Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate PfGW456L13_5067 Ornithine decarboxylase (EC 4.1.1.17) / Arginine decarboxylase (EC 4.1.1.19)
Query= curated2:Q9PII5 (402 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5067 Length = 387 Score = 107 bits (268), Expect = 5e-28 Identities = 110/368 (29%), Positives = 170/368 (46%), Gaps = 29/368 (7%) Query: 7 KQEFNTPFYIYNFDFIKERFLNLKEAFKARKSQIFYAVKANSNLSLLQMLANLDSGFDCV 66 KQE TPF + + I + + +L+ F+ K ++YAVKAN + ++ +L S FD Sbjct: 23 KQE--TPFVVIDTAMISQAYDDLRAGFEFAK--VYYAVKANPAVEIIDLLKEKGSSFDIA 78 Query: 67 SIGEVKRALKAGAKAYKIIFSGVGKTKEELRQALEYDILYINLESEAEMMLLESVAKELN 126 SI E+ + L G A +I + K +++R E + +SEA++ + A Sbjct: 79 SIYELDKVLGRGVSADQISYGNTIKKSKDIRYFYEKGVRLFATDSEADLRNIAKAAPGSK 138 Query: 127 LKARISIRVNPNVDAKTHPYISTGLNENKFGVEIDIARKMYLYAKNSSFLEPVGVHFHIG 186 + RI + D KFG + D+A + + A++ L P G+ FH+G Sbjct: 139 VYVRILTEGSTTADWPL---------SRKFGCQTDMAMDLLILARDLG-LVPYGISFHVG 188 Query: 187 SQLLDISPIHEAAAIVAKLVRELKALQ-IDLKFFDIGGGLGVAYEKNECEPDLYDYAQGI 245 SQ DIS A A V + LK I LK ++GGG Y L YA+ I Sbjct: 189 SQQRDISVWDAAIAKVKVIFERLKEEDGIHLKLINMGGGFPANYITR--TNSLETYAEEI 246 Query: 246 LAQL---HGLDL-TIGMEPGRYLVAKSGEFVCS-VLYEKQNKT--KRFVVVD-GAMNDLI 297 + L G DL I +EPGR L+A +G V VL ++++T +R+V D G + LI Sbjct: 247 IRFLKEDFGDDLPEIILEPGRSLIANAGILVSEVVLVARKSRTAVERWVYTDVGKFSGLI 306 Query: 298 RPSLYEAYHEIILPYNQGEESLCDVVGGICESGDFFAK--ARSLP-STQSDDIMVIKNTG 354 ++ EA I +GE + G C+S D + LP + D + +TG Sbjct: 307 E-TMDEAIKFPIWTEKKGEMEEVVIAGPTCDSADIMYENYKYGLPLNLAIGDRLYWLSTG 365 Query: 355 AYGFSMSS 362 AY S S+ Sbjct: 366 AYTTSYSA 373 Lambda K H 0.319 0.137 0.385 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: 344 Number of extensions: 13 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: 402 Length of database: 387 Length adjustment: 31 Effective length of query: 371 Effective length of database: 356 Effective search space: 132076 Effective search space used: 132076 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: 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