GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24015 in Caulobacter crescentus NA1000

Align ABC transporter related (characterized, see rationale)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA

Query= uniprot:B2TBJ9
         (263 letters)



>FitnessBrowser__Caulo:CCNA_01670
          Length = 339

 Score =  145 bits (366), Expect = 1e-39
 Identities = 86/239 (35%), Positives = 133/239 (55%), Gaps = 19/239 (7%)

Query: 7   VALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVS 66
           + ++++++ K FG +  L  + L+   G+++++LG SGSGK+T LR +  LE PD G V 
Sbjct: 1   MTIAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVL 60

Query: 67  LAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEG---PMRV 123
             G+++                       ++G VFQ + L+ HMTV +N+  G       
Sbjct: 61  FDGQDVTY---------------ASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGK 105

Query: 124 QKRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTS 183
            K S+AE     E LL  V L    G YP+ LSGGQ+QRVA++RALA+ P V+L DEP  
Sbjct: 106 DKPSKAEIARRVEELLKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFG 165

Query: 184 ALDPELVGEVLRVMRSLAE-EGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEV 241
           ALD  +   + R +R + +  G T + VTH+   A  +++RV  L+ G++E  GTPD+V
Sbjct: 166 ALDATVRKSLRRELRRVHDATGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQV 224


Lambda     K      H
   0.318    0.133    0.377 

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: 200
Number of extensions: 9
Number of successful extensions: 4
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: 263
Length of database: 339
Length adjustment: 27
Effective length of query: 236
Effective length of database: 312
Effective search space:    73632
Effective search space used:    73632
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 (21.7 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