Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate Synpcc7942_1029 Synpcc7942_1029 branched-chain amino acid aminotransferase
Query= CharProtDB::CH_024500 (309 letters) >FitnessBrowser__SynE:Synpcc7942_1029 Length = 304 Score = 181 bits (459), Expect = 2e-50 Identities = 105/301 (34%), Positives = 165/301 (54%), Gaps = 13/301 (4%) Query: 8 YIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGP---VVFRHREHMQRLHDS 64 Y +F G++V + +A++ + +HALHYGT F G+R + P ++FR H QRL S Sbjct: 7 YAFFRGQLVPFPEAQLSIATHALHYGTGAFGGLRGIPDPENPDRVLLFRLDRHCQRLSQS 66 Query: 65 AKIYRFPVSQSIDELMEACRDVIRKNNLT-SAYIRPLIFVGDVGMGVNPPAGYSTDVIIA 123 AK F +S +E+ +A ++KN + S YIRP ++ D+G+ D I Sbjct: 67 AKFLHFELSA--EEIFKAIEAFVQKNQPSQSFYIRPFVYTSDLGIAPRLH-NIEKDFFIY 123 Query: 124 AFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEG 183 G YL E G+ +SSW R ++P K G Y++S L +EA G+ E Sbjct: 124 GLQLGDYLSPE----GVSCRISSWYRQEDRSLPLRGKISGAYIASSLAKTEAVASGFDEA 179 Query: 184 IALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLS 243 I ++ G + E G NLF V++G L TP + L GITRD++I++A++LGI V ++ + Sbjct: 180 ILMNSQGKVCEATGMNLFMVRNGRLITPGYDQDILEGITRDSVIRVAQDLGIPVDQRPID 239 Query: 244 RESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGW 303 + L++ADEVF+SGTAA++TPV+ V+ R P+T +I+Q + G W Sbjct: 240 KSELFIADEVFLSGTAAKVTPVKQVENYLTPCDR--PITDQIRQQLTLITEGRLAAYQDW 297 Query: 304 L 304 + Sbjct: 298 V 298 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: 235 Number of extensions: 10 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: 304 Length adjustment: 27 Effective length of query: 282 Effective length of database: 277 Effective search space: 78114 Effective search space used: 78114 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