Align Ornithine aminotransferase; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate RR42_RS26160 RR42_RS26160 4-aminobutyrate aminotransferase
Query= SwissProt::Q6CWC1 (437 letters) >FitnessBrowser__Cup4G11:RR42_RS26160 Length = 424 Score = 195 bits (496), Expect = 2e-54 Identities = 136/412 (33%), Positives = 208/412 (50%), Gaps = 38/412 (9%) Query: 35 RASGAHVWDPEGKEYLDFLSAYSAVNQGHCHPHIIQALVDQASKLTLSSRAF----SNDC 90 RA A +WD EG++Y DF + +N GH HP ++QA++ Q + T ++ S Sbjct: 28 RAENATLWDVEGRQYTDFACGIAVLNTGHRHPRVMQAVIAQLERFTHTAYQIVPYESYVA 87 Query: 91 FASFSKFVTEFFGYESVLPMNTGAEAVESALKLARRWGYMVKKIQPNEAIILGARGNFHG 150 A + G + TGAEAVE+A+K+AR ++ G FHG Sbjct: 88 LAERINALVPIDGLKKTALFTTGAEAVENAVKIARA--------HTGRPGVIAFSGGFHG 139 Query: 151 RTFGAISLSTDEEDSRMNFGPFLENV-----TAKIPGGSDDEFIRYGEIDDYKRAFESHG 205 RT ++L+ ++ FGPF ++ + G S ++ I+ E F++ Sbjct: 140 RTLLGMALTGKVAPYKVGFGPFPSDIYHAPFPCDLHGVSTEQSIQALE-----SLFKTDI 194 Query: 206 D--KICAVIVEPIQGEAGIVVPRADFLTDLQELCKKHQVLLICDEIQTGIARTGKLLCYE 263 D ++ A+I+EP+QGE G DF+ L+ LC KH +LLI DE+QTG RTGKL Sbjct: 195 DPQRVAAIIIEPVQGEGGFHPAPVDFMQTLRALCDKHGILLIADEVQTGFGRTGKLFAMS 254 Query: 264 HSPNCKPDIILLGKAISGGVLPVSCVLSSREIMDCFTPGSHGSTYGGNPLASRVAIAALE 323 H P PD+I + K+++GG +P+S V IMD PG G TY GNPLA A A +E Sbjct: 255 HYP-VAPDLITMAKSLAGG-MPLSAVCGRASIMDAPLPGGLGGTYAGNPLAVAAAHAVIE 312 Query: 324 VVQNENLVERSARLGKFLQDELVKLQHESNGVISEVRGKGLLTAIVINPEKANGRTAWDL 383 ++ E L ER+ LGK L+ L + G I+++RG G + A+ + + A G+ + +L Sbjct: 313 TIEQERLCERATALGKQLKAALQQASQTCPG-IADIRGLGSMVAVEFH-DPATGQPSAEL 370 Query: 384 C----LLMKDQG--VLAKPTHEHIIRLAPPLVISEEDLLKGVDSIRVSLSKL 429 L + G +L T+ + IR PL I + D+ V L+K+ Sbjct: 371 AKRVQLRAMEAGLILLTCGTYGNTIRFLYPLTIPQAQF----DAALVVLTKV 418 Lambda K H 0.318 0.136 0.400 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: 431 Number of extensions: 23 Number of successful extensions: 6 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: 437 Length of database: 424 Length adjustment: 32 Effective length of query: 405 Effective length of database: 392 Effective search space: 158760 Effective search space used: 158760 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 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