Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_046008304.1 OLEAN_RS04885 succinyldiaminopimelate transaminase
Query= curated2:C6BUK3 (388 letters) >NCBI__GCF_000967895.1:WP_046008304.1 Length = 401 Score = 190 bits (482), Expect = 7e-53 Identities = 126/397 (31%), Positives = 204/397 (51%), Gaps = 24/397 (6%) Query: 10 LATLPPYLFAEIDRLKAEVAA-QGVDIISLGIGDPDLPTPDFIIEALHKAAKNPVNHQYP 68 L L PY F ++ LKA+V+ + + I+L IG+P P P F+ + L N YP Sbjct: 5 LQKLQPYPFEKLTALKAQVSPNENLSHIALSIGEPKHPAPKFVTQCLKDNIDKVEN--YP 62 Query: 69 SYVGLLTFRQAVADWYKERFDV-ELDATKEVVSLIGSKEGIAHFPLAFVNPGDLVLVASP 127 + GL R+ +A W ++RF + ++ + +++V + G++E + F A ++ LV P Sbjct: 63 TTKGLPVLRETIAQWLQQRFGLTKICSEQQIVPVNGTREALFAFTQAVIDRSKNGLVVCP 122 Query: 128 N--YPVYPVASGFAGGEVEIVPLLEENDFLPNLDAISDEKWDKCKIFFVNYPNNPTSATA 185 N Y +Y A+ AG E +P LEE F P+ DA+SDE W KC++ F+ P NPT A Sbjct: 123 NPFYQIYEGAAYLAGAEPHFLPCLEEQGFNPDFDAVSDEVWQKCQLLFLCTPGNPTGAVL 182 Query: 186 TPEFYAELVAKAKKHNVIIAADAAYTEVYYDEDKKPISIL---ETPGAKDVA--IEFHSL 240 E +L+A A KH+ IIA+D Y+E++ ++ + PI +L E+ G D A + FHSL Sbjct: 183 ELETLTKLIALADKHDFIIASDECYSEIFVEDKQAPIGLLQACESMGRHDYARCVVFHSL 242 Query: 241 SKTYNMTGWRCGMAVGNASLVAGLGKIKENVDSGIFQAVQEAGIVALKEGEPYVKEFRKI 300 SK N+ G R G G+A ++ + + Q A + A + E +VK+ R+ Sbjct: 243 SKRSNLPGLRSGFVAGDAKILQPFLLYRTYHGCAMSIHTQLASVAAWGD-EGHVKDNRRQ 301 Query: 301 YKERRDCVIEALEKINISCKV----PDASIFVWAKTPEGYTSSEFVSKLLKETGVVVTPG 356 Y + V+E L +++ K+ DAS ++WAKT +F +L + V V PG Sbjct: 302 YSLKFKAVLEILNDPSLAGKIEVKQTDASFYLWAKTE--MDEEQFAQQLFAQQHVTVLPG 359 Query: 357 NGFGES------GEGYFRISLTVDTDRLKEAVSRISK 387 + + G+ R++L + EA RI + Sbjct: 360 SYLSRTVDGINPGKNRVRLALVASVEECIEAAERIKQ 396 Lambda K H 0.317 0.136 0.398 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: 400 Number of extensions: 24 Number of successful extensions: 6 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: 401 Length adjustment: 31 Effective length of query: 357 Effective length of database: 370 Effective search space: 132090 Effective search space used: 132090 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 10 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