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_20255 AO356_20255 arabinose ABC transporter permease

Query= uniprot:D8IZC8
         (344 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_20255
          Length = 322

 Score =  176 bits (446), Expect = 7e-49
 Identities = 100/287 (34%), Positives = 158/287 (55%), Gaps = 14/287 (4%)

Query: 59  NFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGM-------QVS 111
           NF S  N   +   ++   + A  M + + +   DLSVGSV+A + V+          V 
Sbjct: 43  NFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVIACAGVVAAVVMRDTNSVF 102

Query: 112 LGAAPGWAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLN 171
           LG +   A+      GL++G++NG ++A L +NA + TL TM   RG AY+ A+G  V  
Sbjct: 103 LGVSAALAM------GLIVGLINGIVIAKLRVNALITTLATMQIVRGLAYIFANGKAVGV 156

Query: 172 NDIPSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIR 231
           +   SF   GNG    VP  I + +A  L    +L  T  G +  AIGGN +AA L G+ 
Sbjct: 157 SQ-ESFFVFGNGQLFGVPVPILITIACFLFFGWLLNYTTYGRNTMAIGGNQEAALLAGVN 215

Query: 232 VGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSI 291
           V    + ++++ GL   LAG + ASR+       G G+EL  I+A VLGG SL GG+G I
Sbjct: 216 VDRTKIIIFAVHGLIGALAGVILASRMTSGQPMIGQGFELTVISACVLGGVSLSGGIGMI 275

Query: 292 WGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKWRQK 338
              + G LI+ ++ N + +  + +F+QYV +G++++LAV++D+ +Q+
Sbjct: 276 RHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVIDRLKQR 322


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: 268
Number of extensions: 15
Number of successful extensions: 2
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: 322
Length adjustment: 28
Effective length of query: 316
Effective length of database: 294
Effective search space:    92904
Effective search space used:    92904
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