GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04258 in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for D-Cellobiose and D-Salicin, permease component 2 (characterized)
to candidate H281DRAFT_01453 H281DRAFT_01453 carbohydrate ABC transporter membrane protein 1, CUT1 family

Query= reanno::Smeli:SMc04258
         (302 letters)



>FitnessBrowser__Burk376:H281DRAFT_01453
          Length = 319

 Score =  279 bits (714), Expect = 5e-80
 Identities = 129/276 (46%), Positives = 187/276 (67%)

Query: 17  NLNAKIASIPMILTAMVIFVGGTAWTVVYSFTNSKLLPRLAFVGFDQYERLWAAPRWLVS 76
           ++ A +A +PMILT +  ++G   WT   S +NS+  P   F G  QY RL+   RWL+S
Sbjct: 33  SIAAWLALLPMILTVVFAYLGTMVWTARVSLSNSRTFPSGDFAGLTQYVRLFNNARWLLS 92

Query: 77  IQNLAVFGCLSLVFSLVIGFVLAALMDQKIRFENTFRTIMLYPFALSFIVTGLVWQWLLN 136
           +QN+ ++G   +V  +VIG +LA  +DQ++  E   RT+ LYP+A+SF+ TGLVWQW+LN
Sbjct: 93  LQNIVIYGACFIVACMVIGLLLAIFIDQRVVAEGALRTVFLYPYAMSFVATGLVWQWILN 152

Query: 137 PQYGIQSIVRSLGWTSFSFDPLYNSNIVIYGILIAALWQGTGLVMCLMLAGLRGIDEDIW 196
           P+ G Q+++  LG+    FD + + +  IY I+IA +WQ +GLVM L+LAGLRGID+++W
Sbjct: 153 PELGAQAVLHKLGFVHARFDWIVDQDWAIYTIVIATVWQASGLVMALLLAGLRGIDDELW 212

Query: 197 KAARVDGIPMWKTYVLIIIPMMRGVFITTLVIIASGIVKVYDLVVAQTSGGPGIASEVPA 256
           KAAR+DGIP W+ Y  I++PM+     T  V++   +VK+YD VVA T GGPG ASEVPA
Sbjct: 213 KAARIDGIPRWRVYASIVVPMLGPSISTAFVLLFVMVVKLYDAVVAMTQGGPGTASEVPA 272

Query: 257 KYVYDYMFQAQNLGQGFAASTMMLVTVAIIIVPWAY 292
           K++ DY+F   N+G   AAS ++L TV  I+ P+ Y
Sbjct: 273 KFIMDYLFGRANIGLASAASIVLLATVLAILTPFFY 308


Lambda     K      H
   0.329    0.142    0.449 

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: 355
Number of extensions: 15
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: 302
Length of database: 319
Length adjustment: 27
Effective length of query: 275
Effective length of database: 292
Effective search space:    80300
Effective search space used:    80300
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 17 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