YKE +L +IDGG D F+IET QD+LQ+KAA++G++ M E
Sbjct: 115 PGTKLVSLGHISYDDLFYMYKEQSLALIDGGVDLFIIETCQDMLQIKAAINGIRSGMEEK 174
Query: 197 DTFLPIICHVTVETTGTMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHLRYLSKH 256
LPI+ VTVE GTML GS++ A + I +G+NCA GPD M E L LS
Sbjct: 175 KVNLPIMVSVTVEINGTMLTGSDLSAVAVTMAGYPIYSLGINCALGPDLMYEPLTTLSNS 234
Query: 257 ADIPVSVMPNAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTPEHIRAV 316
+S +PNAGLP+ Y +E + +A+ + ++ + +S+VGGCCGT+ EHIR +
Sbjct: 235 WGGRISCIPNAGLPMNINGKFVYNMEPDRMAEIIDDILNHFPISIVGGCCGTSYEHIREM 294
Query: 317 RDAVVGVPEQETSTLTKIPAGPVEQASREVEKEDSVASLYTSVPLSQETGISMIGERTNS 376
R + K+P PV + + AS+YT+ L+QE ++IGER N+
Sbjct: 295 R---------KVCDKHKVP-DPV-----RFQVKGMAASIYTATSLNQEPPPALIGERANA 339
Query: 377 NGSKAFREAMLSGDWEKCVDIAKQQTRDGAHMLDLCVDYVGRDGTADMATLAALLATSST 436
NGSKAFRE ++ D++ + I K Q + AH +D+CV Y GRD DMA +++ S
Sbjct: 340 NGSKAFRELLIKEDFDGMLKIVKDQEEEAAHFVDICVAYAGRDEKRDMARFISMVNRMSL 399
Query: 437 LPIMIDSTEPEVIRTGLEHLGGRSIVNSVNFEDGDGPESRYQRIMKLVKQHGAAVVALTI 496
LP +ID+TEP+V+ L+ G+ I+NS+NFEDG + R++ LVK AAV+ LTI
Sbjct: 400 LPAVIDTTEPDVLEEALKRYSGKPIINSINFEDGG---KKLHRVLNLVKDFPAAVIGLTI 456
Query: 497 DEEGQARTAEHKVRIAKRLIDDITGSYGLDIKDIVVDCLTFPISTGQEETRRDGIETIEA 556
DE+G A TA K IAKR+ T Y LD +D+++D LTF I +G E R ++T+EA
Sbjct: 457 DEDGMAMTAAKKFEIAKRIYTVFTEEYHLDPEDLIIDPLTFSIGSGDETLRYAALQTLEA 516
Query: 557 IRELKKLYPEIHTTLGLSNISFGLNPAARQVLNSVFLNECIEAGLDSAIAHSSKILPMNR 616
I+ +K P + T LGLSN+SFGL+P +R +LNSVFL + +E+GLD AI H+SKILP
Sbjct: 517 IKMIKNELPGVKTVLGLSNVSFGLSPKSRIILNSVFLKKAVESGLDMAIVHASKILPEAS 576
Query: 617 IDDRQREVALDMVYDRRTEDYDPLQEFMQLFEGVS----AADAKDARAEQLAAMPLFERL 672
I + ++AL+++ + L++F+ + + D D E+L L
Sbjct: 577 IPTEEYDLALNLI----NGEEGALEKFINFYSAKKDDDISVDKNDISDEEL--------L 624
Query: 673 AQRIIDGDKNGLEDDLEAGMKEKSPIAIINEDLLNGMKTVGELFGSGQMQLPFVLQSAET 732
++ GDK +E L+ +K +P IIN L++GM+ +GELFG G+M LPFVLQSAE
Sbjct: 625 IVKLKKGDKTDIETLLDRLLKRYTPYDIINNILMSGMQEIGELFGKGKMLLPFVLQSAEV 684
Query: 733 MKTAVAYLEPFMEEEAEATGSAQAEGKGKIVVATVKGDVHDIGKNLVDIILSNNGYDVVN 792
MK +V+YLE FME+ E KGKIV+ATVKGDVHDIGKNLVDIILSNNGY V N
Sbjct: 685 MKKSVSYLEKFMEK-------TDTEPKGKIVLATVKGDVHDIGKNLVDIILSNNGYRVYN 737
Query: 793 LGIKQPLSAMLEAAEEHKADVIGMSGLLVKSTVVMKENLEEMNNAGASNYPVILGGAALT 852
LGIK P+ M+E A E AD IGMSGLLVKST++MKEN+EE+ G V+LGGAALT
Sbjct: 738 LGIKVPVEEMIEKAIEVGADAIGMSGLLVKSTIIMKENIEEIKRRGL-KVKVLLGGAALT 796
Query: 853 RTYVENDLNEVYTGEVYYARDAFEGLRLMDEVMAEKRGEGLDPNSPEAIEQAKKKAERKA 912
YV+N+ VY GEVYY +DAF+ + + E +K E
Sbjct: 797 EGYVKNECAPVYDGEVYYCKDAFDAITYLQE---------------------EKGVESDV 835
Query: 913 RNERSRKIAAERKANAAPVIVPERSDVSTDTPTAAPPFWGTRIVKGLPLAEFLGNLDERA 972
+N+ KI ++ ++ V ++D+S+ T PPF G R+V+ + + L++R
