Align branched-chain amino acid aminotransferase 2; EC 2.6.1.42 (characterized)
to candidate WP_029908713.1 P166_RS0103225 branched-chain-amino-acid transaminase
Query= CharProtDB::CH_012531 (298 letters) >NCBI__GCF_000711315.1:WP_029908713.1 Length = 284 Score = 270 bits (691), Expect = 2e-77 Identities = 136/262 (51%), Positives = 180/262 (68%) Query: 3 EQWIFLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKSIM 62 E++ +LNG+ VP EA +SV DHG LYGDGVFEG+RVY+G FR+REHLVRL +SA+++ Sbjct: 2 EEFCWLNGDLVPVGEAHISVLDHGLLYGDGVFEGMRVYNGRTFRIREHLVRLQQSAQALK 61 Query: 63 LEIPYSLDEITNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCTKPNVVVIAEQLSL 122 L IPY+LD +T I NK+ +GYIRLVV+RG G LGLDP +C PNV ++ L + Sbjct: 62 LVIPYTLDVLTQACEALITANKMDSGYIRLVVTRGEGFLGLDPRNCDTPNVFILYRGLKM 121 Query: 123 FPQEYYEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQGY 182 + G ++T + RR DVL P++K+LNY+NNIL ++EA AG +ALMLN G Sbjct: 122 GEDTIQQHGAKLITTSVRRAPLDVLDPKIKTLNYINNILAKMEANQAGADDALMLNHSGQ 181 Query: 183 VAEGSGDNVFIVKGNKLITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDVYVAD 242 VAE S N+FIVK L TPP AGAL+GITR+A++E+ + V E + +DVY AD Sbjct: 182 VAEASAANLFIVKNGVLSTPPCEAGALQGITRDAVMELAIRSNIAVEESPMSLYDVYNAD 241 Query: 243 EVFLTGTAAEVIAVTTVDGRTI 264 E FLTG+ AE+I V VDGR + Sbjct: 242 EAFLTGSGAELIPVAQVDGRQL 263 Lambda K H 0.317 0.138 0.390 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: 236 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: 298 Length of database: 284 Length adjustment: 26 Effective length of query: 272 Effective length of database: 258 Effective search space: 70176 Effective search space used: 70176 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
Align candidate WP_029908713.1 P166_RS0103225 (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.18339.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-88 283.2 0.0 1.3e-88 283.0 0.0 1.0 1 lcl|NCBI__GCF_000711315.1:WP_029908713.1 P166_RS0103225 branched-chain-am Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000711315.1:WP_029908713.1 P166_RS0103225 branched-chain-amino-acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 283.0 0.0 1.3e-88 1.3e-88 1 285 [. 6 283 .. 6 284 .] 0.95 Alignments for each domain: == domain 1 score: 283.0 bits; conditional E-value: 1.3e-88 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 wl+G+lv+v +a+++vl+h+l+YG+gvfeG+R+Y++ + fr++eh+ Rl +sa++l+l ipy+ + lcl|NCBI__GCF_000711315.1:WP_029908713.1 6 WLNGDLVPVGEAHISVLDHGLLYGDGVFEGMRVYNG----RTFRIREHLVRLQQSAQALKLVIPYTLDV 70 9***********************************....89*************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpk.vdlkveviiaawewgaylgeeale.kGikvkvs 136 l++++ ++ +n+++s YiR +v++G + lgl+p+ +d +++v+i g +ge++++ +G k +++ lcl|NCBI__GCF_000711315.1:WP_029908713.1 71 LTQACEALITANKMDSGYIRLVVTRGEGFLGLDPRnCD-TPNVFIL--YRGLKMGEDTIQqHGAKLITT 136 **********************************8666.6677665..35888999887526******* PP TIGR01122 137 sfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvs 205 s+rra +++ +k+k+ + Y+n++lak+ea++aG+d+a++L+++G vae s n+fivk+gvl tPp + lcl|NCBI__GCF_000711315.1:WP_029908713.1 137 SVRRAPLDVLDPKIKTLN-YINNILAKMEANQAGADDALMLNHSGQVAEASAANLFIVKNGVLSTPPCE 204 *****************9.************************************************** PP TIGR01122 206 esiLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtk 274 +L+gitrdav++la + i v+e+++s++++y aDe+fltG+ ae++P+ +vDgr++ + +Gpv lcl|NCBI__GCF_000711315.1:WP_029908713.1 205 AGALQGITRDAVMELAIRSNIAVEESPMSLYDVYNADEAFLTGSGAELIPVAQVDGRQLQH-AVGPVFL 272 **********************************************************965.79***** PP TIGR01122 275 klqeaffdlve 285 kl+ f +l++ lcl|NCBI__GCF_000711315.1:WP_029908713.1 273 KLKLGFHELTH 283 **999999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (284 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: 00:00:00.00 # Mc/sec: 10.98 // [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