Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_010532048.1 ON01_RS16165 D-amino-acid transaminase
Query= curated2:O29329 (290 letters) >NCBI__GCF_000224785.1:WP_010532048.1 Length = 284 Score = 151 bits (382), Expect = 1e-41 Identities = 95/273 (34%), Positives = 148/273 (54%), Gaps = 6/273 (2%) Query: 11 VPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEIPITKEEF 70 + E + + I D G+ +GDG++E I Y+G + EH++RL SA+ + L +P + E Sbjct: 10 IMERDNVIDIEDRGYQFGDGIYEVIGVYDGEPLMMDEHMERLERSARELRLTLPASTSEL 69 Query: 71 MEIILETLRKNNLRDAYIRPIVTRGIGDLGLDPRKCQNPSIIVITKPWGKLYGDLYEKGL 130 + + + N L + I V+RGI Q P++ V + D+ ++G Sbjct: 70 KSNLEKLVEANGLEEGIIYMQVSRGIASREHGFPASQTPAVTVAYTREEEREPDVEDQGA 129 Query: 131 TAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGYVSEGSGDNIF 190 TA+ R L +IK+LN L N++AK +A EAI L R G V+E S N+F Sbjct: 130 TAVLAEDIR----WLRCDIKTLNLLPNVMAKQKAVENNAVEAI-LHRGGTVTEASASNVF 184 Query: 191 VVKNGAITTPPTINN-LRGITREAVIEIINRLGIPFKETNIGLYDLYTADEVFVTGTAAE 249 +V G + T P N L GITR +I++ + L I E + DL ADEVFV+ T + Sbjct: 185 MVTGGELYTHPADNYILNGITRRKIIQLCDELNINVNEQTYTVDDLLNADEVFVSATKMD 244 Query: 250 IAPIVVIDGRKIGDGKPGEITRKLMEEFSKLTE 282 I PI+ ID + IG+GKPG+IT++++++F L E Sbjct: 245 IIPILKIDDQTIGNGKPGKITKQILQQFRSLYE 277 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: 241 Number of extensions: 12 Number of successful extensions: 3 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: 284 Length adjustment: 26 Effective length of query: 264 Effective length of database: 258 Effective search space: 68112 Effective search space used: 68112 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: 47 (22.7 bits)
This GapMind analysis is from Jul 26 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