Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate BPHYT_RS30200 BPHYT_RS30200 FAD-dependent oxidoreductase
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__BFirm:BPHYT_RS30200 Length = 424 Score = 161 bits (407), Expect = 4e-44 Identities = 118/390 (30%), Positives = 188/390 (48%), Gaps = 12/390 (3%) Query: 14 WEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSGR 73 W + P ++A + + DV VIGGG TGLSAA L ++G +V VL+A +IG G SGR Sbjct: 7 WLDTAPPLLSASEGPLDGQTDVVVIGGGFTGLSAAQALGKRGAAVTVLDAGRIGGGASGR 66 Query: 74 NVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLHM 133 N G VN G + A LG ++ S + +A V +I IDC G L + Sbjct: 67 NGGQVNTGVAQDFVALVAQLGVERASACYRAFSDAVDTVERLIREENIDCNYIATGKLKL 126 Query: 134 AHNATGIADLEARHEQWRRR-GADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYT 192 A +A LE E RR D+EL+ ++ + +D LL R G ++ +T Sbjct: 127 ASKPHHLAHLEKTAEAIRREVDTDIELIDRSRIRSEIQSDSFHGGLLQRHGGQMHMGKFT 186 Query: 193 QGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEGDWSNLQ 252 GLA A R G K+++ ++V + ++G+G+R+ TARG VRA++V+I+TG G + + Sbjct: 187 VGLAEAAVRRGAKLYENAAVTAIAKDGNGYRITTARGEVRAKQVLIATGPSRHGPFGWYR 246 Query: 253 KQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGR--VD 310 ++ + V ++PL +V P+ + TR + + R RLL G R Sbjct: 247 RRLAPVGSFIVVTEPLSPELLAQVFPNRRAYTTTRLMHNYFRVTPDSRLLFGGRARFTAS 306 Query: 311 NKPAWFVRSWADRIQSH----YYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVT 366 +P+ + + RI +P L + W G +D + D L + G+ Sbjct: 307 ERPS---DAKSGRILQEGLAAMFPTLASARIDYCWGGLVDMSADRLPHAGQ-HDGIYFSM 362 Query: 367 GYNGRGNTTGTVIGRAFAEFLLKGEADSLP 396 GY+G G T +G+ A+ ++ G D P Sbjct: 363 GYSGHGTQMSTHMGQVMAD-VMDGHEDKNP 391 Lambda K H 0.319 0.135 0.419 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: 470 Number of extensions: 19 Number of successful extensions: 2 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: 432 Length of database: 424 Length adjustment: 32 Effective length of query: 400 Effective length of database: 392 Effective search space: 156800 Effective search space used: 156800 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 (21.7 bits) S2: 51 (24.3 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