Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate WP_068464489.1 APY04_RS15365 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= BRENDA::P25665
(753 letters)
>NCBI__GCF_001541235.1:WP_068464489.1
Length = 778
Score = 788 bits (2034), Expect = 0.0
Identities = 410/774 (52%), Positives = 517/774 (66%), Gaps = 23/774 (2%)
Query: 1 MTILNHTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLP 60
M++ LGFPR+G RRELK+A ESYWAG S + LL LRA +W +Q+ AGID +P
Sbjct: 1 MSVTVTNLGFPRIGPRRELKQALESYWAGKSDEKTLLESAAALRATNWTKQRAAGIDHIP 60
Query: 61 VGDFAWYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEP----------- 109
DF+ YDHVL ++G +P+ + +DT F + RG G
Sbjct: 61 SNDFSLYDHVLDICAMVGAIPSVYGQVQSKTSVDTYFAMARGSQEYGTVEHPYLSCGHQH 120
Query: 110 ---AAAAEMTKWFNTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVT 166
A EMTKWF+TNYHYMVPE Q F LT T+ +DE EA ALG K +PVLLGPVT
Sbjct: 121 GLGVPAMEMTKWFDTNYHYMVPELSSDQSFALTSTKPVDEFKEAQALGIKTRPVLLGPVT 180
Query: 167 WLWLGKVKGEQFDRLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYK 226
+L L K K E FD L LL+ ++PVY +VL +LA+ G EWVQIDEP L +L A +
Sbjct: 181 FLTLAKSKTEGFDTLKLLSALIPVYVEVLRQLAEAGAEWVQIDEPCLATDLGDGVALALQ 240
Query: 227 PAYDALQG---QVKLLLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSD 283
AY Q++LLLT+YF NLD +LPV G+H+DL + + + + P
Sbjct: 241 TAYGRFAEAVPQLRLLLTSYFGAYGDNLDAALSLPVAGIHLDLARAPEQLETVLAKAPKS 300
Query: 284 WLLSAGLINGRNVWRADLTEKYAQIKDIVGKRD---LWVASSCSLLHSPIDLSVETRLDA 340
LS G+I+GRNVWRA+L +++ +V +R +++A SCS+LH PIDL ET LD
Sbjct: 301 LTLSLGVIDGRNVWRANLPALLDKLEPVVAQRGADKIFIAPSCSMLHVPIDLDAETTLDP 360
Query: 341 EVKSWFAFALQKCHELALLRDALNSGDTAALAEWSAPIQA---RRHSTRVHNPAVEKRLA 397
EVK+W AFA QK EL L ALN G + AE + ++A R+ S ++HNPAV R+A
Sbjct: 361 EVKNWMAFAAQKLGELKTLGRALNEGRDSVKAELTESMRAAASRKSSQKIHNPAVAARMA 420
Query: 398 AITAQDSQRANVYEVRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNY 457
A+T + + R + + R +AQR R +L A+PTTTIGSFPQT E+R R KG L Y
Sbjct: 421 AVTKEMASRKSPFAARQKAQRDRLQLVAYPTTTIGSFPQTPEVRKARAANAKGALGHAEY 480
Query: 458 RTGIAEHIKQAIVEQERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCV 517
+ + + A+ QE +G+DVLVHGE ERNDMV+YFGE LDGF FT+NGWVQSYGSR V
Sbjct: 481 NDFLRKETEAAVRWQEEIGIDVLVHGEFERNDMVQYFGEQLDGFTFTKNGWVQSYGSRYV 540
Query: 518 KPPIVIGDISRPAPITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQI 577
+PPI+ GD++RP P+TVEW YAQSLT KP+KGMLTGPVTIL WSF R+D+ R +QI
Sbjct: 541 RPPIIFGDVTRPKPMTVEWWHYAQSLTKKPMKGMLTGPVTILNWSFVRDDIPRSETCRQI 600
Query: 578 ALALRDEVADLEAAGIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQ 637
ALA+RDEV DLE AG +IQIDE ALREGLPLRRS+W YL W V+AFRI A+ D TQ
Sbjct: 601 ALAIRDEVTDLEKAGAAMIQIDEAALREGLPLRRSEWQHYLDWAVDAFRITASGVDDATQ 660
Query: 638 IHTHMCYCEFNDIMDSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPN 697
IHTHMCY EFNDI+ +I A+DADVI+IETSRS MELL++F ++ YPNEIGPGVYDIHSP
Sbjct: 661 IHTHMCYSEFNDIIAAIGAMDADVISIETSRSKMELLDAFVDYRYPNEIGPGVYDIHSPR 720
Query: 698 VPSVEWIEALLKKAAKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
VP V + LL+KA K + +++WVNPDCGLKTR W E R AL NMV AA+ R
Sbjct: 721 VPDVSEMVDLLQKARKHLSPDQIWVNPDCGLKTRKWDEVRPALVNMVAAAEQAR 774
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: 1598
Number of extensions: 83
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: 778
Length adjustment: 40
Effective length of query: 713
Effective length of database: 738
Effective search space: 526194
Effective search space used: 526194
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 WP_068464489.1 APY04_RS15365 (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.31884.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 1132.0 0.0 0 1131.8 0.0 1.0 1 lcl|NCBI__GCF_001541235.1:WP_068464489.1 APY04_RS15365 5-methyltetrahydro
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001541235.1:WP_068464489.1 APY04_RS15365 5-methyltetrahydropteroyltriglutamate--homocysteine S-methylt
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1131.8 0.0 0 0 1 754 [] 8 776 .. 8 776 .. 0.99
Alignments for each domain:
== domain 1 score: 1131.8 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lgfPrig++Relk+ale+yw+gk+++++ll++a+ lr+++++kq++ag+d+ip+ndfslYDhvLd+ ++
