Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate N515DRAFT_1630 N515DRAFT_1630 methionine synthase (B12-independent)
Query= BRENDA::P25665
(753 letters)
>FitnessBrowser__Dyella79:N515DRAFT_1630
Length = 763
Score = 794 bits (2051), Expect = 0.0
Identities = 413/751 (54%), Positives = 516/751 (68%), Gaps = 8/751 (1%)
Query: 8 LGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFAWY 67
LGFPR+G RRELK+A E+YW + R LL +LR RHW Q++AG ++P DF+ Y
Sbjct: 7 LGFPRMGARRELKQALEAYWRDETQRAPLLDTAGQLRERHWKMQREAGAHVVPCNDFSLY 66
Query: 68 DHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFNTNYHYMV 127
DHVL T+ L +P R++ + + F + RG G A EMTKWF+TNYHY+V
Sbjct: 67 DHVLDTAWLFDAIPERYRALADADPLAGYFAMARGTQRAGVDLHALEMTKWFDTNYHYIV 126
Query: 128 PEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDRLSLLNDI 187
PE GQ F+L + + E EA A GH+ +PVLLGPV++L L K + DRL+LL+ +
Sbjct: 127 PELHAGQAFRLRGDKPVQEFLEARAQGHEARPVLLGPVSFLLLSKTS-DGSDRLALLDRL 185
Query: 188 LPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQGQV--KLLLTTYFE 245
LP Y ++L +L G EWVQ+DEP LVL+L AY+ AY AL G KLLL TYF
Sbjct: 186 LPAYAELLGKLHDAGAEWVQLDEPCLVLDLDHEDAAAYRSAYAALAGTTRPKLLLATYFG 245
Query: 246 GVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRADLTEKY 305
+ NL LPV GLH+DLV + + LP+D +LS G+++GRNVWRADL
Sbjct: 246 ALGDNLPLAQELPVDGLHIDLVRAPAQLDAVLGSLPADRVLSLGVVDGRNVWRADLDRAM 305
Query: 306 AQIK---DIVGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELALLRDA 362
A + + +G++ +W+A SCSLLH P+D S+E L A+V +W AFA QK EL + D
Sbjct: 306 AITRVAIERLGRQRVWLAPSCSLLHVPLDASLEKALPADVHAWLAFARQKLEELRTVADM 365
Query: 363 LNSGDTA--ALAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYEVRAEAQRAR 420
TA AL I ARR S +VH AV +RLA + A + R + Y R Q+ R
Sbjct: 366 CKGVVTAYPALEHAREVIAARRASPKVHRLAVAQRLANLDASAAHRRSTYAFRRGKQQQR 425
Query: 421 FKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERLGLDVL 480
F+LP +PTTTIGSFPQT E+R R +K G A Y IAE + QE +G+DVL
Sbjct: 426 FQLPLFPTTTIGSFPQTAEVREARARYKSGQWSAAEYDALIAEQTAACVQFQEAIGIDVL 485
Query: 481 VHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEWAKYA 540
VHGE ERNDMVEYFGE LDGFVFT++GWVQSYGSRCVKPPI+ GD+ RPAP+TV W+ YA
Sbjct: 486 VHGEFERNDMVEYFGEQLDGFVFTRHGWVQSYGSRCVKPPIIYGDVQRPAPMTVRWSAYA 545
Query: 541 QSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGIIQIDE 600
Q+LT +PVKGMLTGPVT+L WSF R+D R T +Q+ALALRDEV DLEAAGI IIQIDE
Sbjct: 546 QALTGRPVKGMLTGPVTVLQWSFVRDDQPRATTCRQLALALRDEVLDLEAAGIRIIQIDE 605
Query: 601 PALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIAALDAD 660
PALREGLPLRR+DW YL W VE+FR+ A+ DDTQIHTHMCY EFNDI++++AA+DAD
Sbjct: 606 PALREGLPLRRADWAGYLGWAVESFRLAASGVADDTQIHTHMCYSEFNDIIEAVAAMDAD 665
Query: 661 VITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRIPAERL 720
VI+IETSRS MELL +FE F YPNEIGPGVYDIHSP VP V + ALL+KA + + E+L
Sbjct: 666 VISIETSRSRMELLGAFERFRYPNEIGPGVYDIHSPRVPDVAEMVALLEKAGEVLSPEQL 725
Query: 721 WVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
WVNPDCGLKTRGW ETR AL ++V+AA+ +R
Sbjct: 726 WVNPDCGLKTRGWEETRKALVSLVEAARVMR 756
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: 1654
Number of extensions: 92
Number of successful extensions: 9
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: 763
Length adjustment: 40
Effective length of query: 713
Effective length of database: 723
Effective search space: 515499
Effective search space used: 515499
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 N515DRAFT_1630 N515DRAFT_1630 (methionine synthase (B12-independent))
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.31258.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 1092.3 0.0 0 1092.1 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_1630 N515DRAFT_1630 methionine syntha
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_1630 N515DRAFT_1630 methionine synthase (B12-independent)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1092.1 0.0 0 0 1 753 [. 7 757 .. 7 758 .. 0.99
Alignments for each domain:
== domain 1 score: 1092.1 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdt 66
lgfPr+g++Relk+ale+yw+++++++ ll++a +lr++++k q+eag v+p ndfslYDhvLdt
