GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5403 in Williamsia sterculiae CPCC 203464

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

Query= reanno::pseudo6_N2E2:Pf6N2E2_5403
         (375 letters)



>NCBI__GCF_900156495.1:WP_083710231.1
          Length = 589

 Score = 81.3 bits (199), Expect = 7e-20
 Identities = 49/126 (38%), Positives = 81/126 (64%), Gaps = 4/126 (3%)

Query: 248 LALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVIIPPLTSQ 307
           +AL +  AA+I EI RSGI+SV  GQ EA+R++G     ++R V++PQ +R ++P L +Q
Sbjct: 440 VALALLAAAYIGEIFRSGIQSVDDGQLEASRAIGFSYRQSMRLVVVPQGVRRVLPALMNQ 499

Query: 308 YLNLAKNSSLAAGIG-YPEMVSLFA-GTVLN-QTGQAIEVIAITMSVYLAISISISLLMN 364
           +++L K+SSL   +G       LFA G  LN QTG    ++A  + +YL ++I ++ L+N
Sbjct: 500 FISLIKDSSLVYFLGLLASQRELFAVGRDLNAQTGNLSPLVAAGL-IYLVLTIPLTHLVN 558

Query: 365 WYNKRI 370
           + + R+
Sbjct: 559 YIDHRL 564



 Score = 44.7 bits (104), Expect = 7e-09
 Identities = 20/55 (36%), Positives = 37/55 (67%)

Query: 69  GLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQIL 123
           GL NTL+++ +  +L TILG ++ VA +S++  +   A +Y ++FR +P ++ IL
Sbjct: 362 GLPNTLILSVVSGVLGTILGMVLAVAGISRSRWLRWPARIYTDIFRGLPAVVVIL 416


Lambda     K      H
   0.328    0.141    0.430 

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: 433
Number of extensions: 24
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 375
Length of database: 589
Length adjustment: 33
Effective length of query: 342
Effective length of database: 556
Effective search space:   190152
Effective search space used:   190152
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: 51 (24.3 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