Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate WP_057507577.1 ABB28_RS04990 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= BRENDA::P25665
(753 letters)
>NCBI__GCF_001431535.1:WP_057507577.1
Length = 767
Score = 787 bits (2032), Expect = 0.0
Identities = 411/755 (54%), Positives = 512/755 (67%), Gaps = 14/755 (1%)
Query: 8 LGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFAWY 67
LGFPR+G +RELK+A E +W+G L A LRARHW Q +AG+D+ P DF+ Y
Sbjct: 7 LGFPRIGAKRELKRALERHWSGEDDIATLQASAAALRARHWKLQIEAGVDVPPSNDFSLY 66
Query: 68 DHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFNTNYHYMV 127
D VL T+ L +PAR++ + F + RG G A EMTKWF+TNYHY+V
Sbjct: 67 DQVLDTAFLFDALPARYRALAEHEPLAAYFAMARGLQRDGIDLHALEMTKWFDTNYHYLV 126
Query: 128 PEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDRLSLLNDI 187
PE GQ F L + L E EA ALG +PVLLGPV++L L K + L LL+ +
Sbjct: 127 PELQAGQAFALRGDKPLAEFREAKALGIHTRPVLLGPVSFLLLSKTT-DGSAALELLDAL 185
Query: 188 LPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQGQV----KLLLTTY 243
LP Y +LA+LA G +WVQ+DEP LV +L A++ AY L G KLLL TY
Sbjct: 186 LPSYVDLLAQLAAAGADWVQLDEPLLVQDLDAGARSAFERAYGVLGGNAAARPKLLLATY 245
Query: 244 FEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRADLTE 303
F + NL ALPV GLHVDLV + + + + LP+ +LSAGL+NGRN+WR L
Sbjct: 246 FGALDDNLSLAAALPVDGLHVDLVRAPEQLDAVLQALPAGRVLSAGLVNGRNIWRTQLDN 305
Query: 304 -----KYAQIKDIVGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELAL 358
+YAQ G LW+A SCSLLH+P+DL++E +LD E++SW AF+ QK EL +
Sbjct: 306 ALILARYAQTDR--GADLLWLAPSCSLLHTPVDLTLEKKLDDELRSWLAFSRQKLEELRV 363
Query: 359 LRDALNSGDTA--ALAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYEVRAEA 416
L DAL+ +A L ++ARR S RVH+PAV RLA+++A D++R Y R A
Sbjct: 364 LADALDGKPSADAGLGANREALEARRRSPRVHDPAVAARLASLSAADARRHGSYPQRRLA 423
Query: 417 QRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERLG 476
Q A +LP PTTTIGSFPQT ++R R K G L +Y + + + QE LG
Sbjct: 424 QHAALQLPLLPTTTIGSFPQTLDVREARARHKSGKLSLGDYEAFLEQQTAHCVRVQEELG 483
Query: 477 LDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEW 536
LDVLVHGE ERNDMVEYFGE L+GF FT NGWVQSYGSRCVKPP++ GD+SRP P+TV W
Sbjct: 484 LDVLVHGEFERNDMVEYFGEQLEGFAFTGNGWVQSYGSRCVKPPVIFGDVSRPRPMTVRW 543
Query: 537 AKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGII 596
++YAQSLT KP+KGMLTGPVT+L WSF R+D R+ +QIALALRDEV DLEAAGIG+I
Sbjct: 544 SQYAQSLTRKPMKGMLTGPVTVLQWSFVRDDQERDATCRQIALALRDEVNDLEAAGIGVI 603
Query: 597 QIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIAA 656
Q+DEPA+REGLPLRR+ W +YL W VE+FRI+ + +D TQIHTHMCY EFNDI+ S+AA
Sbjct: 604 QVDEPAIREGLPLRRAQWRSYLDWAVESFRISTSGVRDATQIHTHMCYSEFNDIIHSVAA 663
Query: 657 LDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRIP 716
+DADVI+IETSRS MELL++F F+YPNEIGPGVYDIHSP VP + LL+KA +
Sbjct: 664 MDADVISIETSRSRMELLDAFVRFNYPNEIGPGVYDIHSPRVPDKVEMVDLLRKALAVLK 723
Query: 717 AERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
E+LWVNPDCGLKTRGWPETRAAL +V AA LR
Sbjct: 724 PEQLWVNPDCGLKTRGWPETRAALQALVAAAAELR 758
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: 1632
Number of extensions: 82
Number of successful extensions: 7
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: 767
Length adjustment: 40
Effective length of query: 713
Effective length of database: 727
Effective search space: 518351
Effective search space used: 518351
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_057507577.1 ABB28_RS04990 (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.28564.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 1094.9 0.0 0 1094.7 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057507577.1 ABB28_RS04990 5-methyltetrahydro
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057507577.1 ABB28_RS04990 5-methyltetrahydropteroyltriglutamate--homocysteine S-methylt
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1094.7 0.0 0 0 1 754 [] 7 760 .. 7 760 .. 0.98
Alignments for each domain:
