Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate WP_096777659.1 F612_RS0109415 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= BRENDA::P25665
(753 letters)
>NCBI__GCF_000381085.1:WP_096777659.1
Length = 780
Score = 796 bits (2056), Expect = 0.0
Identities = 414/769 (53%), Positives = 530/769 (68%), Gaps = 25/769 (3%)
Query: 6 HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
H LG+PR+G +R+LK ESYW G T EEL AV RE+R ++ Q AGI LLPV DFA
Sbjct: 5 HNLGYPRIGDKRQLKFTLESYWKGEKTVEELEAVAREIRYHNYQTQMNAGIQLLPVNDFA 64
Query: 66 WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGE--------------PAA 111
+YD VL S LLG +P+R + K S +I+ FR+ RGRAP+ +
Sbjct: 65 YYDQVLNMSTLLGVIPSRFRQK--SYNIEVAFRMARGRAPSDDGHVCCASHASSKSKAGY 122
Query: 112 AAEMTKWFNTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGH-----KVKPVLLGPVT 166
A M KWF TNYHY+VPEF + FKLT T+L DEVDEAL + + +VKPVL+GPV+
Sbjct: 123 AGAMKKWFGTNYHYIVPEFEQDTVFKLTDTRLFDEVDEALHIVNDGQNVQVKPVLIGPVS 182
Query: 167 WLWLGKVKGEQFDRLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYK 226
+L+L + K +LS L ++L VYQ++LA LA++GIEWVQIDEP L LEL W +A+
Sbjct: 183 YLFLAENKETTISKLSRLPELLVVYQEILARLAEKGIEWVQIDEPILSLELEPEWQEAFV 242
Query: 227 PAYDAL-QGQVKLLLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWL 285
AY L + +VKLLL +YFE + ++ ++ LPV G+H+D V GK +AE+ +P+D +
Sbjct: 243 QAYGVLAKAEVKLLLASYFETLGEHVSLVSCLPVDGIHIDAVWGKTQLAEIVDAIPADKV 302
Query: 286 LSAGLINGRNVWRADLTEKYAQIKDIVGK--RDLWVASSCSLLHSPIDLSVETRLDAEVK 343
LS GL++GRN+W++DL K K +LW+A SCSLLH P+DL E L E+
Sbjct: 303 LSLGLVDGRNIWKSDLNHALQSAKTAKQKFQDNLWIAPSCSLLHVPVDLDSEEGLSNELT 362
Query: 344 SWFAFALQKCHELALLRDALNSGDTAA-LAEWSAPIQARRHSTRVHNPAVEKRLAAITAQ 402
+ AFA QK E+ LL AL + + L+E + I+AR HS+ V+N AV++RLA + +
Sbjct: 363 GYLAFAKQKLSEVTLLSQALAGHNVESQLSENAKIIEARAHSSMVNNEAVQERLAKLDSI 422
Query: 403 DSQRANVYEVRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIA 462
+R N Y R + Q+ ++ LP +PTTTIGSFPQT EIR R FK L Y +
Sbjct: 423 ALKRQNPYTQRVKVQKPKYNLPLFPTTTIGSFPQTAEIRQARRAFKSEQLTEAQYVKQMQ 482
Query: 463 EHIKQAIVEQERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIV 522
IK + QER+ +DV VHGE ERNDMVEYFGE L G+ FTQ GWVQSYGSRCVKPPI+
Sbjct: 483 AEIKDVVDRQERMNIDVFVHGEPERNDMVEYFGEQLSGYAFTQFGWVQSYGSRCVKPPII 542
Query: 523 IGDISRPAPITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALR 582
GD+SR + +TV W++YAQSLT+K +KGMLTG VT+L WSF R+D RE QIALALR
Sbjct: 543 YGDVSRESAMTVAWSRYAQSLTNKVMKGMLTGAVTMLQWSFVRDDQPREVTCNQIALALR 602
Query: 583 DEVADLEAAGIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHM 642
DEV DLEAAGI +IQIDE ALREGLPL++ DWD YL+W V +F++ + K+ TQIHTHM
Sbjct: 603 DEVLDLEAAGIEMIQIDEAALREGLPLKQRDWDDYLRWAVNSFKLTTSGVKNTTQIHTHM 662
Query: 643 CYCEFNDIMDSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVE 702
CY EFNDI+ ++A +DADVITIETS+S M LL++F F YPNEIGPGVYDIHSPNVP+VE
Sbjct: 663 CYSEFNDIIQAVADMDADVITIETSKSQMTLLDAFVNFHYPNEIGPGVYDIHSPNVPTVE 722
Query: 703 WIEALLKKAAKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
+ L++KAA+ IP ERLWVNPDCGLKTR W ET AL NMV AA+ LR
Sbjct: 723 EMVVLIEKAAQNIPVERLWVNPDCGLKTRAWKETEPALENMVTAAKILR 771
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: 1545
Number of extensions: 56
Number of successful extensions: 10
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: 780
Length adjustment: 41
Effective length of query: 712
Effective length of database: 739
Effective search space: 526168
Effective search space used: 526168
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_096777659.1 F612_RS0109415 (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.26505.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 1070.1 1.6 0 1069.9 1.6 1.0 1 lcl|NCBI__GCF_000381085.1:WP_096777659.1 F612_RS0109415 5-methyltetrahydr
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000381085.1:WP_096777659.1 F612_RS0109415 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyl
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1069.9 1.6 0 0 1 753 [. 7 772 .. 7 773 .. 0.98
Alignments for each domain:
