Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_086508434.1 BZY95_RS02535 aspartate aminotransferase family protein
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >NCBI__GCF_002151265.1:WP_086508434.1 Length = 450 Score = 204 bits (519), Expect = 4e-57 Identities = 150/416 (36%), Positives = 209/416 (50%), Gaps = 45/416 (10%) Query: 29 EGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHT-GNGYTNEPVLRLA 87 +G LWD+ G++Y+D G LGH + +A+ Q + T + N P + LA Sbjct: 21 KGVYLWDETGRQYLDGCSGAISCNLGHGRNDIREAMLAQLDRVAFTYRTQFENAPAVALA 80 Query: 88 KQLIDATFA--DRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRTLFT 145 K L+ T ++VFF +SG+EA E+ALKLAR+Y R ++ V+ + ++HG TL Sbjct: 81 KALVGFTQQQLEKVFFVSSGSEAVESALKLARQYFVARGEPQRRRFVSLRPSYHGSTLGA 140 Query: 146 VSAGGQPAYSQDFAPL---------PPQIQHAIYND-------LDSAKALID----DNTC 185 + G F + P +H +D L +A I+ D Sbjct: 141 LGVTGYQPLEAPFRDIAIGSLKVAGPDFYRHDDTDDGRHVARVLADTRAAIEAAGPDTIA 200 Query: 186 AVIVEPMQGEG-GVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVT 244 A ++EP+ G G D +L G+R LCD LLI DEV TG+GRTG +AY HYGVT Sbjct: 201 AFVLEPVGGASTGARKLDRSYLAGIRALCDEFGCLLILDEVLTGIGRTGTWFAYQHYGVT 260 Query: 245 PDLLSTAKALGGG-FPIGALLA-SERCASVMTVG--THGTTYGGNPLACAVAGEVFATIN 300 PDLLSTAK LG G +P+GA+L+ ++ +VM G HG TY GNPLACA V I Sbjct: 261 PDLLSTAKGLGAGYYPVGAVLSRADIVETVMASGGFQHGHTYAGNPLACATGLAVVEAIE 320 Query: 301 TREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQ--- 357 ++L+ V R + L A+ AR+ ++RGLGLL G L + A KA + Q Sbjct: 321 REKILDNVAARGRQLAAGLEALKARFPWVGDVRGLGLLWGVELVADAASKAPFPAEQNRF 380 Query: 358 ------AAEEGLMIL-------IAGANVVRFAPALIISEDEVNSGLDRFELACKRF 400 A EEGL+I IAG + + P L I + L R E A +RF Sbjct: 381 ARITALAREEGLLIYPRRTLDGIAGDHFL-ITPPLTIDAADTAELLTRLERAMQRF 435 Lambda K H 0.321 0.137 0.412 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: 443 Number of extensions: 22 Number of successful extensions: 4 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: 406 Length of database: 450 Length adjustment: 32 Effective length of query: 374 Effective length of database: 418 Effective search space: 156332 Effective search space used: 156332 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 24 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