Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate GFF3443 PGA1_c34960 putative branched-chain-amino-acid aminotransferase, subunit A
Query= curated2:O29329 (290 letters) >FitnessBrowser__Phaeo:GFF3443 Length = 302 Score = 185 bits (470), Expect = 9e-52 Identities = 109/291 (37%), Positives = 165/291 (56%), Gaps = 17/291 (5%) Query: 2 LYVYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDL 61 + +Y++GE VP+ EAKVS++D GF+ GDGV+EG+R YNG + EH+DRL+++AK IDL Sbjct: 19 ILIYLNGEIVPKAEAKVSVYDSGFMLGDGVWEGLRLYNGTWAFIDEHLDRLFEAAKTIDL 78 Query: 62 EIPITKEEFMEIILETLRKNNLR-DAYIRPIVTRGIGDLGLDPRKCQNPSIIVITKPWGK 120 +I + +++ + +L+T N++ DA+ R +VTRG+ R Q+PS+ G Sbjct: 79 DIGMDRDQVKQAVLDTQDANDMTSDAHARLMVTRGVKS-----RPFQHPSL----SQQGP 129 Query: 121 LYGDLYEKGLTAITVAVRRNSFDAL-------PPNIKSLNYLNNILAKIEANAKGGDEAI 173 + + E + +R + L P + S + LN ILA I A G DE + Sbjct: 130 TFTIIMEHSRPNLPRPIRLATVPHLRGLPMTQDPKLNSHSKLNCILACIAAEKAGADEGL 189 Query: 174 FLDRNGYVSEGSGDNIFVVKNGAITTPPTINNLRGITREAVIEIINRLGIPFKETNIGLY 233 LD NG+V+ + N F+V+ GA+ T + GITR+ VI++ IP E N L Sbjct: 190 MLDVNGFVNTTNACNFFIVRKGAVWTSTGDYCMNGITRQKVIDLCRANDIPVFERNYSLV 249 Query: 234 DLYTADEVFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKLMEEFSKLTESE 284 D Y ADE F+TGT P+ IDGR+IGDG+ G +T++L + L E Sbjct: 250 DTYGADEAFLTGTFGAQTPVGDIDGRQIGDGEMGPVTKRLRALYKDLIAQE 300 Lambda K H 0.319 0.142 0.409 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: 266 Number of extensions: 16 Number of successful extensions: 2 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: 290 Length of database: 302 Length adjustment: 26 Effective length of query: 264 Effective length of database: 276 Effective search space: 72864 Effective search space used: 72864 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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