Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate WP_015887820.1 NGR_RS08385 glycerol-3-phosphate dehydrogenase
Query= SwissProt::O86963 (609 letters) >NCBI__GCF_000018545.1:WP_015887820.1 Length = 503 Score = 171 bits (432), Expect = 9e-47 Identities = 162/587 (27%), Positives = 253/587 (43%), Gaps = 110/587 (18%) Query: 19 TYDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVE 78 TYD+ +IGGGI GAG+A A G+ +L E D A+GTSSRS KLVHGG+RYL+ ++ Sbjct: 6 TYDLFVIGGGINGAGIARDAAGRGLSVLLCEKDDLAQGTSSRSGKLVHGGLRYLEYYEFR 65 Query: 79 VVADTVRERAIVQQIAPHIPKPDPMLLP--IYDEPGATFSLFSVKVAMDLYDRLA---NV 133 +V + + ER ++ Q APHI P +LP D P + V++ + LYD L + Sbjct: 66 LVREALIEREVLLQSAPHIIWPMRFVLPHNPVDRPA-----WLVRLGLLLYDHLGGRKRL 120 Query: 134 TGSKYENYLLTKEEVLAREPQLQAENLVGGGVYLDFRNNDARLVIENIKRAQADGAAMIS 193 G++ + E + +A Y D +DARLV+ N A+ GA +++ Sbjct: 121 PGTRTLDLRTAPEGAPIKPAYRRAFE------YSDCWVDDARLVVLNALDAEQRGARILT 174 Query: 194 KAKVVGILHDEQGIINGVEVEDQLTNERFEVHAKVVINTTGPWSDIVRQLDKNDELPPQM 253 + I +G + VE+ D +T + EV A+ V+NT GPW + V + Sbjct: 175 RTACSNI--RRRGDLWHVEMTDAVTGAKAEVRARCVVNTAGPWVNDVIGRVAGLNSRRSV 232 Query: 254 RPTKGVHLVV-----DREKLKVPQPTYFDTGKNDGRMVFVVPRENK-TYFGTTDTDYTGD 307 R KG H+VV R+ V P D R++F+ P +N GTTD Y G Sbjct: 233 RLVKGSHIVVPKFWEGRQAYLVQNP--------DKRVIFINPYQNDLALIGTTDIPYDGR 284 Query: 308 FAHPTVTQEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLS 367 +++ YL+ VN F Q++ DI S++G+RPL +N + Sbjct: 285 PEDVAADADEIAYLVKSVNRYFKQ-QLSDADIIQSFSGVRPLYDDNAEN----------- 332 Query: 368 DESFEQIVESVKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLE----RSKD 423 PS V+R E + Sbjct: 333 -----------------------------------------PSAVTRDYIFELDAANGEA 351 Query: 424 GLLTLAGGKITDYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGELDAANVEEELA 483 LL++ GGKIT +R ++E A++R+ + G ++ + + GG++ A+ + L Sbjct: 352 PLLSVFGGKITTFRKLSEHALERLKPFFPKIGPAW----TARAHLPGGDMADADFDRFLG 407 Query: 484 KLADQAQTAGFNEAAATYLAHLYGSNLPQVLNYKTKFEGLDEKESTAL-----NYSLHEE 538 +L +++ A + A LYG+ ++ E L S + + E Sbjct: 408 EL--RSRYRWLPADLAKHYARLYGTRTHALIGDANSLEELGTAFSRLFREREARFLIETE 465 Query: 539 MVLTPVDYLLRRTNHILFMRDTLDDVKAGVVAAMTDFFGWSEEEKAA 585 T D L RRT H L M + A F GW E ++AA Sbjct: 466 WARTVEDLLQRRTKHGLHMSE----------AEKRSFSGWLEGQQAA 502 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: 568 Number of extensions: 25 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: 503 Length adjustment: 36 Effective length of query: 573 Effective length of database: 467 Effective search space: 267591 Effective search space used: 267591 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 Apr 09 2024. 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