Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate WP_019867870.1 METMI_RS0118885 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= BRENDA::P25665
(753 letters)
>NCBI__GCF_000384075.1:WP_019867870.1
Length = 755
Score = 837 bits (2161), Expect = 0.0
Identities = 427/751 (56%), Positives = 534/751 (71%), Gaps = 9/751 (1%)
Query: 6 HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
H LGFPR+G RELK A E YW G+ L ++ LR RHW Q +G+DL+PVGDF+
Sbjct: 5 HNLGFPRLGENRELKFALERYWRGDIDHATLGSIAAGLRQRHWQLQANSGLDLIPVGDFS 64
Query: 66 WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFNTNYHY 125
+YD VL TS++LG +P R + S+ +DT FR+ RG+A G P A EMTKWF+TNYHY
Sbjct: 65 YYDQVLDTSIMLGAIPERFGS---SIGLDTYFRMARGQASDGVPFRACEMTKWFDTNYHY 121
Query: 126 MVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDRLSLLN 185
+VPE QQF+L+ +++ DE E ALG++ KPVLLGP+TWLWL K F++L LL+
Sbjct: 122 LVPEVTPDQQFELSGSKIFDEARELQALGYQPKPVLLGPLTWLWLAKT-ASGFNKLDLLD 180
Query: 186 DILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQG-QVKLLLTTYF 244
+LPVY ++L LA +G+EWVQIDEP LVL+LP AW +A++ AY+ LQ VKLLL TYF
Sbjct: 181 RLLPVYGEILRRLAAQGVEWVQIDEPILVLDLPYAWRNAFERAYNRLQSCPVKLLLATYF 240
Query: 245 EGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRADLTEK 304
+ + LPV GLH+DLV + + + + +LS GLI+GRN+WR DL
Sbjct: 241 GELGEHASLTCKLPVAGLHIDLVRAPEQLTAVLDNFANHKVLSLGLIDGRNIWRTDLKAA 300
Query: 305 YAQIKDIVG--KRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELALLRDA 362
A + + K +LW+A SCSLLH P+DL ET LD +K W AFA QK EL +LR A
Sbjct: 301 LATVATVRERFKGELWLAPSCSLLHVPVDLERETDLDPAIKPWLAFARQKLTELEILRLA 360
Query: 363 LNSGDTAA--LAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYEVRAEAQRAR 420
+ A LA + I+ RR S +HNPAV+ LA + +QR N + VR QRA+
Sbjct: 361 IEEPAAAETELAASATAIRTRRESGLIHNPAVQAGLAKLDGTLAQRQNPFPVRQAQQRAK 420
Query: 421 FKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERLGLDVL 480
KLP++PTTTIGSFPQT EIR R +FK+G + +Y + I + EQE LGLDVL
Sbjct: 421 LKLPSYPTTTIGSFPQTPEIRKTRHEFKQGQISEADYVRRMEHTIGFCVREQENLGLDVL 480
Query: 481 VHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEWAKYA 540
VHGEAERNDMVEYFGE LDGF+FT GWVQSYGSRCVKPPI+ GD+SRPAP+TV W+ YA
Sbjct: 481 VHGEAERNDMVEYFGEQLDGFLFTGYGWVQSYGSRCVKPPIIYGDVSRPAPMTVRWSHYA 540
Query: 541 QSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGIIQIDE 600
QSLTDKP+KGMLTGPVT+L WSF R+D R T A Q+ALA+RDEV DLE +GI IIQIDE
Sbjct: 541 QSLTDKPMKGMLTGPVTLLNWSFVRDDQPRSTTAYQLALAIRDEVNDLERSGIPIIQIDE 600
Query: 601 PALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIAALDAD 660
A REGLP R+S W AYL W V AFRI ++ +D TQIHTHMCY EFNDI+ +IA LDAD
Sbjct: 601 AAFREGLPPRQSRWQAYLDWAVRAFRICSSGVQDSTQIHTHMCYSEFNDIIAAIAELDAD 660
Query: 661 VITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRIPAERL 720
VITIETSRS+MELL++F +F+YPNEIGPGVYDIHSPNVP+ + ALLK A +R+ +++L
Sbjct: 661 VITIETSRSNMELLDAFIDFNYPNEIGPGVYDIHSPNVPTTGDMVALLKIAGERVGSDKL 720
Query: 721 WVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
WVNPDCGLKTR W + R +LANM +AA+ LR
Sbjct: 721 WVNPDCGLKTRQWEDVRGSLANMAEAAKVLR 751
Lambda K H
0.319 0.135 0.416
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: 1616
Number of extensions: 74
Number of successful extensions: 7
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: 753
Length of database: 755
Length adjustment: 40
Effective length of query: 713
Effective length of database: 715
Effective search space: 509795
Effective search space used: 509795
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)
Align candidate WP_019867870.1 METMI_RS0118885 (5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase)
to HMM TIGR01371 (metE: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase (EC 2.1.1.14))
# 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/TIGR01371.hmm
# target sequence database: /tmp/gapView.12581.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR01371 [M=754]
Accession: TIGR01371
Description: met_syn_B12ind: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
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 1089.7 0.0 0 1089.5 0.0 1.0 1 lcl|NCBI__GCF_000384075.1:WP_019867870.1 METMI_RS0118885 5-methyltetrahyd
