Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate WP_010961490.1 MCA_RS11060 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
Query= BRENDA::P25665
(753 letters)
>NCBI__GCF_000008325.1:WP_010961490.1
Length = 762
Score = 810 bits (2093), Expect = 0.0
Identities = 419/756 (55%), Positives = 523/756 (69%), Gaps = 12/756 (1%)
Query: 4 LNHTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGD 63
+ H+LGFPR+G RELK+A E+ WAG + EL GRELR RHW Q +GIDL+PVGD
Sbjct: 3 VTHSLGFPRIGAGRELKRAVEACWAGRTGPAELAQTGRELRERHWMIQSGSGIDLVPVGD 62
Query: 64 FAWYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFNTNY 123
FAWYD +L + LLG VP R + ++ +D F++ RG A A EMTKWF+TNY
Sbjct: 63 FAWYDQMLNMTALLGAVPRRFGFQADALSLDQYFQLARGNAEQ----PAMEMTKWFDTNY 118
Query: 124 HYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDRLSL 183
HY+VPEF + F L DEV+EA AL KPVL+GP+T+L LGK + F RL L
Sbjct: 119 HYIVPEFDRETGFGPGTEWLFDEVEEAKALRLNPKPVLIGPLTYLHLGKERQAGFSRLEL 178
Query: 184 LNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDAL-QGQVKLLLTT 242
L +LP Y +L L G+ WVQ+DEP L ++LP WL+A+ PAY AL + KLLL T
Sbjct: 179 LPRLLPAYAAILRRLHASGVPWVQMDEPILGMDLPPEWLEAFAPAYAALAEAGPKLLLAT 238
Query: 243 YFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRADLT 302
YF V + + + V GLH+D V + VA+ K P+D +LS GLI+GRNVWR DL
Sbjct: 239 YFASVAEHAVWLKSSAVAGLHIDAVRAPEQVADFLKDFPADKVLSLGLIDGRNVWRTDLR 298
Query: 303 EKYAQIKD---IVGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELALL 359
Q + ++G+R LW+A SCSLLH P DLS+ET L+ E+K W AFA+QK ELA++
Sbjct: 299 RALEQAESAGAVLGER-LWLAPSCSLLHVPQDLSLETSLNPEIKDWLAFAVQKLEELAVI 357
Query: 360 RDALNSGDTAA---LAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYEVRAEA 416
L G A LAE +Q R S +H+P V++RL ++ D +R + + R+
Sbjct: 358 DKGLRLGRQAVAAELAERDRLLQTRAQSPLIHDPGVKRRLEGLSDADFRRHSPFAERSPL 417
Query: 417 QRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERLG 476
QR R +LP +PTTTIGSFPQT +IR R ++G L+ + YR + I++A+ +QE LG
Sbjct: 418 QRERLRLPPFPTTTIGSFPQTPKIRAARAAHRRGELNGDAYRDAMRAAIREAVYKQESLG 477
Query: 477 LDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEW 536
LD+LVHGEAERNDMVEYFGE L G+ FT++GWVQSYGSRCVKPPI+ GD++RP P+TVEW
Sbjct: 478 LDLLVHGEAERNDMVEYFGERLAGYAFTKHGWVQSYGSRCVKPPIIYGDVARPEPMTVEW 537
Query: 537 AKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGII 596
YAQSLT KPVKGMLTGPVT+L WSF R+D R A QIALA+RDEVADLEAAG+ I
Sbjct: 538 IGYAQSLTKKPVKGMLTGPVTMLQWSFARDDQPRAVTALQIALAIRDEVADLEAAGVAAI 597
Query: 597 QIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIAA 656
QIDEPA REGLPL+ +D YL W V+AFR+ + DDTQIHTHMCY EF DI+ +IA
Sbjct: 598 QIDEPAFREGLPLKAADRADYLDWAVKAFRLASCGVADDTQIHTHMCYSEFGDILPAIAE 657
Query: 657 LDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRIP 716
LDADVITIET RS M+LLE+F F YPN+IGPGVYDIHSP VP+ I ALL+KAA +
Sbjct: 658 LDADVITIETCRSAMDLLEAFGAFGYPNDIGPGVYDIHSPRVPAGAEIRALLEKAAAAVD 717
Query: 717 AERLWVNPDCGLKTRGWPETRAALANMVQAAQNLRR 752
ERLWVNPDCGLKTR WPE ALANMV+AA+ +RR
Sbjct: 718 PERLWVNPDCGLKTRQWPEAEQALANMVEAARAMRR 753
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: 1727
Number of extensions: 84
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: 762
Length adjustment: 40
Effective length of query: 713
Effective length of database: 722
Effective search space: 514786
Effective search space used: 514786
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_010961490.1 MCA_RS11060 (5-methyltetrahydropteroyltriglutamate--homocysteine 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.14175.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 1045.7 0.0 0 1045.4 0.0 1.0 1 lcl|NCBI__GCF_000008325.1:WP_010961490.1 MCA_RS11060 5-methyltetrahydropt
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008325.1:WP_010961490.1 MCA_RS11060 5-methyltetrahydropteroyltriglutamate--homocysteine methyltrans
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1045.4 0.0 0 0 1 753 [. 7 753 .. 7 754 .. 0.99
Alignments for each domain:
