Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate GFF3387 PGA1_c34400 aminotransferase class-III
Query= BRENDA::Q6LFH8 (414 letters) >FitnessBrowser__Phaeo:GFF3387 Length = 464 Score = 160 bits (406), Expect = 6e-44 Identities = 116/405 (28%), Positives = 192/405 (47%), Gaps = 42/405 (10%) Query: 31 VLKRGKGVFVYDIEDRRYYDFLSAYSSVNQGHCHPDILNAMINQAKKLTICSRAFFSDSL 90 ++ R +GV + D E D ++ VN G+ ++ + Q ++L + FF + Sbjct: 38 IITRARGVTLTDSEGNEILDAMAGLWCVNIGYGRDELADVAARQMRELPYYN-TFFQTTH 96 Query: 91 GVCERYLTNLF-----GYDKVLMMNTGAEASETAYKLCRKWGYEVKKIPENSAKIIVCNN 145 + G + V +G+EA++T ++ R + + +K P S II N Sbjct: 97 APAIALAAKIAELAPDGLNHVFFAGSGSEANDTNIRMVRHY-WAMKAKPTKSV-IISRKN 154 Query: 146 NFSGRTLGCVSASTDKKCKNNFGPFVPNFLKVPY--------------------DDLEAL 185 + G ++G S G +P+ + +LE Sbjct: 155 GYHGSSVGSGSLGGMTAMHEQGGLPIPDIHHINQPNWWAEGGDMSAEDFGLARAQELEQA 214 Query: 186 EKELQDPNVCAFIVEPVQGEAGVIVPSDSYFPGVASLCKKYNVLFVADEVQTGLGRTGKL 245 EL + V AFI EPVQG GVIVP +Y+P + +C KY +L +ADEV G GRTG Sbjct: 215 ILELGEDRVAAFIAEPVQGAGGVIVPPATYWPEIQRICDKYEILLIADEVICGFGRTGNW 274 Query: 246 LCTHHYGVKPDVILLGKALSGGHYPISAILANDDVMLVLKPGE--HGSTYGGNPLAAAIC 303 + G++PD++ + K LS G+ PI + +D++ V+ GE HG TY G+P+AAA+ Sbjct: 275 FGSQSVGIRPDIMTIAKGLSSGYAPIGGSIVSDEIASVIGSGEFNHGYTYSGHPVAAAVA 334 Query: 304 VEALKVLINEKLCENADKLGAPFLQNLKEQLKDSKVVREVRGKGLLCAIE---------- 353 +E L++L E + + + AP+L+ E L D +V E + G++ +I Sbjct: 335 LENLRILEEENIIGHVRDVAAPYLKEKWEALADHPLVGEAKIVGMMGSIALTPNKATRAG 394 Query: 354 FKNDLVNVWDICL-KFKENGLITRSVHDKTVRLTPPLCITKEQLD 397 F + V IC + N L+ R V D+ + ++PPL IT E++D Sbjct: 395 FAAEGGTVGYICRERCFANNLVMRHVGDRMI-ISPPLVITPEEID 438 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: 446 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: 414 Length of database: 464 Length adjustment: 32 Effective length of query: 382 Effective length of database: 432 Effective search space: 165024 Effective search space used: 165024 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 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