Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate RR42_RS11930 RR42_RS11930 succinyldiaminopimelate aminotransferase
Query= curated2:A5FRC5 (388 letters) >FitnessBrowser__Cup4G11:RR42_RS11930 Length = 405 Score = 178 bits (451), Expect = 3e-49 Identities = 125/407 (30%), Positives = 201/407 (49%), Gaps = 26/407 (6%) Query: 3 LSKRIENLPPYLFVQISKKIAEKRAKGE-DVISFAIGDPDLPTPKHILAELCKAAEDPSN 61 ++ R++ L PY F ++ +A+ + G ISF IG+P PTP+ I L A + +N Sbjct: 1 MNPRLDLLQPYPFEKLRVLLADVKPNGALPAISFGIGEPKHPTPEFIKTALSNALQGLAN 60 Query: 62 HRYPETEGLPVLRKAMAEWYQKRFGVK-LNPDTEVLPLIGSKEGIGHAAWCFLD---PGD 117 YP T G LR+ MA W Q+R+ + +N T+VLP+ GS+E + A +D PG Sbjct: 61 --YPTTAGSDALRQCMAAWIQRRYNLPAVNATTQVLPVTGSREALFAFAQTVVDASQPGA 118 Query: 118 IALVPNPAYPVYAISSQLAGAEVFNLPLNKGNNFLPNLEAIPQNILSKAKVLWINYPNNP 177 + L PNP Y +Y ++ LAGA + NF P + I +K +++++ P NP Sbjct: 119 LVLCPNPFYQIYEGAALLAGATPVFANSDPARNFAPAFDRIGAETWAKVQLVFVCSPGNP 178 Query: 178 TGAVAGLSFFQEVANFAAKHNLAVCHDGPYSEIAF-DGYKPVSFLE-------ADGAKDV 229 TGAV L ++E+ + +H + D YSEI F +G P+ LE A+GA Sbjct: 179 TGAVLSLEDWRELFALSDRHGFVIASDECYSEIYFKEGEPPLGALEAAHKLGRAEGAHPF 238 Query: 230 G--IEFHSLSKSYNMTGWRIGMAVGNAKMIDALRRFKSNLDSGIPQAIQLMAIAALNGSQ 287 + F SLSK N+ G R G G+A ++ +++ + A+Q ++AA N Sbjct: 239 ERLVMFSSLSKRSNVPGLRSGFVAGDAALLKKFLLYRTYHGGAMNPAVQTASVAAWNDEA 298 Query: 288 EIINQNCAIYQRRRDRLVEALRNIGMEVTAPKASLYIWAPVPES-YTSASFATELLDKTG 346 + N N A Y R+ + L + ++V P A Y+WA V + + FA LL + Sbjct: 299 HVRN-NRAAYARKFAEVTPMLAEV-LDVALPDAGFYLWADVSRTGLSDTEFAARLLAEQN 356 Query: 347 VVVTPGTGYGTAGEGY------IRLSLTVPDEQIEKGIAKLAGYKKS 387 V V PG+ +G +R++L E+ +G ++ + KS Sbjct: 357 VTVLPGSYLAREADGINPGANRVRMALVATPEECLEGARRIVAFCKS 403 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: 390 Number of extensions: 19 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