Align Glycerol-3-phosphate dehydrogenase SDP6, mitochondrial; Protein SUGAR-DEPENDENT 6; EC 1.1.5.3 (characterized)
to candidate RR42_RS16760 RR42_RS16760 FAD-dependent oxidoreductase
Query= SwissProt::Q9SS48 (629 letters) >FitnessBrowser__Cup4G11:RR42_RS16760 Length = 559 Score = 259 bits (662), Expect = 2e-73 Identities = 203/591 (34%), Positives = 293/591 (49%), Gaps = 63/591 (10%) Query: 52 TASVPSRSAQESALIAATASDPLDVLVIGGGATGSGVALDAVTRGLRVGLVEREDFSSGT 111 T++ P R A+++ L S+ D+L++GGG TG+ ALDA RG RV LVE+ DF+SGT Sbjct: 17 TSTEPLRLARQAQL-DRLGSETFDILIVGGGVTGAYAALDASLRGYRVALVEKNDFASGT 75 Query: 112 SSRSTKLIHGGVRYLEKAVFNLDYGQLKLVFHALEERKQLIENAPHLCHALPCMTP---- 167 SS+S+K++HGG+RY+E+ G L LV H+L ER++L NA HL LP + P Sbjct: 76 SSKSSKMVHGGLRYIEQ-------GNLGLVRHSLLERQRLRRNARHLVQRLPFLFPVMEK 128 Query: 168 --CFDWFEVIYFWMGLKMYDLVAGPRLLHLSRYYSAKESIELFPTLARKGKDKNLRGTVV 225 FD F L YDL G R L + + E + PT ++NL G + Sbjct: 129 DGVFDKRLSKAFESLLWTYDLAGGWREGILHQKLTKAEVLSHCPTF----NEENLLGGFM 184 Query: 226 YYDGQMNDSRLNVGLACTAALAGAAVLNHAEVVSLITDDATKRIIGARIRNNLTGQEFNS 285 Y+D +++D+RL + +A TAA GAAV+NHA+VV IT + ++ GA I + +E + Sbjct: 185 YFDARVDDARLTLNIARTAAFHGAAVVNHAKVVE-ITRNGHGKVDGAII--HAGDREIRA 241 Query: 286 YAKVVVNAAGPFC-DSIRKMIDEDTKPMICPSSGVHIVLPDYYSPEGMGLIVPKTKDGRV 344 A VVV A G + D + E+ I P+ GVH+ +P + +P R Sbjct: 242 RAGVVVMATGVWLRDWTGRKKGEEKTLHIRPAKGVHVAIPWLKVRNDCTVTIPVPGRNRR 301 Query: 345 VFMLPWLGRTVAGTTD-------SNTSITSLPEPHEDEIQFILDAISDYLNIKVRRTDVL 397 + W + GTTD N T +E+ F+LD L ++ DVL Sbjct: 302 ATITRWGNVSYLGTTDEDYEGDLDNVCCT------REELDFLLDGARWALKTDLQAEDVL 355 Query: 398 SAWSGIRPLAMDPTAKSTESISRDHVVFEENPGLVTITGGKWTTYRSMAEDAVDAAIKSG 457 + +G RPL P K+ E I R+H + GLVTI GGK TT R MAE +DAA K Sbjct: 356 GSIAGCRPLVAPPGGKTLE-IKRNHEIHTAADGLVTIVGGKLTTSRHMAEQTIDAAQK-- 412 Query: 458 QLKPTNECVTQKLQLLGSYGWEPSSFTTLAQQYVRMKKTYGGKVVPGAMDTAAAKHLSHA 517 L N C T+ LLG+ G++ + V G + + HL Sbjct: 413 VLGQRNRCQTKSAYLLGAAGYDAQAI-----------------VASGGL----SAHLGER 451 Query: 518 YGSMADRVATIAQEEG-LGKRLAHGHPFLEAEVAYCARHEYCESAVDFIARRCRIAFLDT 576 YG+ A V+ I Q + L + G P+ EAE+ Y ARHE S D ++RR R + Sbjct: 452 YGTEARFVSDILQADARLQAPIVEGLPYTEAEIVYAARHELAGSVDDVLSRRIRARLMAR 511 Query: 577 DAAARALQRVVEILASEHKWDKSRQKQELQKAKEFLETFKSSKNAQFNDGK 627 DA+ARA RV IL +E +S Q++ ++L K+ D + Sbjct: 512 DASARAASRVGAILQAELGLSESVVAQQV---NDYLAAVAHEKSVLLGDAQ 559 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: 713 Number of extensions: 34 Number of successful extensions: 8 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: 629 Length of database: 559 Length adjustment: 37 Effective length of query: 592 Effective length of database: 522 Effective search space: 309024 Effective search space used: 309024 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