Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate GFF1415 Psest_1452 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= BRENDA::P25665 (753 letters) >FitnessBrowser__psRCH2:GFF1415 Length = 769 Score = 908 bits (2346), Expect = 0.0 Identities = 460/758 (60%), Positives = 552/758 (72%), Gaps = 13/758 (1%) Query: 6 HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65 H LGFPR+G RELKKA E+YW G L VGR+LRA+HW Q AGI LLPVGDFA Sbjct: 5 HNLGFPRIGADRELKKALEAYWKGELDELGLRQVGRQLRAQHWQAQADAGIQLLPVGDFA 64 Query: 66 WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRG-RAPTGEPAAAAEMTKWFNTNYH 124 WYD VLT SL+ G VP R + DG +DT+F + RG + A EMTKWF+TNYH Sbjct: 65 WYDQVLTHSLMFGVVPQRFRPADGQPTLDTVFAMARGVTSSCCGGGQAQEMTKWFDTNYH 124 Query: 125 YMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQ---FDRL 181 Y+VPEF QQF+L+W+QL +EV+EA ALGH +KPVL+GP+T+LWLGK+KGE FD+L Sbjct: 125 YLVPEFTVDQQFQLSWSQLFEEVEEAQALGHAIKPVLVGPLTYLWLGKLKGEDTEGFDKL 184 Query: 182 SLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQ-GQVKLLL 240 LL +LPVY +VL LA +GIEWVQIDEP L L+LPQ W +A++ AY+ LQ +K L+ Sbjct: 185 ELLERLLPVYGEVLDRLAAQGIEWVQIDEPILALDLPQDWKNAFERAYNLLQRAPLKKLV 244 Query: 241 TTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRAD 300 TYF G+ NL ALPV GLH+DLV + + LP+ +LS GL+NGRNVWR D Sbjct: 245 ATYFGGLEDNLSLAAALPVDGLHIDLVRAPEQYPLILDWLPTYKVLSLGLVNGRNVWRCD 304 Query: 301 LT---EKYAQIKDIVGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELA 357 L E + +G R LW+A SCSLLHSP+DL E RLD E+K W AFA+QKC E+A Sbjct: 305 LDKALEVARHAAERLGDR-LWLAPSCSLLHSPVDLEREDRLDHELKGWLAFAVQKCAEVA 363 Query: 358 LLRDALNSGDT----AALAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYEVR 413 L A+N LA A AR+HS R+H P V+ RL+AI QDSQR +V+ R Sbjct: 364 TLARAINEPTNEDVVVELARSRAVQAARQHSPRIHKPQVQTRLSAIQPQDSQRTSVFAAR 423 Query: 414 AEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQE 473 E QRAR LPA+PTTTIGSFPQT IR R +K+G L +Y + I+ A+ QE Sbjct: 424 IEQQRARLDLPAFPTTTIGSFPQTPAIRLARQAYKQGRLSLGDYTEAMQAEIRHAVAVQE 483 Query: 474 RLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPIT 533 ++GLDVLVHGEAERNDMVEYF E LDG+ FT+ GWVQSYGSRCVKP ++ GD+SRP P+T Sbjct: 484 QIGLDVLVHGEAERNDMVEYFAEQLDGYAFTRFGWVQSYGSRCVKPAVIYGDLSRPQPMT 543 Query: 534 VEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGI 593 V+W +YAQ TD+ +KGMLTGPVT+L WSF REDVSRE A+Q+ALA+RDEV DLEAAGI Sbjct: 544 VDWIRYAQQQTDRVMKGMLTGPVTMLMWSFAREDVSREVQARQLALAIRDEVCDLEAAGI 603 Query: 594 GIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDS 653 IIQIDE A REGLPLRR+ W YL W VEAFR+ A+ +D+TQIHTHMCY EFND+++S Sbjct: 604 RIIQIDEAAFREGLPLRRAQWQHYLDWAVEAFRLCASGVRDETQIHTHMCYSEFNDVIES 663 Query: 654 IAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAK 713 IAA+DADVITIETSRS MELLE+F FDYPN+IGPGVYDIHSP VP + LL+KAA+ Sbjct: 664 IAAMDADVITIETSRSQMELLEAFRAFDYPNDIGPGVYDIHSPRVPDTAEMVQLLEKAAE 723 Query: 714 RIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751 RIPAERLWVNPDCGLKTR WPET AAL NMV AA+ LR Sbjct: 724 RIPAERLWVNPDCGLKTRAWPETEAALVNMVAAARQLR 761 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: 1726 Number of extensions: 82 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: 769 Length adjustment: 40 Effective length of query: 713 Effective length of database: 729 Effective search space: 519777 Effective search space used: 519777 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 GFF1415 Psest_1452 ( 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.7983.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 1092.7 0.0 0 1092.5 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF1415 Psest_1452 5-methyltetrahydropt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF1415 Psest_1452 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransfera # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1092.5 0.0 0 0 1 753 [. 7 762 .. 7 763 .. 