Sbjct: 836 QNDVDVKIDSKNDKDSLKPSV--KNDLSS-TIVPQPPFLGVRVVECINFDDVEKFLNKRT 892
Query: 973 LFMGQWGLKSTRGNEGPSYEDLVETEGRPRLRYWLDRLKSEGILDHVALVYGYFPAVAEG 1032
L+ +WG K + YE L+E +P L+++K ++D + L+YGYF V+ G
Sbjct: 893 LWTNRWGYKKLKEQSNTEYEKLLEEVVKPEYNSILEKVKLSKLVD-MKLIYGYFRVVSVG 951
Query: 1033 DDVVILESPDPHAAERMRFSFPRQQRGRFLCIADFIRPREQAVKDGQVDVMPFQLVTMGN 1092
DDV+IL D E R +FPRQ+ +LC+AD+ +P ++ G VD++P Q+VT+G+
Sbjct: 952 DDVIIL---DERENEVERLTFPRQRVEPYLCLADYFKPLDK----GIVDILPLQIVTLGD 1004
Query: 1093 PIADFANELFAANEYREYLEVHGIGVQLTEALAEYWHSRVRSELKLNDGGSVADFDPEDK 1152
+F +L +N Y+EY HG + TEA+AEYWH +R EL + + +P+
Sbjct: 1005 RPVEFLKKLKDSN-YKEYFLYHGFFTEFTEAVAEYWHRHIRYEL------GITENEPQSV 1057
Query: 1153 TKFFDLDYRGARFSFGYGSCPDLEDRAKLVELLEPGRIGVELSEELQLHPEQSTDAFVLY 1212
YRG R+SFGY SCPDLE K++ELL+ +IGV ++E Q+ PE +T A +++
Sbjct: 1058 EGILTNRYRGLRYSFGYPSCPDLEGNKKIIELLDASKIGVSITETFQMVPEFTTSAIIVH 1117
Query: 1213 HPEAKYFNV 1221
+AKYF V
Sbjct: 1118 SDKAKYFVV 1126
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: 3045
Number of extensions: 130
Number of successful extensions: 15
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: 1126
Length adjustment: 47
Effective length of query: 1174
Effective length of database: 1079
Effective search space: 1266746
Effective search space used: 1266746
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: 58 (26.9 bits)
Align candidate WP_013450377.1 CALNI_RS01215 (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.28401.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 1131.5 0.4 0 1131.1 0.4 1.1 1 lcl|NCBI__GCF_000183405.1:WP_013450377.1 CALNI_RS01215 methionine synthas
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000183405.1:WP_013450377.1 CALNI_RS01215 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1131.1 0.4 0 0 2 1182 .] 9 1126 .] 8 1126 .] 0.95
Alignments for each domain:
== domain 1 score: 1131.1 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDive 68
+ r++++DGamGt++q++ + +a ++g+ +G+n++Ln+ P +i++ih +++eaGaD++e
lcl|NCBI__GCF_000183405.1:WP_013450377.1 9 KDRVILFDGAMGTNIQKYSISDATWQGK--------NGCNEYLNIVAPHIIEEIHGNFLEAGADVLE 67
679************************5........9****************************** PP
TIGR02082 69 tntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdver 135
tn F++t ++l++Y+led +ye+n +aa++ar+vad+++ RfvaGs+GP++kl +l+
lcl|NCBI__GCF_000183405.1:WP_013450377.1 68 TNSFGGTRLVLSEYGLEDAVYEINLQAARIARRVADKYG------RFVAGSVGPGTKLVSLG----- 123
***************************************......*****************..... PP
TIGR02082 136 pefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvi 202
++ yd+l Ykeq +l+dGGvDl++iet++D+l++kaa++++++ +eek+++lPi++s v+
