GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16925 in Pseudomonas putida KT2440

Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate PP_2456 PP_2456 D-ribose ABC transporter - permease subunit

Query= uniprot:B2SYR4
         (338 letters)



>FitnessBrowser__Putida:PP_2456
          Length = 331

 Score =  145 bits (366), Expect = 1e-39
 Identities = 90/297 (30%), Positives = 153/297 (51%), Gaps = 5/297 (1%)

Query: 39  IVIFVVMFATMSLTVDHFFSIENMLGLALSISQIGMVSCTMMFCLASRDFDLSVGSTVAF 98
           ++  +V+F+ +S    HF+S      LA  I  + +++  M F L     DLSVGS +A 
Sbjct: 33  LLAMIVLFSFLS---SHFWSYGTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSVGSVLAL 89

Query: 99  AGVLCAMVLNATG-NTFIAIVAAVAAGGVIGFVNGAVIAYLRINALITTLATMEIVRGLG 157
           A    ++ +   G     + +  +A   + G + G V    RI + I +L  +E+ RGL 
Sbjct: 90  AASTVSVAILGWGWGVLPSALLGMAVAALAGSITGGVTVAWRIPSFIVSLGVLEMARGLA 149

Query: 158 FIVSHGQAVGVSSDTFIALGGLSFFGVSLPIWVTLLCFIVFGVMLNQTVYGRNTLAIGGN 217
           +  +  +   +  D +        FGVS    + LL  ++  ++L +TV+GR  + IG N
Sbjct: 150 YQFTDSRTAYIG-DAYAWFSNPVAFGVSPAFIIALLVIVLAQLVLTRTVFGRYLIGIGTN 208

Query: 218 PEASRLAGINVERTRVYIFLIQGAVTALAGVILASRITSGQPNAAQGFELNVISACVLGG 277
            EA RLAGI+    +V +F + G +  LA +   SR+ +  PNA  G EL VI+A V+GG
Sbjct: 209 EEAVRLAGIDPRPYKVLVFALMGLLAGLAALFQISRLEAADPNAGSGLELQVIAAVVIGG 268

Query: 278 VSLLGGRATISGVVIGVLIMGTVENVMNLMNIDAFYQYLVRGAILLAAVLLDQLKNR 334
            SL+GGR ++     GVLI+  +   +  +      + ++ GA+++ AV+LD  ++R
Sbjct: 269 TSLMGGRGSVISTFFGVLIISVLAAGLAQIGASEPTKRIITGAVIVIAVVLDTYRSR 325


Lambda     K      H
   0.326    0.139    0.396 

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: 281
Number of extensions: 17
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 338
Length of database: 331
Length adjustment: 28
Effective length of query: 310
Effective length of database: 303
Effective search space:    93930
Effective search space used:    93930
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 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