Align branched-chain-amino-acid aminotransferase subunit (EC 2.6.1.42) (characterized)
to candidate WP_012502762.1 CPAR_RS07765 branched-chain amino acid transaminase
Query= metacyc::MONOMER-11914 (306 letters) >NCBI__GCF_000020505.1:WP_012502762.1 Length = 303 Score = 373 bits (958), Expect = e-108 Identities = 173/299 (57%), Positives = 229/299 (76%), Gaps = 1/299 (0%) Query: 8 KIWLNGEMVEWEEATVHVLSHVVHYGSSVFEGIRCYRNSKGSAIFRLREHVKRLFDSAKI 67 KIW+NGE+V+W +A +HV+SHV HYGSS FEGIRCY +KGSAI L EHV+RL++S+KI Sbjct: 6 KIWMNGELVDWNDAKIHVMSHVAHYGSSTFEGIRCYDTAKGSAILFLDEHVRRLWESSKI 65 Query: 68 YRMDIPYTQEQICDAIVETVRENGLEECYIRPVVFRGYGEMGVHPVNCPVDVAVAAWEWG 127 YR++IPY++ +I DAI+ T++ NG + CYIRP+V+RG G +GV+P ++VA+A WEWG Sbjct: 66 YRIEIPYSETEIKDAIIATIKANGHKACYIRPLVYRGQGALGVNPHRASIEVAIATWEWG 125 Query: 128 AYLGAEALEVGVDAGVSTWRRMAPNTMPNMAKAGGNYLNSQLAKMEAVRHGYDEAIMLDY 187 +YLG + LE GVD VS+W R+APNT+P+ AKAGGNY+NSQL KMEA+ GY E + LD Sbjct: 126 SYLGEDVLETGVDVKVSSWHRLAPNTLPSWAKAGGNYMNSQLIKMEAISDGYAEGLALDQ 185 Query: 188 HGYISEGSGENIFLVSEGEIYTPPVSSSLLRGITRDSVIKIARTEGVTVHEEPITREMLY 247 +GY++EGSGENIF+V +YTP + S+L G TR +V++IA+ G V E I RE LY Sbjct: 186 NGYVAEGSGENIFVVRHNVLYTPFAAQSILPGFTRHAVMEIAKKLGYEVRETLIPRESLY 245 Query: 248 IADEAFFTGTAAEITPIRSVDGIEIGAGRRGPVTKLLQDEFFRIIRAETEDSFGWLTYI 306 IADE F TGTAAEITP+RSVD +G +RGPVT+ LQ E+ +I+ + ED F WLT+I Sbjct: 246 IADEIFLTGTAAEITPVRSVDKYPVGQEKRGPVTEALQHEYLKIVHS-GEDPFNWLTFI 303 Lambda K H 0.320 0.136 0.414 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: 342 Number of extensions: 10 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: 306 Length of database: 303 Length adjustment: 27 Effective length of query: 279 Effective length of database: 276 Effective search space: 77004 Effective search space used: 77004 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_012502762.1 CPAR_RS07765 (branched-chain amino acid transaminase)
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.29001.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-130 419.1 0.0 5.3e-130 418.9 0.0 1.0 1 lcl|NCBI__GCF_000020505.1:WP_012502762.1 CPAR_RS07765 branched-chain amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020505.1:WP_012502762.1 CPAR_RS07765 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 418.9 0.0 5.3e-130 5.3e-130 1 297 [. 8 302 .. 8 303 .] 0.99 Alignments for each domain: == domain 1 score: 418.9 bits; conditional E-value: 5.3e-130 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w++Gelvd++dak+hv++h+ hYG++ feGiR+Y+t kg+ai++l+ehv Rl++s+ki+r+eipys+ e lcl|NCBI__GCF_000020505.1:WP_012502762.1 8 WMNGELVDWNDAKIHVMSHVAHYGSSTFEGIRCYDTAKGSAILFLDEHVRRLWESSKIYRIEIPYSETE 76 9******************************************************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 + ++++ ++++n+ k +YiRplvy+G++ lg++p +++ev+ia+wewg ylge+ le+G++vkvss+ lcl|NCBI__GCF_000020505.1:WP_012502762.1 77 IKDAIIATIKANGHKACYIRPLVYRGQGALGVNP-HRASIEVAIATWEWGSYLGEDVLETGVDVKVSSW 144 **********************************.8889****************************** PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 +r a+n++p+ aka+gnY+ns+l+k+ea++ Gy e+++Ld++GyvaeGsGenif+v+++vl+tP ++s lcl|NCBI__GCF_000020505.1:WP_012502762.1 145 HRLAPNTLPSWAKAGGNYMNSQLIKMEAISDGYAEGLALDQNGYVAEGSGENIFVVRHNVLYTPFAAQS 213 ********************************************************************* PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 iL g tr av+++ak+lg+ev+e+ i re+ly+aDe+fltGtaae+tP+r+vD+ +g+ krGpvt+ l lcl|NCBI__GCF_000020505.1:WP_012502762.1 214 ILPGFTRHAVMEIAKKLGYEVRETLIPRESLYIADEIFLTGTAAEITPVRSVDKYPVGQEKRGPVTEAL 282 ********************************************************************* PP TIGR01122 277 qeaffdlvegktekkeewlty 297 q+++ ++v+++ e+ +wlt lcl|NCBI__GCF_000020505.1:WP_012502762.1 283 QHEYLKIVHSG-EDPFNWLTF 302 *********98.677789986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (303 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.81 // [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