lcl|NCBI__GCF_000183405.1:WP_013450377.1 124 ----HISYDDLFYMYKEQSLALIDGGVDLFIIETCQDMLQIKAAINGIRSGMEEKKVNLPIMVS-VT 185
....************************************************************.** PP
TIGR02082 203 vdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalg 269
v+ G++L+G++l a+++++ ++i +lG+nCalG+d++ e + +ls+ +s+iPnaGLP ++
lcl|NCBI__GCF_000183405.1:WP_013450377.1 186 VEINGTMLTGSDLSAVAVTMAGYPIYSLGINCALGPDLMYEPLTTLSNSWGGRISCIPNAGLPMNIN 252
***************************************************************9998 PP
TIGR02082 270 ...eYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqele.eksvlsgl 332
Y+ +p+++a+++ + +++ ++ivGGCCGt ehir++ ++ ++ k ++ +++ + +++s++
lcl|NCBI__GCF_000183405.1:WP_013450377.1 253 gkfVYNMEPDRMAEIIDDILNHFPISIVGGCCGTSYEHIREMRKVCDKHKVPDPVRFQvKGMAASIY 319
7989******************************************999988887765156899*** PP
TIGR02082 333 ealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgead 399
+a +++qe iGeR n++Gsk fr+l+++ed++ +lki k+q ee a+ +Di+v ++++D ++d
lcl|NCBI__GCF_000183405.1:WP_013450377.1 320 TATSLNQEPPPALIGERANANGSKAFRELLIKEDFDGMLKIVKDQEEEAAHFVDICVAYAGRDEKRD 386
******************************************************************* PP
TIGR02082 400 mkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaa 466
m +++s++ + +P ++D +e +vle Lk+ Gk i+nsi+++dG ++ + ++l+k++ aa
lcl|NCBI__GCF_000183405.1:WP_013450377.1 387 MARFISMVNRM---SLLPAVIDTTEPDVLEEALKRYSGKPIINSINFEDGGKKLHRVLNLVKDFPAA 450
*****987665...89*************************************************** PP
TIGR02082 467 vvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieai 533
v+ +++De+G+a ta+kk+eiakR+y++ te++ ++ped+i+Dp++++i+ G e + a++++eai
lcl|NCBI__GCF_000183405.1:WP_013450377.1 451 VIGLTIDEDGMAMTAAKKFEIAKRIYTVFTEEYHLDPEDLIIDPLTFSIGSGDETLRYAALQTLEAI 517
******************************************************************* PP
TIGR02082 534 reikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelr 600
+ ik+elP +k+ +G+snvsF+l ++ R +l+svFL +a+++GlDm+iv+a+k+++ + i+ e
lcl|NCBI__GCF_000183405.1:WP_013450377.1 518 KMIKNELPGVKTVLGLSNVSFGLS--PKSRIILNSVFLKKAVESGLDMAIVHASKILPEASIPTEEY 582
************************..***************************************** PP
TIGR02082 601 evvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedle 667
+++++li L ++++ y +k + + + +++ ee L +l kG + ie l+
lcl|NCBI__GCF_000183405.1:WP_013450377.1 583 DLALNLINGE----EGALEKFINFYSAKKDD-D---ISVDKNDISDEELLIVKLKKGDKTDIETLLD 641
******9543....34577777777777766.3...3455667888999****************** PP
TIGR02082 668 earkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskG 734
+ k ++p +ii++ L+ Gm+ +G+LFG+Gkm LP+v++sa+vmkk+v+yLe ++ek + ++ kG
