Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_017752177.1 PN53_RS07220 D-amino acid aminotransferase
Query= curated2:Q58414 (288 letters) >NCBI__GCF_000816635.1:WP_017752177.1 Length = 287 Score = 122 bits (306), Expect = 9e-33 Identities = 89/271 (32%), Positives = 141/271 (52%), Gaps = 9/271 (3%) Query: 4 YLNGKFVDEKDAKVSVFDHGLLYGDGVFEGIRAYDGVVFMLKEHIDRLYDSAKSLCIDIP 63 Y NGK+ ++ + + D +GDGV++ + + V+F L EHIDR ++SA L I IP Sbjct: 6 YYNGKYDLIENMTIPMNDRVCYFGDGVYDATYSRNHVIFALDEHIDRFFNSAGLLKIKIP 65 Query: 64 LTKEEMIDVVLETLRVNNLRDAYIRLVVTRGVGDLG-LDPRKCGKPTIFCIAIPMPPLLG 122 TK+E+ +++ + ++ + + ++ VTRG + P K ++ I P Sbjct: 66 YTKDELKELLNDMVKKVDSGEQFVYWQVTRGTAMRNHIFPGDDVKANVWIILKPQKVKDM 125 Query: 123 EDGIRAITVSVRRLPVDVLNPAVKSLNYLNSVLAKIQANYAGVDEA-FLLDDKGFVVEGT 181 +R IT+ R L+ +K+LN L SV+A +A+ EA F D+ V E Sbjct: 126 SQKLRLITLEDTRF----LHCNIKTLNLLPSVMAAQKADEKDCQEAVFHRGDR--VTECA 179 Query: 182 GDNIFIVKNGVLKTPPVYQSILKGITRDVVIKLAKEEGIEVVEEPLTLHDLYTADELFIT 241 N+ I+K+G+ KT P IL GI R +IK+ K+ I V E P TL +L ADE+ +T Sbjct: 180 HSNVSIIKDGIFKTAPADNLILPGIARAHIIKMCKKFEIPVNETPFTLEELMDADEVIVT 239 Query: 242 GTAAEIVPVFEIDGRVINNKQVGEITKKLKE 272 + + EIDG + K EI KKL++ Sbjct: 240 SSGQFCMTTCEIDGTPVGGK-APEIVKKLQD 269 Lambda K H 0.321 0.143 0.411 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: 226 Number of extensions: 17 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: 288 Length of database: 287 Length adjustment: 26 Effective length of query: 262 Effective length of database: 261 Effective search space: 68382 Effective search space used: 68382 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: 47 (22.7 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