Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate GFF2392 PGA1_c24230 acetylornithine aminotransferase ArgD
Query= reanno::WCS417:GFF4238 (406 letters) >FitnessBrowser__Phaeo:GFF2392 Length = 394 Score = 327 bits (838), Expect = 4e-94 Identities = 171/386 (44%), Positives = 241/386 (62%), Gaps = 9/386 (2%) Query: 17 MVPNYAPAAFIPVRGEGSRVWDQAGRELIDFAGGIAVNVLGHAHPALVGALTEQAHKLWH 76 ++P Y A V+GEG+ + + GR +D A GIAVN LGHAHPALV ALT+QA LWH Sbjct: 5 VLPTYNRAPLSFVKGEGAWLIEADGRRFLDLAAGIAVNALGHAHPALVKALTDQAETLWH 64 Query: 77 VSNVFTNEPALRLAHKLIDATFAERVFFCNSGAEANEAAFKLARRVAFDRFGSEKYEIIA 136 VSN++ LA +L++ +FA+ VFF NSG E+ E A K+AR+ D+ E+ EI+ Sbjct: 65 VSNLYHIPQQQALADRLVEHSFADTVFFTNSGTESCELAVKMARKYFHDKGQPERVEILT 124 Query: 137 ALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLDALKAAVSDKTCAVVLEPIQ 196 SFHGR+ ++ G K + GFGP + G H+ + DLD + A++D+T A+++EP+Q Sbjct: 125 FSGSFHGRSSAGISAAGSEKMTAGFGPMLPGFKHLMFGDLDGVTDAITDQTAAILIEPVQ 184 Query: 197 GEGGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLFAYQHYGVTPDILTSAKS 256 GEGG+ P A L+ R +CD + LL+ DEVQ G+GR+G LFA++ G+TPDI+ AK Sbjct: 185 GEGGIRPVPDAELKALRQICDEHGLLLILDEVQCGVGRTGKLFAHEWAGITPDIMMVAKG 244 Query: 257 LGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLAGVNAKHD 316 +GGGFP+ A+L TE A + GTHG+TYGGNPL CAV AV+D + PE LA V+ K Sbjct: 245 IGGGFPLGAVLATEEAASGMTAGTHGSTYGGNPLGCAVGCAVMDHVTDPEFLAEVSRKAG 304 Query: 317 LFKARLE-QIGKQYGIFTEVRGMGLLLG--CVLSDAFKGKAKDVFNAAEKENLMILQAGP 373 L + +LE + +F VRG GL+LG CV ++ DV A + ++ + A Sbjct: 305 LLRQKLEGLVASHPQVFEAVRGSGLMLGLKCVAANT------DVVAAGYEAEVVTVPAAD 358 Query: 374 DVVRFAPSLVVEDADIKEGLDRFERA 399 +VVR P L + D DI E R ++A Sbjct: 359 NVVRLLPPLTLTDEDIAEAFARLDQA 384 Lambda K H 0.320 0.137 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: 416 Number of extensions: 17 Number of successful extensions: 3 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: 394 Length adjustment: 31 Effective length of query: 375 Effective length of database: 363 Effective search space: 136125 Effective search space used: 136125 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: 50 (23.9 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