Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate GFF2214 HP15_2168 FAD dependent oxidoreductase
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__Marino:GFF2214 Length = 507 Score = 178 bits (451), Expect = 6e-49 Identities = 159/558 (28%), Positives = 249/558 (44%), Gaps = 99/558 (17%) Query: 20 YDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVEV 79 +DV+++GGG+ G G+A+ A G+K +L EM D A TSS S+KL+HGG+RYL+ ++ + Sbjct: 6 FDVIVVGGGVNGTGIAMDAAGRGLKVLLCEMNDLASATSSSSSKLIHGGLRYLEHYEFRL 65 Query: 80 VADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLANVTGSKYE 139 V + + ER + + +PHI P LP P + ++ + LYD LA Sbjct: 66 VREALAERESLLRNSPHIMWPMRFRLP--HRPHLR-PAWMIRTGLFLYDHLA-------- 114 Query: 140 NYLLTKEEVL--AREPQLQAE-----NLVGGGVYLDFRNNDARLVIENIKRAQADGAAMI 192 K E+L +R + A+ ++ G Y D +DARLV+ K+AQ GA ++ Sbjct: 115 -----KREILPGSRSIKFGADDPLKPDITKGFEYSDGWVDDARLVVLTAKKAQQFGAQIL 169 Query: 193 SKAKVVGILHDEQGIIN-GVEVEDQLTNERFEVHAKVVINTTGPWSDIVRQLDKNDELPP 251 ++ K V EQG V + D V AK ++N +GPW + + P Sbjct: 170 TRTKCV---KAEQGSREWQVTLRDMTDETEKTVSAKAIVNASGPWVSRLFGETLSMPAPK 226 Query: 252 QMRPTKGVHLVVDREKLKVPQPTYFDTGKNDGRMVFVVPRENK-TYFGTTDTDYTGDFAH 310 +R KG H+VV R L Y D R+VFV+P E++ + GTTD DY GD Sbjct: 227 MIRMVKGSHIVVPR--LNKGTEAYI-LQNEDERIVFVIPYEDEFSLVGTTDVDYEGDPKK 283 Query: 311 PTVTQEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLSDES 370 ++ E+ DYLL IVN F Q+ D+ S++G+RPL+ D+ Sbjct: 284 AKISPEETDYLLNIVNSHFKR-QLVPSDVIWSYSGVRPLM-----------------DDE 325 Query: 371 FEQIVESVKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLERSKDGLLTLAG 430 E ++ ++Y S + E+ K L+++ G Sbjct: 326 QENAQKASRDY-------------------------------SFEINSEKGKAPLISVFG 354 Query: 431 GKITDYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGELDAANVEEELAKLADQAQ 490 GKIT YR +AE A ++ + E+G + + + GG+ EE + D Sbjct: 355 GKITTYRKLAEAATDKLCQFFPEAGGRW----TKKGVLPGGDFANHEALEETLR-RDYPW 409 Query: 491 TAGFNEAAATYLAHLYGSNLPQVLNYKTKFEGLD--------EKESTALNYSLHEEMVLT 542 A E + YG+ +L T E L E+E + + + E +T Sbjct: 410 LA---EKVISRYVRTYGTTSYDILRNCTSMEDLGIHFAGTLYERE---VEHLVKNEWAMT 463 Query: 543 PVDYLLRRTNHILFMRDT 560 D L RRT L+ D+ Sbjct: 464 SEDILWRRTKQGLYASDS 481 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: 640 Number of extensions: 33 Number of successful extensions: 5 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: 507 Length adjustment: 36 Effective length of query: 573 Effective length of database: 471 Effective search space: 269883 Effective search space used: 269883 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