GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Pseudomonas fluorescens FW300-N2E2

Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate Pf6N2E2_5970 L-arabinose transport system permease protein (TC 3.A.1.2.2)

Query= uniprot:A0A0C4Y7K0
         (337 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5970
          Length = 322

 Score =  175 bits (444), Expect = 1e-48
 Identities = 98/299 (32%), Positives = 165/299 (55%), Gaps = 5/299 (1%)

Query: 38  VLVLLCIGFSVLT----ENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSIL 93
           V++L  IG  VL     +NF    N+  +    S   + A  M + + +G  DLSVGS++
Sbjct: 25  VMLLAAIGIFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVI 84

Query: 94  SISAVVAMLVSLMPQLGMLSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVRGL 153
           + + VVA +V        L + AAL+ GL+ G++NG ++A +++   I TL T+  VRGL
Sbjct: 85  ACAGVVAAVVMRDTNSVFLGISAALVMGLIVGLINGIVIAKLRVNALITTLATMQIVRGL 144

Query: 154 ARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGG 213
           A +  N   +      F   GNG++ GVP  ++I         ++L  T  G    A+GG
Sbjct: 145 AYIFANGKAVGVSQESFFVFGNGQMFGVPVPILITIVCFLFFGWLLNYTTYGRNTMAIGG 204

Query: 214 NAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVIL 273
           N EAA L+G+ V    + ++AV G++  L GV+ ++R+ +   + +GQ +EL  I+A +L
Sbjct: 205 NQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPM-IGQGFELTVISACVL 263

Query: 274 GGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDSYRRK 332
           GG S  GG G I   + G LI+A++ N + L  +   +QY+I+G +++ AV +D  +++
Sbjct: 264 GGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVIDRLKQR 322


Lambda     K      H
   0.325    0.141    0.409 

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: 302
Number of extensions: 24
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: 337
Length of database: 322
Length adjustment: 28
Effective length of query: 309
Effective length of database: 294
Effective search space:    90846
Effective search space used:    90846
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