Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate RR42_RS13815 RR42_RS13815 FAD-dependent oxidoreductase
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__Cup4G11:RR42_RS13815 Length = 534 Score = 205 bits (522), Expect = 3e-57 Identities = 147/432 (34%), Positives = 213/432 (49%), Gaps = 70/432 (16%) Query: 20 YDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVEV 79 +DV++IGGG TG G AV A+ G +T+L+E DFA+GTSS++TKLVHGG+RYL ++ + Sbjct: 26 WDVIVIGGGATGLGTAVDAASRGYRTLLVEAADFAKGTSSKATKLVHGGVRYLAQGNISL 85 Query: 80 VADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLA---NVTGS 136 V + + ER ++ + APH+ P ++P Y F + + LYD LA N++GS Sbjct: 86 VREALHERGLLARNAPHLVWPLGFVVPAYQ----LFDQPFYGIGLKLYDMLAGGLNLSGS 141 Query: 137 KYENYLLTKEEVLAREPQLQ----AENLVGGGVYLDFRNNDARLVIENIKRAQADGAAMI 192 ++ N+ E LA P L L GG +Y D + +DARL I ++ G I Sbjct: 142 RWLNH----RETLAAAPTLAEHVGGRPLRGGNLYFDGQFDDARLAIALMRTLFDVGGTAI 197 Query: 193 SKAKVVGILHDEQGIINGVEVEDQLTNERFEVHAKVVINTTGPWSDIVRQLDKNDELPPQ 252 + +V G L G+I+GV V+D L + F++ A VIN TG W D VRQ++ + + Sbjct: 198 NYLRVSG-LSQRNGVIDGVTVQDVLGDASFDLKASCVINATGVWVDAVRQME-DGQARSM 255 Query: 253 MRPTKGVHLVVDREKLKVPQPTYFDTGKNDGRMVFVVPRENKTYFGTTDTDYTGDFAHPT 312 + P++GVHL + R L + +DGR++FVVP T GTTDT P Sbjct: 256 VAPSQGVHLTLPRSFLPGDRAILIPK-TDDGRVLFVVPWNGHTIIGTTDTPRKDLPLEPR 314 Query: 313 VTQEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLSDESFE 372 +DVD++L A T D+ + WAGLRPL+ G Sbjct: 315 AGADDVDFILETATRYLSRAP-TRADVTSVWAGLRPLVKATG------------------ 355 Query: 373 QIVESVKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLERSKDGLLTLAGGK 432 EAS + +SR ++ SK GL+T+ GGK Sbjct: 356 ------------------------------EAS---TASLSREHTILVSKAGLITVTGGK 382 Query: 433 ITDYRLMAEGAV 444 T YR MAE V Sbjct: 383 WTTYRKMAEDVV 394 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: 679 Number of extensions: 34 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: 534 Length adjustment: 36 Effective length of query: 573 Effective length of database: 498 Effective search space: 285354 Effective search space used: 285354 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