GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araF in Pseudomonas fluorescens FW300-N2C3

Align L-arabinose-binding periplasmic protein; ABP (characterized)
to candidate AO356_20245 AO356_20245 sugar ABC transporter substrate-binding protein

Query= SwissProt::P02924
         (329 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_20245
          Length = 334

 Score =  372 bits (956), Expect = e-108
 Identities = 189/321 (58%), Positives = 244/321 (76%), Gaps = 4/321 (1%)

Query: 9   AAIGLAAVMSQSAM--AENLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVPDG 66
           AA+ + AV   S++  A+ +K+GFLVKQ EEPWFQTEW FA+KA KD GFE+IKIAVPDG
Sbjct: 13  AALAVTAVSLSSSLLAADPVKIGFLVKQAEEPWFQTEWAFAEKASKDKGFELIKIAVPDG 72

Query: 67  EKTLNAIDSLAASGAKGFVICTPDPKLGSAIVAKARGYDMKVIAVDDQFVNAKGKPMDTV 126
           EKTL+AIDSLAA+GAKGFVIC PD  LG AI+AKA+  D+KVIAVDD+FV+A GK M+ V
Sbjct: 73  EKTLSAIDSLAANGAKGFVICPPDVSLGPAIMAKAKLNDLKVIAVDDRFVDANGKFMEDV 132

Query: 127 PLVMMAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMDALKAAG 186
           P + MAA ++G++QG  +  E +KR W+ K++  +  T NELDT ++RT GS+DALK AG
Sbjct: 133 PYLGMAAFEVGQKQGAAMAAEAKKRNWEWKDTYAVINTFNELDTGKKRTDGSVDALKKAG 192

Query: 187 FPEKQIYQVPTKSNDIPGAFDAANSMLVQHPE-VKHWLIVGMNDSTVLGGVRATEGQGFK 245
            P   I     K+ D+PG+ D+ NS LV+ P   K+ +I GMND+TVLGGVRATE  GFK
Sbjct: 193 MPADHILYSALKTLDVPGSMDSTNSALVKLPSAAKNLIIGGMNDNTVLGGVRATEAAGFK 252

Query: 246 AADIIGIGINGVDAVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKDVEPPKFTE 305
           AA++IGIGING DA+ EL K   +GF+GS+LPSP + GYK++EM+Y W+    EPPK+T 
Sbjct: 253 AANVIGIGINGTDAIGELKKPD-SGFFGSMLPSPHIEGYKTAEMMYEWITTGKEPPKYTA 311

Query: 306 VTDVVLITRDNFKEELEKKGL 326
           + +V LITR+NFK+ELEK GL
Sbjct: 312 MDEVTLITRENFKQELEKIGL 332


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: 373
Number of extensions: 18
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: 334
Length adjustment: 28
Effective length of query: 301
Effective length of database: 306
Effective search space:    92106
Effective search space used:    92106
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: 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