GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treU in Rhodobacter viridis JA737

Align TreU, component of Trehalose porter (characterized)
to candidate WP_110804034.1 C8J30_RS01980 carbohydrate ABC transporter permease

Query= TCDB::Q97ZC1
         (267 letters)



>NCBI__GCF_003217355.1:WP_110804034.1
          Length = 382

 Score = 81.6 bits (200), Expect = 2e-20
 Identities = 70/243 (28%), Positives = 114/243 (46%), Gaps = 27/243 (11%)

Query: 41  SLLPVSLTLNNLLTALQGTAFIDPFIKSLETATLVGIITIALAIPAGYGLS--RLP-RAI 97
           ++ P  LT  N    +        F+ ++       +I I +A  A Y L+  R P RA+
Sbjct: 150 TVAPPRLTTGNYARVITAEGIGRAFLNTMTVTIPATVIPILIAAFAAYALAWMRFPGRAL 209

Query: 98  AYSIIILLLVTNMMPAIVIGIPIAVDFLKLH----LFESVVGLALAQTLITLPLATFILQ 153
             + I+ LLV  +  A++         LKLH    L +S +G+ LA T   LPLA ++L+
Sbjct: 210 LVATIVGLLVVPLQLALI-------PLLKLHNQIGLNQSYLGIWLAHTGFGLPLAIYLLR 262

Query: 154 GTFSSIPIDLEHQARVDGANLFNRLFSVLLPLAAPGIAAAFLISWMFSWDEFTYAILLIP 213
                +P ++   ARVDGA  F     ++LPL+ P +A+  +  +++ W++   A + + 
Sbjct: 263 NYMVGLPREIIESARVDGATEFQIFRRIVLPLSFPALASFAIFQFLWVWNDLLVATVFL- 321

Query: 214 YHSTLPVTIYQDVTRG---------NLLAGIAFSLIFTLPVIILTFALQKYLRGEYLAGG 264
             +     +     R           +LA  AF  I  +P+I+  FALQKYL    LAG 
Sbjct: 322 -GNATDTQVMTGALRALLGSRGGDWEILAASAFVSI-AVPLIVF-FALQKYLVRGLLAGS 378

Query: 265 IKG 267
           +KG
Sbjct: 379 VKG 381


Lambda     K      H
   0.330    0.146    0.431 

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: 270
Number of extensions: 17
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: 267
Length of database: 382
Length adjustment: 28
Effective length of query: 239
Effective length of database: 354
Effective search space:    84606
Effective search space used:    84606
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.

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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