GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoK in Pseudomonas putida KT2440

Align deoxyribose kinase (EC 2.7.1.15) (characterized)
to candidate PP_4934 PP_4934 heptose 7-phosphate kinase/heptose 1-phosphate adenylyltransferase

Query= reanno::Burk376:H281DRAFT_01116
         (320 letters)



>FitnessBrowser__Putida:PP_4934
          Length = 473

 Score = 58.5 bits (140), Expect = 3e-13
 Identities = 45/142 (31%), Positives = 66/142 (46%), Gaps = 5/142 (3%)

Query: 157 LEVARKHGVTTVFNPAPALPLDDDIFPLCDYITPNETEAAALTGVPIANVDDARRAADVL 216
           ++ AR  G+  + +P      D  I+     ITPN +E   + G  +   +   +   +L
Sbjct: 163 IQAARAKGIPVLADPKGK---DFSIYRGASLITPNLSEFETIVGRCVDEAELVAKGLQLL 219

Query: 217 LAKGVGTVIVTLGEGG-ALLHDATQSIWLPAFRCGAVVETAGAGDGFTGGFAAALARGED 275
               +G ++VT GE G  LL     ++ LPA R   V +  GAGD      AAA+A GED
Sbjct: 220 QDLDLGALLVTRGEHGMTLLRVGQPALHLPA-RAREVFDVTGAGDTVISTLAAAIAAGED 278

Query: 276 AISAMRFGCALAGISVTRAGTA 297
              A+      AGI V + GTA
Sbjct: 279 LPHAVALANLAAGIVVGKLGTA 300


Lambda     K      H
   0.318    0.132    0.377 

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: 264
Number of extensions: 12
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: 320
Length of database: 473
Length adjustment: 30
Effective length of query: 290
Effective length of database: 443
Effective search space:   128470
Effective search space used:   128470
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 (21.7 bits)
S2: 50 (23.9 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