Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate GFF469 HP15_457 5-methyltetrahydropteroyltriglutamate- homocysteine S-methyltransferase
Query= BRENDA::P25665
(753 letters)
>FitnessBrowser__Marino:GFF469
Length = 759
Score = 838 bits (2164), Expect = 0.0
Identities = 428/760 (56%), Positives = 541/760 (71%), Gaps = 17/760 (2%)
Query: 3 ILNHTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVG 62
+ H LGFPR+G RRELK AQE++W G + E+L G +LR RHW Q Q +D +PVG
Sbjct: 2 VTTHNLGFPRIGARRELKFAQEAFWKGRISEEDLQISGADLRRRHW--QNQRPLDRVPVG 59
Query: 63 DFAWYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAA-----AAEMTK 117
DF++YD +L S+ LGN+P R + GS ++D FR+ RGR+ G+ +A A EMTK
Sbjct: 60 DFSFYDQILDMSVTLGNLPERVNDTKGS-ELDRYFRVARGRS--GQESACCGVQAGEMTK 116
Query: 118 WFNTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQ 177
WF+TNYHY+VPEF + +F+L +L+D++DEA A G KPV++GPVT+LWLGK K +
Sbjct: 117 WFDTNYHYIVPEFHQNTRFRLNGNRLIDQIDEARAQGVTPKPVIIGPVTYLWLGKAKDDS 176
Query: 178 FDRLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQGQV- 236
DRL LL +LPVY ++L LA RG+EWVQ+DEPALV +L W A+ AY L+
Sbjct: 177 -DRLLLLESLLPVYSELLELLADRGVEWVQVDEPALVTDLDADWRHAFSLAYHHLKTSTP 235
Query: 237 KLLLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNV 296
KLL+TTYF + NL LPV GLH+D + +V + LP LS G+INGRN+
Sbjct: 236 KLLVTTYFGELRENLQLACELPVAGLHLDAISAPQEVPRVVDWLPPHKQLSLGVINGRNI 295
Query: 297 WRADLTEKYAQIKDIVGK--RDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCH 354
WR+DL + ++ + K LW+A SCSL+H P+DL+ E +LD E++SW AFA+QK
Sbjct: 296 WRSDLEKTLDWLEPVYEKLGNRLWLAPSCSLIHVPVDLTSEDKLDPEIRSWLAFAVQKLD 355
Query: 355 ELALLRDALNSGDTAA---LAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYE 411
EL L ALN+G A LAE + + +R S RVH+ +V+ RLA ++ QR + +
Sbjct: 356 ELKTLATALNNGRAAVRKQLAESTVAVNSRAKSERVHSASVQARLADVSPALGQRQSRFP 415
Query: 412 VRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVE 471
R Q+ + LP +PTTTIGSFPQT +IR RL F+KG L Y I E +++ IVE
Sbjct: 416 DRIAIQQRKLGLPRFPTTTIGSFPQTRDIRQTRLQFRKGELTEPQYNARIREEVRRCIVE 475
Query: 472 QERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAP 531
QE LGLDVLVHGEAERNDMVEYFGE LDG+ F+Q GWVQSYGSRCVKPPI+ GDISRP
Sbjct: 476 QEALGLDVLVHGEAERNDMVEYFGEQLDGYTFSQFGWVQSYGSRCVKPPILFGDISRPKA 535
Query: 532 ITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAA 591
+TVEW +YAQSLT KP+KGMLTGPVTIL WSF R+D R Q+ALA+R+EV DLEA+
Sbjct: 536 MTVEWIRYAQSLTKKPLKGMLTGPVTILNWSFVRDDQPRRETCLQLALAIREEVLDLEAS 595
Query: 592 GIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIM 651
G IIQIDE ALREGLPLR++DW YL W +E+FRI+A +D+TQIHTHMCY EFNDI+
Sbjct: 596 GARIIQIDEAALREGLPLRQADWKNYLDWAIESFRISANGVRDETQIHTHMCYSEFNDII 655
Query: 652 DSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKA 711
++IA +DADVITIETSRSDMELL++F F YPN+IGPGVYDIHSPN+P E I +L+ KA
Sbjct: 656 EAIARMDADVITIETSRSDMELLDAFRGFHYPNDIGPGVYDIHSPNIPDSEQIRSLMIKA 715
Query: 712 AKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
A+RIPAERLWVNPDCGLKTR W E R AL +MV AA+ LR
Sbjct: 716 AERIPAERLWVNPDCGLKTRQWEEVRPALKSMVAAARELR 755
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: 1708
Number of extensions: 76
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: 759
Length adjustment: 40
Effective length of query: 713
Effective length of database: 719
Effective search space: 512647
Effective search space used: 512647
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 GFF469 HP15_457 (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.25111.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 1105.4 0.0 0 1105.2 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF469 HP15_457 5-methyltetrahydroptero
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF469 HP15_457 5-methyltetrahydropteroyltriglutamate- homocysteine S-methyltransferase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1105.2 0.0 0 0 1 753 [. 7 756 .. 7 757 .. 0.98
Alignments for each domain:
