GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Desulfovibrio vulgaris Miyazaki F

Align Putative aldehyde dehydrogenase YwdH; EC 1.2.1.3 (uncharacterized)
to candidate 8501918 DvMF_2633 Aldehyde Dehydrogenase (RefSeq)

Query= curated2:P39616
         (456 letters)



>FitnessBrowser__Miya:8501918
          Length = 460

 Score =  248 bits (633), Expect = 3e-70
 Identities = 146/458 (31%), Positives = 238/458 (51%), Gaps = 7/458 (1%)

Query: 6   SIISKHKAYFAAGHTRPLESRLNILRKLKQAVRTHEADLIAALYQDLHKSEQEAYSTEIG 65
           ++ ++ KA+ A+G   P  +R++ LR+L++ V+ +   L  A+  D  + E      E+ 
Sbjct: 3   ALAARQKAFIASGAVLPSGARVDALRRLREGVQGYRDRLADAIRADYGRPEHPFLVREVV 62

Query: 66  IVLEEISFVMKRLRKWSKPKRVKTPLTHLGSKSIIIPEPYGTVLVIAPWNYPLQLALSPL 125
            VL EI +++K +  +   +RV   L    ++S +  +P G V+  A W  P +  L PL
Sbjct: 63  PVLHEIDWLIKAVPGFCGGRRVLPSLGQFKARSYVRRQPLGRVVAYAHWADPFRSLLVPL 122

Query: 126 IGAIAAGNTVVLKPSEYTPAVSAILSKLISSVFPTDYVAMAEGGPDVSTALLQQPFDYIF 185
             AI AGN VVL+PS   PA + ++++++   F  ++VA+  GG +   ALL    D+++
Sbjct: 123 ADAIGAGNAVVLRPSAEAPATAEMVTRMVRQYFEPEHVAVVGGGAETDEALLATAPDFVW 182

Query: 186 FTGSVAVGKIVMEAAAKQLIPVTLELGGKSPCIVHKDADIQLAAKRIVFGKFTNAGQTCI 245
           + G     + +   AA  L P     GG S  +VH DAD+ +AA+RIV+ KF +AGQ   
Sbjct: 183 YDGDARGARTIAVLAAPTLTPYAAITGGPSAALVHGDADMAMAARRIVWAKFLHAGQLRA 242

Query: 246 APDYLFVHEDIKTKLTEEMKRAIREFYGPQPERNPQYGKIVSERHYQRLLSFLNDGIPLT 305
           APD L V   +  ++ + ++  +   +GPQP  +  +G++VS   + R    L  G  L 
Sbjct: 243 APDVLLVQRTVLDRVLDALRTELERAFGPQPRTSADFGRMVSAAGFARQAERLAIGRALP 302

Query: 306 GGQSDPNHHK------IAPTILEQVRDDSPVMQEEIFGPILPLFTYRNIGEVIEKVQSRP 359
            G  D  +        + PT+L  V DDSPV++EE FGP+L +  Y  + E    +   P
Sbjct: 303 FGPGDAANQPDRASLYVPPTLLTDVPDDSPVLREEGFGPVLVVRPYTRLDEATAFLAGLP 362

Query: 360 KPLALYLFTTNKEIERAVLGNLSFGGGCVNDTLMHVATPYLPFGGVGESGIGSYHGFDSF 419
              ALY FTT       ++ N   G   +ND   H+A P LP GGVGE+G G+  G    
Sbjct: 363 ALTALYAFTTAHARGERLMENTRAGAVLINDAATHLANPRLPQGGVGETGHGAMAGPAGL 422

Query: 420 NTFTHKKSVVKQTNRFDFAFRY-PSSKNGLRMIRKILK 456
            TF+  ++    +N FD   R+ P S   L++++++ K
Sbjct: 423 ATFSAPRATAVGSNFFDIPLRFAPGSDLKLKVLKRLYK 460


Lambda     K      H
   0.320    0.137    0.401 

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: 474
Number of extensions: 16
Number of successful extensions: 2
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: 456
Length of database: 460
Length adjustment: 33
Effective length of query: 423
Effective length of database: 427
Effective search space:   180621
Effective search space used:   180621
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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