== domain 1 score: 1094.7 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lgfPrig+kRelk+ale++w+g+ + ++l+++a+ lr++++k q eagvdv p+ndfslYD+vLdta l
lcl|NCBI__GCF_001431535.1:WP_057507577.1 7 LGFPRIGAKRELKRALERHWSGEDDIATLQASAAALRARHWKLQIEAGVDVPPSNDFSLYDQVLDTAFL 75
79******************************************************************* PP
TIGR01371 70 lgaiperfkeladdesdldtyFaiaRGtek..kdvaalemtkwfntnYhYlvPelskeeefklsknkll 136
++a+p+r++ la++e l+ yFa+aRG ++ d++alemtkwf+tnYhYlvPel++ ++f+l+ +k+l
lcl|NCBI__GCF_001431535.1:WP_057507577.1 76 FDALPARYRALAEHE-PLAAYFAMARGLQRdgIDLHALEMTKWFDTNYHYLVPELQAGQAFALRGDKPL 143
***********8877.8***********99556789********************************* PP
TIGR01371 137 eeykeakelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePv 205
e++eak+lg++t+PvllGp++fl+L+k+++ +++lell++llp Y ++l +la+ag++wvq+deP+
lcl|NCBI__GCF_001431535.1:WP_057507577.1 144 AEFREAKALGIHTRPVLLGPVSFLLLSKTTD--GSAALELLDALLPSYVDLLAQLAAAGADWVQLDEPL 210
******************************8..5589******************************** PP
TIGR01371 206 lvldlskeelaavkeayeelee.askelklllqtYfdsveealeklvslpvealglDlveakeelelak 273
lv dl++ +++a+++ay l a+++ klll+tYf++++++l+ ++ lpv++l++Dlv+a+e+l+++
lcl|NCBI__GCF_001431535.1:WP_057507577.1 211 LVQDLDAGARSAFERAYGVLGGnAAARPKLLLATYFGALDDNLSLAAALPVDGLHVDLVRAPEQLDAVL 279
********************86156789***************************************** PP
TIGR01371 274 akfeedkvLvaGvidGrniwkadlekslkllkkleakag.dklvvstscsllhvpvdleleekldkelk 341
+++++ +vL+aG+++Grniw+++l ++l l + ++ +g d l++++scsllh+pvdl+le+kld+el+
lcl|NCBI__GCF_001431535.1:WP_057507577.1 280 QALPAGRVLSAGLVNGRNIWRTQLDNALILARYAQTDRGaDLLWLAPSCSLLHTPVDLTLEKKLDDELR 348
****************************99999999888899*************************** PP
TIGR01371 342 ellafakekleelkvlkealegeaavaealeaeaaaiaarkkskrvadekvkerlealkekkarressf 410
++laf+++kleel+vl++al+g+ ++ + l a+++a++ar++s+rv+d +v++rl++l++++arr+ s+
lcl|NCBI__GCF_001431535.1:WP_057507577.1 349 SWLAFSRQKLEELRVLADALDGKPSADAGLGANREALEARRRSPRVHDPAVAARLASLSAADARRHGSY 417
**********************9999******************************************* PP
TIGR01371 411 eeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDv 479
+R+ aq++ l+lPllPtttiGsfPqt +vR+aRa+++ g++s +Ye+f+++++++++++qeelglDv
lcl|NCBI__GCF_001431535.1:WP_057507577.1 418 PQRRLAQHAALQLPLLPTTTIGSFPQTLDVREARARHKSGKLSLGDYEAFLEQQTAHCVRVQEELGLDV 486
********************************************************************* PP
TIGR01371 480 LvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpv 548
LvhGefeRnDmveyFge+l+Gfaft ngWvqsYGsRcvkPp+i+gdvsrp+pmtv++s+yaqslt+kp+
lcl|NCBI__GCF_001431535.1:WP_057507577.1 487 LVHGEFERNDMVEYFGEQLEGFAFTGNGWVQSYGSRCVKPPVIFGDVSRPRPMTVRWSQYAQSLTRKPM 555
********************************************************************* PP
TIGR01371 549 kGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdkeeY 617
kGmLtGPvt+l+WsfvR+D++r +++qialalrdev+dLe+agi +iq+Depa+ReglPlr++++++Y
lcl|NCBI__GCF_001431535.1:WP_057507577.1 556 KGMLTGPVTVLQWSFVRDDQERDATCRQIALALRDEVNDLEAAGIGVIQVDEPAIREGLPLRRAQWRSY 624
********************************************************************* PP
TIGR01371 618 ldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyeke 686
ldwave+Fr+++sgv+d+tqihthmCYsefn+ii+++aa+daDvisie+srs mellda+ ++y++e
lcl|NCBI__GCF_001431535.1:WP_057507577.1 625 LDWAVESFRISTSGVRDATQIHTHMCYSEFNDIIHSVAAMDADVISIETSRSRMELLDAFVR-FNYPNE 692
**************************************************************.67**** PP
TIGR01371 687 iGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRek 754
iG+GvyDihsprvP k e+ +ll+kal++l+ e+lWvnPDCGLktR w+e++aal+ lv+aa elR++
lcl|NCBI__GCF_001431535.1:WP_057507577.1 693 IGPGVYDIHSPRVPDKVEMVDLLRKALAVLKPEQLWVNPDCGLKTRGWPETRAALQALVAAAAELRAE 760
*****************************************************************985 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (767 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: 9.81
//
[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