Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate Ga0059261_3811 Ga0059261_3811 branched-chain amino acid aminotransferase, group II
Query= CharProtDB::CH_024500 (309 letters) >FitnessBrowser__Korea:Ga0059261_3811 Length = 362 Score = 144 bits (364), Expect = 2e-39 Identities = 114/327 (34%), Positives = 166/327 (50%), Gaps = 44/327 (13%) Query: 15 MVRWEDAK--------------VHVMSHALHYGTSVFEGIRCYDS-HKGPVVFRHREHMQ 59 MVRW D K + + LHY +FEG++ Y + +G +FR E+ + Sbjct: 39 MVRWSDTKGWHDAKVVARGPLSLDPATAVLHYAQEIFEGLKAYRTGDEGTALFRPLENAR 98 Query: 60 RLHDSAKIYRFPVSQ------SIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPP 113 R +SA+ P SI+ L++A R+ I + S Y+RP +F +V +GV P Sbjct: 99 RFRESAQRMAMPELPDDLFLGSIEALVKADREWIPQIEGGSLYLRPFMFASEVFLGVKPA 158 Query: 114 AGYSTDVIIAAFPWGAYL--GAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLV 171 + Y ++ A P GAY GA A+ + + RAAP AAK GGNY SSL+ Sbjct: 159 SEYL--YLVIASPAGAYFKGGAPAVTIWVS---DHYTRAAPGGTG-AAKCGGNYASSLVA 212 Query: 172 GSEARRHGYQEGIALDV--NGYISEGAGENLFEV-KDGVLFTPPFTSSALPGITRDAIIK 228 +EA R G + + LD ++ E G NLF V DG + TPP + LPGITR++I+ Sbjct: 213 QAEAIREGCDQVVFLDAVERRWVEELGGMNLFFVFDDGSMVTPPLGGTILPGITRESILT 272 Query: 229 LAKELGIEVREQVLSRESLYLAD-------EVFMSGTAAEITP---VRSVDG-IQVGEGR 277 LA+E GI VRE+ + + + AD E F GTAA +TP V+S DG +G G Sbjct: 273 LAREQGITVREEPYAIDQ-WKADAGSGKLVETFACGTAAVVTPVGKVKSRDGEFTIGSGG 331 Query: 278 CGPVTKRIQQAFFGLFTGETEDKWGWL 304 G VT+ ++ + G+ D GW+ Sbjct: 332 PGQVTEALKARLTAIQRGQAPDIHGWV 358 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: 303 Number of extensions: 18 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 309 Length of database: 362 Length adjustment: 28 Effective length of query: 281 Effective length of database: 334 Effective search space: 93854 Effective search space used: 93854 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: 49 (23.5 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