Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate SMc01620 SMc01620 glycerol-3-phosphate dehydrogenase
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__Smeli:SMc01620 Length = 504 Score = 178 bits (452), Expect = 4e-49 Identities = 167/584 (28%), Positives = 262/584 (44%), Gaps = 104/584 (17%) Query: 19 TYDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVE 78 TYD+ +IGGGI GAG+A A G+ +L E D A+GTSSRS KLVHGG+RYL+ ++ Sbjct: 7 TYDLFVIGGGINGAGIARDAAGRGLSVLLCEKDDLAQGTSSRSGKLVHGGLRYLEYYEFR 66 Query: 79 VVADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLA---NVTG 135 +V + + ER ++ + APHI P +LP A + V++ + LYD L + G Sbjct: 67 LVREALIEREVLLESAPHIIWPMRFVLP---HNPADRPAWLVRLGLFLYDHLGGRKRLPG 123 Query: 136 SKYENYLLTKEEVLAREPQLQAENLVGGGVYLDFRNNDARLVIENIKRAQADGAAMISKA 195 ++ N L T E A +P + Y D +DARLV+ N A+ GA ++++ Sbjct: 124 TRVLN-LRTAPEGAAIKPAYRK-----AFEYSDCWVDDARLVVLNALDAKKKGARILTRT 177 Query: 196 KVVGILHDEQGIINGVEVEDQLTNERFEVHAKVVINTTGPWSDIVRQLDKNDELPPQMRP 255 I +G + VE+ D T + E A+ V+NT GPW + V +R Sbjct: 178 ACTSI--RRRGDLWHVEMTDAETGAKTEAKARCVVNTAGPWVNDVIGRVAGLNSSRSVRL 235 Query: 256 TKGVHLVV-----DREKLKVPQPTYFDTGKNDGRMVFVVPRENK-TYFGTTDTDYTGDFA 309 KG H+VV R+ V P D R++F+ P +N GTTD Y G Sbjct: 236 VKGSHIVVPKFWEGRQAYLVQNP--------DKRVIFINPYQNDLALIGTTDIPYDGRPE 287 Query: 310 HPTVTQEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLSDE 369 T + +V YLL VN F Q+ DI S++G+RPL D+ Sbjct: 288 DVTADENEVAYLLKSVNRYFKQ-QLAPGDILHSFSGVRPLY-----------------DD 329 Query: 370 SFEQIVESVKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLERSKDGLLTLA 429 + E ++Y+ + ++ A K+A LL++ Sbjct: 330 NAENPSAVTRDYIFE------LDAAGKEAP-------------------------LLSVF 358 Query: 430 GGKITDYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGELDAANVEEELAKLADQA 489 GGKIT +R ++E A++R+ G ++ + + GG++ A+ ++ L +L +A Sbjct: 359 GGKITTFRKLSEHALERLRPFFPTMGPAW----TARAHLPGGDMADADFDQFLGEL--RA 412 Query: 490 QTAGFNEAAATYLAHLYGSNLPQVLNYKTKFEGLD--------EKESTALNYSLHEEMVL 541 + A + A LYG+ ++ T + L E+E+ + + E Sbjct: 413 RYRWLPADLAKHYARLYGTRAHDLIGGATSLDELGTAFTPLFREREA---RFLIENEWAR 469 Query: 542 TPVDYLLRRTNHILFMRDTLDDVKAGVVAAMTDFFGWSEEEKAA 585 T D + RRT H L M + A F GW E ++AA Sbjct: 470 TAEDLIERRTKHGLHMSE----------AEKRAFSGWFEGQQAA 503 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: 583 Number of extensions: 28 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 609 Length of database: 504 Length adjustment: 36 Effective length of query: 573 Effective length of database: 468 Effective search space: 268164 Effective search space used: 268164 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