GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1B in Williamsia sterculiae CPCC 203464

Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_083710231.1 BW971_RS16650 ABC transporter permease subunit

Query= TCDB::A1VZQ3
         (250 letters)



>NCBI__GCF_900156495.1:WP_083710231.1
          Length = 589

 Score =  108 bits (271), Expect = 2e-28
 Identities = 65/216 (30%), Positives = 116/216 (53%), Gaps = 8/216 (3%)

Query: 42  DAFINGFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPLVIQIF 101
           D    G   TL +S+++ ++ TI G +  V   SR + +R   RIY ++F+ +P V+ I 
Sbjct: 357 DLLKTGLPNTLILSVVSGVLGTILGMVLAVAGISRSRWLRWPARIYTDIFRGLPAVVVIL 416

Query: 102 FLFYALPVLGIRL---DIFTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGFTY 158
            +   +  +   L   + + +G + +     AY+ E+ RSGI +V  GQ EAS + GF+Y
Sbjct: 417 VVGLGIGPVVKNLTGNNPYWLGAVALALLAAAYIGEIFRSGIQSVDDGQLEASRAIGFSY 476

Query: 159 IQQMRYIIVPQTIRIILPPMTNQMVNLIKNTSVL----LIVGGAELMHSADSYAADYGNY 214
            Q MR ++VPQ +R +LP + NQ ++LIK++S++    L+    EL        A  GN 
Sbjct: 477 RQSMRLVVVPQGVRRVLPALMNQFISLIKDSSLVYFLGLLASQRELFAVGRDLNAQTGNL 536

Query: 215 APAYIFAAVLYFIICYPLAYFAKAYENKLKKAHLTR 250
           +P  + A ++Y ++  PL +     +++L+    T+
Sbjct: 537 SP-LVAAGLIYLVLTIPLTHLVNYIDHRLRTGRPTQ 571


Lambda     K      H
   0.328    0.143    0.422 

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: 329
Number of extensions: 15
Number of successful extensions: 1
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: 250
Length of database: 589
Length adjustment: 30
Effective length of query: 220
Effective length of database: 559
Effective search space:   122980
Effective search space used:   122980
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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