Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate 8499751 DvMF_0516 aminotransferase class-III (RefSeq)
Query= reanno::Marino:GFF3099 (404 letters) >FitnessBrowser__Miya:8499751 Length = 459 Score = 169 bits (429), Expect = 1e-46 Identities = 127/431 (29%), Positives = 207/431 (48%), Gaps = 57/431 (13%) Query: 22 GSIIPVRGEGSRIWDQEGREFIDL-QGGIAVTCLGHSHPGLVGALHDQAEKIWHLSNVMT 80 G +I V GEG + D G+E++D GG+ +G+ + A+++Q + + + + Sbjct: 34 GPMIVVEGEGLTLRDINGKEYLDATSGGVWCVNVGYGRERIARAVYEQMKAMPYYAATAG 93 Query: 81 NEPALRLA-KTLCDLTFAERVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSF 139 N P + A K L + R + +NSG+EANE A+K+ R A K +I+ + Sbjct: 94 NIPYIEFAQKLLAHMPGLTRAYLSNSGSEANEKAYKMVRSLAHLSGNPAKKKILFRARDY 153 Query: 140 HGRTLFTVSVGGQPKYLEGFEP-APGGI-------HHAEFN------DLE---SVKKLIS 182 HG TL +S GQ + E F P PG + + FN D++ +V+++I Sbjct: 154 HGTTLGALSSTGQAERKEWFGPLVPGFVEFPHACCYRCAFNKTYPGCDIDCARAVERIIE 213 Query: 183 KE---KTCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYA 239 +E ++VEPI GGV+P + L D+C + LL+ DEV G+GR+G + Sbjct: 214 QEGPETVGGLIVEPITAGGGVIPPVAEYYTVLADICRRHGVLLIMDEVVCGMGRTGTMFG 273 Query: 240 YQMYGVVPDILSSAKGLGGGF-PVAAMLTTAKV--------AASLGVGTHGSTYGGNALA 290 YQ YGV PDI++ AKG+ + P++ TT +V A + STYGG A Sbjct: 274 YQHYGVTPDIVTMAKGVASAYMPISVTATTEEVFKAFLNDPADKMAYFRDISTYGGCAAG 333 Query: 291 CAVAQRVVDTVSQPEILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQ 350 C+ A + + + ++L V A D L G+ ++G+ V +VRG GLL G L + Sbjct: 334 CSAALENMAIIEEEKLLDNVNAMGDYLLAGLKELGDLPYV-GDVRGKGLLCGIELVQDKA 392 Query: 351 GKAKDFLNAGLEEGVMVLVAGA-------------------NVIRLAPSLIIPEPDIELA 391 GK + EG ++ V G N+I +AP+ ++ +I++ Sbjct: 393 GKKP------MAEGKVIQVVGEMAANAVLVGRTNRSLPGFNNIINIAPAYVVTRDNIDVI 446 Query: 392 LERFEAAVKKL 402 L AA+ K+ Sbjct: 447 LRTLRAALVKV 457 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: 472 Number of extensions: 35 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: 404 Length of database: 459 Length adjustment: 32 Effective length of query: 372 Effective length of database: 427 Effective search space: 158844 Effective search space used: 158844 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: 51 (24.3 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