Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate PfGW456L13_4923 Branched-chain amino acid aminotransferase (EC 2.6.1.42)
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4923 Length = 293 Score = 219 bits (557), Expect = 8e-62 Identities = 114/266 (42%), Positives = 162/266 (60%), Gaps = 5/266 (1%) Query: 6 RDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKRLLN 65 R+G IW+DG+ ++W A++HVLTH LHY V+EG R Y IF+L+EH++RL Sbjct: 11 REGVIWLDGEFVEWSRAQLHVLTHGLHYASTVYEGERVYNGR-----IFKLREHSERLYR 65 Query: 66 SAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVAIAA 125 SA+ +P++ L AA E+++ NK+ YLRP+ W GSE + SA+ N +HVAIA Sbjct: 66 SAQWMDFAIPYEMAELEAASHELLQRNKVADGYLRPVAWRGSEMISTSARFNRVHVAIAC 125 Query: 126 WPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEAL 185 W W +Y GIR+KT+S+ R + S AKASG Y + L+ +A GY +AL Sbjct: 126 WQWPSYFDPAARMAGIRLKTASWRRPPPSSSPFEAKASGHYQIATLSKHDAENTGYHDAL 185 Query: 186 LLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRITRD 245 +LD G+V+E + N F V L+TP L+GITR TVI LA+ QV+E+ I Sbjct: 186 MLDWRGHVAEATSANVFFVKGRTLHTPLPDCFLNGITRQTVIELAKALDYQVVERTILPT 245 Query: 246 EVYTCDEAFFTGTAAEVTPIRELDNR 271 E+ DE F TGTAAE+TP++ +D + Sbjct: 246 ELGDFDECFLTGTAAEITPVQSIDEQ 271 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: 258 Number of extensions: 6 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: 293 Length adjustment: 27 Effective length of query: 280 Effective length of database: 266 Effective search space: 74480 Effective search space used: 74480 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 PfGW456L13_4923 (Branched-chain amino acid aminotransferase (EC 2.6.1.42))
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.8122.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-83 265.3 0.0 3.6e-83 265.1 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4923 Branched-chain amino acid aminot Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4923 Branched-chain amino acid aminotransferase (EC 2.6.1.42) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 265.1 0.0 3.6e-83 3.6e-83 1 265 [. 16 274 .. 16 292 .. 0.97 Alignments for each domain: == domain 1 score: 265.1 bits; conditional E-value: 3.6e-83 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlyds 55 wldGe+v++ a++hvlth+lhY ++v+eG R+Y++ +if+l+eh eRly s lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4923 16 WLDGEFVEWSRAQLHVLTHGLHYASTVYEGERVYNG----RIFKLREHSERLYRS 66 9***********************************....9************** PP TIGR01122 56 akilrleipyskeelvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkve 110 a+ +++ ipy el + +e+l++n++ + Y+Rp++++G+e + +++ + +v+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4923 67 AQWMDFAIPYEMAELEAASHELLQRNKVADGYLRPVAWRGSEMISTSARFN-RVH 120 ************************************************998.9** PP TIGR01122 111 viiaawewgaylgeealekGikvkvssfrraavnsiptkakaagnYlnsllakse 165 v+ia w+w+ y++ a Gi+ k++s+rr ++s p +aka+g Y ++l k++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4923 121 VAIACWQWPSYFDPAARMAGIRLKTASWRRPPPSSSPFEAKASGHYQIATLSKHD 175 ******************************************************* PP TIGR01122 166 alraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavikl 220 a ++Gy++a++Ld G+vae + n+f vk +l tP + L+gitr++vi+l lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4923 176 AENTGYHDALMLDWRGHVAEATSANVFFVKGRTLHTPLP-DCFLNGITRQTVIEL 229 *************************************99.99************* PP TIGR01122 221 akelgievkeerisreelytaDevfltGtaaevtPirevDgrkig 265 ak l ++v+e++i +el De fltGtaae+tP++++D+++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4923 230 AKALDYQVVERTILPTELGDFDECFLTGTAAEITPVQSIDEQHYR 274 ****************************************98754 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (293 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 7.91 // [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