lcl|NCBI__GCF_000183405.1:WP_013450377.1 642 RLL-KRYTPYDIINNILMSGMQEIGELFGKGKMLLPFVLQSAEVMKKSVSYLEKFMEKTD--TEPKG 705
*99.7889*************************************************988..7899* PP
TIGR02082 735 kivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldem 801
kivlatvkGDvhDiGkn+vd++Ls+ngy+v +lG+kvPve+++e+a + aD ig+sGL+vks+ m
lcl|NCBI__GCF_000183405.1:WP_013450377.1 706 KIVLATVKGDVHDIGKNLVDIILSNNGYRVYNLGIKVPVEEMIEKAIEVGADAIGMSGLLVKSTIIM 772
******************************************************************* PP
TIGR02082 802 vevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeele 868
+e++ee++rrg+k+ +llGGaal++ +v++++a+ Y+gev y kda++a++ + +e+k +e
lcl|NCBI__GCF_000183405.1:WP_013450377.1 773 KENIEEIKRRGLKVKVLLGGAALTEGYVKNECAPVYDGEVYYCKDAFDAITYL----QEEK---GVE 832
*************************************************9864....4443...234 PP
TIGR02082 869 kikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiD 934
++++ +++ + ++ k+ k++++ d+s + vp+p+flG++v+e + +++ k+++
lcl|NCBI__GCF_000183405.1:WP_013450377.1 833 SDVQNDVDVKIDSKN---------DKDSLKPSVKNDLS-STIVPQPPFLGVRVVECInFDDVEKFLN 889
445555555555554.........33444566677888.7889**************9********* PP
TIGR02082 935 wkalFv.qWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddie 1000
+++l++ W+ ++ ++ +++ e+e+l+++ + ++ +++l+k++ kl+ + ++G+f svgdd+
lcl|NCBI__GCF_000183405.1:WP_013450377.1 890 KRTLWTnRWGYKKLKE-QSNTEYEKLLEEVVKPEYNSILEKVKLSKLVDMKLIYGYFRVVSVGDDVI 955
******99****9999.99************************************************ PP
TIGR02082 1001 iytdetvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvtaglgaeelakkl 1067
i++++ v e+l ++rq + ylclaD++++ + Gi+D l++++vt g e+ kkl
lcl|NCBI__GCF_000183405.1:WP_013450377.1 956 ILDEREN--------EV-ERLTFPRQRVEPYLCLADYFKPLDKGIVDILPLQIVTLGDRPVEFLKKL 1013
**95443........33.57899******************************************** PP
TIGR02082 1068 eakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacP 1134
++ ++++++ l ++ ++ea+ae++h+++R el + e+e++++e +l +rYrG r++fGYp+cP
lcl|NCBI__GCF_000183405.1:WP_013450377.1 1014 KD-SNYKEYFLYHGFFTEFTEAVAEYWHRHIRYELGIT-ENEPQSVEGILTNRYRGLRYSFGYPSCP 1078
86.589*****************************988.**************************** PP
TIGR02082 1135 dhtekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfav 1182
d++ +++++eLl+a +iG+ +te +++ Pe ++s+++++ +akYf v
lcl|NCBI__GCF_000183405.1:WP_013450377.1 1079 DLEGNKKIIELLDASKIGVSITETFQMVPEFTTSAIIVHSDKAKYFVV 1126
**********************************************76 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1126 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: 0.11u 0.04s 00:00:00.15 Elapsed: 00:00:00.13
# Mc/sec: 9.79
//
[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