Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate GFF1639 HP15_1598 FAD dependent oxidoreductase
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__Marino:GFF1639 Length = 532 Score = 197 bits (501), Expect = 9e-55 Identities = 138/426 (32%), Positives = 214/426 (50%), Gaps = 62/426 (14%) Query: 20 YDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVEV 79 +DV+++GGGITGAGVA + A +G++T+L+E +DF+ GTSSRS+K+VHGG+RYL + + Sbjct: 17 FDVVVVGGGITGAGVAREAAGSGLRTLLVEQKDFSWGTSSRSSKMVHGGLRYLGSGHYGL 76 Query: 80 VADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLANVTGSKYE 139 D VRER + AP + +P ++P + LF + + +YD +A Sbjct: 77 TRDAVRERERLMAEAPGLIEPLRFIMPHFKGQFPGPRLF--QTLLRVYDLIAR----NQS 130 Query: 140 NYLLTKEEVLAREPQLQAENLVGGGVYLDFRNNDARLVIENIKRAQADGAAMISKAKVVG 199 + LT E + P L +ENL G + D +D+RLV+ I A+ DGA ++ + Sbjct: 131 RHFLTPAESMLWVPGLTSENLAGASGFTDAVTDDSRLVLRLIAEARRDGAMCLNYTRADE 190 Query: 200 ILHDEQGIINGVEVEDQLTNERFEVHAKVVINTTGPWSDIVRQLDKNDELPPQMRPTKGV 259 I G ++G+ ++ + + EV A +VIN TG W+D + Q K E +RP +G Sbjct: 191 IKR-SNGDVSGLLIQAEENDTPIEVFAPLVINATGAWADRL-QSSKTSEDAMHIRPLRGS 248 Query: 260 HLVVDREKLKVPQPTYFDTGKNDGRMVFVVPRENKTYFGTTDTDYTGDF-AHPTVTQEDV 318 HLV+ L V DGR VF P T GTTD D+ G P +++ + Sbjct: 249 HLVLPWSSLPVSCSVSL-FHPEDGRPVFAFPWLGTTVLGTTDIDHEGSLDQEPVISESET 307 Query: 319 DYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLSDESFEQIVESV 378 YLL I + FP + IT +DI ++WAG+RP++T+ G GK Sbjct: 308 AYLLEIASRLFPGSPITRNDILSTWAGVRPVVTD---------GTGK------------- 345 Query: 379 KEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLERSKDGLLTLAGGKITDYRL 438 PS+ +R +L R GL+++AGGK+T +R+ Sbjct: 346 -----------------------------SPSKENREHAL-RVDRGLVSIAGGKLTTFRV 375 Query: 439 MAEGAV 444 +A A+ Sbjct: 376 IAREAL 381 Lambda K H 0.314 0.132 0.368 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: 634 Number of extensions: 35 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: 609 Length of database: 532 Length adjustment: 36 Effective length of query: 573 Effective length of database: 496 Effective search space: 284208 Effective search space used: 284208 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 53 (25.0 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