GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Marinobacter adhaerens HP15

Align Triosephosphate isomerase; TIM; TPI; EC 5.3.1.1; Triose-phosphate isomerase (uncharacterized)
to candidate GFF3332 HP15_3274 thiazole synthase

Query= curated2:Q9YBR1
         (223 letters)



>FitnessBrowser__Marino:GFF3332
          Length = 269

 Score = 42.7 bits (99), Expect = 7e-09
 Identities = 40/132 (30%), Positives = 58/132 (43%), Gaps = 16/132 (12%)

Query: 93  EHKVTYRHLQAVVSKARSL---GLEVLA-CADTPEEAAAAALLRPSMVALEPPELIGTGI 148
           E K  Y ++   +  A  L   G +V+  C+D P    A  L     VA+ P      G 
Sbjct: 117 EEKTLYPNMTETLVAAEELIKDGFKVMVYCSDDP--LLAKRLEEMGCVAIMP-----LGA 169

Query: 149 PVSQAKPEVITRGVEAVARVAPGVAVLAGAGITAGEDARRAVELGAQGVLVASAVMKAKD 208
           P+           +  +   A  V VL  AG+    DA  A+ELG  GVL+ +A+ +AKD
Sbjct: 170 PIGSGLGIQNRYNIRLIVENA-NVPVLVDAGVGTASDATIAMELGCDGVLMNTAIAQAKD 228

Query: 209 PHGKMLELAEAM 220
           P    + +A AM
Sbjct: 229 P----IRMANAM 236


Lambda     K      H
   0.316    0.130    0.359 

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: 111
Number of extensions: 4
Number of successful extensions: 1
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: 223
Length of database: 269
Length adjustment: 24
Effective length of query: 199
Effective length of database: 245
Effective search space:    48755
Effective search space used:    48755
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 (21.6 bits)
S2: 46 (22.3 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