Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_011612205.1 TERY_RS12675 aspartate aminotransferase family protein
Query= BRENDA::Q3ZCF5 (439 letters) >NCBI__GCF_000014265.1:WP_011612205.1 Length = 423 Score = 263 bits (672), Expect = 8e-75 Identities = 141/395 (35%), Positives = 220/395 (55%), Gaps = 12/395 (3%) Query: 50 YGAHNYHPLPVALERGKGIYVWDVEGRKYFDFLSAYSAVNQGHCHPKIVDALKSQVDKLT 109 Y + Y P+A+ERG+G VWD EG++Y DF++ + GH HP ++ + Q+ +L Sbjct: 28 YVMNTYGRFPIAIERGEGCRVWDTEGKEYLDFVAGIATCTLGHAHPVMMATVSEQIKRLH 87 Query: 110 LTSRAFYNNVLGEYEEYVTKLFNYHKVLPMNTGVEAGETACKLARKWGYTVKGIPKYKAK 169 S +Y V GE +++ + K N+G EA E A KLARK+ + I Sbjct: 88 HVSNLYYIPVQGELAQWLIQHSCADKAFFCNSGAEANEGAIKLARKYAHEKLNIE--NPT 145 Query: 170 IVFAAGNFWGRTLSAISSSTDPTSYDGFGPFMPGFEIIPYNDLPALERALQD-----PNV 224 I+ A +F GRTL+ ++++ P + GF P MPGF +PYND+ A+E A+++ V Sbjct: 146 ILTAHASFHGRTLATMTATGQPKYHKGFSPLMPGFYYVPYNDIAAIESAIEELDKDKRQV 205 Query: 225 AAFMVEPIQGEAGVVVPDPGYLVGVRELCTQHQVLFIADEIQTGLARTGRWLAIDHENVR 284 AA M+E +QGE G+ D Y +RE+C + +L I DE+Q G+ R+G+ ++ + Sbjct: 206 AAIMLEALQGEGGIRPGDMTYFKRIREICNEKGILLILDEVQAGMGRSGKIWGYENLGIE 265 Query: 285 PDIVLLGKALSGGLYPVSAVLCDDEIMLTIKPGEHGSTYGGNPLGCRVAIAALEVLEEEN 344 PDI K L GG+ P+ A+LC + +PG H ST+GGNP C VA+A LE+EN Sbjct: 266 PDIFTSAKGLGGGI-PIGAMLCKSHCDV-FEPGSHASTFGGNPFACAVALAVCHTLEQEN 323 Query: 345 LAENAEKMGIILRNELMKLPS---DVVTTVRGKGLLNAIVIRETKDCDAWKVCLRLRDNG 401 L N ++ G LR EL + ++ + VRG GL+N + + T + + + G Sbjct: 324 LLANVQQRGDELRIELKAIADKYPNLFSEVRGWGLINGLELNATATLTSIDIVKAAMNEG 383 Query: 402 LLAKPTHGDIIRFAPPLVIKEDEILEAVEIINKTI 436 LL P ++RF PPL++ E E+ EA++++ K I Sbjct: 384 LLIVPAGPKVLRFVPPLIVTETEVKEAMDLLAKAI 418 Lambda K H 0.319 0.138 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: 451 Number of extensions: 21 Number of successful extensions: 5 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: 439 Length of database: 423 Length adjustment: 32 Effective length of query: 407 Effective length of database: 391 Effective search space: 159137 Effective search space used: 159137 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: 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