Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate 200004 SO0818 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (NCBI ptt file)
Query= BRENDA::P25665
(753 letters)
>FitnessBrowser__MR1:200004
Length = 760
Score = 843 bits (2178), Expect = 0.0
Identities = 425/755 (56%), Positives = 543/755 (71%), Gaps = 9/755 (1%)
Query: 6 HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
++LGFPR+G RRELK A E YW G ST+ EL V RELR HW Q AGI+ +PVGDFA
Sbjct: 4 NSLGFPRIGRRRELKFALEKYWRGESTQAELHEVARELRRTHWQWQVAAGIEQVPVGDFA 63
Query: 66 WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFNTNYHY 125
+YD VLT S L +P RH+ +G++D+DTLFR+ RGRAPTG A A+EMTK+FNTNYHY
Sbjct: 64 FYDQVLTLSATLNAIPDRHRG-EGAIDLDTLFRVARGRAPTGTDAPASEMTKYFNTNYHY 122
Query: 126 MVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDRLSLLN 185
+VPE + Q F + + Q DEV EA ALG+K KPVLLGPV++L+L K G+ FD+LSLL
Sbjct: 123 LVPELKQDQVFSIAYEQFFDEVAEAQALGYKAKPVLLGPVSYLYLAKTVGQDFDKLSLLP 182
Query: 186 DILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQ-GQVKLLLTTYF 244
++L Y ++LA A +G+ WVQ++EP L LEL W A +Y AL+ QVK+LLT+Y+
Sbjct: 183 NLLKAYAEILARFAAQGVTWVQLEEPILALELTHEWQAAISESYQALKTAQVKILLTSYY 242
Query: 245 EGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRAD---L 301
++ + ++ALPV GLH+DLV + +A L D +LS G++NGRNVW A+ +
Sbjct: 243 GSISHHQALVSALPVAGLHLDLVTAPEQLALFANALRPDQILSVGVVNGRNVWAAEVDLI 302
Query: 302 TEKYAQIKDIVGKRD---LWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELAL 358
E+ + + +D LW+ +SCSLLHSP+DL VET L ++ AFA QK ELA
Sbjct: 303 VERIGSVARDLCSQDGSRLWIGTSCSLLHSPVDLEVETTLAPTLRQQLAFAKQKLLELAN 362
Query: 359 LRDALNSGDTAALAEWSAPIQARRHS-TRVHNPAVEKRLAAITAQDSQRANVYEVRAEAQ 417
+R L + ++ A E ARR + + + V R+AA+T D +R + + R Q
Sbjct: 363 VRQLLQAPESVAAKEIVNTCLARREAKAQAADAKVIARVAALTPADYERVSEFTERQAVQ 422
Query: 418 RARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERLGL 477
+ +++LP PTTTIGSFPQT IR LR ++KG L Y + + + I Q +LG+
Sbjct: 423 QRKYRLPLLPTTTIGSFPQTPAIRGLRSRWRKGELSDAQYTEQLQQVTRDTIDRQLKLGI 482
Query: 478 DVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEWA 537
DVLVHGEAERNDMVEYFGE L+G FT+NGWVQSYGSRCVKPP++ GD+SRP +TV+WA
Sbjct: 483 DVLVHGEAERNDMVEYFGEQLEGVGFTKNGWVQSYGSRCVKPPLIYGDVSRPKAMTVDWA 542
Query: 538 KYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGIIQ 597
+AQSLTDKPVKGMLTGPVTIL WSF RED+SR+TIA Q+ALA+RDEV DL+ AGIGIIQ
Sbjct: 543 VFAQSLTDKPVKGMLTGPVTILHWSFAREDISRDTIATQLALAIRDEVVDLQHAGIGIIQ 602
Query: 598 IDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIAAL 657
IDEPA REGLPL++S+W AYL W V AF+++AA D+TQIHTHMCY EFND + +IAA+
Sbjct: 603 IDEPAFREGLPLKQSEWQAYLDWAVNAFKLSAAGVVDETQIHTHMCYSEFNDTIAAIAAM 662
Query: 658 DADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRIPA 717
DADVITIETSRS MELL +FE+F+YPNEIGPGVYDIHSPN PSVE + L++KAA+++P
Sbjct: 663 DADVITIETSRSRMELLNAFEDFEYPNEIGPGVYDIHSPNTPSVEAMVHLIEKAAQKVPV 722
Query: 718 ERLWVNPDCGLKTRGWPETRAALANMVQAAQNLRR 752
+LWVNPDCGLKTR W E AL NMV A + LRR
Sbjct: 723 RQLWVNPDCGLKTRTWDEVEPALKNMVDATRELRR 757
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: 1566
Number of extensions: 71
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: 760
Length adjustment: 40
Effective length of query: 713
Effective length of database: 720
Effective search space: 513360
Effective search space used: 513360
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 200004 SO0818 (5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (NCBI ptt file))
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.25949.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 1066.5 0.0 0 1066.4 0.0 1.0 1 lcl|FitnessBrowser__MR1:200004 SO0818 5-methyltetrahydropteroyl
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200004 SO0818 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (NCBI pt
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1066.4 0.0 0 0 1 753 [. 6 757 .. 6 758 .. 0.97
