GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c12640 in Caulobacter crescentus NA1000

Align D-lactate transporter, ATP-binding component (characterized)
to candidate CCNA_03714 CCNA_03714 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF1248
         (251 letters)



>FitnessBrowser__Caulo:CCNA_03714
          Length = 252

 Score =  130 bits (327), Expect = 3e-35
 Identities = 81/250 (32%), Positives = 130/250 (52%), Gaps = 19/250 (7%)

Query: 4   LEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMFD 63
           L V +VGK FG    + +V+L ++   V  ++GPNGAGK+T    + G +  D G++  D
Sbjct: 11  LFVDSVGKSFGDRPVVKNVSLRLKRGEVAGLLGPNGAGKTTCFYMVTGLIAADYGAIYLD 70

Query: 64  GKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQR 123
           G+++  +  ++  ++G+  + Q   IF  ++V +N+M           EM         R
Sbjct: 71  GENITAQPMFQRARLGVGYLPQEASIFRGMTVEQNVM--------AVVEMRE----RDPR 118

Query: 124 DILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAG---MA 180
              E+   +LEE+ +   R   A ++S G++RR+EI   L+ EP  +LLDEP AG   +A
Sbjct: 119 KAREQVTSILEELRITHIRKSPAVALSGGERRRVEIARALASEPSFMLLDEPFAGIDPLA 178

Query: 181 RADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKGNP 240
            AD    I  LK     R I I I +H++     + DR +++  G  L E  P+ I  NP
Sbjct: 179 IADIREVIGYLK----GRGIGILITDHNVRETLDIIDRASIIHAGEVLFEGSPREIVENP 234

Query: 241 KVREAYLGES 250
           +V+  YLGES
Sbjct: 235 EVKRVYLGES 244


Lambda     K      H
   0.318    0.135    0.379 

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: 171
Number of extensions: 9
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: 251
Length of database: 252
Length adjustment: 24
Effective length of query: 227
Effective length of database: 228
Effective search space:    51756
Effective search space used:    51756
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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