Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate H281DRAFT_00600 H281DRAFT_00600 succinyldiaminopimelate aminotransferase apoenzyme
Query= curated2:A5FRC5 (388 letters) >FitnessBrowser__Burk376:H281DRAFT_00600 Length = 405 Score = 158 bits (400), Expect = 2e-43 Identities = 120/399 (30%), Positives = 200/399 (50%), Gaps = 25/399 (6%) Query: 7 IENLPPYLFVQISKKIAEKR-AKGEDVISFAIGDPDLPTPKHILAELCKAAEDPSNHRYP 65 +++L PY F ++ + A G ISF IG+P PTP I + + S YP Sbjct: 5 LDSLQPYPFEKLRALFKDVAPAAGFPHISFGIGEPKHPTPTLITDAVIASLGGLS--AYP 62 Query: 66 ETEGLPVLRKAMAEWYQKRFGVK-LNPDTEVLPLIGSKEGIGHAAWCFLDP-----GDIA 119 T G LR+++A+W +R+G+ ++P T+VLP+ GS+E + A +DP G+ A Sbjct: 63 ATVGSLPLRESIAKWVTQRYGLPPVDPATQVLPVSGSREALFALAQTVIDPRRNAKGEPA 122 Query: 120 LV--PNPAYPVYAISSQLAGAEVFNLPLNKGNNFLPNLEAIPQNILSKAKVLWINYPNNP 177 +V PNP Y +Y ++ LAGAE + + + NF + A+P ++ ++ ++L++ P NP Sbjct: 123 IVLCPNPFYQIYEGAAILAGAEPYFVNSDPARNFACDYSAVPADVWARTQLLYVCSPGNP 182 Query: 178 TGAVAGLSFFQEVANFAAKHNLAVCHDGPYSEIAFD-GYKPVSFLEADGAKDVG----IE 232 TGAV L ++E+ + +H + D YSEI FD P+ LEA G I Sbjct: 183 TGAVLTLEDWRELFALSDRHGFVIASDECYSEIYFDEANAPLGGLEAAHKLGRGYDRLIM 242 Query: 233 FHSLSKSYNMTGWRIGMAVGNAKMIDALRRFKSNLDSGIPQAIQLMAIAALNGSQEIINQ 292 SLSK N+ G R G G+A ++ +++ + + Q +IAA N + + + Sbjct: 243 LSSLSKRSNVPGMRSGFVAGDAAILKDFLLYRTYHGAALSTVFQSASIAAWN-DEAHVRE 301 Query: 293 NCAIYQRRRDRLVEALRNIGMEVTAPKASLYIWAPVPES-YTSASFATELLDKTGVVVTP 351 N A Y ++ + L + ++V P A+ Y+WA V + T FA L V V P Sbjct: 302 NRAKYVQKFSTVTPMLAAV-LDVRLPDAAFYLWADVSRTGLTDTEFAQRLYADYNVTVLP 360 Query: 352 G-----TGYG-TAGEGYIRLSLTVPDEQIEKGIAKLAGY 384 G T +G G ++RL+L ++ +G ++ + Sbjct: 361 GSFLARTAHGVNPGRNFVRLALVADVDECTQGAQRIVDF 399 Lambda K H 0.317 0.135 0.401 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: 365 Number of extensions: 17 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: 388 Length of database: 405 Length adjustment: 31 Effective length of query: 357 Effective length of database: 374 Effective search space: 133518 Effective search space used: 133518 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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