Align Glycerol-3-phosphate dehydrogenase SDP6, mitochondrial; Protein SUGAR-DEPENDENT 6; EC 1.1.5.3 (characterized)
to candidate CA265_RS07875 CA265_RS07875 FAD-dependent oxidoreductase
Query= SwissProt::Q9SS48 (629 letters) >lcl|FitnessBrowser__Pedo557:CA265_RS07875 CA265_RS07875 FAD-dependent oxidoreductase Length = 530 Score = 367 bits (943), Expect = e-106 Identities = 214/537 (39%), Positives = 305/537 (56%), Gaps = 51/537 (9%) Query: 75 DVLVIGGGATGSGVALDAVTRGLRVGLVEREDFSSGTSSRSTKLIHGGVRYLEKAVFNLD 134 D ++IGGGATG G ALDA +RG + LVE+ DF+ GTSSRSTKL+HGGVRYL + Sbjct: 16 DFIIIGGGATGLGTALDAASRGFKTLLVEQSDFAKGTSSRSTKLVHGGVRYLAQ------ 69 Query: 135 YGQLKLVFHALEERKQLIENAPHLCHALPCMTPCFDWFEVIYFWMGLKMYDLVAGPRLLH 194 G + LV HAL+ER L +NA HL + + PC+DWF V+ + GL +YD +AG Sbjct: 70 -GDIGLVKHALKERGLLQQNAKHLVNKEEFLIPCYDWFSVVKYLTGLTLYDWLAGKYSFG 128 Query: 195 LSRYYSAKESIELFPTLARKGKDKNLRGTVVYYDGQMNDSRLNVGLACTAALAGAAVLNH 254 S+++S KE++ + P + K+K L+G++ YYDG+ +D+RL + +A TA GA++LN+ Sbjct: 129 KSKFFSKKETLTMMPGI----KEKGLKGSIRYYDGKFDDARLAINIAQTAIENGASLLNY 184 Query: 255 AEVVSLITDDATKRIIGARIRNNLTGQEFNSYAKVVVNAAGPFCDSIRKMIDEDTKPMIC 314 +V L+ + ++ G + +TG K+V+NA G F D I +M + ++K M+ Sbjct: 185 TKVTGLL--KSGDQVTGIETEDTITGLTAKYNGKIVINATGVFVDDILQMNNPNSKKMVR 242 Query: 315 PSSGVHIVLPDYYSPEGMGLIVPKTKDGRVVFMLPWLGRTVAGTTDSNTSITSL-PEPHE 373 PS GVH+VL + L++PKT DGRV+F +PW + GTTD+ SL P + Sbjct: 243 PSQGVHVVLDKSFLNSESALMIPKTSDGRVLFAVPWHDHLLVGTTDTPLDEHSLEPRALK 302 Query: 374 DEIQFILDAISDYLNIKVRRTDVLSAWSGIRPLAMDPT---AKSTESISRDHVVFEENPG 430 E+ FI+ + Y N K D+LS +SG+RPLA PT ST+ ISRDH + G Sbjct: 303 KEVDFIMSTAASYFNRKPLEKDILSVFSGLRPLAA-PTNGDGNSTKEISRDHKLIVSAKG 361 Query: 431 LVTITGGKWTTYRSMAEDAVDAAIKSGQLKPTNECVTQKLQLLGSYGWEPSSFTTLAQQY 490 L+TITGGKWTTYR MAE+ VD AI G L+ + CVTQ L + GS Sbjct: 362 LITITGGKWTTYRRMAEETVDLAITHGGLE-SKACVTQNLSIHGS--------------- 405 Query: 491 VRMKKTYGGKVVPGAMDTAAAKHLSHAYGSMADRV-ATIAQEEGLGKRLAHGHPFLEAEV 549 T H YG+ ++ A I Q+ GLG +L PF EAEV Sbjct: 406 ----------------STTTGDHHLAIYGTDRSKIEALIVQDPGLGNKLNPAFPFTEAEV 449 Query: 550 AYCARHEYCESAVDFIARRCRIAFLDTDAAARALQRVVEILASEHKWDKSRQKQELQ 606 + AR+E E+ D ++RR RI F++ AA RV +LA E DK+ + +++ Sbjct: 450 IWSARNEMAETVEDILSRRLRILFINAQAAKDMAPRVASLLAQELSADKNWETNQIE 506 Lambda K H 0.318 0.133 0.390 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: 717 Number of extensions: 25 Number of successful extensions: 7 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: 629 Length of database: 530 Length adjustment: 36 Effective length of query: 593 Effective length of database: 494 Effective search space: 292942 Effective search space used: 292942 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 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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