lcl|NCBI__GCF_001541235.1:WP_068464489.1 8 LGFPRIGPRRELKQALESYWAGKSDEKTLLESAAALRATNWTKQRAAGIDHIPSNDFSLYDHVLDICAM 76
79******************************************************************* PP
TIGR01371 70 lgaiperfkeladdesdldtyFaiaRGtek................kdvaalemtkwfntnYhYlvPel 122
+gaip+ + +++++ +++dtyFa+aRG+++ +v+a+emtkwf+tnYhY+vPel
lcl|NCBI__GCF_001541235.1:WP_068464489.1 77 VGAIPSVYGQVQSK-TSVDTYFAMARGSQEygtvehpylscghqhgLGVPAMEMTKWFDTNYHYMVPEL 144
**********9666.58***********99*************99988********************* PP
TIGR01371 123 skeeefklsknklleeykeakelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkkl 191
s++++f+l+++k+++e+kea++lg++t+PvllGp+tfl+Lak+k e +++l+ll++l+pvY evl++l
lcl|NCBI__GCF_001541235.1:WP_068464489.1 145 SSDQSFALTSTKPVDEFKEAQALGIKTRPVLLGPVTFLTLAKSKT-EGFDTLKLLSALIPVYVEVLRQL 212
******************************************996.88********************* PP
TIGR01371 192 aeagvewvqidePvlvldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealgl 260
aeag+ewvqideP+l++dl + a+++ay ++ea +l+lll++Yf+++ ++l++++slpv++++l
lcl|NCBI__GCF_001541235.1:WP_068464489.1 213 AEAGAEWVQIDEPCLATDLGDGVALALQTAYGRFAEAVPQLRLLLTSYFGAYGDNLDAALSLPVAGIHL 281
********************************************************************* PP
TIGR01371 261 DlveakeelelakakfeedkvLvaGvidGrniwkadlekslkllkkleakag.dklvvstscsllhvpv 328
Dl +a+e+le++ ak +++ +L++GvidGrn+w+a+l + l++l+ + a++g dk+++++scs+lhvp+
lcl|NCBI__GCF_001541235.1:WP_068464489.1 282 DLARAPEQLETVLAKAPKSLTLSLGVIDGRNVWRANLPALLDKLEPVVAQRGaDKIFIAPSCSMLHVPI 350
************************************************99999**************** PP
TIGR01371 329 dleleekldkelkellafakekleelkvlkealeg.eaavaealeaeaaaiaarkkskrvadekvkerl 396
dl++e++ld+e+k+++afa++kl elk+l +al++ +++v+++l+++ +a a+rk+s+++++ +v++r+
lcl|NCBI__GCF_001541235.1:WP_068464489.1 351 DLDAETTLDPEVKNWMAFAAQKLGELKTLGRALNEgRDSVKAELTESMRAAASRKSSQKIHNPAVAARM 419
***********************************9********************************* PP
TIGR01371 397 ealkekkarressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeei 465
+a+++++a r+s+f++R++aq+++l+l ++PtttiGsfPqt evRkaRa+ kg + ++eY++f+++e+
lcl|NCBI__GCF_001541235.1:WP_068464489.1 420 AAVTKEMASRKSPFAARQKAQRDRLQLVAYPTTTIGSFPQTPEVRKARAANAKGALGHAEYNDFLRKET 488
********************************************************************* PP
TIGR01371 466 kkviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtv 534
+ ++++qee+g+DvLvhGefeRnDmv+yFge+l+Gf+ft+ngWvqsYGsR+v+Ppii+gdv+rpkpmtv
lcl|NCBI__GCF_001541235.1:WP_068464489.1 489 EAAVRWQEEIGIDVLVHGEFERNDMVQYFGEQLDGFTFTKNGWVQSYGSRYVRPPIIFGDVTRPKPMTV 557
********************************************************************* PP
TIGR01371 535 keskyaqsltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepal 603
++++yaqslt+kp+kGmLtGPvtilnWsfvR+D+pr+e+++qiala+rdev+dLe+ag+++iqiDe+al
lcl|NCBI__GCF_001541235.1:WP_068464489.1 558 EWWHYAQSLTKKPMKGMLTGPVTILNWSFVRDDIPRSETCRQIALAIRDEVTDLEKAGAAMIQIDEAAL 626
********************************************************************* PP
TIGR01371 604 ReglPlrksdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdme 672
ReglPlr+s++++Yldwav+aFr++asgv d+tqihthmCYsefn+ii+ai a+daDvisie+srs+me
lcl|NCBI__GCF_001541235.1:WP_068464489.1 627 REGLPLRRSEWQHYLDWAVDAFRITASGVDDATQIHTHMCYSEFNDIIAAIGAMDADVISIETSRSKME 695
********************************************************************* PP
TIGR01371 673 lldalkeikkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaal 741
llda+ + ++y++eiG+GvyDihsprvP + e+ +ll+ka k+l +++WvnPDCGLktRkw+ev++al
lcl|NCBI__GCF_001541235.1:WP_068464489.1 696 LLDAFVD-YRYPNEIGPGVYDIHSPRVPDVSEMVDLLQKARKHLSPDQIWVNPDCGLKTRKWDEVRPAL 763
*******.66*********************************************************** PP
TIGR01371 742 knlveaakelRek 754
n+v+aa ++R+k
lcl|NCBI__GCF_001541235.1:WP_068464489.1 764 VNMVAAAEQARAK 776
***********86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (778 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: 8.63
//
[ok]
This GapMind analysis is from Apr 10 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