Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate BPHYT_RS26655 BPHYT_RS26655 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase
Query= BRENDA::P25665
(753 letters)
>FitnessBrowser__BFirm:BPHYT_RS26655
Length = 764
Score = 820 bits (2119), Expect = 0.0
Identities = 428/752 (56%), Positives = 525/752 (69%), Gaps = 11/752 (1%)
Query: 6 HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
H GFPR+G +RELK AQES+W G S + LL V RELRARHW Q+ A +D + VGDFA
Sbjct: 5 HIPGFPRIGAQRELKFAQESFWRGESDEQYLLGVARELRARHWQLQQDAKLDFVTVGDFA 64
Query: 66 WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFNTNYHY 125
+YD +L S LLG +P R ++ + + + RG A +PA EMTKWF+TNYHY
Sbjct: 65 YYDQMLNLSALLGALPQRFGFDAKTLSLARYYELARGNA--AQPAM--EMTKWFDTNYHY 120
Query: 126 MVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDRLSLLN 185
+VPE F L DE+DEALAL VKPVL+GP+T+LWL K FDRLSLL
Sbjct: 121 LVPELGPQTTFDGGVEWLFDEIDEALALNLPVKPVLIGPITYLWLSKSHVAGFDRLSLLP 180
Query: 186 DILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDAL-QGQVKLLLTTYF 244
++ Y ++L +L +RGIEWVQ+DEPAL ++LP WLDA+ AYD L VK+LL TYF
Sbjct: 181 KLVIRYSRLLEKLKQRGIEWVQLDEPALCVDLPVEWLDAFSAAYDVLGTSGVKVLLATYF 240
Query: 245 EGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRADLTEK 304
E + + LPV G+H+DLV + LP +LSAG+I+GRN+WRADL E
Sbjct: 241 ESAAEHAPRVAVLPVAGVHLDLVRAPQQLDAWRAALPKHAVLSAGVIDGRNIWRADLGEI 300
Query: 305 YAQIKDI---VGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELALLRD 361
+ ++ + G+R LWV+SSCSLLH P+ L E +LDA++KSW AFA +K E+A L
Sbjct: 301 FESLQALHAEFGER-LWVSSSCSLLHVPVSLDAEQKLDADLKSWLAFATEKLGEVATLAL 359
Query: 362 ALN--SGDTAALAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYEVRAEAQRA 419
AL + A LA + ARRHS+ V N V+KR+AA+++ + R + + R QR
Sbjct: 360 ALRDPAAAEATLAAADRALDARRHSSTVVNALVQKRVAAVSSAMADRQSPFAERNRLQRE 419
Query: 420 RFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERLGLDV 479
LP PTTTIGSFPQT IR R +K+G L A +Y + I+ A+ +QE LGLDV
Sbjct: 420 ALGLPLLPTTTIGSFPQTPAIRQARAAYKRGELRALDYLQRMRAEIEIAVRKQEELGLDV 479
Query: 480 LVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEWAKY 539
LVHGEAERNDMVEYFGE L G+ FT+NGWVQSYGSRCVKPPI+ GD+ RP P+TVE +Y
Sbjct: 480 LVHGEAERNDMVEYFGEQLWGYAFTENGWVQSYGSRCVKPPIIYGDVYRPEPMTVETTRY 539
Query: 540 AQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGIIQID 599
AQSLT + +KGMLTGPVT+L WSF R+D R T A Q+ALA+RDEV DLE AGI IIQID
Sbjct: 540 AQSLTQRLMKGMLTGPVTMLQWSFVRDDQPRSTTALQLALAIRDEVVDLEKAGIRIIQID 599
Query: 600 EPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIAALDA 659
EPA REGLPLRR DW AYL+W FRI+AA D TQIHTHMCY EFNDI+ SIAA+DA
Sbjct: 600 EPAFREGLPLRRGDWAAYLEWATRVFRISAAGVADQTQIHTHMCYSEFNDILPSIAAMDA 659
Query: 660 DVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRIPAER 719
DVITIETSRS MELL+ F F YPNEIGPGVYDIHSP VP + ++ LL++A + IPAER
Sbjct: 660 DVITIETSRSAMELLDGFGAFAYPNEIGPGVYDIHSPRVPDAQAMQRLLERACEVIPAER 719
Query: 720 LWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
LWVNPDCGLKTRGWPET AAL NMV+AA+ LR
Sbjct: 720 LWVNPDCGLKTRGWPETEAALTNMVRAAKALR 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: 1695
Number of extensions: 74
Number of successful extensions: 9
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: 764
Length adjustment: 40
Effective length of query: 713
Effective length of database: 724
Effective search space: 516212
Effective search space used: 516212
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 BPHYT_RS26655 BPHYT_RS26655 (5-methyltetrahydropteroyltriglutamate-- homocysteine 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.18309.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 1075.1 0.0 0 1074.9 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS26655 BPHYT_RS26655 5-methyltetrahydro
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS26655 BPHYT_RS26655 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltra
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1074.9 0.0 0 0 2 754 .] 8 753 .. 7 753 .. 0.99
Alignments for each domain:
== domain 1 score: 1074.9 bits; conditional E-value: 0
