Align branched-chain-amino-acid aminotransferase subunit (EC 2.6.1.42) (characterized)
to candidate GFF3358 PGA1_c34110 branched-chain-amino-acid aminotransferase IlvE
Query= metacyc::MONOMER-11914 (306 letters) >FitnessBrowser__Phaeo:GFF3358 Length = 288 Score = 228 bits (580), Expect = 2e-64 Identities = 117/265 (44%), Positives = 167/265 (63%), Gaps = 7/265 (2%) Query: 4 EASGKIWLNGEMVEWEEATVHVLSHVVHYGSSVFEGIRCYRNSKGSAIFRLREHVKRLFD 63 + G IW++GEMV W +A VH+LSH +HY SSVFEG R Y IF+ REH +RL Sbjct: 6 DRDGLIWMDGEMVNWRDAKVHILSHAMHYASSVFEGERAYNGK----IFKSREHSERLIA 61 Query: 64 SAKIYRMDIPYTQEQICDAIVETVRENGLEECYIRPVVFRGYGE-MGVHPVNCPVDVAVA 122 SA+ M +PYT +QI A ET++ +GL++ Y+R VV+RG GE MGV PV +A+A Sbjct: 62 SAEALDMPMPYTVDQIEAAKEETLKASGLQDAYVRAVVWRGSGEDMGVASAKNPVRMAIA 121 Query: 123 AWEWGAYLGAEALEVGVDAGVSTWRRMAPNTMPNMAKAGGNYLNSQLAKMEAVRHGYDEA 182 W WGAY G ++ G ++ W+R +P T+P AKA G Y+ ++K +A G +A Sbjct: 122 VWGWGAYYGDAKMQ-GAKLDIAEWKRPSPETIPVHAKAAGLYMICTISKHKAEAKGCSDA 180 Query: 183 IMLDYHGYISEGSGENIFLVSEGEIYTPPVSSSLLRGITRDSVIKIARTEGVTVHEEPIT 242 + +DY GY++E +G NIF V +GE++TP L GITR +VI + + G+TVHE I Sbjct: 181 LFMDYRGYVAEATGANIFFVKDGEVHTPK-PDCFLNGITRQTVIGMLKDRGITVHERHIM 239 Query: 243 REMLYIADEAFFTGTAAEITPIRSV 267 E L ++ + TGTAAE+TP+ + Sbjct: 240 PEELDGFEQCWLTGTAAEVTPVGQI 264 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: 306 Number of extensions: 18 Number of successful extensions: 5 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: 288 Length adjustment: 26 Effective length of query: 280 Effective length of database: 262 Effective search space: 73360 Effective search space used: 73360 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 GFF3358 PGA1_c34110 (branched-chain-amino-acid aminotransferase IlvE)
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.16991.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-89 285.4 0.0 2.7e-89 285.2 0.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF3358 PGA1_c34110 branched-chain-amino Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF3358 PGA1_c34110 branched-chain-amino-acid aminotransferase IlvE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 285.2 0.0 2.7e-89 2.7e-89 1 285 [. 12 287 .. 12 288 .] 0.97 Alignments for each domain: == domain 1 score: 285.2 bits; conditional E-value: 2.7e-89 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvevtke 76 w+dGe+v+++dakvh+l+ha+hY ++vfeG RaY++ if+ +eh eRl sa++l++++py+ +++ + e lcl|FitnessBrowser__Phaeo:GFF3358 12 WMDGEMVNWRDAKVHILSHAMHYASSVFEGERAYNG----KIFKSREHSERLIASAEALDMPMPYTVDQIEAAKEE 83 9***********************************....9*********************************** PP TIGR01122 77 vlrknnlksaYiRplvyvGa.edlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkak 151 +l++++l++aY+R +v++G+ ed+g+ ++ +v+++ia+w wgay+g+ a +G k ++ ++r ++++ip +ak lcl|FitnessBrowser__Phaeo:GFF3358 84 TLKASGLQDAYVRAVVWRGSgEDMGVAS-AKNPVRMAIAVWGWGAYYGD-AKMQGAKLDIAEWKRPSPETIPVHAK 157 *******************8458****9.889****************7.7889********************** PP TIGR01122 152 aagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgie 227 aag Y+ ++ k++a ++G +a+++d Gyvae +G nif vkdg++ tP+ + L+gitr++vi ++k++gi+ lcl|FitnessBrowser__Phaeo:GFF3358 158 AAGLYMICTISKHKAEAKGCSDALFMDYRGYVAEATGANIFFVKDGEVHTPKP-DCFLNGITRQTVIGMLKDRGIT 232 ****************************************************9.99******************** PP TIGR01122 228 vkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlve 285 v+e++i eel + +ltGtaaevtP+ ++ + ++G++t+ + +a+ +lv+ lcl|FitnessBrowser__Phaeo:GFF3358 233 VHERHIMPEELDGFEQCWLTGTAAEVTPVGQIGPHSF---EVGELTQDIAKAYEELVR 287 ******************************9988765...799***********9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (288 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: 8.23 // [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