GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG in Pseudovibrio axinellae Ad2

Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate WP_068002934.1 PsAD2_RS04495 carbohydrate ABC transporter permease

Query= reanno::Smeli:SMc03063
         (380 letters)



>NCBI__GCF_001623255.1:WP_068002934.1
          Length = 290

 Score =  123 bits (308), Expect = 7e-33
 Identities = 69/216 (31%), Positives = 118/216 (54%), Gaps = 6/216 (2%)

Query: 164 GRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLAVVVGLLVVPLQMSLIPLL 223
           GR+  NSL V + ST + + I   AAYAL    F GR  +    + + +VP  + L+P+ 
Sbjct: 81  GRALNNSLIVGLLSTGLTLTIGCMAAYALVRFQFMGRGTVSMGTLLMRIVPPAVLLVPVF 140

Query: 224 QLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAGLPREIMESARVDGASDFD 283
               G+  F     +TY GI L +T   LP  I++L++++  +P ++ E+AR+DGA+ F 
Sbjct: 141 ----GIWTFQYGLDQTYAGIILIYTAMNLPFVIWILQSFIVQVPIQLEEAARMDGANPFQ 196

Query: 284 IFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDKLVLTGRLVNLLGSRGGNW 343
           +F  ++LP+  P LA+ AIF F   WN+ L+A    G       +T  +VN +     +W
Sbjct: 197 VFFLVVLPIIQPGLAAAAIFTFRIAWNEFLLANALSGRSTRTAPVT--IVNSITEYDIDW 254

Query: 344 EILTASAFITIVVPLIVFFALQRYLVRGLLAGSVKG 379
            ++ A+  +  + P++  F   + ++ G+ AG+VKG
Sbjct: 255 GVIMATGMLLAIPPILFTFVASKQIITGMTAGAVKG 290


Lambda     K      H
   0.324    0.139    0.418 

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: 245
Number of extensions: 10
Number of successful extensions: 3
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: 380
Length of database: 290
Length adjustment: 28
Effective length of query: 352
Effective length of database: 262
Effective search space:    92224
Effective search space used:    92224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 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