Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate 5210966 Shew_3392 ornithine decarboxylase (RefSeq)
Query= curated2:Q9Z661 (421 letters) >FitnessBrowser__PV4:5210966 Length = 391 Score = 113 bits (282), Expect = 1e-29 Identities = 101/342 (29%), Positives = 161/342 (47%), Gaps = 25/342 (7%) Query: 58 VAFAVKANPSQAILASFAKEGLGADVVSAGEIRRAVHAGIPPERIVFSGVGKTAEEMRYA 117 + +AVKANP++ +L G D+ S E+ G+ P+R+ + K +++R Sbjct: 56 IYYAVKANPAKEVLTLLRDRGANFDIASIYELDMVSDIGVTPDRVSYGNTIKKRKDVRAF 115 Query: 118 LEIGIGQFNIESVSEIEMLAEVATSLGKKAAVALRINPDVDPHTHAKIATGKADTKFGIA 177 E G+ + +S +++ M+AE A + V +RI + TH A KFG Sbjct: 116 YERGVRMYASDSEADLRMIAEEAPG----SRVYVRI---LTEGTHT--ADWPLSRKFGCQ 166 Query: 178 AEDALSAYEKLASYPSLKIQGIASHIGSQITDLAPFEAAAERIYEIITAL-EKAGHAIET 236 E A LA L+ GI+ H+GSQ D+ +++A ++ I L E+ G ++ Sbjct: 167 NEMAFELL-VLAKTLGLEPYGISFHVGSQQRDIGAWDSAIAKVKSIFERLREEHGIELKM 225 Query: 237 ADLGGGLGVRYKDDQPEPPSVEAYGEMIKRVTK----GWNCRLIFEPGRSLIANAGVLLS 292 +LGGG Y D E + Y E I K ++I EPGRSL++NAGVL+S Sbjct: 226 INLGGGFPANYLDKTNE---LGTYAEQITHFLKEDFGDQLPQIILEPGRSLLSNAGVLVS 282 Query: 293 KVIRI-KESKTA--RFVILDAAMNDLVRPTLYDAYHEIKAVTPSAQTYQADIVGPVCETG 349 +V+ I K+S+TA R+V D + T+ +A + + I GP C++ Sbjct: 283 EVVLISKKSQTALERWVFTDVGKFSGLIETMDEAIKFPIYTERQGELDRCVIAGPTCDSA 342 Query: 350 DIFARNRSISA---VKADDLMAIMSAGAYGAT-MASAYNSRP 387 DI + S + D M ++AGAY T A +N P Sbjct: 343 DIMYEHYSYGLPLDLAIGDRMYWLTAGAYTTTYSAVCFNGFP 384 Lambda K H 0.317 0.132 0.372 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: 353 Number of extensions: 17 Number of successful extensions: 3 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: 421 Length of database: 391 Length adjustment: 31 Effective length of query: 390 Effective length of database: 360 Effective search space: 140400 Effective search space used: 140400 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