GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Shewanella loihica PV-4

Align 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)
to candidate 5209195 Shew_1673 3-ketoacyl-(acyl-carrier-protein) reductase (RefSeq)

Query= SwissProt::O18404
         (255 letters)



>FitnessBrowser__PV4:5209195
          Length = 252

 Score =  142 bits (357), Expect = 9e-39
 Identities = 97/257 (37%), Positives = 138/257 (53%), Gaps = 12/257 (4%)

Query: 2   IKNAVSLVTGGASGLGRATAERLAKQGASVILADLPSSKGNEVAKELGD--KVVFVPVDV 59
           +K+ V ++TGGA GLG A A+ LA  GA + L D+   K      ++GD  +V     D+
Sbjct: 3   LKDKVVVITGGAGGLGFAMAQELAAAGAKLALIDVDQEKLERACADIGDTTEVQGYAFDI 62

Query: 60  TSEKDVSAALQTAKDKFGRLDLTVNCAGT---ATAVKTFNFNKNVAHRLEDFQRVININT 116
           T E+DV A      + FG++++ VN AG       VK           L  FQ VIN+N 
Sbjct: 63  TDEEDVVAGFGYILEDFGQVNVLVNNAGILLDGMLVKAKEGEVTDRMSLAQFQAVINVNL 122

Query: 117 VGTFNVIRLSAGLMGANEPNQDGQRGVIVNTASVAAFDGQIGQAAYSASKAAVVGMTLPI 176
            G+F   R +A  M  ++     Q+GVIVN +S+A   G IGQ  Y+ASKA V  M++  
Sbjct: 123 TGSFLCGREAAAAMITSK-----QQGVIVNISSLAKA-GNIGQTNYAASKAGVAAMSVGW 176

Query: 177 ARDLSTQGIRICTIAPGLFNTPMLAALPEKVRTFLAKSIPFPQRLGEPSEYAHLVQAIYE 236
           A++L+   IR   +APG+  T M AA+  +    L K +P   RLG+ SE A  V+ I E
Sbjct: 177 AKELARYNIRSAAVAPGVIETEMTAAMKPEALERLEKMVPV-GRLGQASEIASTVKFIIE 235

Query: 237 NPLLNGEVIRIDGALRM 253
           N  +NG V  IDG +R+
Sbjct: 236 NDYVNGRVFEIDGGIRI 252


Lambda     K      H
   0.317    0.133    0.369 

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: 158
Number of extensions: 13
Number of successful extensions: 5
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: 255
Length of database: 252
Length adjustment: 24
Effective length of query: 231
Effective length of database: 228
Effective search space:    52668
Effective search space used:    52668
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