Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate GFF1415 Psest_1452 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= BRENDA::P25665
(753 letters)
>FitnessBrowser__psRCH2:GFF1415
Length = 769
Score = 908 bits (2346), Expect = 0.0
Identities = 460/758 (60%), Positives = 552/758 (72%), Gaps = 13/758 (1%)
Query: 6 HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
H LGFPR+G RELKKA E+YW G L VGR+LRA+HW Q AGI LLPVGDFA
Sbjct: 5 HNLGFPRIGADRELKKALEAYWKGELDELGLRQVGRQLRAQHWQAQADAGIQLLPVGDFA 64
Query: 66 WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRG-RAPTGEPAAAAEMTKWFNTNYH 124
WYD VLT SL+ G VP R + DG +DT+F + RG + A EMTKWF+TNYH
Sbjct: 65 WYDQVLTHSLMFGVVPQRFRPADGQPTLDTVFAMARGVTSSCCGGGQAQEMTKWFDTNYH 124
Query: 125 YMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQ---FDRL 181
Y+VPEF QQF+L+W+QL +EV+EA ALGH +KPVL+GP+T+LWLGK+KGE FD+L
Sbjct: 125 YLVPEFTVDQQFQLSWSQLFEEVEEAQALGHAIKPVLVGPLTYLWLGKLKGEDTEGFDKL 184
Query: 182 SLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQ-GQVKLLL 240
LL +LPVY +VL LA +GIEWVQIDEP L L+LPQ W +A++ AY+ LQ +K L+
Sbjct: 185 ELLERLLPVYGEVLDRLAAQGIEWVQIDEPILALDLPQDWKNAFERAYNLLQRAPLKKLV 244
Query: 241 TTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRAD 300
TYF G+ NL ALPV GLH+DLV + + LP+ +LS GL+NGRNVWR D
Sbjct: 245 ATYFGGLEDNLSLAAALPVDGLHIDLVRAPEQYPLILDWLPTYKVLSLGLVNGRNVWRCD 304
Query: 301 LT---EKYAQIKDIVGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELA 357
L E + +G R LW+A SCSLLHSP+DL E RLD E+K W AFA+QKC E+A
Sbjct: 305 LDKALEVARHAAERLGDR-LWLAPSCSLLHSPVDLEREDRLDHELKGWLAFAVQKCAEVA 363
Query: 358 LLRDALNSGDT----AALAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYEVR 413
L A+N LA A AR+HS R+H P V+ RL+AI QDSQR +V+ R
Sbjct: 364 TLARAINEPTNEDVVVELARSRAVQAARQHSPRIHKPQVQTRLSAIQPQDSQRTSVFAAR 423
Query: 414 AEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQE 473
E QRAR LPA+PTTTIGSFPQT IR R +K+G L +Y + I+ A+ QE
Sbjct: 424 IEQQRARLDLPAFPTTTIGSFPQTPAIRLARQAYKQGRLSLGDYTEAMQAEIRHAVAVQE 483
Query: 474 RLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPIT 533
++GLDVLVHGEAERNDMVEYF E LDG+ FT+ GWVQSYGSRCVKP ++ GD+SRP P+T
Sbjct: 484 QIGLDVLVHGEAERNDMVEYFAEQLDGYAFTRFGWVQSYGSRCVKPAVIYGDLSRPQPMT 543
Query: 534 VEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGI 593
V+W +YAQ TD+ +KGMLTGPVT+L WSF REDVSRE A+Q+ALA+RDEV DLEAAGI
Sbjct: 544 VDWIRYAQQQTDRVMKGMLTGPVTMLMWSFAREDVSREVQARQLALAIRDEVCDLEAAGI 603
Query: 594 GIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDS 653
IIQIDE A REGLPLRR+ W YL W VEAFR+ A+ +D+TQIHTHMCY EFND+++S
Sbjct: 604 RIIQIDEAAFREGLPLRRAQWQHYLDWAVEAFRLCASGVRDETQIHTHMCYSEFNDVIES 663
Query: 654 IAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAK 713
IAA+DADVITIETSRS MELLE+F FDYPN+IGPGVYDIHSP VP + LL+KAA+
Sbjct: 664 IAAMDADVITIETSRSQMELLEAFRAFDYPNDIGPGVYDIHSPRVPDTAEMVQLLEKAAE 723
Query: 714 RIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
RIPAERLWVNPDCGLKTR WPET AAL NMV AA+ LR
Sbjct: 724 RIPAERLWVNPDCGLKTRAWPETEAALVNMVAAARQLR 761
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: 1726
Number of extensions: 82
Number of successful extensions: 8
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: 769
Length adjustment: 40
Effective length of query: 713
Effective length of database: 729
Effective search space: 519777
Effective search space used: 519777
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 GFF1415 Psest_1452 ( 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.7037.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 1092.7 0.0 0 1092.5 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF1415 Psest_1452 5-methyltetrahydropt
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF1415 Psest_1452 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransfera
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1092.5 0.0 0 0 1 753 [. 7 762 .. 7 763 .. 0.98
Alignments for each domain:
== domain 1 score: 1092.5 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavllgaipe 75
