Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_086509870.1 BZY95_RS10460 aspartate aminotransferase family protein
Query= BRENDA::Q6LFH8 (414 letters) >NCBI__GCF_002151265.1:WP_086509870.1 Length = 485 Score = 158 bits (399), Expect = 4e-43 Identities = 123/428 (28%), Positives = 198/428 (46%), Gaps = 63/428 (14%) Query: 31 VLKRGKGVFVYDIEDRRYYDFLSAYSSVNQGHCHPDILNAMINQAKKLTICSRAFFSD-- 88 ++ +G++++D E R D ++ VN G+ +++ A Q ++L + F S Sbjct: 31 IVTHAEGIYIHDSEGNRILDAMAGLWCVNLGYGREELVAAATAQLRELPYYNNFFKSTHP 90 Query: 89 -SLGVCERYLTNLFGY-DKVLMMNTGAEASETAYKLCRK-WGYEVKKIPENSAKIIVCNN 145 ++ + E + ++V +G+EA++T ++ R+ W E K + +I N Sbjct: 91 PAVKLAEMLCRLAPAHMNRVFFTGSGSEANDTVLRMVRRYWALEGKP---DKQWVIAREN 147 Query: 146 NFSGRTLGCVSASTDKKCKNNFGPFVPNFLKV--PY------------------------ 179 + G T+ +S GP VP V PY Sbjct: 148 AYHGSTVAGLSLGGMAPMHAQGGPLVPKIAHVRQPYWFGEGKVAQGRVGEGRDTSPEAFG 207 Query: 180 ----DDLEALEKELQDPNVCAFIVEPVQGEAGVIVPSDSYFPGVASLCKKYNVLFVADEV 235 LEA L + NV AFI EPVQG G I+P SY+P V + +Y++L V DEV Sbjct: 208 RECAAALEAKILALGEENVAAFIAEPVQGAGGAIIPPQSYWPAVKEVLARYDILLVVDEV 267 Query: 236 QTGLGRTGKLLCTHHYGVKPDVILLGKALSGGHYPISAILANDDV--MLVLKPGE--HGS 291 G GR G+ + HY +KPD++ + K LS G+ PI +L D V L+ + GE HG Sbjct: 268 ICGFGRLGEWFGSIHYDLKPDLMPIAKGLSSGYLPIGGVLVGDRVAETLIERGGEFFHGF 327 Query: 292 TYGGNPLAAAICVEALKVLINEKLCENADKLGAPFLQNLKEQLKDSKVVREVRGKGLLCA 351 TY G+P+ AA+ ++ L+++ E + E P+L L D +V EVR GL+ A Sbjct: 328 TYSGHPVCAAVALKNLELMQAEGIVERVRDDVGPYLAERWATLADHPLVGEVRSLGLIGA 387 Query: 352 IEFKNDLVN-----------------VWDICLKFKENGLITRSVHDKTVRLTPPLCITKE 394 +E + DIC ++GL+ RSV D T+ ++PPL IT+ Sbjct: 388 LELIDPDTGERFDKARFPKGFGVGTLCRDICF---DHGLVMRSVGD-TMIISPPLVITRA 443 Query: 395 QLDECTEI 402 ++DE + Sbjct: 444 EIDELVRL 451 Lambda K H 0.320 0.138 0.418 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: 526 Number of extensions: 26 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 414 Length of database: 485 Length adjustment: 33 Effective length of query: 381 Effective length of database: 452 Effective search space: 172212 Effective search space used: 172212 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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