Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate WP_028310300.1 H566_RS0103220 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= BRENDA::P25665
(753 letters)
>NCBI__GCF_000482785.1:WP_028310300.1
Length = 799
Score = 749 bits (1934), Expect = 0.0
Identities = 419/787 (53%), Positives = 501/787 (63%), Gaps = 40/787 (5%)
Query: 4 LNHTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGD 63
L HTLGFPR+G RRELK A ES+W G+S+ +L R +RAR W Q +AG+ L+ VGD
Sbjct: 3 LVHTLGFPRIGERRELKFALESFWRGDSSAAQLEEAARFVRARRWQTQARAGLGLVTVGD 62
Query: 64 FAWYDHVLTTSLLLGNVPARH--------------------QNKDGSVDIDTLFRIGRGR 103
FA YDHVL SLLLG VPAR VD L G
Sbjct: 63 FALYDHVLDASLLLGAVPARFGFGGDAGTAGHGAGADNAPATGAQAVVDRAPLGLAGHFA 122
Query: 104 APTGEPA-AAAEMTKWFNTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLL 162
G A A EMTKWF+TNYHY+VPE + L LLDEV EA A GH+VK L+
Sbjct: 123 LARGNAAQPALEMTKWFDTNYHYLVPELDSRTRLSLHAAALLDEVREAQAFGHRVKVALV 182
Query: 163 GPVTWLWLGKVKGEQFDRLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWL 222
GP+TWL L K FDR +L D+ Y + L G+EWVQ+DE ALV +L WL
Sbjct: 183 GPLTWLRLAKSHEAGFDRRALAADLAECYATLFGRLGGLGVEWVQLDETALVTDLDDDWL 242
Query: 223 ---DAYKPAYDALQGQVKLLLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKR 279
D ++ +G+ +LLL T F V+ + D + P+ GLH+DLV D +A
Sbjct: 243 HAADLIYARFNRAEGRPRLLLATAFGDVSRHADRLAGWPIDGLHLDLVRAPDQLAAFLPD 302
Query: 280 LPSDWLLSAGLINGRNVWRADLTEKYAQIKDI---VGKRDLWVASSCSLLHSPIDLSVET 336
P +LSAG+++GRN+WR DL A + + +G R LW+A SCSLLH P+ L E
Sbjct: 303 WPEGRVLSAGVVDGRNIWRNDLRLSLATLAPLHAALGDR-LWLAPSCSLLHVPVTLDGED 361
Query: 337 RLDAEVKSWFAFALQKCHELALLRDALNSGDTA------------ALAEWSAPIQARRHS 384
+LDAEVK W AFA +K ELALL AL++GD A ALA A AR S
Sbjct: 362 KLDAEVKPWLAFATEKLGELALLARALDAGDNADAPAHEATAIARALAASDAARGARLAS 421
Query: 385 TRVHNPAVEKRLAAITAQDSQRANVYEVRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLR 444
R + V R+ AIT ++R + + RA AQ+A LP PTTTIGSFPQT IR R
Sbjct: 422 RRTRHRTVRARVEAITPDMAERFSPHAGRAVAQQAALGLPPLPTTTIGSFPQTPAIRAAR 481
Query: 445 LDFKKGNLDANNYRTGIAEHIKQAIVEQERLGLDVLVHGEAERNDMVEYFGEHLDGFVFT 504
K+G L A +Y + + + I QE LGLDVLVHGE ER DMVEYF E L G+ T
Sbjct: 482 AAHKRGELGALDYLNAMRAEVAEVIRRQEALGLDVLVHGEPERTDMVEYFAEKLWGYAVT 541
Query: 505 QNGWVQSYGSRCVKPPIVIGDISRPAPITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFP 564
NGWVQSYGSRCVKPPI+ GD+ RP +TV+ A +AQSLT KPVKGMLTGPVT+L WSF
Sbjct: 542 ANGWVQSYGSRCVKPPILFGDVLRPEAMTVDTAVHAQSLTGKPVKGMLTGPVTMLQWSFV 601
Query: 565 REDVSRETIAKQIALALRDEVADLEAAGIGIIQIDEPALREGLPLRRSDWDAYLQWGVEA 624
R+D+ RE + Q+ALALRDEV LEAAGI IIQIDEPA REGLPLR +D A+L V A
Sbjct: 602 RDDLPREQVQLQLALALRDEVQALEAAGIRIIQIDEPAFREGLPLRAADQGAWLDAAVRA 661
Query: 625 FRINAAVAKDDTQIHTHMCYCEFNDIMDSIAALDADVITIETSRSDMELLESFEEFDYPN 684
FR++AA D TQIHTHMCY EFND++ IAA+DADVITIETSRS MELL+ F FDYPN
