Align D-lactate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate N515DRAFT_2104 N515DRAFT_2104 glycolate oxidase iron-sulfur subunit
Query= reanno::Phaeo:GFF2923 (444 letters) >FitnessBrowser__Dyella79:N515DRAFT_2104 Length = 400 Score = 140 bits (352), Expect = 9e-38 Identities = 123/400 (30%), Positives = 171/400 (42%), Gaps = 35/400 (8%) Query: 25 CVHCGFCTATCPTYQVLGDELDSPRGRIYLIKDMLENERVPDAKTVKHIDRCLSCLACMT 84 CV CG C CPTY + +E +SPRGRI + + + P A+ +H+D CL C+ C Sbjct: 20 CVQCGLCLPVCPTYALDRNEAESPRGRIAIAAALARGQASPTAELREHLDHCLGCMGCEK 79 Query: 85 TCPSGVHYMHLVDHARAYIDKHYNRPWSDRAL-----RWLLARILPYPGRFRLALIGAKL 139 CP+ V Y L+ RA + RP + L RW R G L G K Sbjct: 80 VCPANVRYGELLVETRALLGPALQRPEHEIGLVRDPRRWRRLR----RGLGWLGFAGWKS 135 Query: 140 AQPFKRLVPDARLRAMLDMAPRHIPPVSRNDDPQSFAAKAPRRKRVALMTGCAQKALNTD 199 A K L + LR+ L + PR P+ Q + KA VAL GC + D Sbjct: 136 ALA-KSLPARSALRSALALWPR--TPLPEPYLAQPASDKAADGDTVALFPGCIASVEDAD 192 Query: 200 INDATIRLLTRLGCEVVVAAGAGCCGALTHHMGREEESHATAAKNIRAWTDEIDGQGLDA 259 A LL G VV A CCGA+ H G + AA+ AW D D Sbjct: 193 AQRAARTLLRAAGYR-VVELPAFCCGAMDLHGGDTARAEQAAAQVSAAWQD----AQADH 247 Query: 260 IVINTSGCGTTVKDYGHMFRNDALAEDAARVSAIAMDISELLMQLDLPEGEDKETTVAYH 319 +V T GC T++ H+ +A+ A ++A A +S LP T VA H Sbjct: 248 LVTVTPGCVGTLR---HVLPGVRVADPMALLAARAQRLS----FRPLP------TRVAVH 294 Query: 320 AACSLQHGQQIKTHPKTLLKRA-GFTVVEPADSHLCCGSAGTYNLLQPEISAELKARKVT 378 C+ + + LL+R G V CCG+AGT+ L PE +A L+ + Sbjct: 295 LPCTQSNVARSDDALLRLLRRVPGLDVAPLPKPPHCCGAAGTHVLEFPERAARLREDTLR 354 Query: 379 SLEARQPDLIAAGNIGCMMQIGSA----TDIPILHTVELL 414 + A P + + NIGC + + + D P H + LL Sbjct: 355 QVAALAPRRLLSSNIGCRLHLAAGMQNERDWPHQHPLVLL 394 Lambda K H 0.321 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: 487 Number of extensions: 28 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 444 Length of database: 400 Length adjustment: 32 Effective length of query: 412 Effective length of database: 368 Effective search space: 151616 Effective search space used: 151616 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