GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Desulfovibrio vulgaris Hildenborough

Align BadH (characterized)
to candidate 206645 3-oxoacyl-(acyl-carrier-protein) reductase

Query= metacyc::MONOMER-893
         (255 letters)



>MicrobesOnline__882:206645
          Length = 259

 Score =  168 bits (426), Expect = 9e-47
 Identities = 98/245 (40%), Positives = 147/245 (60%), Gaps = 7/245 (2%)

Query: 8   TAVITGGGGGIGGATCRRFAQEGAKIAVFDLNL-DAAEKVAGAIRDAGGTAEAVRCDIAD 66
           TA++TGG  GIG A     A+ G ++ +  ++  D AE VA  IRDAGG+A A R D++D
Sbjct: 19  TAIVTGGSRGIGKAVAETLARAGLQVFLTYVSKPDEAEAVAAGIRDAGGSATAFRLDVSD 78

Query: 67  RTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHAVL 126
             +V A   +       +D+LVNNAG        + +  ++ER++ +NL GA        
Sbjct: 79  AAAVAAFFQSEIKDKVRLDVLVNNAGITKDGLIMRMKDEDFERVLDVNLCGAFTCLREAS 138

Query: 127 PGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVCPG 186
             M  +R GRI+NI S   ++G++G+A Y A K GL+  +K+ A+E A   +TVN V PG
Sbjct: 139 KLMTRQRLGRIINITSVVGQMGNAGQANYCAAKAGLIGLTKSAAKELAARNVTVNAVAPG 198

Query: 187 PTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQVLS 246
             +T    D+T+G   PE++ +A+ +AIPL RLG   D+A A+AF  S+ A +ITGQVL+
Sbjct: 199 FIET----DMTAGL--PEEVRKAYVEAIPLRRLGSAQDIADAVAFLASERASYITGQVLA 252

Query: 247 VSGGL 251
           V+GG+
Sbjct: 253 VNGGM 257



 Score = 23.1 bits (48), Expect = 0.006
 Identities = 26/100 (26%), Positives = 37/100 (37%), Gaps = 10/100 (10%)

Query: 156 AACKGGLVAFSKTLAREHARHGITVNVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIP 215
           A   GG     K +A   AR G+ V +      D A    V +G  +      AF   + 
Sbjct: 20  AIVTGGSRGIGKAVAETLARAGLQVFLTYVSKPDEA--EAVAAGIRDAGGSATAFRLDV- 76

Query: 216 LGRLGKPDDLAGAIAFFGSDDAGFITGQVLSVSGGLTMNG 255
                   D A   AFF S+    +   VL  + G+T +G
Sbjct: 77  -------SDAAAVAAFFQSEIKDKVRLDVLVNNAGITKDG 109


Lambda     K      H
   0.318    0.135    0.398 

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: 178
Number of extensions: 9
Number of successful extensions: 4
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: 255
Length of database: 259
Length adjustment: 24
Effective length of query: 231
Effective length of database: 235
Effective search space:    54285
Effective search space used:    54285
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: 47 (22.7 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