GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araF in Pseudomonas simiae WCS417

Align L-arabinose-binding periplasmic protein; ABP (characterized)
to candidate GFF4165 PS417_21335 sugar ABC transporter substrate-binding protein

Query= SwissProt::P02924
         (329 letters)



>FitnessBrowser__WCS417:GFF4165
          Length = 326

 Score =  375 bits (963), Expect = e-109
 Identities = 191/324 (58%), Positives = 241/324 (74%), Gaps = 2/324 (0%)

Query: 4   FTKALAAIGLAAVMSQSAMAENLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAV 63
           F K L  + LA   S  A+AE +K+GFLVKQ EEPWFQTEW FA+KAGKD GF VIKIAV
Sbjct: 2   FKKTLGTLALAMAFSSVALAEEVKIGFLVKQAEEPWFQTEWAFAEKAGKDQGFTVIKIAV 61

Query: 64  PDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIVAKARGYDMKVIAVDDQFVNAKGKPM 123
           PDGEKTL+AID+LAA+GAKGFVIC PD  LG AI+AKA+  ++KV+AVDD+FV+AKGKPM
Sbjct: 62  PDGEKTLSAIDTLAANGAKGFVICPPDVSLGPAIMAKAKLNNLKVLAVDDRFVDAKGKPM 121

Query: 124 DTVPLVMMAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMDALK 183
           + VP V + A KIG++QG+ +  E + R WD K++  +  T +EL+T ++RT GS++ LK
Sbjct: 122 EDVPYVGLDAYKIGQKQGEAMATEAKHRNWDWKDTYAVINTFDELETGKKRTDGSVEGLK 181

Query: 184 AAGFPEKQIYQVPTKSNDIPGAFDAANSMLVQHPE-VKHWLIVGMNDSTVLGGVRATEGQ 242
           AAG P   I     K+ D+PG+ DA NS LV+ P   K+ +I GMNDSTVLGGVRATE  
Sbjct: 182 AAGLPADHILFSAQKTLDVPGSMDATNSALVKLPSGAKNLIIGGMNDSTVLGGVRATESA 241

Query: 243 GFKAADIIGIGINGVDAVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKDVEPPK 302
           GFKAA++IG+GING DA+ EL K+  TGFYGS+L SPD  GYK++  ++ WV +  EP K
Sbjct: 242 GFKAANVIGVGINGTDAIEELKKSD-TGFYGSMLLSPDASGYKTASAMFEWVTQGTEPAK 300

Query: 303 FTEVTDVVLITRDNFKEELEKKGL 326
           FT + +V LITR NFKEEL K GL
Sbjct: 301 FTALDNVTLITRANFKEELSKIGL 324


Lambda     K      H
   0.315    0.132    0.381 

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: 359
Number of extensions: 19
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: 329
Length of database: 326
Length adjustment: 28
Effective length of query: 301
Effective length of database: 298
Effective search space:    89698
Effective search space used:    89698
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 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