0.98 Alignments for each domain: == domain 1 score: 1092.5 bits; conditional E-value: 0 TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavllgaipe 75 lgfPrig+ Relkkale+ywkg++++ l +v ++lr++++++q++ag++++pv+df++YD+vL+ ++++g++p+ lcl|FitnessBrowser__psRCH2:GFF1415 7 LGFPRIGADRELKKALEAYWKGELDELGLRQVGRQLRAQHWQAQADAGIQLLPVGDFAWYDQVLTHSLMFGVVPQ 81 79************************************************************************* PP TIGR01371 76 rfkeladdesdldtyFaiaRGtek...kdvaalemtkwfntnYhYlvPelskeeefklsknklleeykeakelgv 147 rf+ d++ +ldt Fa+aRG ++ + +a+emtkwf+tnYhYlvPe++ +++f+ls+++l+ee++ea++lg+ lcl|FitnessBrowser__psRCH2:GFF1415 82 RFRPA-DGQPTLDTVFAMARGVTSsccGGGQAQEMTKWFDTNYHYLVPEFTVDQQFQLSWSQLFEEVEEAQALGH 155 ****8.66779**********9888887889******************************************** PP TIGR01371 148 etkPvllGpitflkLakakee..eekellellekllpvYkevlkklaeagvewvqidePvlvldlskeelaavke 220 kPvl+Gp+t+l+L+k k e e +++lelle+llpvY evl++la++g+ewvqideP+l+ldl++++++a+++ lcl|FitnessBrowser__psRCH2:GFF1415 156 AIKPVLVGPLTYLWLGKLKGEdtEGFDKLELLERLLPVYGEVLDRLAAQGIEWVQIDEPILALDLPQDWKNAFER 230 ****************9887666899************************************************* PP TIGR01371 221 ayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakeelelakakfeedkvLvaGvidGrniwka 295 ay+ l++ + lk l++tYf+ +e++l+ ++ lpv++l++Dlv+a+e+ l +++ kvL++G+++Grn+w+ lcl|FitnessBrowser__psRCH2:GFF1415 231 AYNLLQR--APLKKLVATYFGGLEDNLSLAAALPVDGLHIDLVRAPEQYPLILDWLPTYKVLSLGLVNGRNVWRC 303 *****97..4777789*********************************************************** PP TIGR01371 296 dlekslkllkkleakagdklvvstscsllhvpvdleleekldkelkellafakekleelkvlkealeg..eaava 368 dl k+l++ ++ +++ gd+l++++scsllh+pvdle+e++ld+elk +lafa++k++e+++l++a+++ +++v lcl|FitnessBrowser__psRCH2:GFF1415 304 DLDKALEVARHAAERLGDRLWLAPSCSLLHSPVDLEREDRLDHELKGWLAFAVQKCAEVATLARAINEptNEDVV 378 *******************************************************************99667788 PP TIGR01371 369 ealeaeaaaiaarkkskrvadekvkerlealkekkarressfeeRaeaqekklnlPllPtttiGsfPqtkevRka 443 +l+ ++a aar++s+r+++ +v++rl+a++ ++++r+s f++R e+q+++l+lP++PtttiGsfPqt +R a lcl|FitnessBrowser__psRCH2:GFF1415 379 VELARSRAVQAARQHSPRIHKPQVQTRLSAIQPQDSQRTSVFAARIEQQRARLDLPAFPTTTIGSFPQTPAIRLA 453 888888888899*************************************************************** PP TIGR01371 444 RakfrkgeiseeeYekfikeeikkviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvk 518 R+++++g++s +Y++++++ei++++++qe++glDvLvhGe+eRnDmveyF+e+l+G+aft++gWvqsYGsRcvk lcl|FitnessBrowser__psRCH2:GFF1415 454 RQAYKQGRLSLGDYTEAMQAEIRHAVAVQEQIGLDVLVHGEAERNDMVEYFAEQLDGYAFTRFGWVQSYGSRCVK 528 *************************************************************************** PP TIGR01371 519 PpiiygdvsrpkpmtvkeskyaqsltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagi 593 P++iygd+srp+pmtv++++yaq t++ +kGmLtGPvt+l Wsf ReD++r+ +a+q+ala+rdev dLe+agi lcl|FitnessBrowser__psRCH2:GFF1415 529 PAVIYGDLSRPQPMTVDWIRYAQQQTDRVMKGMLTGPVTMLMWSFAREDVSREVQARQLALAIRDEVCDLEAAGI 603 *************************************************************************** PP TIGR01371 594 kiiqiDepalReglPlrksdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasr 668 +iiqiDe+a+ReglPlr++++++YldwaveaFrl asgv+detqihthmCYsefn++ie+iaa+daDvi+ie+sr lcl|FitnessBrowser__psRCH2:GFF1415 604 RIIQIDEAAFREGLPLRRAQWQHYLDWAVEAFRLCASGVRDETQIHTHMCYSEFNDVIESIAAMDADVITIETSR 678 *************************************************************************** PP TIGR01371 669 sdmelldalkeikkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalkn 743 s+mell+a+++ ++y+++iG+GvyDihsprvP + e+ +lleka +++p+erlWvnPDCGLktR+w+e++aal n lcl|FitnessBrowser__psRCH2:GFF1415 679 SQMELLEAFRA-FDYPNDIGPGVYDIHSPRVPDTAEMVQLLEKAAERIPAERLWVNPDCGLKTRAWPETEAALVN 752 ***********.77************************************************************* PP TIGR01371 744 lveaakelRe 753 +v+aa++lR+ lcl|FitnessBrowser__psRCH2:GFF1415 753 MVAAARQLRA 762 ********96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (754 nodes) Target sequences: 1 (769 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: 11.76 // [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