GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligJ in Klebsiella michiganensis M5al

Align 4-oxalmesaconate hydratase; OMA hydratase; Gallate degradation protein B; EC 4.2.1.83 (characterized)
to candidate BWI76_RS14190 BWI76_RS14190 DNA-binding protein

Query= SwissProt::Q88JX8
         (258 letters)



>FitnessBrowser__Koxy:BWI76_RS14190
          Length = 246

 Score =  425 bits (1092), Expect = e-124
 Identities = 200/240 (83%), Positives = 220/240 (91%)

Query: 19  QKSALVVSAHSADFVWRAGGAIALHAEQGYAMHVVCLSFGERGESAKLWRKGEMTEAKVK 78
           +KSALVVSAHSADFVWRAGGAIALH EQGY +H+VCLSFGERGESAKLWRKG MTE  VK
Sbjct: 7   EKSALVVSAHSADFVWRAGGAIALHVEQGYQVHIVCLSFGERGESAKLWRKGNMTEETVK 66

Query: 79  DARREEAMAAAEILGASVEFFDIGDYPMRADKDTLFRLADVYRRVQPEFVLSHSLKDPYN 138
             RREEA AAA+ILGASVEFFDIGDYP+RADK+TLFRLADVYRRVQP FVL+HS++DPYN
Sbjct: 67  HHRREEAQAAADILGASVEFFDIGDYPLRADKETLFRLADVYRRVQPHFVLTHSMQDPYN 126

Query: 139 YDHPLAMHLAQEARIIAQAEGYKPGEKIVGAPPVYAFEPHQPEQCEWRPDTFLDITSVWD 198
           YDHP+A +LAQEARIIAQAEGY+PGE +V APPVY FEPHQPEQC W+PD  LDIT VW+
Sbjct: 127 YDHPMASNLAQEARIIAQAEGYRPGEPVVQAPPVYCFEPHQPEQCSWKPDVLLDITRVWE 186

Query: 199 KKYAAIQCMAGQEHLWEYYTRVALQRGVQAKRNVGITSARNIVYAEGLQSVFPRVTENLA 258
           KKY AIQCM GQEHLWEYYTRVALQRGVQAKRN+GIT+AR+IV+AEG QS+FPRVTENLA
Sbjct: 187 KKYQAIQCMQGQEHLWEYYTRVALQRGVQAKRNIGITAARDIVHAEGFQSIFPRVTENLA 246


Lambda     K      H
   0.320    0.132    0.408 

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: 325
Number of extensions: 8
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: 258
Length of database: 246
Length adjustment: 24
Effective length of query: 234
Effective length of database: 222
Effective search space:    51948
Effective search space used:    51948
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: 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