Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate GFF1354 PGA1_c13710 diaminopimelate decarboxylase-like protein
Query= curated2:O27390 (428 letters) >FitnessBrowser__Phaeo:GFF1354 Length = 828 Score = 159 bits (402), Expect = 3e-43 Identities = 128/418 (30%), Positives = 204/418 (48%), Gaps = 33/418 (7%) Query: 22 ELADEYGTPLYVIDEMRIRENYRRLYRAFSGEYSRFQVFYACKANTNLAVMRILEEEGSG 81 E+A GTP Y+ D +R RRL A + FY+ K+N NL+V R+L G+G Sbjct: 15 EIATTAGTPFYLYDASVLR---RRL-DALRAALPQVDFFYSLKSNPNLSVTRVLHGHGAG 70 Query: 82 IDAVSPGEIYTALMAGFDPDRILYTGNNVRDDELQFALDSGVR-INVDSRSQLLRLSEIA 140 + S E+ T+L AG P+RIL G + EL A++ G++ I V+S +L ++ +A Sbjct: 71 CEVSSLLELETSLQAGATPERILMVGPGKSETELTRAIELGIKAIVVESAYELTQIDALA 130 Query: 141 PEGLR---ISFRVNPLVGAGHHEHCITGGEMSKFGVMEREAPEVYRMAMDLG-FEPVGIH 196 + R I+ RVNP AG + ++G ++FG+ + E P+V + A G+H Sbjct: 131 RQQGRVQNIALRVNPDFHAGGAKLNMSG-RPTQFGIDQSELPDVLKQAEGCAQLRLCGLH 189 Query: 197 AHIGSGILDPEPFMLAVETLMDIAGRVHEATGVEFEFIDFGGGLGIPYTPEEEPLDIDEF 256 A++G+ IL E + V ++++A V + V +F+D GGG GIPY E LD+D Sbjct: 190 AYMGTRILTHETVVANVGNILNLATEVVSSLKVPLDFVDVGGGFGIPYYDGETELDLDAL 249 Query: 257 ASKITGLFKDKLSEYGLGRP--MMCLEPGRYIVGDASYLLTRVNTIKESY-RKFAGVDAG 313 +T L + +G P + +E GRY+ G + +TRV K S FA D G Sbjct: 250 GQAVTPL----VQSFGTTHPKTRVVIELGRYLSGPSGQFVTRVQQTKSSKGEHFAVCDGG 305 Query: 314 FNTLLRPAMYGSYHHILVAERPL-----------DEPSEKMDVAGNVCESGDLFARDRQL 362 N + A G L P+ DE ++ + G +C D+ + + Sbjct: 306 SNVHVAAAGQG----FLRKNFPIRLLRDGKAEIDDEAAQPWTLTGPLCTPQDVIGKSVLM 361 Query: 363 PEINEGDVLAIMNAGAYSFSMSS-QYNSRPRPAEVLVREGKVDVVRERETFSDLLRGQ 419 GD+++I +GAY + S + PAEV++ ++ +VR R+T L GQ Sbjct: 362 ATPQVGDLISIGQSGAYGPTASPVNFLGFGAPAEVMIDGTELRLVRSRDTVEARLAGQ 419 Lambda K H 0.320 0.140 0.408 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: 802 Number of extensions: 37 Number of successful extensions: 7 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: 428 Length of database: 828 Length adjustment: 37 Effective length of query: 391 Effective length of database: 791 Effective search space: 309281 Effective search space used: 309281 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 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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