GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Pseudomonas litoralis 2SM5

Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_090275047.1 BLU11_RS15865 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::Q0AVM2
         (279 letters)



>NCBI__GCF_900105005.1:WP_090275047.1
          Length = 504

 Score =  218 bits (556), Expect = 2e-61
 Identities = 113/279 (40%), Positives = 171/279 (61%), Gaps = 1/279 (0%)

Query: 2   KIMVLGAGTMGAGIVQTAAQAGFEVVVRDIKQEFVDRGIAGIDKLLSKNVDKGRMTAEDK 61
           +I V+GAG MG GI Q  A +G +V++ D + E ++  +A    LL + V KG+++  + 
Sbjct: 4   RIGVIGAGAMGRGIAQLFASSGQQVLLFDTRAEAIEDALAFNRNLLQRQVAKGKLSEAEF 63

Query: 62  AAVMGRISGTVDMGAAADCDLVIEAALEVMDIKKAIFKELDSICKPECILASNTSALSVT 121
            AV  R+    ++    DCDL+IEA +E++++K+ +F +L++I    C+LA+NTS+LSVT
Sbjct: 64  EAVNARMQPAAELEQLKDCDLIIEAIVEILEVKQKLFTDLEAIVSEACLLATNTSSLSVT 123

Query: 122 EIAAATGRADKVIGMHFFNPVPAMKLVEVIRGASTSQATYDAIKDLSVKMGKSPVEINEA 181
            IAA   R ++V G HFFNPV  MK+VEV+RG+ T +     + +L+ K G  P    + 
Sbjct: 124 RIAAGCNRPERVAGFHFFNPVTLMKIVEVVRGSRTDERYIQGLVELAEKAGHFPAITPDT 183

Query: 182 PGFVVNRLLIPMLNEGMYCLMEGVANAADIDTSMKFGAGHPMGPLALADMIGLDICLKIM 241
           PGF+VN        E +  L EGVA A  ID  ++ G G  MGP  L D+ GLD+   +M
Sbjct: 184 PGFLVNHAGRAFGTEALRMLSEGVATAQQIDRILRDGPGFRMGPFELFDLTGLDVSHAVM 243

Query: 242 ETLYKEF-GDPKYRPCPLLAKMVRANKLGRKTGEGFFAY 279
           E++Y++F  DP+Y P  +  + V A  LGRKTG+GF+ Y
Sbjct: 244 ESVYEQFYHDPRYTPSFIAGQRVAAGLLGRKTGQGFYRY 282



 Score = 68.9 bits (167), Expect = 2e-16
 Identities = 31/91 (34%), Positives = 52/91 (57%), Gaps = 1/91 (1%)

Query: 175 PVE-INEAPGFVVNRLLIPMLNEGMYCLMEGVANAADIDTSMKFGAGHPMGPLALADMIG 233
           PVE IN++PGFV+ RL+  + N G     +G+A    +D +++   G+P GPLA  +  G
Sbjct: 402 PVEVINDSPGFVIQRLIASVTNLGCEIAQKGIATPETLDRAIQLALGYPKGPLAFGEHYG 461

Query: 234 LDICLKIMETLYKEFGDPKYRPCPLLAKMVR 264
                 ++  +   +G+P+YRP P L + V+
Sbjct: 462 KQALFTVLNNMQATYGEPRYRPSPWLRRRVQ 492


Lambda     K      H
   0.321    0.137    0.389 

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: 311
Number of extensions: 12
Number of successful extensions: 3
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: 279
Length of database: 504
Length adjustment: 30
Effective length of query: 249
Effective length of database: 474
Effective search space:   118026
Effective search space used:   118026
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: 50 (23.9 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