GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Caulobacter crescentus NA1000

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA

Query= reanno::Smeli:SM_b21216
         (360 letters)



>FitnessBrowser__Caulo:CCNA_01670
          Length = 339

 Score =  216 bits (549), Expect = 9e-61
 Identities = 117/273 (42%), Positives = 165/273 (60%), Gaps = 8/273 (2%)

Query: 4   LEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIG 63
           + IR++ K++G    L  +D+ +  GE L LLG SG GK+TLL  IAGL  P  G +L  
Sbjct: 3   IAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFD 62

Query: 64  ERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRR----VPQAEHDKAVRDTAR 119
            + V       R +  VFQ YAL+ +++VA+NI FGL++R+      +AE  + V +  +
Sbjct: 63  GQDVTYASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEELLK 122

Query: 120 LLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRL 179
           L+++E L  R PSQLSGGQRQRVA+ RAL   P V L DEP   LDA +R  +R EL+R+
Sbjct: 123 LVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELRRV 182

Query: 180 HQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPM 239
           H     T ++VTHDQ EA+ LA R+A++ +GRIEQ+  PD+V+D P T +V GFVG    
Sbjct: 183 HDATGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCGFVGE--A 240

Query: 240 NILDAEMTANGLKIEGCEEVLPLPAAFNGAAWA 272
           N  D +++    K       +P  A  +GAA A
Sbjct: 241 NRFDGQVSGGRFKAGAL--TVPASALKDGAATA 271


Lambda     K      H
   0.320    0.136    0.385 

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: 331
Number of extensions: 15
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: 360
Length of database: 339
Length adjustment: 29
Effective length of query: 331
Effective length of database: 310
Effective search space:   102610
Effective search space used:   102610
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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