lcl|FitnessBrowser__Dyella79:N515DRAFT_1630 7 LGFPRMGARRELKQALEAYWRDETQRAPLLDTAGQLRERHWKMQREAGAHVVPCNDFSLYDHVLDT 72
79**************************************************************** PP
TIGR01371 67 avllgaiperfkeladdesdldtyFaiaRGtek..kdvaalemtkwfntnYhYlvPelskeeefkl 130
a l++aiper++ lad++ l+ yFa+aRGt++ d++alemtkwf+tnYhY+vPel++ ++f+l
lcl|FitnessBrowser__Dyella79:N515DRAFT_1630 73 AWLFDAIPERYRALADAD-PLAGYFAMARGTQRagVDLHALEMTKWFDTNYHYIVPELHAGQAFRL 137
**************7766.8***********9977899**************************** PP
TIGR01371 131 sknklleeykeakelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagv 196
+ +k+++e++ea+++g+e++PvllGp++fl+L+k+++ +++l+ll++llp+Y e+l kl++ag+
lcl|FitnessBrowser__Dyella79:N515DRAFT_1630 138 RGDKPVQEFLEARAQGHEARPVLLGPVSFLLLSKTSD--GSDRLALLDRLLPAYAELLGKLHDAGA 201
************************************8..5699*********************** PP
TIGR01371 197 ewvqidePvlvldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDl 262
ewvq+deP+lvldl++e+ aa+++ay++l+ +++ klll+tYf+++ ++l +++lpv++l++Dl
lcl|FitnessBrowser__Dyella79:N515DRAFT_1630 202 EWVQLDEPCLVLDLDHEDAAAYRSAYAALAG-TTRPKLLLATYFGALGDNLPLAQELPVDGLHIDL 266
******************************8.699******************************* PP
TIGR01371 263 veakeelelakakfeedkvLvaGvidGrniwkadlekslkllkkleakag.dklvvstscsllhvp 327
v+a+++l+++ ++++d+vL++Gv+dGrn+w+adl +++++ + ++ g +++++++scsllhvp
lcl|FitnessBrowser__Dyella79:N515DRAFT_1630 267 VRAPAQLDAVLGSLPADRVLSLGVVDGRNVWRADLDRAMAITRVAIERLGrQRVWLAPSCSLLHVP 332
***************************************999988888888*************** PP
TIGR01371 328 vdleleekldkelkellafakekleelkvlkealegeaavaealeaeaaaiaarkkskrvadekvk 393
+d +le++l ++++ +lafa++kleel++++++ +g +++ ale++++ iaar+ s++v+ +v+
lcl|FitnessBrowser__Dyella79:N515DRAFT_1630 333 LDASLEKALPADVHAWLAFARQKLEELRTVADMCKGVVTAYPALEHAREVIAARRASPKVHRLAVA 398
************************************9999999*********************** PP
TIGR01371 394 erlealkekkarressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYek 459
+rl++l+++ a+r+s ++ R+ +q+++++lPl+PtttiGsfPqt+evR+aRa+++ g++s++eY++
lcl|FitnessBrowser__Dyella79:N515DRAFT_1630 399 QRLANLDASAAHRRSTYAFRRGKQQQRFQLPLFPTTTIGSFPQTAEVREARARYKSGQWSAAEYDA 464
****************************************************************** PP
TIGR01371 460 fikeeikkviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygd 525
i e+++ ++++qe++g+DvLvhGefeRnDmveyFge+l+Gf+ft++gWvqsYGsRcvkPpiiygd
lcl|FitnessBrowser__Dyella79:N515DRAFT_1630 465 LIAEQTAACVQFQEAIGIDVLVHGEFERNDMVEYFGEQLDGFVFTRHGWVQSYGSRCVKPPIIYGD 530
****************************************************************** PP
TIGR01371 526 vsrpkpmtvkeskyaqsltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeea 591
v+rp+pmtv++s+yaq+lt +pvkGmLtGPvt+l+WsfvR+D+pr+++++q+alalrdev dLe+a
lcl|FitnessBrowser__Dyella79:N515DRAFT_1630 531 VQRPAPMTVRWSAYAQALTGRPVKGMLTGPVTVLQWSFVRDDQPRATTCRQLALALRDEVLDLEAA 596
****************************************************************** PP
TIGR01371 592 gikiiqiDepalReglPlrksdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaal 657
gi+iiqiDepalReglPlr++d++ Yl wave+Frlaasgv+d+tqihthmCYsefn+iiea+aa+
lcl|FitnessBrowser__Dyella79:N515DRAFT_1630 597 GIRIIQIDEPALREGLPLRRADWAGYLGWAVESFRLAASGVADDTQIHTHMCYSEFNDIIEAVAAM 662
****************************************************************** PP
TIGR01371 658 daDvisieasrsdmelldalkeikkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWv 723
daDvisie+srs mell a++ ++y++eiG+GvyDihsprvP + e+ +lleka ++l e+lWv
lcl|FitnessBrowser__Dyella79:N515DRAFT_1630 663 DADVISIETSRSRMELLGAFER-FRYPNEIGPGVYDIHSPRVPDVAEMVALLEKAGEVLSPEQLWV 727
**********************.66***************************************** PP
TIGR01371 724 nPDCGLktRkweevkaalknlveaakelRe 753
nPDCGLktR wee+++al lveaa+ +Re
lcl|FitnessBrowser__Dyella79:N515DRAFT_1630 728 NPDCGLKTRGWEETRKALVSLVEAARVMRE 757
*****************************8 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (763 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 12.58
//
[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