Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate 208718 DVU3197 branched-chain amino acid aminotransferase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >MicrobesOnline__882:208718 Length = 309 Score = 369 bits (946), Expect = e-107 Identities = 172/304 (56%), Positives = 224/304 (73%) Query: 1 MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT 60 MSM + IW DGK + W +A +HVLTH LHYG+GVFEG+RAY+ ADG +A+FRL+EH Sbjct: 1 MSMVQKSETIWFDGKQVPWDEANVHVLTHALHYGVGVFEGIRAYRCADGSSAVFRLREHV 60 Query: 61 KRLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH 120 +RL +SAKI +M++PF + + A E ++ N+L Y+RP+ +VG+ +GV N + Sbjct: 61 QRLFSSAKILRMEIPFTEDAIFDAIVETLQRNRLAEGYIRPLSFVGAGAMGVYPGDNPVQ 120 Query: 121 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180 IA WPWGAYLG + + KGIRVKTSSF RHHVN M +AKASG YVNS+LA EA ADG Sbjct: 121 TIIAVWPWGAYLGAEALEKGIRVKTSSFARHHVNAMMTKAKASGNYVNSVLAKMEAKADG 180 Query: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEK 240 YDEAL+LDV G+VSE +GEN F+V NG + T L+S LDGITR++++TLARD G +V+E+ Sbjct: 181 YDEALMLDVSGFVSEATGENIFMVRNGVIKTTPLTSILDGITRNSLMTLARDLGYEVVEQ 240 Query: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY 300 + TRDE+Y DEAFF GTAAEVTPIRE+D R IG G+ GP+T+ LQ +F V G + Y Sbjct: 241 QFTRDELYVADEAFFCGTAAEVTPIREVDRRVIGKGSAGPVTKHLQQEYFKAVKGDNPSY 300 Query: 301 ANWL 304 +WL Sbjct: 301 DHWL 304 Lambda K H 0.319 0.136 0.411 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: 348 Number of extensions: 6 Number of successful extensions: 1 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: 307 Length of database: 309 Length adjustment: 27 Effective length of query: 280 Effective length of database: 282 Effective search space: 78960 Effective search space used: 78960 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: 48 (23.1 bits)
Align candidate 208718 DVU3197 (branched-chain amino acid aminotransferase)
to HMM TIGR01122 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))
# 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/TIGR01122.hmm # target sequence database: /tmp/gapView.32574.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01122 [M=298] Accession: TIGR01122 Description: ilvE_I: branched-chain amino acid aminotransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-136 440.6 0.0 1.4e-136 440.4 0.0 1.0 1 lcl|MicrobesOnline__882:208718 DVU3197 branched-chain amino aci Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:208718 DVU3197 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 440.4 0.0 1.4e-136 1.4e-136 1 296 [. 11 305 .. 11 307 .. 0.98 Alignments for each domain: == domain 1 score: 440.4 bits; conditional E-value: 1.4e-136 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdk.glaifrlkehveRlydsakilrleipyskeelvevtkevl 78 w+dG+ v++++a+vhvlthalhYG gvfeGiRaY+ + +a+frl+ehv+Rl+ sakilr+eip++++ + ++++e+l lcl|MicrobesOnline__882:208718 11 WFDGKQVPWDEANVHVLTHALHYGVGVFEGIRAYRCADgSSAVFRLREHVQRLFSSAKILRMEIPFTEDAIFDAIVETL 89 9**********************************9883579************************************* PP TIGR01122 79 rknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkakaagnYl 157 ++n l + YiRpl +vGa+ +g++p d +v+ iia+w+wgaylg+ealekGi+vk+ssf+r++vn+++tkaka+gnY+ lcl|MicrobesOnline__882:208718 90 QRNRLAEGYIRPLSFVGAGAMGVYP-GDNPVQTIIAVWPWGAYLGAEALEKGIRVKTSSFARHHVNAMMTKAKASGNYV 167 *************************.999************************************************** PP TIGR01122 158 nsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgievkeerisre 236 ns+lak+ea++ Gydea++Ld +G+v+e +Genif+v++gv++t p+ +siL+gitr+++++la++lg+ev+e++++r+ lcl|MicrobesOnline__882:208718 168 NSVLAKMEAKADGYDEALMLDVSGFVSEATGENIFMVRNGVIKTTPL-TSILDGITRNSLMTLARDLGYEVVEQQFTRD 245 **********************************************9.78***************************** PP TIGR01122 237 elytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekkeewlt 296 ely+aDe+f+ GtaaevtPirevD r ig+g++Gpvtk+lq+++f+ v+g+++++++wl+ lcl|MicrobesOnline__882:208718 246 ELYVADEAFFCGTAAEVTPIREVDRRVIGKGSAGPVTKHLQQEYFKAVKGDNPSYDHWLH 305 **********************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (309 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.93 // [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