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.7983.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: 00:00:00.04
# Mc/sec: 11.76
//
[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