== domain 1 score: 1105.2 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavllgaiper 76
lgfPrig++Relk+a+e++wkg+is+e+l+ + +dlr++++++q+ +d +pv+dfs+YD++Ld++v lg++per
lcl|FitnessBrowser__Marino:GFF469 7 LGFPRIGARRELKFAQEAFWKGRISEEDLQISGADLRRRHWQNQR--PLDRVPVGDFSFYDQILDMSVTLGNLPER 80
79****************************************999..78*************************** PP
TIGR01371 77 fkeladdesdldtyFaiaRGtek.....kdvaalemtkwfntnYhYlvPelskeeefklsknklleeykeakelgv 147
+++++++ +ld+yF++aRG + +v+a emtkwf+tnYhY+vPe++++++f+l+ n+l+++++ea+++gv
lcl|FitnessBrowser__Marino:GFF469 81 VNDTKGS--ELDRYFRVARGRSGqesacCGVQAGEMTKWFDTNYHYIVPEFHQNTRFRLNGNRLIDQIDEARAQGV 154
***9555..5**********988777887899******************************************** PP
TIGR01371 148 etkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvlvldlskeelaavkeaye 223
kPv++Gp+t+l+L+kak+ ++++l lle+llpvY+e+l+ la++gvewvq+deP+lv+dl++++++a+ ay+
lcl|FitnessBrowser__Marino:GFF469 155 TPKPVIIGPVTYLWLGKAKD--DSDRLLLLESLLPVYSELLELLADRGVEWVQVDEPALVTDLDADWRHAFSLAYH 228
*******************8..5689************************************************** PP
TIGR01371 224 eleeaskelklllqtYfdsveealeklvslpvealglDlveakeelelakakfeedkvLvaGvidGrniwkadlek 299
+l+ ++ kll++tYf++++e+l+ + +lpv++l+lD ++a++e ++ ++ +k L++Gvi+Grniw++dlek
lcl|FitnessBrowser__Marino:GFF469 229 HLKT--STPKLLVTTYFGELRENLQLACELPVAGLHLDAISAPQEVPRVVDWLPPHKQLSLGVINGRNIWRSDLEK 302
**97..799************************************9999999999********************* PP
TIGR01371 300 slkllkkleakagdklvvstscsllhvpvdleleekldkelkellafakekleelkvlkealeg.eaavaealeae 374
+l+ l+ + +k g++l++++scsl+hvpvdl+ e+kld+e++++lafa++kl+elk+l++al++ +aav ++l+++
lcl|FitnessBrowser__Marino:GFF469 303 TLDWLEPVYEKLGNRLWLAPSCSLIHVPVDLTSEDKLDPEIRSWLAFAVQKLDELKTLATALNNgRAAVRKQLAES 378
***************************************************************99*********** PP
TIGR01371 375 aaaiaarkkskrvadekvkerlealkekkarressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkg 450
+ a+++r+ks+rv++++v++rl++++ + +r+s f +R ++q++kl lP +PtttiGsfPqt+++R++R +frkg
lcl|FitnessBrowser__Marino:GFF469 379 TVAVNSRAKSERVHSASVQARLADVSPALGQRQSRFPDRIAIQQRKLGLPRFPTTTIGSFPQTRDIRQTRLQFRKG 454
**************************************************************************** PP
TIGR01371 451 eiseeeYekfikeeikkviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdv 526
e++e +Y++ i+ee++++i qe+lglDvLvhGe+eRnDmveyFge+l+G++f q+gWvqsYGsRcvkPpi++gd+
lcl|FitnessBrowser__Marino:GFF469 455 ELTEPQYNARIREEVRRCIVEQEALGLDVLVHGEAERNDMVEYFGEQLDGYTFSQFGWVQSYGSRCVKPPILFGDI 530
**************************************************************************** PP
TIGR01371 527 srpkpmtvkeskyaqsltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepa 602
srpk+mtv++++yaqslt+kp+kGmLtGPvtilnWsfvR+D+pr+e++ q+ala+r+ev dLe++g++iiqiDe+a
lcl|FitnessBrowser__Marino:GFF469 531 SRPKAMTVEWIRYAQSLTKKPLKGMLTGPVTILNWSFVRDDQPRRETCLQLALAIREEVLDLEASGARIIQIDEAA 606
**************************************************************************** PP
TIGR01371 603 lReglPlrksdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalk 678
lReglPlr++d+++Yldwa+e+Fr++a+gv+detqihthmCYsefn+iieaia +daDvi+ie+srsdmellda++
lcl|FitnessBrowser__Marino:GFF469 607 LREGLPLRQADWKNYLDWAIESFRISANGVRDETQIHTHMCYSEFNDIIEAIARMDADVITIETSRSDMELLDAFR 682
**************************************************************************** PP
TIGR01371 679 eikkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRe 753
++y+++iG+GvyDihsp++P +e++++l+ ka +++p+erlWvnPDCGLktR+weev++alk +v+aa+elRe
lcl|FitnessBrowser__Marino:GFF469 683 G-FHYPNDIGPGVYDIHSPNIPDSEQIRSLMIKAAERIPAERLWVNPDCGLKTRQWEEVRPALKSMVAAARELRE 756
*.66**********************************************************************8 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (759 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 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 9.55
//
[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