GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpD in Arenitalea lutea P7-3-5

Align Glycerol-3-phosphate dehydrogenase SDP6, mitochondrial; Protein SUGAR-DEPENDENT 6; EC 1.1.5.3 (characterized)
to candidate WP_143148086.1 P735_RS0108625 FAD-dependent oxidoreductase

Query= SwissProt::Q9SS48
         (629 letters)



>NCBI__GCF_000283015.1:WP_143148086.1
          Length = 520

 Score =  330 bits (845), Expect = 1e-94
 Identities = 203/546 (37%), Positives = 306/546 (56%), Gaps = 50/546 (9%)

Query: 75  DVLVIGGGATGSGVALDAVTRGLRVGLVEREDFSSGTSSRSTKLIHGGVRYLEKAVFNLD 134
           DV+VIGGGATG GVALD++TRG +  L+E+ DF+ GTSSRSTKL+HGGVRYL +      
Sbjct: 18  DVIVIGGGATGLGVALDSITRGYKTLLLEQVDFAKGTSSRSTKLVHGGVRYLAQ------ 71

Query: 135 YGQLKLVFHALEERKQLIENAPHLCHALPCMTPCFDWFEVIYFWMGLKMYDLVAGPRLLH 194
            G + LV  AL ER  L++NA HL      + P ++W++ + + +GLK+YD +AG     
Sbjct: 72  -GNIDLVKEALYERGLLLKNASHLVSNQSFIIPNYNWWDNLKYTIGLKIYDALAGKLSFG 130

Query: 195 LSRYYSAKESIELFPTLARKGKDKNLRGTVVYYDGQMNDSRLNVGLACTAALAGAAVLNH 254
            S   S KE+++   T+    K+  L+G VVY+DGQ +DSRL V +A T    GA VLNH
Sbjct: 131 KSTRISKKETLKRLSTI----KNGKLKGGVVYHDGQFDDSRLAVNIAQTCIEHGATVLNH 186

Query: 255 AEVVSLITDDATKRIIGARIRNNL-TGQEFNSYAKVVVNAAGPFCDSIRKMIDEDTKPMI 313
            +V  L+ +D  + ++ A +  +  T + +    KVV+NA G F D I KM + + K ++
Sbjct: 187 FKVKQLLKND--RGVVNAVVAEDAETHKSYTLKTKVVINATGVFTDEILKMDNAEAKDIV 244

Query: 314 CPSSGVHIVLPDYYSPEGMGLIVPKTKDGRVVFMLPWLGRTVAGTTDSNTSITSL-PEPH 372
            PS G+H+V+   + P    +++PKT DGRV+F++PW  + V GTTD+     SL P+  
Sbjct: 245 RPSQGIHLVIDKSFLPGNDAIMIPKTNDGRVLFLVPWHNKIVVGTTDTLLDSHSLEPKAL 304

Query: 373 EDEIQFILDAISDYLNIKVRRTDVLSAWSGIRPLAMDPTAKS--TESISRDHVVFEENPG 430
           + E+ FI+   ++YL   + + DVLS ++G+RPLA  P  KS  T+ ISR H +   +  
Sbjct: 305 DAEVDFIIATANNYLTKTLAKEDVLSIFAGLRPLAA-PKDKSEKTKEISRSHKIIVSDSD 363

Query: 431 LVTITGGKWTTYRSMAEDAVDAAIKSGQLKPTNECVTQKLQLLGSYGWEPSSFTTLAQQY 490
           L+TITGGKWTTYR MA+D ++ AI  G+L P   C T+ ++                   
Sbjct: 364 LITITGGKWTTYRRMAQDTINKAIFIGKL-PKVACETKAIK------------------- 403

Query: 491 VRMKKTYGGKVVPGAMDTAAAKHLSHAYGSMADRVAT-IAQEEGLGKRLAHGHPFLEAEV 549
                      + GA+  +  K   + YGS    +   I +   LG +L    PF + EV
Sbjct: 404 -----------IHGAIKPSEKKSHQYVYGSDETNIQNLIKKHPELGAQLHKSLPFTKGEV 452

Query: 550 AYCARHEYCESAVDFIARRCRIAFLDTDAAARALQRVVEILASEHKWDKSRQKQELQKAK 609
            +  R+E   +  D +ARR R  FLD  A    +  V +IL+ E   D   ++Q++++ K
Sbjct: 453 VWAIRNEMARTIEDVLARRVRTLFLDAKATLEIIPIVAKILSEELNKDAIWEQQQIEEFK 512

Query: 610 EFLETF 615
              + +
Sbjct: 513 SIAKQY 518


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: 674
Number of extensions: 36
Number of successful extensions: 7
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: 520
Length adjustment: 36
Effective length of query: 593
Effective length of database: 484
Effective search space:   287012
Effective search space used:   287012
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 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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