Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate BPHYT_RS00645 BPHYT_RS00645 diaminopimelate decarboxylase
Query= BRENDA::C9W982 (420 letters) >FitnessBrowser__BFirm:BPHYT_RS00645 Length = 402 Score = 79.0 bits (193), Expect = 2e-19 Identities = 106/352 (30%), Positives = 152/352 (43%), Gaps = 55/352 (15%) Query: 29 YAVKCNPDPVMLRVLANLGCGFDCASAKEMATVLDMGVEAESIVFAHPCKRPLDLEFAIE 88 Y++K NP P ++ LA GFD ASA+EMA LD G +SI FA P K DL A+ Sbjct: 58 YSIKANPMPAVIHYLAQRVDGFDVASAQEMALALDAGATPDSIGFAGPGKSHDDLRRAVA 117 Query: 89 TNVTRMTFDCVDELEKVAA----ECPHAELVLRIRADDPSAVVQFGHK----------YG 134 + V + + +L V A +V+RI D Q GH +G Sbjct: 118 SGV-NVHVESDTQLRLVTALGWELGVQPNVVIRINPD-----FQVGHSGMRMGGSAAPFG 171 Query: 135 ADPQTEAPMLLAAAKQLEMNVVGVSFHVGSGSQSCDAYPLAVEAARRVFD----QAADLG 190 D + P LL + E+ + G FHV GSQ A + +EA R+ D A+DL Sbjct: 172 VDVD-QIPALLHELETREVALAG--FHVFWGSQCLHASTI-IEAQRQSVDLILRLASDLP 227 Query: 191 YEMQLLDLGGGFWGRFDATGHVPLED--VSEAINSALDRF-------FPVNSSGRKVEVI 241 ++ ++LGGGF G G PL+ V EA++ L R P+ GR ++ Sbjct: 228 RPLRFVNLGGGF-GIPYFPGETPLDTKVVCEAMHDWLPRLCERLPGTTPILELGR--YLV 284 Query: 242 AEPGRYFAEACTTMYALVTTVKDRP-DGSRSYYITDGVYGSFNNLVYDHGSVTAKVLRGP 300 E G Y V V DR R++ ITDG G ++L G+ + R Sbjct: 285 GEAGIY-----------VCRVIDRKVSRGRTFVITDG--GLHHHLAAS-GNFGQVLRRNF 330 Query: 301 GMPPVQPVETETRLPSTVFGPTCDGVDLIFKDVPMPLLRRGDWLQFPNFGAY 352 + + +R V G C +D + DV +P GD++ GAY Sbjct: 331 PVVIGNRPDGISRERCYVVGCLCTPLDRLADDVELPEAHIGDFVVVKQSGAY 382 Lambda K H 0.321 0.137 0.426 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: 416 Number of extensions: 19 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: 420 Length of database: 402 Length adjustment: 31 Effective length of query: 389 Effective length of database: 371 Effective search space: 144319 Effective search space used: 144319 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