Alignments for each domain:
== domain 1 score: 1066.4 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavllgaiperfke 79
lgfPrig++Relk+alekyw+g+++++el++va++lr+++++ q +ag++ +pv+df++YD+vL++++ l+aip+r++
lcl|FitnessBrowser__MR1:200004 6 LGFPRIGRRRELKFALEKYWRGESTQAELHEVARELRRTHWQWQVAAGIEQVPVGDFAFYDQVLTLSATLNAIPDRHRG 84
79***************************************************************************99 PP
TIGR01371 80 laddesdldtyFaiaRGtek..kdvaalemtkwfntnYhYlvPelskeeefklsknklleeykeakelgvetkPvllGp 156
+++dldt+F++aRG + +d++a+emtk+fntnYhYlvPel++++ f+++ ++ ++e+ ea++lg ++kPvllGp
lcl|FitnessBrowser__MR1:200004 85 E--GAIDLDTLFRVARGRAPtgTDAPASEMTKYFNTNYHYLVPELKQDQVFSIAYEQFFDEVAEAQALGYKAKPVLLGP 161
7..7889**********98777899****************************************************** PP
TIGR01371 157 itflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvlvldlskeelaavkeayeeleeaskelkll 235
+++l+Lak++ ++++++l+ll++ll++Y e+l ++a++gv+wvq++eP+l+l+l++e++aa+ e y++l+ +++k+l
lcl|FitnessBrowser__MR1:200004 162 VSYLYLAKTV-GQDFDKLSLLPNLLKAYAEILARFAAQGVTWVQLEEPILALELTHEWQAAISESYQALKT--AQVKIL 237
**********.599*******************************************************97..69**** PP
TIGR01371 236 lqtYfdsveealeklvslpvealglDlveakeelelakakfeedkvLvaGvidGrniwkadlekslkllkklea....k 310
l++Y++s++++ + ++ lpv++l+lDlv+a+e+l+l +++++ d++L++Gv++Grn+w+a++ +++++ ++++ +
lcl|FitnessBrowser__MR1:200004 238 LTSYYGSISHHQALVSALPVAGLHLDLVTAPEQLALFANALRPDQILSVGVVNGRNVWAAEVDLIVERIGSVARdlcsQ 316
********99999999*********************************************999998887765411115 PP
TIGR01371 311 agdklvvstscsllhvpvdleleekldkelkellafakekleelkvlkealeg.eaavaealeaeaaaiaarkkskrva 388
g++l++ tscsllh+pvdle e++l ++l++ lafak+kl el+ ++++l+ e+ +a+++ + + +a+r+ ++++a
lcl|FitnessBrowser__MR1:200004 317 DGSRLWIGTSCSLLHSPVDLEVETTLAPTLRQQLAFAKQKLLELANVRQLLQApESVAAKEIVN--TCLARREAKAQAA 393
569*************************************************966666666655..5899999999*** PP
TIGR01371 389 dekvkerlealkekkarressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikk 467
d+kv +r++al+ ++ +r s+f+eR++ q++k++lPllPtttiGsfPqt +R R+++rkge+s+++Y++ +++ +++
lcl|FitnessBrowser__MR1:200004 394 DAKVIARVAALTPADYERVSEFTERQAVQQRKYRLPLLPTTTIGSFPQTPAIRGLRSRWRKGELSDAQYTEQLQQVTRD 472
******************************************************************************* PP
TIGR01371 468 viklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltsk 546
+i+ q +lg+DvLvhGe+eRnDmveyFge+l+G ft+ngWvqsYGsRcvkPp+iygdvsrpk+mtv++ ++aqslt+k
lcl|FitnessBrowser__MR1:200004 473 TIDRQLKLGIDVLVHGEAERNDMVEYFGEQLEGVGFTKNGWVQSYGSRCVKPPLIYGDVSRPKAMTVDWAVFAQSLTDK 551
******************************************************************************* PP
TIGR01371 547 pvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdkeeYldwaveaF 625
pvkGmLtGPvtil+Wsf ReD++r +ia+q+ala+rdev+dL++agi iiqiDepa+ReglPl++s++++Yldwav+aF
lcl|FitnessBrowser__MR1:200004 552 PVKGMLTGPVTILHWSFAREDISRDTIATQLALAIRDEVVDLQHAGIGIIQIDEPAFREGLPLKQSEWQAYLDWAVNAF 630
******************************************************************************* PP
TIGR01371 626 rlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyekeiGlGvyDihsprvPskee 704
+l+a+gv detqihthmCYsefn+ i+aiaa+daDvi+ie+srs mell+a+++ ++y++eiG+GvyDihsp+ Ps+e
lcl|FitnessBrowser__MR1:200004 631 KLSAAGVVDETQIHTHMCYSEFNDTIAAIAAMDADVITIETSRSRMELLNAFED-FEYPNEIGPGVYDIHSPNTPSVEA 708
******************************************************.67********************** PP
TIGR01371 705 laellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRe 753
+ +l+eka +k+p ++lWvnPDCGLktR w+ev++alkn+v+a++elR
lcl|FitnessBrowser__MR1:200004 709 MVHLIEKAAQKVPVRQLWVNPDCGLKTRTWDEVEPALKNMVDATRELRR 757
**********************************************996 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (760 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: 12.75
//
[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