Sbjct: 662 FRLSAAGVADTTQIHTHMCYSEFNDVLPWIAAMDADVITIETSRSAMELLDGFAAFDYPN 721
Query: 685 EIGPGVYDIHSPNVPSVEWIEALLKKAAKRIPAERLWVNPDCGLKTRGWPETRAALANMV 744
+IGPGVYDIHSP VPSVE + ALL++A IP ERLWVNPDCGLKTRGW ET AALANMV
Sbjct: 722 QIGPGVYDIHSPRVPSVEAMLALLERACSVIPRERLWVNPDCGLKTRGWAETEAALANMV 781
Query: 745 QAAQNLR 751
AA+ LR
Sbjct: 782 AAARRLR 788
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: 1667
Number of extensions: 72
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 753
Length of database: 799
Length adjustment: 41
Effective length of query: 712
Effective length of database: 758
Effective search space: 539696
Effective search space used: 539696
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_028310300.1 H566_RS0103220 (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.28788.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
4.1e-301 987.4 0.0 7.7e-301 986.5 0.0 1.4 1 lcl|NCBI__GCF_000482785.1:WP_028310300.1 H566_RS0103220 5-methyltetrahydr
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000482785.1:WP_028310300.1 H566_RS0103220 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyl
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 986.5 0.0 7.7e-301 7.7e-301 1 753 [. 7 789 .. 7 790 .. 0.96
Alignments for each domain:
== domain 1 score: 986.5 bits; conditional E-value: 7.7e-301
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lgfPrige+Relk+ale++w+g++s+++l++ a+ +r++ +++q++ag+ +++v+df+lYDhvLd+++l
lcl|NCBI__GCF_000482785.1:WP_028310300.1 7 LGFPRIGERRELKFALESFWRGDSSAAQLEEAARFVRARRWQTQARAGLGLVTVGDFALYDHVLDASLL 75
79******************************************************************* PP
TIGR01371 70 lgaiperfkeladdesd........................ldtyFaiaRGtekkdvaalemtkwfntn 114
lga+p+rf d+ + l+ Fa+aRG++ +alemtkwf+tn
lcl|NCBI__GCF_000482785.1:WP_028310300.1 76 LGAVPARFGFGGDAGTAghgagadnapatgaqavvdraplgLAGHFALARGNAA--QPALEMTKWFDTN 142
********87655444456778889999******9999999999*******966..89*********** PP
TIGR01371 115 YhYlvPelskeeefklsknklleeykeakelgvetkPvllGpitflkLakakeeeekellellekllpv 183
YhYlvPel+++++++l++ +ll+e++ea++ g+ +k l+Gp+t+l Lak++e +++++l +l +
lcl|NCBI__GCF_000482785.1:WP_028310300.1 143 YHYLVPELDSRTRLSLHAAALLDEVREAQAFGHRVKVALVGPLTWLRLAKSHE-AGFDRRALAADLAEC 210
**************************************************996.88************* PP
TIGR01371 184 YkevlkklaeagvewvqidePvlvldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvs 252
Y ++ +l gvewvq+de +lv+dl++++l+a+ +y+ +++a+ + +lll+t f++v+++ + l+
lcl|NCBI__GCF_000482785.1:WP_028310300.1 211 YATLFGRLGGLGVEWVQLDETALVTDLDDDWLHAADLIYARFNRAEGRPRLLLATAFGDVSRHADRLAG 279
********************************************************************* PP
TIGR01371 253 lpvealglDlveakeelelakakfeedkvLvaGvidGrniwkadlekslkllkkleakagdklvvstsc 321
