Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate 353284 BT3758 acetylornithine aminotransferase (NCBI ptt file)
Query= reanno::Marino:GFF3099 (404 letters) >FitnessBrowser__Btheta:353284 Length = 373 Score = 227 bits (578), Expect = 5e-64 Identities = 133/372 (35%), Positives = 208/372 (55%), Gaps = 18/372 (4%) Query: 27 VRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLSNVMTNEPALR 86 V+G+G ++WD+ G E++DL GG AV +GH+HP V + +Q + SN + N+ + Sbjct: 15 VKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATLGFYSNSVINKLQQQ 74 Query: 87 LAKTLCDLTFAE--RVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSFHGRTL 144 +A+ L ++ E +F NSGAEANE A KLA Y +G+ K +ISF +FHGRT Sbjct: 75 VAERLGKISGYEDYSLFLINSGAEANENALKLASFY----NGRTK--VISFSKAFHGRTS 128 Query: 145 FTVSVGGQPKYLEGFEPAPGGIHHAEFNDLESVKKLISKEKTCAIVVEPIQGEGGVMPGD 204 V P + G + + ND+E++K+ ++K CA+++E IQG GG+ Sbjct: 129 LAVEATNNPTIIAPINNN-GHVTYLPLNDIEAMKQELAKGDVCAVIIEGIQGVGGIKIPT 187 Query: 205 QAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQMYGVVPDILSSAKGLGGGFPVAA 264 F+Q LR +C E +L+ DE+QSG GRSG F+A+Q + PDI++ AKG+G GFP+A Sbjct: 188 TEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITVAKGIGNGFPMAG 247 Query: 265 MLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDTVSQPEILKGVKARSDKLRKGMMDI 324 +L + G G+T+GGN LAC+ A V+D + Q +++ KA D L + + Sbjct: 248 VLISPMFKPV--YGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKAVGDYLLEEL--- 302 Query: 325 GERYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAGLEEGVMVLVAGANVIRLAPSLIIP 384 +++ EVRG GL++G E + + +E V +G NV+RL P L + Sbjct: 303 -KKFPQIKEVRGRGLMIGLEFEEPIKELRSRLI---YDEHVFTGASGTNVLRLLPPLCLS 358 Query: 385 EPDIELALERFE 396 + + L RF+ Sbjct: 359 MEEADEFLARFK 370 Lambda K H 0.318 0.137 0.406 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: 368 Number of extensions: 20 Number of successful extensions: 7 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: 404 Length of database: 373 Length adjustment: 30 Effective length of query: 374 Effective length of database: 343 Effective search space: 128282 Effective search space used: 128282 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 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