GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2554 in Williamsia sterculiae CPCC 203464

Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate WP_083710231.1 BW971_RS16650 ABC transporter permease subunit

Query= reanno::acidovorax_3H11:Ac3H11_2554
         (222 letters)



>NCBI__GCF_900156495.1:WP_083710231.1
          Length = 589

 Score =  102 bits (255), Expect = 1e-26
 Identities = 69/219 (31%), Positives = 120/219 (54%), Gaps = 10/219 (4%)

Query: 12  VPQLLAGALV-TVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLV 70
           +P LL   L  T+ ++  S +LG ++G+++ +  ++  R + +     Y    RG P +V
Sbjct: 355 LPDLLKTGLPNTLILSVVSGVLGTILGMVLAVAGISRSRWLRWP-ARIYTDIFRGLPAVV 413

Query: 71  QLFILFFGLPQFGILLPA---FVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAARSIG 127
            + ++  G+      L     +  G + L + + AY+ E+ R  IQS+D GQ+EA+R+IG
Sbjct: 414 VILVVGLGIGPVVKNLTGNNPYWLGAVALALLAAAYIGEIFRSGIQSVDDGQLEASRAIG 473

Query: 128 MSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTI----HDLMHEGQKIISVS 183
            S   +MR VV+PQ V R++P L N+FI+LIK+S+LV  L +     +L   G+  ++  
Sbjct: 474 FSYRQSMRLVVVPQGVRRVLPALMNQFISLIKDSSLVYFLGLLASQRELFAVGRD-LNAQ 532

Query: 184 YRSLEVYLAIAVVYFILTGATTLVLRRIELRLRAGGMVQ 222
             +L   +A  ++Y +LT   T ++  I+ RLR G   Q
Sbjct: 533 TGNLSPLVAAGLIYLVLTIPLTHLVNYIDHRLRTGRPTQ 571


Lambda     K      H
   0.328    0.143    0.412 

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: 264
Number of extensions: 13
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: 222
Length of database: 589
Length adjustment: 29
Effective length of query: 193
Effective length of database: 560
Effective search space:   108080
Effective search space used:   108080
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: 49 (23.5 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