Align Ornithine aminotransferase; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate 15866 b1748 succinylornithine transaminase, PLP-dependent (NCBI)
Query= SwissProt::Q6CWC1 (437 letters) >FitnessBrowser__Keio:15866 Length = 406 Score = 226 bits (575), Expect = 1e-63 Identities = 144/412 (34%), Positives = 214/412 (51%), Gaps = 21/412 (5%) Query: 9 LSSAKTIEYEQEYSAHNYHPLPVVFSRASGAHVWDPEGKEYLDFLSAYSAVNQGHCHPHI 68 +S T E E+ Y P P + R G+ +WD +GKEY+DF + GH HP + Sbjct: 1 MSQPITRENFDEWMIPVYAPAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPEL 60 Query: 69 IQALVDQASKLTLSSRAFSNDCFASFSKFVTEFFGYESVLPMNTGAEAVESALKLARRWG 128 +AL +QASK + ++N+ +K + + + V N+GAEA E+ALKLAR++ Sbjct: 61 REALNEQASKFWHTGNGYTNEPVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFA 120 Query: 129 YMVKKIQPNEAIILGARGNFHGRTFGAISLSTDEEDSRMNFGPFLENVTAKIPGGSDDEF 188 + + +++ I+ + FHGRT +S S+ +F P + Sbjct: 121 H--DRYGSHKSGIVAFKNAFHGRTLFTVSAGGQPAYSQ-DFAPLPAD------------- 164 Query: 189 IRYGEIDDYKRAFESHGDKICAVIVEPIQGEAGIVVPRADFLTDLQELCKKHQVLLICDE 248 IR+ +D A D CAVIVEPIQGE G+V FL L+ELC +H LLI DE Sbjct: 165 IRHAAYNDINSASALIDDSTCAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDE 224 Query: 249 IQTGIARTGKLLCYEHSPNCKPDIILLGKAISGGVLPVSCVLSSREIMDCFTPGSHGSTY 308 +QTG+ RTG+L Y H PD++ KA+ GG PV +L++ E T G+HG+TY Sbjct: 225 VQTGVGRTGELYAYMHY-GVTPDLLTTAKALGGG-FPVGALLATEECARVMTVGTHGTTY 282 Query: 309 GGNPLASRVAIAALEVVQNENLVERSARLGKFLQDELVKLQHESNGVISEVRGKGLLTAI 368 GGNPLAS VA LE++ ++ + + + L + H G+ SEVRG GLL Sbjct: 283 GGNPLASAVAGKVLELINTPEMLNGVKQRHDWFVERLNTINHR-YGLFSEVRGLGLLIGC 341 Query: 369 VINPEKANGRTAWDLCLLMKDQGVLAKPTHEHIIRLAPPLVISEEDLLKGVD 420 V+N + A A + GV+ +++R AP L +SEE++ G+D Sbjct: 342 VLNADYAG--QAKQISQEAAKAGVMVLIAGGNVVRFAPALNVSEEEVTTGLD 391 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: 400 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: 437 Length of database: 406 Length adjustment: 32 Effective length of query: 405 Effective length of database: 374 Effective search space: 151470 Effective search space used: 151470 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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