GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1D in Pseudomonas fluorescens FW300-N1B4

Align Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale)
to candidate Pf1N1B4_2211 Putative amino acid ABC transporter, permease protein

Query= uniprot:A0A0H3PA28
         (219 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2211
          Length = 216

 Score = 96.3 bits (238), Expect = 4e-25
 Identities = 66/202 (32%), Positives = 105/202 (51%), Gaps = 3/202 (1%)

Query: 13  LMQGLFLTLKIALATCIISIVFGTFLAITKNYGDRLSKFLAACYIDIFRNTPLLLWMLAA 72
           L+ GL  TL ++L   I   + G  + + +     L    A  YI++F+ TPLL+ +   
Sbjct: 13  LLTGLQWTLALSLVAFIGGGLIGLLIMVMRISKKSLPSHFARTYIELFQGTPLLMQLFLV 72

Query: 73  CFVLPVFFGQFPQAFWGTIGFSLYTSSVMAEIIRGGLNSIPKGQFEAAYSQGFGKFFTLF 132
            F + +   +        I  +L+TS+ +AEI RG ++SIP GQ+EA+ S        L 
Sbjct: 73  FFGVALAGVEISPWMAAAIALTLFTSAYLAEIWRGCVDSIPHGQWEASSSLALNPLEQLR 132

Query: 133 YIILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNSKTILAKLTSFEEILAMIGV 192
           Y+ILPQ  R  +   +   V  VK TA  + +G  ELT  +  +LA  T FE  + + G+
Sbjct: 133 YVILPQALRIAVAPTVGFSVQVVKGTAVTSIIGFTELT-KTGGMLANAT-FEPFM-VYGL 189

Query: 193 VAGIYFIICFSLSMLVRYYAKK 214
           VA  YF++C+ LS+  RY  ++
Sbjct: 190 VALGYFLLCYPLSLSARYLERR 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: 124
Number of extensions: 7
Number of successful extensions: 3
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: 216
Length adjustment: 22
Effective length of query: 197
Effective length of database: 194
Effective search space:    38218
Effective search space used:    38218
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