Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate GFF4238 PS417_21710 acetylornithine aminotransferase
Query= curated2:Q5SHH5 (395 letters) >FitnessBrowser__WCS417:GFF4238 Length = 406 Score = 270 bits (691), Expect = 4e-77 Identities = 162/379 (42%), Positives = 221/379 (58%), Gaps = 21/379 (5%) Query: 32 VRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPT-PMRG 90 VRG+G+RVWD G E ID GG V LGH +P +V A+ QA L + P Sbjct: 29 VRGEGSRVWDQAGRELIDFAGGIAVNVLGHAHPALVGALTEQAHKLWHVSNVFTNEPALR 88 Query: 91 EFYRTLTAILPPELNRVFPVNSGTEANEAALKFARA----HTGRKKF--VAAMRGFSGRT 144 ++ + A RVF NSG EANEAA K AR G +K+ +AA+ F GRT Sbjct: 89 LAHKLIDATFA---ERVFFCNSGAEANEAAFKLARRVAFDRFGSEKYEIIAALNSFHGRT 145 Query: 145 MGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQGEGGVRPAT 204 + +++V + KY + F P + + +PYND++ALK AV ++T AV+LEP+QGEGGV PA Sbjct: 146 LFTVNVGGQSKYSDGFGPKITGITHVPYNDLDALKAAVSDKTCAVVLEPIQGEGGVLPAE 205 Query: 205 PEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGVPLGA 264 +L+ AR++ ALL+ DE+QTGMGR+G FA++H+G+ PDILT AK+LGGG P+ A Sbjct: 206 LAYLQGARDLCDANNALLVFDEVQTGMGRSGHLFAYQHYGVTPDILTSAKSLGGGFPIAA 265 Query: 265 AVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLRAI 324 + E +A+ + G HGTT+GGNPLA A A I + + F +L I Sbjct: 266 MLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLAGVNAKHDLFKARLEQI 325 Query: 325 PSPK--IREVRGMGLMVGLEL----KEKAAPYIARLEKEHRVLALQAGPTVIRFLPPLVI 378 EVRGMGL++G L K KA EKE+ ++ LQAGP V+RF P LV+ Sbjct: 326 GKQYGIFTEVRGMGLLLGCVLSDAFKGKAKDVFNAAEKEN-LMILQAGPDVVRFAPSLVV 384 Query: 379 E----KEDLERVVEAVRAV 393 E KE L+R AV+A+ Sbjct: 385 EDADIKEGLDRFERAVKAL 403 Lambda K H 0.319 0.137 0.402 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: 392 Number of extensions: 18 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: 395 Length of database: 406 Length adjustment: 31 Effective length of query: 364 Effective length of database: 375 Effective search space: 136500 Effective search space used: 136500 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 Aug 03 2021. The underlying query database was built on Aug 03 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