Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate GFF3358 PGA1_c34110 branched-chain-amino-acid aminotransferase IlvE
Query= CharProtDB::CH_024500 (309 letters) >FitnessBrowser__Phaeo:GFF3358 Length = 288 Score = 185 bits (470), Expect = 1e-51 Identities = 104/270 (38%), Positives = 156/270 (57%), Gaps = 10/270 (3%) Query: 9 IWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIY 68 IW +GEMV W DAKVH++SHA+HY +SVFEG R Y+ +F+ REH +RL SA+ Sbjct: 11 IWMDGEMVNWRDAKVHILSHAMHYASSVFEGERAYNGK----IFKSREHSERLIASAEAL 66 Query: 69 RFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGD-VGMGVNPPAGYSTDVIIAAFPW 127 P+ ++D++ A + ++ + L AY+R +++ G MGV A + IA + W Sbjct: 67 DMPMPYTVDQIEAAKEETLKASGLQDAYVRAVVWRGSGEDMGV-ASAKNPVRMAIAVWGW 125 Query: 128 GAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALD 187 GAY G +A QG ++ W R +P TIP AKA G Y+ + +A G + + +D Sbjct: 126 GAYYG-DAKMQGAKLDIAEWKRPSPETIPVHAKAAGLYMICTISKHKAEAKGCSDALFMD 184 Query: 188 VNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESL 247 GY++E G N+F VKDG + TP L GITR +I + K+ GI V E+ + E L Sbjct: 185 YRGYVAEATGANIFFVKDGEVHTPK-PDCFLNGITRQTVIGMLKDRGITVHERHIMPEEL 243 Query: 248 YLADEVFMSGTAAEITPVRSV--DGIQVGE 275 ++ +++GTAAE+TPV + +VGE Sbjct: 244 DGFEQCWLTGTAAEVTPVGQIGPHSFEVGE 273 Lambda K H 0.319 0.136 0.413 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: 261 Number of extensions: 11 Number of successful extensions: 4 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: 309 Length of database: 288 Length adjustment: 27 Effective length of query: 282 Effective length of database: 261 Effective search space: 73602 Effective search space used: 73602 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)
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