TIGR01371 2 gfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavllg 71
gfPrig++Relk+a+e++w+g+++++ ll va++lr+++++ q++a++d+++v+df++YD++L++++llg
lcl|FitnessBrowser__BFirm:BPHYT_RS26655 8 GFPRIGAQRELKFAQESFWRGESDEQYLLGVARELRARHWQLQQDAKLDFVTVGDFAYYDQMLNLSALLG 77
9********************************************************************* PP
TIGR01371 72 aiperfkeladdesdldtyFaiaRGtekkdvaalemtkwfntnYhYlvPelskeeefklsknklleeyke 141
a+p+rf ++ +l++y+++aRG++ +a+emtkwf+tnYhYlvPel ++++f + l++e++e
lcl|FitnessBrowser__BFirm:BPHYT_RS26655 78 ALPQRFGFD-AKTLSLARYYELARGNAA--QPAMEMTKWFDTNYHYLVPELGPQTTFDGGVEWLFDEIDE 144
*******98.55569**********966..89************************************** PP
TIGR01371 142 akelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvlvldls 211
a +l++ +kPvl+Gpit+l+L+k++ +++l+ll+kl+ Y+++l+kl+++g+ewvq+deP+l +dl+
lcl|FitnessBrowser__BFirm:BPHYT_RS26655 145 ALALNLPVKPVLIGPITYLWLSKSHV-AGFDRLSLLPKLVIRYSRLLEKLKQRGIEWVQLDEPALCVDLP 213
***********************996.88***************************************** PP
TIGR01371 212 keelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakeelelakakfeedkv 281
e+l+a+ +ay+ l + +k+ll+tYf+s e+ ++ lpv++++lDlv+a+++l++ a+++++ v
lcl|FitnessBrowser__BFirm:BPHYT_RS26655 214 VEWLDAFSAAYDVLGT--SGVKVLLATYFESAAEHAPRVAVLPVAGVHLDLVRAPQQLDAWRAALPKHAV 281
**************97..79************************************************** PP
TIGR01371 282 LvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvpvdleleekldkelkellafakekl 351
L+aGvidGrniw+adl +++++l++l+a+ g++l+vs+scsllhvpv+l++e+kld++lk++lafa+ekl
lcl|FitnessBrowser__BFirm:BPHYT_RS26655 282 LSAGVIDGRNIWRADLGEIFESLQALHAEFGERLWVSSSCSLLHVPVSLDAEQKLDADLKSWLAFATEKL 351
********************************************************************** PP
TIGR01371 352 eelkvlkealegeaavaealeaeaaaiaarkkskrvadekvkerlealkekkarressfeeRaeaqekkl 421
e+++l+ al++ aa++++l+a+++a+ ar++s++v ++ v++r++a+++++a r+s+f+eR++ q++ l
lcl|FitnessBrowser__BFirm:BPHYT_RS26655 352 GEVATLALALRDPAAAEATLAAADRALDARRHSSTVVNALVQKRVAAVSSAMADRQSPFAERNRLQREAL 421
************999999999999********************************************** PP
TIGR01371 422 nlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLvhGefeRnDmv 491
lPllPtttiGsfPqt +R+aRa++++ge+ + +Y + +++ei+ +++ qeelglDvLvhGe+eRnDmv
lcl|FitnessBrowser__BFirm:BPHYT_RS26655 422 GLPLLPTTTIGSFPQTPAIRQARAAYKRGELRALDYLQRMRAEIEIAVRKQEELGLDVLVHGEAERNDMV 491
********************************************************************** PP
TIGR01371 492 eyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkGmLtGPvtilnW 561
eyFge+l G+aft+ngWvqsYGsRcvkPpiiygdv rp+pmtv+ ++yaqslt++ +kGmLtGPvt+l+W
lcl|FitnessBrowser__BFirm:BPHYT_RS26655 492 EYFGEQLWGYAFTENGWVQSYGSRCVKPPIIYGDVYRPEPMTVETTRYAQSLTQRLMKGMLTGPVTMLQW 561
********************************************************************** PP
TIGR01371 562 sfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdkeeYldwaveaFrlaasg 631
sfvR+D+pr+++a q+ala+rdev+dLe+agi+iiqiDepa+ReglPlr+ d+++Yl+wa ++Fr++a+g
lcl|FitnessBrowser__BFirm:BPHYT_RS26655 562 SFVRDDQPRSTTALQLALAIRDEVVDLEKAGIRIIQIDEPAFREGLPLRRGDWAAYLEWATRVFRISAAG 631
********************************************************************** PP
TIGR01371 632 vkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyekeiGlGvyDihsprvPs 701
v+d+tqihthmCYsefn+i+ +iaa+daDvi+ie+srs melld + + ++y++eiG+GvyDihsprvP
lcl|FitnessBrowser__BFirm:BPHYT_RS26655 632 VADQTQIHTHMCYSEFNDILPSIAAMDADVITIETSRSAMELLDGFGA-FAYPNEIGPGVYDIHSPRVPD 700
************************************************.67******************* PP
TIGR01371 702 keelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRek 754
++ +++lle+a +++p+erlWvnPDCGLktR w+e++aal+n+v aak+lR+k
lcl|FitnessBrowser__BFirm:BPHYT_RS26655 701 AQAMQRLLERACEVIPAERLWVNPDCGLKTRGWPETEAALTNMVRAAKALRAK 753
***************************************************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (764 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: 9.26
//
[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