GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08260 in Pseudomonas fluorescens GW456-L13

Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate PfGW456L13_4606 High-affinity leucine-specific transport system, periplasmic binding protein LivK (TC 3.A.1.4.1)

Query= uniprot:G8ALJ3
         (366 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4606
          Length = 375

 Score =  274 bits (700), Expect = 3e-78
 Identities = 143/352 (40%), Positives = 204/352 (57%), Gaps = 1/352 (0%)

Query: 11  VAATAMTASVAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQKLKLEV 70
           V A   + S A   I +  AGP TG  A +G+    G + A+  INA GGV G+KL+   
Sbjct: 16  VLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGAKMAIEQINAKGGVDGKKLEAVE 75

Query: 71  GDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPASTNPKLTE 130
            DDACDPKQAVAVAN++   GVKFV GH CS S+ PAS +Y +EGV+ I+PA+T+P +T 
Sbjct: 76  YDDACDPKQAVAVANKVVNDGVKFVVGHLCSSSTQPASDIYEDEGVIMITPAATSPDITA 135

Query: 131 QNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKALNAGGQK 190
           +  K VFR  G D  QG  AG Y+ +  K K VA+LHDK  YG+G+A   +K L   G K
Sbjct: 136 RGYKMVFRTIGLDSAQGPAAGNYIADFVKPKIVAVLHDKQQYGEGIASAVKKTLEGKGVK 195

Query: 191 EKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNAPIVSGDAL 250
             ++E   AG+KD+S++++KLKQ  VD VY GGYH E GL+ RQ  ++GL A  +  + +
Sbjct: 196 VAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQSAEKGLKAKFMGPEGV 255

Query: 251 VTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEKFRKAGYEPEG-YTLYTYAALQIWA 309
             +    I   A E  ++T      + P      + F+    +P G +    Y+A+ + A
Sbjct: 256 GNDSISQIAKDASEGLLVTLPKSFDQDPANVALADAFKAKKEDPSGPFVFPAYSAVTVIA 315

Query: 310 EAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWNNGQ 361
           +  K A S DSAK+A+ +   ++ T  G + FD KGD+    +V Y W+ G+
Sbjct: 316 DGIKAAKSEDSAKVAEAIHAGTFKTPTGDLSFDEKGDLKDFKFVVYEWHFGK 367


Lambda     K      H
   0.312    0.129    0.366 

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: 398
Number of extensions: 20
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: 366
Length of database: 375
Length adjustment: 30
Effective length of query: 336
Effective length of database: 345
Effective search space:   115920
Effective search space used:   115920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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