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000384075.1:WP_019867870.1 METMI_RS0118885 5-methyltetrahydropteroyltriglutamate--homocysteine S-methy
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1089.5 0.0 0 0 1 753 [. 7 752 .. 7 753 .. 0.99
Alignments for each domain:
== domain 1 score: 1089.5 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lgfPr+ge+Relk+ale+yw+g+i++++l + a+ lr+++++ q+++g+d+ipv+dfs+YD+vLdt+++
lcl|NCBI__GCF_000384075.1:WP_019867870.1 7 LGFPRLGENRELKFALERYWRGDIDHATLGSIAAGLRQRHWQLQANSGLDLIPVGDFSYYDQVLDTSIM 75
79******************************************************************* PP
TIGR01371 70 lgaiperfkeladdesdldtyFaiaRGtekkdv..aalemtkwfntnYhYlvPelskeeefklsknkll 136
lgaiperf ++ + ldtyF++aRG+++++v a+emtkwf+tnYhYlvPe++++++f+ls +k++
lcl|NCBI__GCF_000384075.1:WP_019867870.1 76 LGAIPERFGSS----IGLDTYFRMARGQASDGVpfRACEMTKWFDTNYHYLVPEVTPDQQFELSGSKIF 140
********997....679**********99665226********************************* PP
TIGR01371 137 eeykeakelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePv 205
+e +e ++lg + kPvllGp+t+l+Lak+++ +++l+ll++llpvY e+l++la++gvewvqideP+
lcl|NCBI__GCF_000384075.1:WP_019867870.1 141 DEARELQALGYQPKPVLLGPLTWLWLAKTAS--GFNKLDLLDRLLPVYGEILRRLAAQGVEWVQIDEPI 207
*****************************96..899********************************* PP
TIGR01371 206 lvldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakeelelaka 274
lvldl+ ++++a+++ay+ l++ +klll+tYf+++ e+ + + +lpv++l++Dlv+a+e+l+++
lcl|NCBI__GCF_000384075.1:WP_019867870.1 208 LVLDLPYAWRNAFERAYNRLQS--CPVKLLLATYFGELGEHASLTCKLPVAGLHIDLVRAPEQLTAVLD 274
*********************8..699****************************************** PP
TIGR01371 275 kfeedkvLvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvpvdleleekldkelkel 343
+f+++kvL++G+idGrniw++dl+++l++++++ ++ + +l++++scsllhvpvdle+e++ld+++k +
lcl|NCBI__GCF_000384075.1:WP_019867870.1 275 NFANHKVLSLGLIDGRNIWRTDLKAALATVATVRERFKGELWLAPSCSLLHVPVDLERETDLDPAIKPW 343
**************************************99***************************** PP
TIGR01371 344 lafakekleelkvlkealegeaavaealeaeaaaiaarkkskrvadekvkerlealkekkarressfee 412
lafa++kl+el++l+ a+e+ aa++++l+a+a+ai++r++s +++ +v++ l++l+ + a+r+++f
lcl|NCBI__GCF_000384075.1:WP_019867870.1 344 LAFARQKLTELEILRLAIEEPAAAETELAASATAIRTRRESGLIHNPAVQAGLAKLDGTLAQRQNPFPV 412
********************999999******************************************* PP
TIGR01371 413 RaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLv 481
R+++q++kl+lP +PtttiGsfPqt e+Rk+R++f++g+ise++Y++ +++ i +++ qe+lglDvLv
lcl|NCBI__GCF_000384075.1:WP_019867870.1 413 RQAQQRAKLKLPSYPTTTIGSFPQTPEIRKTRHEFKQGQISEADYVRRMEHTIGFCVREQENLGLDVLV 481
********************************************************************* PP
TIGR01371 482 hGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkG 550
hGe+eRnDmveyFge+l+Gf+ft +gWvqsYGsRcvkPpiiygdvsrp+pmtv++s+yaqslt+kp+kG
lcl|NCBI__GCF_000384075.1:WP_019867870.1 482 HGEAERNDMVEYFGEQLDGFLFTGYGWVQSYGSRCVKPPIIYGDVSRPAPMTVRWSHYAQSLTDKPMKG 550
********************************************************************* PP
TIGR01371 551 mLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdkeeYld 619
mLtGPvt+lnWsfvR+D+pr+++a+q+ala+rdev+dLe +gi iiqiDe+a+ReglP r+s +++Yld
lcl|NCBI__GCF_000384075.1:WP_019867870.1 551 MLTGPVTLLNWSFVRDDQPRSTTAYQLALAIRDEVNDLERSGIPIIQIDEAAFREGLPPRQSRWQAYLD 619
********************************************************************* PP
TIGR01371 620 waveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyekeiG 688
wav+aFr+ +sgv+d+tqihthmCYsefn+ii+aia+ldaDvi+ie+srs+mellda+ + ++y++eiG
lcl|NCBI__GCF_000384075.1:WP_019867870.1 620 WAVRAFRICSSGVQDSTQIHTHMCYSEFNDIIAAIAELDADVITIETSRSNMELLDAFID-FNYPNEIG 687
************************************************************.67****** PP
TIGR01371 689 lGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRe 753
+GvyDihsp+vP++ ++ +ll+ a +++ +++lWvnPDCGLktR+we+v+ +l n+ eaak lR+
lcl|NCBI__GCF_000384075.1:WP_019867870.1 688 PGVYDIHSPNVPTTGDMVALLKIAGERVGSDKLWVNPDCGLKTRQWEDVRGSLANMAEAAKVLRA 752
**************************************************************997 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (755 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 9.02
//
[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