Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate 7026327 Shewana3_3469 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase (RefSeq)
Query= BRENDA::P25665
(753 letters)
>FitnessBrowser__ANA3:7026327
Length = 756
Score = 848 bits (2191), Expect = 0.0
Identities = 427/752 (56%), Positives = 545/752 (72%), Gaps = 7/752 (0%)
Query: 6 HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
++LGFPR+G RRELK A E YW G ST+ EL V +ELR HW Q AGI+ +PVGDFA
Sbjct: 4 NSLGFPRIGRRRELKFALEKYWRGESTQAELHEVAKELRRTHWQWQVAAGIEQVPVGDFA 63
Query: 66 WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFNTNYHY 125
+YD VLT S L +P RH+ +G++D+DTLFR+ RGRAPTG A A+EMTK+FNTNYHY
Sbjct: 64 FYDQVLTLSATLNAIPDRHRG-EGAIDLDTLFRVARGRAPTGTDAPASEMTKYFNTNYHY 122
Query: 126 MVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDRLSLLN 185
+VPE + Q F + + Q DEV EA ALG++ KPVLLGPV++L+L K G+ FD+LSLL
Sbjct: 123 LVPELKQDQVFSIAYEQFFDEVAEAQALGYQAKPVLLGPVSYLYLAKTVGQDFDKLSLLP 182
Query: 186 DILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQ-GQVKLLLTTYF 244
++L Y +LA A +G+ WVQ++EP L LEL W A AY AL+ QVK+LLT+Y+
Sbjct: 183 NLLKAYADILARFAAQGVTWVQLEEPILALELTHDWQAAISEAYQALKTAQVKILLTSYY 242
Query: 245 EGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRAD---L 301
++ + ++ALPV GLH+DLV + +A L SD +LSAG++NGRNVW A+ +
Sbjct: 243 GSISHHQALVSALPVAGLHLDLVTAPEQLALFANALRSDQILSAGVVNGRNVWAAEVDLI 302
Query: 302 TEKYAQIKDIVGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELALLRD 361
E+ + +G R LW+ +SCSLLHSP+DL VET L ++ AFA QK ELA +R
Sbjct: 303 VERIGSVARDLGAR-LWIGTSCSLLHSPVDLEVETTLTPALRQQLAFAKQKLLELANVRQ 361
Query: 362 ALNSGDTAALAEWSAPIQARRHS-TRVHNPAVEKRLAAITAQDSQRANVYEVRAEAQRAR 420
L + ++ A E ARR + + + V R+AA+T D +R + + R Q+ +
Sbjct: 362 LLQAPESIAAKEIVNTCLARREAKAQAADAKVIARVAALTQADYERVSEFTERQAVQQRK 421
Query: 421 FKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERLGLDVL 480
++LP PTTTIGSFPQT IR LR ++KG L Y + + + I Q +LG+DVL
Sbjct: 422 YRLPLLPTTTIGSFPQTPAIRGLRSRWRKGELSDAQYTEQLQQVTRDTIDRQLKLGIDVL 481
Query: 481 VHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEWAKYA 540
VHGEAERNDMVEYFGE L+G FT+NGWVQSYGSRCVKPP++ GD+SRP +TV+WA++A
Sbjct: 482 VHGEAERNDMVEYFGEQLEGVGFTKNGWVQSYGSRCVKPPLIYGDVSRPKAMTVDWAEFA 541
Query: 541 QSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGIIQIDE 600
QSLTDKPVKGMLTGPVTIL WSF RED+SR+TIA Q+ALA+RDEV DL+ AGIGIIQIDE
Sbjct: 542 QSLTDKPVKGMLTGPVTILHWSFAREDISRDTIATQLALAIRDEVVDLQNAGIGIIQIDE 601
Query: 601 PALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIAALDAD 660
PA REGLPL++S+W AYL W V AF+++AA D+TQIHTHMCY EFND + +IAA+DAD
Sbjct: 602 PAFREGLPLKQSEWQAYLDWAVNAFKLSAAGVVDETQIHTHMCYSEFNDTIAAIAAMDAD 661
Query: 661 VITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRIPAERL 720
VITIETSRS MELL +FE+F+YPNEIGPGVYDIHSPN PSVE + L++KAA+++P +L
Sbjct: 662 VITIETSRSRMELLNAFEDFEYPNEIGPGVYDIHSPNTPSVEAMVHLIEKAAQKVPVRQL 721
Query: 721 WVNPDCGLKTRGWPETRAALANMVQAAQNLRR 752
WVNPDCGLKTR W E AL NMV A + LRR
Sbjct: 722 WVNPDCGLKTRTWDEVEPALKNMVDATRELRR 753
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: 1572
Number of extensions: 68
Number of successful extensions: 6
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: 756
Length adjustment: 40
Effective length of query: 713
Effective length of database: 716
Effective search space: 510508
Effective search space used: 510508
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 7026327 Shewana3_3469 (5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase (RefSeq))
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.25984.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 1075.0 0.0 0 1074.8 0.0 1.0 1 lcl|FitnessBrowser__ANA3:7026327 Shewana3_3469 5-methyltetrahydro
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026327 Shewana3_3469 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransfer
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1074.8 0.0 0 0 1 753 [. 6 753 .. 6 754 .. 0.98
