Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_012114576.1 XAUT_RS12870 branched-chain amino acid aminotransferase
Query= CharProtDB::CH_024500 (309 letters) >NCBI__GCF_000017645.1:WP_012114576.1 Length = 297 Score = 194 bits (493), Expect = 2e-54 Identities = 105/261 (40%), Positives = 152/261 (58%), Gaps = 6/261 (2%) Query: 8 YIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKI 67 +IW++G V W DAK+HV+SH LHYG++VFEG R Y G +F+ EH +RL SA++ Sbjct: 14 WIWYDGVFVPWADAKLHVLSHGLHYGSTVFEGERAY----GGTIFKSAEHSERLRLSAEM 69 Query: 68 YRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPW 127 F + +I E+ A + + KNNL AYIRP+ + G MGV + + I + W Sbjct: 70 LDFTIPYTIGEIDAAKKATLEKNNLVDAYIRPVAWRGSEMMGVAAQKN-TIHLAIGVWEW 128 Query: 128 GAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALD 187 +Y E ++G+ +S W R P TIP AKA G Y+ + A R G+ + + LD Sbjct: 129 PSYFDPEQRQKGLRLDLSEWRRPDPATIPCKAKAAGLYMICTISKHRAERRGFADALMLD 188 Query: 188 VNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESL 247 GY++E G N+F VKDGV+ TP L G+TR +I +A+ G+EV E+ + E L Sbjct: 189 YRGYVAECTGANVFFVKDGVIHTPT-PDCFLDGLTRRTVIDIARRHGMEVVERHIKPEEL 247 Query: 248 YLADEVFMSGTAAEITPVRSV 268 E F++GTAAE+TPV S+ Sbjct: 248 SSFTECFITGTAAEVTPVGSI 268 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: 237 Number of extensions: 16 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: 297 Length adjustment: 27 Effective length of query: 282 Effective length of database: 270 Effective search space: 76140 Effective search space used: 76140 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 Jul 25 2024. The underlying query database was built on Jul 25 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