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) >FitnessBrowser__Pedo557:CA265_RS07875 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:
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