Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_012567072.1 RC1_RS09070 branched-chain amino acid aminotransferase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >NCBI__GCF_000016185.1:WP_012567072.1 Length = 299 Score = 234 bits (596), Expect = 2e-66 Identities = 125/292 (42%), Positives = 177/292 (60%), Gaps = 8/292 (2%) Query: 5 DRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKRLL 64 DRDG IW DG+++ WRDAKIHVLTH LHY VFEG R Y +F+L EH++RL+ Sbjct: 8 DRDGVIWFDGEMVPWRDAKIHVLTHGLHYASCVFEGERVYNGK-----VFKLTEHSERLV 62 Query: 65 NSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVAIA 124 S +I +P+ + A +VV+ + + Y+RP+ W GSE +GVSA+ N IH+AIA Sbjct: 63 RSGEILGFRIPYSAAEIEKATNDVVKAAGMVNGYVRPVAWRGSEMMGVSAQANKIHLAIA 122 Query: 125 AWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEA 184 AW W +Y + KGI ++ S + R + + +KA+G Y+ ++ A DG+ +A Sbjct: 123 AWEWPSYFSPELRMKGISLQISKWRRPAPDTAPTASKAAGLYMICTMSKHAAENDGFQDA 182 Query: 185 LLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRITR 244 L+LD G V+E +G N FLV +G ++TP LDGITR TVI LAR G QV+E+ I+ Sbjct: 183 LMLDYRGLVAEATGANIFLVKDGAIHTPTPDCFLDGITRRTVIGLARRRGYQVVERAISA 242 Query: 245 DEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGK 296 DE+ E F TGTAAEVT + + + T G IT+ L + +VNG+ Sbjct: 243 DELKDFTEVFLTGTAAEVTAVGRIGDITY---TPGEITKALMLDYDALVNGR 291 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: 300 Number of extensions: 5 Number of successful extensions: 2 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: 299 Length adjustment: 27 Effective length of query: 280 Effective length of database: 272 Effective search space: 76160 Effective search space used: 76160 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 WP_012567072.1 RC1_RS09070 (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.14973.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.1e-91 290.1 0.0 1.1e-90 289.8 0.0 1.0 1 lcl|NCBI__GCF_000016185.1:WP_012567072.1 RC1_RS09070 branched-chain amino Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016185.1:WP_012567072.1 RC1_RS09070 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 289.8 0.0 1.1e-90 1.1e-90 1 290 [. 14 294 .. 14 298 .. 0.98 Alignments for each domain: == domain 1 score: 289.8 bits; conditional E-value: 1.1e-90 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w+dGe+v+++dak+hvlth+lhY + vfeG R+Y++ +f+l+eh eRl s +il + ipys+ e lcl|NCBI__GCF_000016185.1:WP_012567072.1 14 WFDGEMVPWRDAKIHVLTHGLHYASCVFEGERVYNG----KVFKLTEHSERLVRSGEILGFRIPYSAAE 78 9***********************************....9**************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 + ++t++v+++ ++ + Y+Rp++++G+e +g++++++ k++++iaawew+ y+ e kGi+ ++s + lcl|NCBI__GCF_000016185.1:WP_012567072.1 79 IEKATNDVVKAAGMVNGYVRPVAWRGSEMMGVSAQAN-KIHLAIAAWEWPSYFSPELRMKGISLQISKW 146 **********************************777.******************************* PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 rr a+++ pt+ kaag Y+ ++ k+ a + G+++a++Ld G vae +G nif+vkdg++ tP + lcl|NCBI__GCF_000016185.1:WP_012567072.1 147 RRPAPDTAPTASKAAGLYMICTMSKHAAENDGFQDALMLDYRGLVAEATGANIFLVKDGAIHTPTP-DC 214 *****************************************************************9.99 PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 L+gitr +vi la+++g++v+e+ is +el evfltGtaaevt + ++ +++ + G++tk l lcl|NCBI__GCF_000016185.1:WP_012567072.1 215 FLDGITRRTVIGLARRRGYQVVERAISADELKDFTEVFLTGTAAEVTAVGRIGDITY---TPGEITKAL 280 *****************************************************9986...6799***** PP TIGR01122 277 qeaffdlvegktek 290 + + lv+g+ + lcl|NCBI__GCF_000016185.1:WP_012567072.1 281 MLDYDALVNGRLAD 294 ********998665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (299 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.75 // [ok]
This GapMind analysis is from Apr 10 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