GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Pedobacter sp. GW460-11-11-14-LB5

Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate CA265_RS07715 CA265_RS07715 3-hydroxybutyryl-CoA dehydrogenase

Query= SwissProt::Q0AVM2
         (279 letters)



>FitnessBrowser__Pedo557:CA265_RS07715
          Length = 297

 Score =  290 bits (741), Expect = 3e-83
 Identities = 149/279 (53%), Positives = 187/279 (67%), Gaps = 1/279 (0%)

Query: 2   KIMVLGAGTMGAGIVQTAAQAGFEVVVRDIKQEFVDRGIAGIDKLLSKNVDKGRMTAEDK 61
           +I V+G+GTMG GI  T AQ  ++V + DI Q+ +D+ I  I K L + V KG +TA+ K
Sbjct: 3   QIAVIGSGTMGNGIAHTFAQFNYQVNLIDINQDALDKAIQTITKNLDRQVAKGTLTADQK 62

Query: 62  AAVMGRISG-TVDMGAAADCDLVIEAALEVMDIKKAIFKELDSICKPECILASNTSALSV 120
           A  +  I+  T         DL++EAA E +D+K  IF++LD       ILASNTS++S+
Sbjct: 63  ATTLNNITTYTSTKDGVQQADLIVEAATENVDLKLKIFRDLDDYAPAHAILASNTSSISI 122

Query: 121 TEIAAATGRADKVIGMHFFNPVPAMKLVEVIRGASTSQATYDAIKDLSVKMGKSPVEINE 180
           T+IAA T R DKVIGMHF NPVP MKLVEVIRG +TS  T   I  LS  + K PVE+N+
Sbjct: 123 TQIAAVTNRGDKVIGMHFMNPVPVMKLVEVIRGYATSDETTSTIMTLSQNLEKVPVEVND 182

Query: 181 APGFVVNRLLIPMLNEGMYCLMEGVANAADIDTSMKFGAGHPMGPLALADMIGLDICLKI 240
            PGFV NR+L+PM+NE +Y L EGVA   +IDT MK G  HPMGPL LAD IGLD+CL I
Sbjct: 183 YPGFVANRILMPMINEAIYTLYEGVAGVYEIDTVMKLGMAHPMGPLQLADFIGLDVCLAI 242

Query: 241 METLYKEFGDPKYRPCPLLAKMVRANKLGRKTGEGFFAY 279
           ++ L   FG+PKY PCPLL  MV A K G KT EGF+ Y
Sbjct: 243 LKVLNDGFGNPKYAPCPLLVNMVAAGKKGVKTSEGFYKY 281


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: 256
Number of extensions: 8
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: 279
Length of database: 297
Length adjustment: 26
Effective length of query: 253
Effective length of database: 271
Effective search space:    68563
Effective search space used:    68563
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: 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