GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0211 in Caulobacter crescentus NA1000

Align Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate CCNA_00647 CCNA_00647 nitrate transport ATP-binding protein nrtD

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__Caulo:CCNA_00647
          Length = 261

 Score =  131 bits (329), Expect = 2e-35
 Identities = 78/211 (36%), Positives = 121/211 (57%), Gaps = 24/211 (11%)

Query: 23  NLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIGDRLVNDVPPKDRDIAMVFQ 82
           +L+ + GEFV  +G SGCGK+T L ++AGL  ++ G + +  + VN   P   D A+VFQ
Sbjct: 29  DLKIDKGEFVSIIGHSGCGKSTLLNVVAGLVPVTTGAVILDRQEVNAPGP---DRAVVFQ 85

Query: 83  NYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAAR----------ILKIEHLLNRKPR 132
           N++L P ++V EN++  +       D++   VK AA           ++K+ H L+++P 
Sbjct: 86  NHSLLPWLSVRENVSLAV-------DKVFGGVKSAAERKEWVLHNLELVKMTHALDKRPA 138

Query: 133 ELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRLGVTTIYVTH 192
           E+SGG +QRV + RA+  EPKV L+DEP   LDA  R  ++  + ++   L  T + +TH
Sbjct: 139 EISGGMKQRVGIARALSMEPKVLLLDEPFGALDALTRAHLQDSVMEIHSALKNTVLMITH 198

Query: 193 DQVEAMTLGHRIVVMKDGEI----QQVDTPL 219
           D  EA  L  RIV+M +G      Q +D PL
Sbjct: 199 DVDEATLLSDRIVMMTNGPRACVGQVLDVPL 229


Lambda     K      H
   0.320    0.139    0.400 

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: 204
Number of extensions: 11
Number of successful extensions: 3
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: 376
Length of database: 261
Length adjustment: 27
Effective length of query: 349
Effective length of database: 234
Effective search space:    81666
Effective search space used:    81666
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: 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