GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21715 in Williamsia sterculiae CPCC 203464

Align ABC transporter for D-Glucosamine Hydrochloride, permease component 2 (characterized)
to candidate WP_083710231.1 BW971_RS16650 ABC transporter permease subunit

Query= reanno::pseudo6_N2E2:Pf6N2E2_2052
         (220 letters)



>NCBI__GCF_900156495.1:WP_083710231.1
          Length = 589

 Score =  101 bits (251), Expect = 3e-26
 Identities = 70/213 (32%), Positives = 108/213 (50%), Gaps = 8/213 (3%)

Query: 15  DTLLAGLGLGLSLALVSIAIGCVIGLAMAFALLSKHRVLRVLASVYVTVIRNTPILVLIL 74
           D L  GL   L L++VS  +G ++G+ +A A +S+ R LR  A +Y  + R  P +V+IL
Sbjct: 357 DLLKTGLPNTLILSVVSGVLGTILGMVLAVAGISRSRWLRWPARIYTDIFRGLPAVVVIL 416

Query: 75  LIYFALPSLGIRLDKLPSF---VITLSLYAGAYLTEVFRGGLLSIHKGQREAGLAIGLGE 131
           ++   +  +   L     +    + L+L A AY+ E+FR G+ S+  GQ EA  AIG   
Sbjct: 417 VVGLGIGPVVKNLTGNNPYWLGAVALALLAAAYIGEIFRSGIQSVDDGQLEASRAIGFSY 476

Query: 132 WQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAV----PELTYYARKINVESYRV 187
            Q    V VP  +R VLPAL N FISL KD+SL   + +     EL    R +N ++   
Sbjct: 477 RQSMRLVVVPQGVRRVLPALMNQFISLIKDSSLVYFLGLLASQRELFAVGRDLNAQTGN- 535

Query: 188 IETWLVTTALYVAACYLIAMLLRYFEQRLAIRR 220
           +   +    +Y+     +  L+ Y + RL   R
Sbjct: 536 LSPLVAAGLIYLVLTIPLTHLVNYIDHRLRTGR 568


Lambda     K      H
   0.330    0.142    0.414 

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: 266
Number of extensions: 11
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: 220
Length of database: 589
Length adjustment: 29
Effective length of query: 191
Effective length of database: 560
Effective search space:   106960
Effective search space used:   106960
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