lgfPrig+ Relkkale+ywkg++++ l +v ++lr++++++q++ag++++pv+df++YD+vL+ ++++g++p+
lcl|FitnessBrowser__psRCH2:GFF1415 7 LGFPRIGADRELKKALEAYWKGELDELGLRQVGRQLRAQHWQAQADAGIQLLPVGDFAWYDQVLTHSLMFGVVPQ 81
79************************************************************************* PP
TIGR01371 76 rfkeladdesdldtyFaiaRGtek...kdvaalemtkwfntnYhYlvPelskeeefklsknklleeykeakelgv 147
rf+ d++ +ldt Fa+aRG ++ + +a+emtkwf+tnYhYlvPe++ +++f+ls+++l+ee++ea++lg+
lcl|FitnessBrowser__psRCH2:GFF1415 82 RFRPA-DGQPTLDTVFAMARGVTSsccGGGQAQEMTKWFDTNYHYLVPEFTVDQQFQLSWSQLFEEVEEAQALGH 155
****8.66779**********9888887889******************************************** PP
TIGR01371 148 etkPvllGpitflkLakakee..eekellellekllpvYkevlkklaeagvewvqidePvlvldlskeelaavke 220
kPvl+Gp+t+l+L+k k e e +++lelle+llpvY evl++la++g+ewvqideP+l+ldl++++++a+++
lcl|FitnessBrowser__psRCH2:GFF1415 156 AIKPVLVGPLTYLWLGKLKGEdtEGFDKLELLERLLPVYGEVLDRLAAQGIEWVQIDEPILALDLPQDWKNAFER 230
****************9887666899************************************************* PP
TIGR01371 221 ayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakeelelakakfeedkvLvaGvidGrniwka 295
ay+ l++ + lk l++tYf+ +e++l+ ++ lpv++l++Dlv+a+e+ l +++ kvL++G+++Grn+w+
lcl|FitnessBrowser__psRCH2:GFF1415 231 AYNLLQR--APLKKLVATYFGGLEDNLSLAAALPVDGLHIDLVRAPEQYPLILDWLPTYKVLSLGLVNGRNVWRC 303
*****97..4777789*********************************************************** PP
TIGR01371 296 dlekslkllkkleakagdklvvstscsllhvpvdleleekldkelkellafakekleelkvlkealeg..eaava 368
dl k+l++ ++ +++ gd+l++++scsllh+pvdle+e++ld+elk +lafa++k++e+++l++a+++ +++v
lcl|FitnessBrowser__psRCH2:GFF1415 304 DLDKALEVARHAAERLGDRLWLAPSCSLLHSPVDLEREDRLDHELKGWLAFAVQKCAEVATLARAINEptNEDVV 378
*******************************************************************99667788 PP
TIGR01371 369 ealeaeaaaiaarkkskrvadekvkerlealkekkarressfeeRaeaqekklnlPllPtttiGsfPqtkevRka 443
+l+ ++a aar++s+r+++ +v++rl+a++ ++++r+s f++R e+q+++l+lP++PtttiGsfPqt +R a
lcl|FitnessBrowser__psRCH2:GFF1415 379 VELARSRAVQAARQHSPRIHKPQVQTRLSAIQPQDSQRTSVFAARIEQQRARLDLPAFPTTTIGSFPQTPAIRLA 453
888888888899*************************************************************** PP
TIGR01371 444 RakfrkgeiseeeYekfikeeikkviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvk 518
R+++++g++s +Y++++++ei++++++qe++glDvLvhGe+eRnDmveyF+e+l+G+aft++gWvqsYGsRcvk
lcl|FitnessBrowser__psRCH2:GFF1415 454 RQAYKQGRLSLGDYTEAMQAEIRHAVAVQEQIGLDVLVHGEAERNDMVEYFAEQLDGYAFTRFGWVQSYGSRCVK 528
*************************************************************************** PP
TIGR01371 519 PpiiygdvsrpkpmtvkeskyaqsltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagi 593
P++iygd+srp+pmtv++++yaq t++ +kGmLtGPvt+l Wsf ReD++r+ +a+q+ala+rdev dLe+agi
lcl|FitnessBrowser__psRCH2:GFF1415 529 PAVIYGDLSRPQPMTVDWIRYAQQQTDRVMKGMLTGPVTMLMWSFAREDVSREVQARQLALAIRDEVCDLEAAGI 603
*************************************************************************** PP
TIGR01371 594 kiiqiDepalReglPlrksdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasr 668
+iiqiDe+a+ReglPlr++++++YldwaveaFrl asgv+detqihthmCYsefn++ie+iaa+daDvi+ie+sr
lcl|FitnessBrowser__psRCH2:GFF1415 604 RIIQIDEAAFREGLPLRRAQWQHYLDWAVEAFRLCASGVRDETQIHTHMCYSEFNDVIESIAAMDADVITIETSR 678
*************************************************************************** PP
TIGR01371 669 sdmelldalkeikkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalkn 743
s+mell+a+++ ++y+++iG+GvyDihsprvP + e+ +lleka +++p+erlWvnPDCGLktR+w+e++aal n
lcl|FitnessBrowser__psRCH2:GFF1415 679 SQMELLEAFRA-FDYPNDIGPGVYDIHSPRVPDTAEMVQLLEKAAERIPAERLWVNPDCGLKTRAWPETEAALVN 752
***********.77************************************************************* PP
TIGR01371 744 lveaakelRe 753
+v+aa++lR+
lcl|FitnessBrowser__psRCH2:GFF1415 753 MVAAARQLRA 762
********96 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (769 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: 10.37
//
[ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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