== domain 1 score: 1045.4 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lgfPrig+ Relk+a+e+ w+g++ +el+++ ++lr++++ q+ +g+d++pv+df++YD++L++++l
lcl|NCBI__GCF_000008325.1:WP_010961490.1 7 LGFPRIGAGRELKRAVEACWAGRTGPAELAQTGRELRERHWMIQSGSGIDLVPVGDFAWYDQMLNMTAL 75
79******************************************************************* PP
TIGR01371 70 lgaiperfkeladdesdldtyFaiaRGtekkdvaalemtkwfntnYhYlvPelskeeefklsknkllee 138
lga+p+rf +ad+ +ld+yF++aRG+++ +a+emtkwf+tnYhY+vPe+++e+ f ++ l++e
lcl|NCBI__GCF_000008325.1:WP_010961490.1 76 LGAVPRRFGFQADA-LSLDQYFQLARGNAE--QPAMEMTKWFDTNYHYIVPEFDRETGFGPGTEWLFDE 141
*********98555.69**********955..89*********************************** PP
TIGR01371 139 ykeakelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvlv 207
++eak+l ++ kPvl+Gp+t+l L+k+ + +++lell++llp+Y +l++l+++gv wvq+deP+l
lcl|NCBI__GCF_000008325.1:WP_010961490.1 142 VEEAKALRLNPKPVLIGPLTYLHLGKERQ-AGFSRLELLPRLLPAYAAILRRLHASGVPWVQMDEPILG 209
***************************97.88************************************* PP
TIGR01371 208 ldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakeelelakakf 276
+dl++e+l+a+ ay++l+e + klll+tYf sv e+ l+s v++l++D v+a+e+ + ++f
lcl|NCBI__GCF_000008325.1:WP_010961490.1 210 MDLPPEWLEAFAPAYAALAE--AGPKLLLATYFASVAEHAVWLKSSAVAGLHIDAVRAPEQVADFLKDF 276
*******************8..599******************************************** PP
TIGR01371 277 eedkvLvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvpvdleleekldkelkella 345
++dkvL++G+idGrn+w++dl+++l++ ++ a g++l++++scsllhvp dl+le++l++e+k++la
lcl|NCBI__GCF_000008325.1:WP_010961490.1 277 PADKVLSLGLIDGRNVWRTDLRRALEQAESAGAVLGERLWLAPSCSLLHVPQDLSLETSLNPEIKDWLA 345
********************************************************************* PP
TIGR01371 346 fakekleelkvlkealeg.eaavaealeaeaaaiaarkkskrvadekvkerlealkekkarressfeeR 413
fa++kleel+v+ + l+ ++ava++l+++++ +++r++s+ ++d vk+rle l+++++rr+s+f+eR
lcl|NCBI__GCF_000008325.1:WP_010961490.1 346 FAVQKLEELAVIDKGLRLgRQAVAAELAERDRLLQTRAQSPLIHDPGVKRRLEGLSDADFRRHSPFAER 414
****************988************************************************** PP
TIGR01371 414 aeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLvh 482
+ q+++l+lP +PtttiGsfPqt ++R aRa++r+ge++ ++Y +++++ i++++ qe+lglD Lvh
lcl|NCBI__GCF_000008325.1:WP_010961490.1 415 SPLQRERLRLPPFPTTTIGSFPQTPKIRAARAAHRRGELNGDAYRDAMRAAIREAVYKQESLGLDLLVH 483
********************************************************************* PP
TIGR01371 483 GefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkGm 551
Ge+eRnDmveyFge+laG+aft++gWvqsYGsRcvkPpiiygdv rp+pmtv+++ yaqslt+kpvkGm
lcl|NCBI__GCF_000008325.1:WP_010961490.1 484 GEAERNDMVEYFGERLAGYAFTKHGWVQSYGSRCVKPPIIYGDVARPEPMTVEWIGYAQSLTKKPVKGM 552
********************************************************************* PP
TIGR01371 552 LtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdkeeYldw 620
LtGPvt+l+Wsf R+D+pr+ +a qiala+rdev+dLe+ag++ iqiDepa+ReglPl+++d+++Yldw
lcl|NCBI__GCF_000008325.1:WP_010961490.1 553 LTGPVTMLQWSFARDDQPRAVTALQIALAIRDEVADLEAAGVAAIQIDEPAFREGLPLKAADRADYLDW 621
********************************************************************* PP
TIGR01371 621 aveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyekeiGl 689
av+aFrla++gv+d+tqihthmCYsef +i+ aia+ldaDvi+ie+ rs m+ll+a+ + ++y+++iG+
lcl|NCBI__GCF_000008325.1:WP_010961490.1 622 AVKAFRLASCGVADDTQIHTHMCYSEFGDILPAIAELDADVITIETCRSAMDLLEAFGA-FGYPNDIGP 689
***********************************************************.88******* PP
TIGR01371 690 GvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRe 753
GvyDihsprvP+ e+++lleka ++++ erlWvnPDCGLktR+w+e ++al n+veaa+++R
lcl|NCBI__GCF_000008325.1:WP_010961490.1 690 GVYDIHSPRVPAGAEIRALLEKAAAAVDPERLWVNPDCGLKTRQWPEAEQALANMVEAARAMRR 753
**************************************************************96 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (762 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 0.03s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 8.17
//
[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