GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03645 in Pseudomonas putida KT2440

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate PP_2456 PP_2456 D-ribose ABC transporter - permease subunit

Query= uniprot:D8IZC8
         (344 letters)



>FitnessBrowser__Putida:PP_2456
          Length = 331

 Score =  184 bits (466), Expect = 4e-51
 Identities = 129/343 (37%), Positives = 183/343 (53%), Gaps = 20/343 (5%)

Query: 4   TKMTHTHDAVPPGARRSSSTTAQWLLHRLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASA 63
           T   +  DA P   RRS   T   L   LG+   L+ + +LF  L+ +    GT  F++ 
Sbjct: 3   TTPLNNQDAAP--VRRSG--TYFGLGTYLGLAGALLAMIVLFSFLSSHFWSYGT--FSTL 56

Query: 64  ENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLGAAPGWAIPMF 123
            N      Q+   +VLA GMTFV++  GIDLSVGSVLA++A       LG   GW +   
Sbjct: 57  AN------QIPDLMVLAVGMTFVLIIGGIDLSVGSVLALAASTVSVAILGW--GWGVLPS 108

Query: 124 IFSGLVM----GMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPSFEW 179
              G+ +    G + G +     I +F+V+LG +   RG AY   D  T    D  ++ W
Sbjct: 109 ALLGMAVAALAGSITGGVTVAWRIPSFIVSLGVLEMARGLAYQFTDSRTAYIGD--AYAW 166

Query: 180 IGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFV 239
             N     V     +A+ V++L+ ++L +TV G ++  IG N +A RL GI      + V
Sbjct: 167 FSNPVAFGVSPAFIIALLVIVLAQLVLTRTVFGRYLIGIGTNEEAVRLAGIDPRPYKVLV 226

Query: 240 YSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGAL 299
           +++ GL +GLA     SRL  A+ N GSG EL  IAAVV+GGTSLMGG GS+  T  G L
Sbjct: 227 FALMGLLAGLAALFQISRLEAADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVL 286

Query: 300 IIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKWRQKDAAQ 342
           II V+  GL  +G S   + +  GAVIV+AV+LD +R + A +
Sbjct: 287 IISVLAAGLAQIGASEPTKRIITGAVIVIAVVLDTYRSRRAGR 329


Lambda     K      H
   0.324    0.138    0.417 

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: 305
Number of extensions: 13
Number of successful extensions: 4
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: 344
Length of database: 331
Length adjustment: 28
Effective length of query: 316
Effective length of database: 303
Effective search space:    95748
Effective search space used:    95748
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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