GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglF in Nocardiopsis gilva YIM 90087

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate WP_152471781.1 CDO52_RS22265 ABC transporter permease subunit

Query= uniprot:A8LLL5
         (334 letters)



>NCBI__GCF_002263495.1:WP_152471781.1
          Length = 265

 Score = 91.3 bits (225), Expect = 2e-23
 Identities = 73/246 (29%), Positives = 113/246 (45%), Gaps = 31/246 (12%)

Query: 91  WVGLDNYAQMASE---PKFWEAMRNNMFWLIVVPALSTAFGLLAAQLTDRIKWGN-VAKS 146
           + GLDN+A + S     + W A  +N+ +      + T  GL  A L    + G    ++
Sbjct: 12  FAGLDNFAHLFSGVYGDRLWRAFGHNLAFFAGTMLVQTTLGLAFAVLLRHTRAGRRFLQT 71

Query: 147 IIFMPMAISFVGASVIWKLVYDGRPIEQEQIGILNAIIVGLG---------GDPVTFLTI 197
              +P  +S +    +W L+         Q G +NA +  +G         GDP   L +
Sbjct: 72  AYVLPHLVSPIVVGYLWSLMLS------PQFGAVNAALRAVGLDALAQPWTGDPA--LAL 123

Query: 198 PFWNNFFLMIVLVWVQTGFAMVILSAALRGIPEETIEAAIIDGASPLQIFFKIKVPQIMP 257
           P      L++V  W   GF M++ SAAL GIP E  EAA +DGAS  Q F  + +P +MP
Sbjct: 124 PT-----LILVNAWQWIGFPMLLFSAALAGIPPEYEEAARVDGASGWQAFRTVTLPLLMP 178

Query: 258 TVVVVWTTITLVVLKVFDIVFAMTNGQ----WETQVLANYMFDKLFRANDWG-VGSASAM 312
            + +V     +  + V D+V+AM   Q      T VL    +   F   D G +G ASA+
Sbjct: 179 AIGIVTVLTFIGNMNVLDLVYAMQGSQGAPAGATDVLGLLFYRTAFNNPDPGAIGQASAL 238

Query: 313 VIMLLV 318
            +++ V
Sbjct: 239 AVVMFV 244


Lambda     K      H
   0.329    0.143    0.455 

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: 200
Number of extensions: 13
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: 334
Length of database: 265
Length adjustment: 26
Effective length of query: 308
Effective length of database: 239
Effective search space:    73612
Effective search space used:    73612
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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