GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1896 in Rhodobacter viridis JA737

Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate WP_110804034.1 C8J30_RS01980 carbohydrate ABC transporter permease

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1896
         (281 letters)



>NCBI__GCF_003217355.1:WP_110804034.1
          Length = 382

 Score =  129 bits (323), Expect = 1e-34
 Identities = 80/242 (33%), Positives = 124/242 (51%), Gaps = 14/242 (5%)

Query: 42  SPEDIRTGNLLSWPTVIDGIGWIKAWDVVGGYFWNSVKITVPAVLISTFIGAMNGYVLSM 101
           +P  + TGN   +  VI   G       +G  F N++ +T+PA +I   I A   Y L+ 
Sbjct: 152 APPRLTTGN---YARVITAEG-------IGRAFLNTMTVTIPATVIPILIAAFAAYALAW 201

Query: 102 WRFRGSQLFFGLLLFGCFLPFQTVLLPASFTLGKFGLANTTTGLVLVHVVYGLAFTTLFF 161
            RF G  L    ++    +P Q  L+P      + GL  +  G+ L H  +GL       
Sbjct: 202 MRFPGRALLVATIVGLLVVPLQLALIPLLKLHNQIGLNQSYLGIWLAHTGFGLPLAIYLL 261

Query: 162 RNYYVSIPDALVKAARLDGAGFFTIFLKILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFA 221
           RNY V +P  ++++AR+DGA  F IF +I+LP+S P +    I+QF  +WND L   VF 
Sbjct: 262 RNYMVGLPREIIESARVDGATEFQIFRRIVLPLSFPALASFAIFQFLWVWNDLLVATVFL 321

Query: 222 SG--DAQPITVALNNLVNTSTGAKEYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAV 279
               D Q +T AL  L+ +  G  ++ +  A+A ++    L+V+    KY +RGL +G+V
Sbjct: 322 GNATDTQVMTGALRALLGSRGG--DWEILAASAFVSIAVPLIVFFALQKYLVRGLLAGSV 379

Query: 280 KG 281
           KG
Sbjct: 380 KG 381


Lambda     K      H
   0.329    0.143    0.447 

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: 291
Number of extensions: 16
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: 281
Length of database: 382
Length adjustment: 28
Effective length of query: 253
Effective length of database: 354
Effective search space:    89562
Effective search space used:    89562
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