GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1D in Cupriavidus basilensis 4G11

Align Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale)
to candidate RR42_RS27120 RR42_RS27120 amino acid ABC transporter permease

Query= uniprot:A0A0H3PA28
         (219 letters)



>FitnessBrowser__Cup4G11:RR42_RS27120
          Length = 218

 Score = 90.5 bits (223), Expect = 2e-23
 Identities = 60/202 (29%), Positives = 102/202 (50%), Gaps = 3/202 (1%)

Query: 13  LMQGLFLTLKIALATCIISIVFGTFLAITKNYGDRLSKFLAACYIDIFRNTPLLLWMLAA 72
           L+  +  T+ ++L       V G  + + +      ++  A  +I++F+ TPLL+ +  A
Sbjct: 13  LLMAVRWTVVLSLVAFAGGAVIGLLVLLMRISRRAPARRAAWAFIEVFQGTPLLMQLFLA 72

Query: 73  CFVLPVFFGQFPQAFWGTIGFSLYTSSVMAEIIRGGLNSIPKGQFEAAYSQGFGKFFTLF 132
            F L +F  + P      +  SL++ + +AEI RG + +IPKGQ+EAA     G    + 
Sbjct: 73  FFGLALFGVEIPAWLAAGLALSLWSGAYLAEIWRGCVEAIPKGQWEAAGCLSLGHLQQMR 132

Query: 133 YIILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNSKTILAKLTSFEEILAMIGV 192
           Y+ILPQ  R  I   +  +V  +K TA  + +G  EL+  + T++   T       +  +
Sbjct: 133 YVILPQALRIAIAPTVGFVVQIIKGTALASIIGFVELS-KAGTVITNATF--SPFTVYAL 189

Query: 193 VAGIYFIICFSLSMLVRYYAKK 214
           VA IYF +C+ LS   RY  +K
Sbjct: 190 VALIYFALCWPLSRYSRYLERK 211


Lambda     K      H
   0.331    0.144    0.428 

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: 118
Number of extensions: 5
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: 219
Length of database: 218
Length adjustment: 22
Effective length of query: 197
Effective length of database: 196
Effective search space:    38612
Effective search space used:    38612
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 45 (21.9 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