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.32357.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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06 # Mc/sec: 8.79 // [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