p+++l+lDlv+a+++l++ + +e +vL+aGv+dGrniw++dl+ sl++l+ l+a+ gd+l++++sc
lcl|NCBI__GCF_000482785.1:WP_028310300.1 280 WPIDGLHLDLVRAPDQLAAFLPDWPEGRVLSAGVVDGRNIWRNDLRLSLATLAPLHAALGDRLWLAPSC 348
********************************************************************* PP
TIGR01371 322 sllhvpvdleleekldkelkellafakekleelkvlkealeg.eaav.........aealeaeaaaiaa 380
sllhvpv+l+ e+kld+e+k +lafa+ekl el++l++al+ ++a+ a al+a++aa a
lcl|NCBI__GCF_000482785.1:WP_028310300.1 349 SLLHVPVTLDGEDKLDAEVKPWLAFATEKLGELALLARALDAgDNADapaheataiARALAASDAARGA 417
****************************************87544331111111102233444445556 PP
TIGR01371 381 rkkskrvadekvkerlealkekkarressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrk 449
r s+r+ +++v++r+ea++ ++a+r s+ + Ra aq++ l lP lPtttiGsfPqt +R aRa++++
lcl|NCBI__GCF_000482785.1:WP_028310300.1 418 RLASRRTRHRTVRARVEAITPDMAERFSPHAGRAVAQQAALGLPPLPTTTIGSFPQTPAIRAARAAHKR 486
67788899999********************************************************** PP
TIGR01371 450 geiseeeYekfikeeikkviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvk 518
ge+ + +Y +++++e+++vi+ qe+lglDvLvhGe+eR+DmveyF+ekl G+a+t+ngWvqsYGsRcvk
lcl|NCBI__GCF_000482785.1:WP_028310300.1 487 GELGALDYLNAMRAEVAEVIRRQEALGLDVLVHGEPERTDMVEYFAEKLWGYAVTANGWVQSYGSRCVK 555
********************************************************************* PP
TIGR01371 519 PpiiygdvsrpkpmtvkeskyaqsltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkd 587
Ppi++gdv rp++mtv+ ++aqslt kpvkGmLtGPvt+l+WsfvR+Dlpr++++ q+alalrdev++
lcl|NCBI__GCF_000482785.1:WP_028310300.1 556 PPILFGDVLRPEAMTVDTAVHAQSLTGKPVKGMLTGPVTMLQWSFVRDDLPREQVQLQLALALRDEVQA 624
********************************************************************* PP
TIGR01371 588 LeeagikiiqiDepalReglPlrksdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaa 656
Le+agi+iiqiDepa+ReglPlr++d+ ++ld av+aFrl+a+gv+d+tqihthmCYsefn+++ iaa
lcl|NCBI__GCF_000482785.1:WP_028310300.1 625 LEAAGIRIIQIDEPAFREGLPLRAADQGAWLDAAVRAFRLSAAGVADTTQIHTHMCYSEFNDVLPWIAA 693
********************************************************************* PP
TIGR01371 657 ldaDvisieasrsdmelldalkeikkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnP 725
+daDvi+ie+srs melld + + ++y+++iG+GvyDihsprvPs+e + +lle+a +++p+erlWvnP
lcl|NCBI__GCF_000482785.1:WP_028310300.1 694 MDADVITIETSRSAMELLDGFAA-FDYPNQIGPGVYDIHSPRVPSVEAMLALLERACSVIPRERLWVNP 761
***********************.77******************************************* PP
TIGR01371 726 DCGLktRkweevkaalknlveaakelRe 753
DCGLktR w e++aal n+v+aa++lR+
lcl|NCBI__GCF_000482785.1:WP_028310300.1 762 DCGLKTRGWAETEAALANMVAAARRLRA 789
**************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (799 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 0.02s 00:00:00.15 Elapsed: 00:00:00.14
# Mc/sec: 4.06
//
[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