Alignments for each domain:
== domain 1 score: 1074.8 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavllgaiperf 77
lgfPrig++Relk+alekyw+g+++++el++vak+lr+++++ q +ag++ +pv+df++YD+vL++++ l+aip+r+
lcl|FitnessBrowser__ANA3:7026327 6 LGFPRIGRRRELKFALEKYWRGESTQAELHEVAKELRRTHWQWQVAAGIEQVPVGDFAFYDQVLTLSATLNAIPDRH 82
79*************************************************************************** PP
TIGR01371 78 keladdesdldtyFaiaRGtek..kdvaalemtkwfntnYhYlvPelskeeefklsknklleeykeakelgvetkPv 152
+ +++dldt+F++aRG + +d++a+emtk+fntnYhYlvPel++++ f+++ ++ ++e+ ea++lg ++kPv
lcl|FitnessBrowser__ANA3:7026327 83 RGE--GAIDLDTLFRVARGRAPtgTDAPASEMTKYFNTNYHYLVPELKQDQVFSIAYEQFFDEVAEAQALGYQAKPV 157
997..7889**********98777899************************************************** PP
TIGR01371 153 llGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvlvldlskeelaavkeayeeleeas 229
llGp+++l+Lak++ ++++++l+ll++ll++Y ++l ++a++gv+wvq++eP+l+l+l+++++aa+ eay++l+
lcl|FitnessBrowser__ANA3:7026327 158 LLGPVSYLYLAKTV-GQDFDKLSLLPNLLKAYADILARFAAQGVTWVQLEEPILALELTHDWQAAISEAYQALKT-- 231
**************.599*******************************************************97.. PP
TIGR01371 230 kelklllqtYfdsveealeklvslpvealglDlveakeelelakakfeedkvLvaGvidGrniwkadlekslkllkk 306
+++k+ll++Y++s++++ + ++ lpv++l+lDlv+a+e+l+l ++++++d++L+aGv++Grn+w+a++ +++++ +
lcl|FitnessBrowser__ANA3:7026327 232 AQVKILLTSYYGSISHHQALVSALPVAGLHLDLVTAPEQLALFANALRSDQILSAGVVNGRNVWAAEVDLIVERIGS 308
69************99999999******************************************************* PP
TIGR01371 307 leakagdklvvstscsllhvpvdleleekldkelkellafakekleelkvlkealeg.eaavaealeaeaaaiaark 382
+++ g++l++ tscsllh+pvdle e++l ++l++ lafak+kl el+ ++++l+ e+ +a+++ + + +a+r+
lcl|FitnessBrowser__ANA3:7026327 309 VARDLGARLWIGTSCSLLHSPVDLEVETTLTPALRQQLAFAKQKLLELANVRQLLQApESIAAKEIVN--TCLARRE 383
********************************************************955555555544..6899999 PP
TIGR01371 383 kskrvadekvkerlealkekkarressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYek 459
++++ad+kv +r++al++++ +r s+f+eR++ q++k++lPllPtttiGsfPqt +R R+++rkge+s+++Y++
lcl|FitnessBrowser__ANA3:7026327 384 AKAQAADAKVIARVAALTQADYERVSEFTERQAVQQRKYRLPLLPTTTIGSFPQTPAIRGLRSRWRKGELSDAQYTE 460
999************************************************************************** PP
TIGR01371 460 fikeeikkviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvke 536
+++ ++++i+ q +lg+DvLvhGe+eRnDmveyFge+l+G ft+ngWvqsYGsRcvkPp+iygdvsrpk+mtv++
lcl|FitnessBrowser__ANA3:7026327 461 QLQQVTRDTIDRQLKLGIDVLVHGEAERNDMVEYFGEQLEGVGFTKNGWVQSYGSRCVKPPLIYGDVSRPKAMTVDW 537
***************************************************************************** PP
TIGR01371 537 skyaqsltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksd 613
++aqslt+kpvkGmLtGPvtil+Wsf ReD++r +ia+q+ala+rdev+dL++agi iiqiDepa+ReglPl++s+
lcl|FitnessBrowser__ANA3:7026327 538 AEFAQSLTDKPVKGMLTGPVTILHWSFAREDISRDTIATQLALAIRDEVVDLQNAGIGIIQIDEPAFREGLPLKQSE 614
***************************************************************************** PP
TIGR01371 614 keeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyekeiGlG 690
+++Yldwav+aF+l+a+gv detqihthmCYsefn+ i+aiaa+daDvi+ie+srs mell+a+++ ++y++eiG+G
lcl|FitnessBrowser__ANA3:7026327 615 WQAYLDWAVNAFKLSAAGVVDETQIHTHMCYSEFNDTIAAIAAMDADVITIETSRSRMELLNAFED-FEYPNEIGPG 690
******************************************************************.67******** PP
TIGR01371 691 vyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRe 753
vyDihsp+ Ps+e + +l+eka +k+p ++lWvnPDCGLktR w+ev++alkn+v+a++elR
lcl|FitnessBrowser__ANA3:7026327 691 VYDIHSPNTPSVEAMVHLIEKAAQKVPVRQLWVNPDCGLKTRTWDEVEPALKNMVDATRELRR 753
************************************************************996 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (756 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: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 7.89
//
[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