Align Ornithine decarboxylase; ODC; EC 4.1.1.17 (characterized)
to candidate GFF5387 PS417_27580 diaminopimelate decarboxylase
Query= SwissProt::P07805 (423 letters) >FitnessBrowser__WCS417:GFF5387 Length = 415 Score = 108 bits (269), Expect = 4e-28 Identities = 112/400 (28%), Positives = 177/400 (44%), Gaps = 38/400 (9%) Query: 14 LEGFNTRDA--LCKKISMNTCDE--GDPFFVADLGDIVRKHETWKKCLPRVTPF--YAVK 67 ++ FN RD + ++++ + G P +V I ++ ++ L V+ YAVK Sbjct: 1 MDAFNYRDGELFAEGVALSAIAQRFGTPTYVYSRAHIEAQYRSFTDALDGVSHLVCYAVK 60 Query: 68 CNDDWRVLGTLAALGTGFDCASNTEIQRVRGIGVPPEKIIYANPCKQISHIRYARDSGVD 127 N + VL LA LG GFD S E++RV G EKI+++ K +R A + GV Sbjct: 61 ANSNLGVLNVLARLGAGFDIVSRGELERVLAAGGKAEKIVFSGVGKTREDMRRALEVGVH 120 Query: 128 VMTFDCVDELEKV----AKTHPKAKMVLRISTD-DSLARCRLSV-----KFGAKVEDCRF 177 + DELE++ A+ +A + LR++ D D+ +S KFG + D Sbjct: 121 CFNIESTDELERLQVVAAEMGVRAPISLRVNPDVDAGTHPYISTGLKENKFGIAIADAED 180 Query: 178 ILEQAKKL-NIDVTGVSFHVGSGSTDASTFAQAISDSRFVFDMGTELGFNMHILDIGGGF 236 + +A +L N++V GV H+GS T F A+ + D E G +H +D+GGG Sbjct: 181 VYIRAAQLPNLEVLGVDCHIGSQLTTLPPFLDALDRLLALIDRLGECGIYLHHIDLGGGV 240 Query: 237 PGTRDAPLKFEEIAGVINNALEKHFPPDLKLTIVAEPGRYYVASAFTLAVNVIAKKVTPG 296 G R + IA I E+ D LT++ EPGRY VA+A L V K T Sbjct: 241 -GVRYRDEEPPLIADYIKAVRERIEGRD--LTLMFEPGRYIVANAGVLLTQVEYLKHTEH 297 Query: 297 VQTDVGAHAESNAQSFMYYVNDGVYGSFNCILYDHAVVRPLPQREPIPNEKLYPSSVWGP 356 + A +ND + + + V P + Y + GP Sbjct: 298 KDFAIVDAA----------MNDLIRPALYQAWMNVTAVTPRAS-----EARAY--DIVGP 340 Query: 357 TCDGLDQIVERYYLPEMQVGEWLLFEDMGAYTVVGTSSFN 396 C+ D + + L ++ G+ L GAY V +S++N Sbjct: 341 ICETGDFLAKDRQL-ALEEGDLLAIHSAGAYGFVMSSNYN 379 Lambda K H 0.321 0.138 0.424 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: 382 Number of extensions: 24 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: 423 Length of database: 415 Length adjustment: 32 Effective length of query: 391 Effective length of database: 383 Effective search space: 149753 Effective search space used: 149753 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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