GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Halomonas xinjiangensis TRM 0175

Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_052384180.1 JH15_RS15780 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::Q0AVM2
         (279 letters)



>NCBI__GCF_000759345.1:WP_052384180.1
          Length = 498

 Score =  213 bits (541), Expect = 9e-60
 Identities = 114/274 (41%), Positives = 161/274 (58%), Gaps = 1/274 (0%)

Query: 5   VLGAGTMGAGIVQTAAQAGFEVVVRDIKQEFVDRGIAGIDKLLSKNVDKGRMTAEDKAAV 64
           V+GAG MG GI Q AA AG    + D +Q         I    +K V  G+M+AE+    
Sbjct: 13  VVGAGAMGGGIAQVAAAAGIRTRLHDARQGAAAETCEKIRDRFAKRVTAGKMSAEEANVA 72

Query: 65  MGRISGTVDMGAAADCDLVIEAALEVMDIKKAIFKELDSICKPECILASNTSALSVTEIA 124
              +     +   ADCD+VIEA +E +++K A+FKEL+ + + + ILASNTS+L +  IA
Sbjct: 73  TANLLPVAGLNELADCDVVIEAIVEKLEVKTALFKELEELVREDAILASNTSSLPIGAIA 132

Query: 125 AATGRADKVIGMHFFNPVPAMKLVEVIRGASTSQATYDAIKDLSVKMGKSPVEINEAPGF 184
           A   R D+V GMHFFNPVPAMKLVEVI+ A TS    DA+ +L  ++G+ PV + + PGF
Sbjct: 133 AGLKRRDRVAGMHFFNPVPAMKLVEVIQAADTSAVVMDALIELGGRLGRVPVVVKDTPGF 192

Query: 185 VVNRLLIPMLNEGMYCLMEGVANAADIDTSMKFGAGHPMGPLALADMIGLDICLKIMETL 244
           +VN        E +  + EGVA  A +D  M+   G  MGP  L D+ G+D+   +   +
Sbjct: 193 LVNFGGRAYTTEALAIVHEGVATPAQVDAIMRDCFGFRMGPFELMDLTGMDVNFPVTRFV 252

Query: 245 YKE-FGDPKYRPCPLLAKMVRANKLGRKTGEGFF 277
           ++  FGDP+ R  PL   M+   +LGRKTG+GF+
Sbjct: 253 HENFFGDPRLRSTPLHRYMLETGQLGRKTGQGFY 286



 Score = 60.8 bits (146), Expect = 6e-14
 Identities = 33/96 (34%), Positives = 50/96 (52%), Gaps = 1/96 (1%)

Query: 178 INEAPGFVVNRLLIPMLNEGMYCLMEGVANAADIDTSMKFGAGHPMGPLALADMIGLDIC 237
           I ++PGFV  R+   + N G      G+A   DID +++ G  +P GPL LAD +G  + 
Sbjct: 404 IGDSPGFVGQRIAAMVANLGCEMAQMGLAKIDDIDLALRLGLNYPYGPLELADHLGSKVT 463

Query: 238 LKIMETLYKEFGDPKYRPCPLLAKMVRANKLGRKTG 273
            +I+E      GD +YRP   L +  +   L  +TG
Sbjct: 464 YRILEQAQLLSGDDRYRPSQWLRRRAQLG-LSARTG 498


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: 13
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: 279
Length of database: 498
Length adjustment: 30
Effective length of query: 249
Effective length of database: 468
Effective search space:   116532
Effective search space used:   116532
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: 49 (23.5 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