GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03645 in Pseudomonas fluorescens FW300-N2C3

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate AO356_00960 AO356_00960 ABC transporter permease

Query= uniprot:D8IZC8
         (344 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_00960
          Length = 325

 Score =  185 bits (470), Expect = 1e-51
 Identities = 118/314 (37%), Positives = 171/314 (54%), Gaps = 20/314 (6%)

Query: 45  FYGLTLYLSGDG------------TSNFASAENTMNILRQVAINLVLAAGMTFVILTAGI 92
           FYGL  YL   G            +S+F S +    +  Q+   +VLA GMTF+++  GI
Sbjct: 14  FYGLGTYLGLAGALLAMVALFSTLSSHFLSYDTFSTLANQIPDLMVLAVGMTFILIIGGI 73

Query: 93  DLSVGSVLAVSAVLGMQVSLGAAPGWAIPMFIFSGLVM----GMVNGAMVALLNINAFVV 148
           DLSVGSVLA++A       LG   GW++      G+ +    G V G++     I +F+V
Sbjct: 74  DLSVGSVLALAASTVSVAVLGW--GWSVWPSALLGMAVAALAGTVTGSITVAWRIPSFIV 131

Query: 149 TLGTMTAFRGAAYLLADGTTVLNNDIPSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRK 208
           +LG +   RG AY +    T    D  SF W+ N     +     +A+ V+ ++  +L +
Sbjct: 132 SLGVLEMARGLAYQMTGSRTAYIGD--SFAWLSNPIAFGISPSFIIALLVIFIAQAVLTR 189

Query: 209 TVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSG 268
           TV G ++  IG N +A RL GI      + V+S+ GL +G+A     SRL  A+ N GSG
Sbjct: 190 TVFGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGVAALFQISRLEAADPNAGSG 249

Query: 269 YELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVL 328
            EL  IAAVV+GGTSLMGG GS+  T  G LII V+  GL  +G +   + +  GAVIV+
Sbjct: 250 LELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVV 309

Query: 329 AVILDKWRQKDAAQ 342
           AV+LD +R + A++
Sbjct: 310 AVVLDTYRSQRASR 323


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: 288
Number of extensions: 16
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: 325
Length adjustment: 28
Effective length of query: 316
Effective length of database: 297
Effective search space:    93852
Effective search space used:    93852
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