== domain 1 score: 1069.9 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lg+Prig kR lk+ le+ywkg+ + eel++va+++r +++++q +ag++++pvndf++YD+vL+++ l
lcl|NCBI__GCF_000381085.1:WP_096777659.1 7 LGYPRIGDKRQLKFTLESYWKGEKTVEELEAVAREIRYHNYQTQMNAGIQLLPVNDFAYYDQVLNMSTL 75
79******************************************************************* PP
TIGR01371 70 lgaiperfkeladdesdldtyFaiaRGtek................kdvaalemtkwfntnYhYlvPel 122
lg+ip+rf+++ + ++++ F++aRG + k a +m+kwf tnYhY+vPe+
lcl|NCBI__GCF_000381085.1:WP_096777659.1 76 LGVIPSRFRQK---SYNIEVAFRMARGRAPsddghvccashassksKAGYAGAMKKWFGTNYHYIVPEF 141
*********97...45699********98899***********988777899***************** PP
TIGR01371 123 skeeefklsknklleeykeake.....lgvetkPvllGpitflkLakakeeeekellellekllpvYke 186
++++ fkl+ ++l++e++ea + ++v++kPvl+Gp+++l+La +ke ++ ++l++l++ll vY+e
lcl|NCBI__GCF_000381085.1:WP_096777659.1 142 EQDTVFKLTDTRLFDEVDEALHivndgQNVQVKPVLIGPVSYLFLAENKE-TTISKLSRLPELLVVYQE 209
******************9975333336799***************8885.8899************** PP
TIGR01371 187 vlkklaeagvewvqidePvlvldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpv 255
+l +lae+g+ewvqideP+l l+l++e+++a+ +ay l++ +e+klll++Yf+++ e+++ ++ lpv
lcl|NCBI__GCF_000381085.1:WP_096777659.1 210 ILARLAEKGIEWVQIDEPILSLELEPEWQEAFVQAYGVLAK--AEVKLLLASYFETLGEHVSLVSCLPV 276
****************************************8..699*********************** PP
TIGR01371 256 ealglDlveakeelelakakfeedkvLvaGvidGrniwkadlekslkllkkleakagdklvvstscsll 324
+++++D v +k++l+ + ++++dkvL++G++dGrniwk+dl+++l++ k+ ++k +d+l++++scsll
lcl|NCBI__GCF_000381085.1:WP_096777659.1 277 DGIHIDAVWGKTQLAEIVDAIPADKVLSLGLVDGRNIWKSDLNHALQSAKTAKQKFQDNLWIAPSCSLL 345
********************************************************************* PP
TIGR01371 325 hvpvdleleekldkelkellafakekleelkvlkealegeaavaealeaeaaaiaarkkskrvadekvk 393
hvpvdl+ ee l++el +lafak+kl+e+++l++al+g ++v+++l+++a+ i+ar++s++v++e+v+
lcl|NCBI__GCF_000381085.1:WP_096777659.1 346 HVPVDLDSEEGLSNELTGYLAFAKQKLSEVTLLSQALAG-HNVESQLSENAKIIEARAHSSMVNNEAVQ 413
**************************************9.88999999999****************** PP
TIGR01371 394 erlealkekkarressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfik 462
erl++l++ +r++++++R++ q+ k+nlPl+PtttiGsfPqt+e+R+aR++f+ ++++e++Y+k ++
lcl|NCBI__GCF_000381085.1:WP_096777659.1 414 ERLAKLDSIALKRQNPYTQRVKVQKPKYNLPLFPTTTIGSFPQTAEIRQARRAFKSEQLTEAQYVKQMQ 482
********************************************************************* PP
TIGR01371 463 eeikkviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkp 531
+eik+v++ qe++++Dv vhGe+eRnDmveyFge+l+G+aftq+gWvqsYGsRcvkPpiiygdvsr+ +
lcl|NCBI__GCF_000381085.1:WP_096777659.1 483 AEIKDVVDRQERMNIDVFVHGEPERNDMVEYFGEQLSGYAFTQFGWVQSYGSRCVKPPIIYGDVSRESA 551
********************************************************************* PP
TIGR01371 532 mtvkeskyaqsltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDe 600
mtv++s+yaqslt+k +kGmLtG vt+l+WsfvR+D+pr+ +++qialalrdev dLe+agi++iqiDe
lcl|NCBI__GCF_000381085.1:WP_096777659.1 552 MTVAWSRYAQSLTNKVMKGMLTGAVTMLQWSFVRDDQPREVTCNQIALALRDEVLDLEAAGIEMIQIDE 620
********************************************************************* PP
TIGR01371 601 palReglPlrksdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrs 669
+alReglPl+++d+++Yl+wav++F+l++sgvk++tqihthmCYsefn+ii+a+a++daDvi+ie+s+s
lcl|NCBI__GCF_000381085.1:WP_096777659.1 621 AALREGLPLKQRDWDDYLRWAVNSFKLTTSGVKNTTQIHTHMCYSEFNDIIQAVADMDADVITIETSKS 689
********************************************************************* PP
TIGR01371 670 dmelldalkeikkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevk 738
+m llda+ + ++y++eiG+GvyDihsp+vP++ee+ l+eka +++p erlWvnPDCGLktR+w+e++
lcl|NCBI__GCF_000381085.1:WP_096777659.1 690 QMTLLDAFVN-FHYPNEIGPGVYDIHSPNVPTVEEMVVLIEKAAQNIPVERLWVNPDCGLKTRAWKETE 757
**********.66******************************************************** PP
TIGR01371 739 aalknlveaakelRe 753
+al+n+v+aak lRe
lcl|NCBI__GCF_000381085.1:WP_096777659.1 758 PALENMVTAAKILRE 772
**************8 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (780 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 11.28
//
[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