Align Anaerobic glycerol-3-phosphate dehydrogenase subunit A2; G-3-P dehydrogenase A2; G3PDH A2; EC 1.1.5.3 (characterized)
to candidate WP_012709582.1 NGR_RS26605 glycerol-3-phosphate dehydrogenase
Query= SwissProt::D4GQU6 (563 letters) >NCBI__GCF_000018545.1:WP_012709582.1 Length = 505 Score = 121 bits (304), Expect = 6e-32 Identities = 141/461 (30%), Positives = 189/461 (40%), Gaps = 67/461 (14%) Query: 3 YSVVVIGGGATGTGTARDLAMRGFDVTLVERGNLTEGTTGRTHGHLHSGARYAVSDKESA 62 + V VIGGG G G ARD RG+ V L E + GT+ + +H G RY + Sbjct: 7 FDVFVIGGGINGCGIARDAVGRGYSVALAEMDDFASGTSSGSTKLIHGGLRYLEHYEFRL 66 Query: 63 V-DCMRENRVLHRIAGHCIEDTGGLFVQLEGDS-------------DDYFERKLAGCAEC 108 V + + E VL +A H I + +G D RKL Sbjct: 67 VREALMEREVLWAMAPHVIWPMRFVLPYHKGGPRPAWLIRLGLFLYDHIGGRKLLPATST 126 Query: 109 DIPTEVISGEEARRREPYLTDAVERAIWVPDGAVDPFRLCVANAASAVEHGARIETHAEV 168 T +G +R T A E + DG VD RL V NA A + GARI V Sbjct: 127 LDMTRDAAGGPLKR---LFTKAFEYS----DGWVDDARLVVLNARDAADRGARIMARTRV 179 Query: 169 VDLVVEGGRVAGVEVKRQGPNHHSEGAAGDTETFEADYVVSATGAWAGQLAAMAGVDLEM 228 V E GR A +E + + G ET A +V+ATG W VD + Sbjct: 180 VSARRENGRWA-IETE--------DAQTGARETLRARLLVNATGPW---------VDRVL 221 Query: 229 AISKGAMVVTNVRQLD---TVINRCL----------PKGEGDTIIPHETT-VLLGAND-D 273 A + G V NVR + V+ R P G IP++ L+G D D Sbjct: 222 ADTLGKNDVHNVRLVQGSHIVVKRKFDDPRAYFFQNPDGRIMFAIPYQNDFTLIGTTDRD 281 Query: 274 PVDDPDDYPEEQWEVDMMIDIASEMV--PVVADARMIRAYWGVRPLYDPNPKSTTDPGDV 331 +P D E+D + ASE PV D ++ Y VRPLYD + Sbjct: 282 FTGNPADVRISDAEIDYLCKSASEYFSDPVTTDD-IVWTYSAVRPLYDDGASKAQE---A 337 Query: 332 TRNYFVLDHAERDGVAGFASVVGGKLTTYREMAESVSDHVCEVLGVEEPCRTDEVPLP-G 390 TR+Y VL ++G A +V GGKLTTYR +AES + + E +G + T LP G Sbjct: 338 TRDY-VLRVEGQNGQAPLLNVFGGKLTTYRRLAESALEKIGEAIGTKGSKWTATSHLPGG 396 Query: 391 SADPSALDEYMDEFDLRSPI-----ARRSGQRLGDRAPEVL 426 +A D +D R P ARR + G +A +L Sbjct: 397 DFAATAYDTEVDMLKARYPFLALSHARRLVRLYGTQAASLL 437 Lambda K H 0.316 0.134 0.405 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: 662 Number of extensions: 30 Number of successful extensions: 3 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: 563 Length of database: 505 Length adjustment: 35 Effective length of query: 528 Effective length of database: 470 Effective search space: 248160 Effective search space used: 248160 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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