Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate GFF2721 Psest_2775 Glycerol-3-phosphate dehydrogenase
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__psRCH2:GFF2721 Length = 511 Score = 161 bits (408), Expect = 5e-44 Identities = 152/545 (27%), Positives = 235/545 (43%), Gaps = 91/545 (16%) Query: 20 YDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVEV 79 YDV +IGGGI G G+A A G+ L E D A TSS S+KL+HGG+RYL+ ++ + Sbjct: 12 YDVAVIGGGINGVGIAADAAGRGLSVFLCERDDLASHTSSASSKLIHGGLRYLEHYEFRL 71 Query: 80 VADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLANVTGSKYE 139 V + + ER ++ APHI KP +LP P + ++ + LYD L Sbjct: 72 VREALAEREMLLAKAPHIVKPMRFVLP--HRPHLR-PAWMIRAGLFLYDNLG-------- 120 Query: 140 NYLLTKEEVLAREPQLQAEN-----LVGGGVYLDFRNNDARLVIENIKRAQADGAAMISK 194 + K+ +R + +E+ + G Y D +DARLV+ N A+ GA + ++ Sbjct: 121 ---MRKKLPASRGLRFGSESPLKPVITRGFEYSDCWVDDARLVVLNAMAAREKGAHIHTR 177 Query: 195 AKVVGILHDEQGIINGVEVEDQLTNERFEVHAKVVINTTGPWSDIVRQLDKNDELPPQMR 254 + + G I VE++ + RF + AK ++N GPW + P +R Sbjct: 178 TQCLSA--KRAGGIWHVELQRE-DGSRFSLRAKALVNAAGPWVAQFIGENLQQRSPYGIR 234 Query: 255 PTKGVHLVVDREKLKVPQPTYFDTGKNDGRMVFVVP-RENKTYFGTTDTDYTGDFAHPTV 313 +G H++V KL + Y D R+VF +P + T GTTD +Y GD A ++ Sbjct: 235 LIQGSHIIV--PKLYEGEQAYI-MQNEDRRIVFAIPYLDRYTMIGTTDREYRGDPAKVSI 291 Query: 314 TQEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLSDESFEQ 373 ++E++ Y+L + N F Q+ DI ++AG+RPL + SD Sbjct: 292 SEEEIAYVLGVANTHF-RKQLEPRDIVHTFAGVRPLCDDE-------------SDNPSAV 337 Query: 374 IVESVKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLERSKDGLLTLAGGKI 433 + A+E+Q P LL++ GGK+ Sbjct: 338 TRDYTLSLAAEEKQAP-----------------------------------LLSVFGGKL 362 Query: 434 TDYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGE--LDAANVEEELAKLADQAQT 491 T YR +AE A+ ++ G S+ + + GGE A + EEL A+ Sbjct: 363 TTYRKLAESAMAQLKPFFPAMGGSW----TAQAALPGGEDMSTADALTEELV-----AKV 413 Query: 492 AGFNEAAATYLAHLYGSNLPQVLNYKTKFEGLDEKESTAL-----NYSLHEEMVLTPVDY 546 G A A LYG+ + ++L + L E L Y EE D Sbjct: 414 QGLKLPLAKRWATLYGNRVWRMLGEAHSLDALGEDLGQQLYAQEVEYLRREEWATQVDDI 473 Query: 547 LLRRT 551 L RRT Sbjct: 474 LWRRT 478 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: 562 Number of extensions: 30 Number of successful extensions: 4 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: 511 Length adjustment: 36 Effective length of query: 573 Effective length of database: 475 Effective search space: 272175 Effective search space used: 272175 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