GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Caulobacter crescentus NA1000

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc02869
         (352 letters)



>FitnessBrowser__Caulo:CCNA_02751
          Length = 332

 Score =  150 bits (378), Expect = 6e-41
 Identities = 88/242 (36%), Positives = 131/242 (54%), Gaps = 5/242 (2%)

Query: 28  AFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQIDGVEVGHVA 87
           A G H  L G+ L VK GE    +G SG GKSTL+R I GLE  ++G V +DG +V  + 
Sbjct: 12  AQGGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQVIVDGDDVAALG 71

Query: 88  PA-----KRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGMLSLEPY 142
            A     +R + M+FQ + L    TV  N+   LK AG P AE++ + A+    + L  +
Sbjct: 72  VAGLRALRRRVGMIFQHFNLLSGKTVAQNVAFPLKLAGRPAAEVKARTAELLERVGLSAH 131

Query: 143 LARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLHRSLKAT 202
             + PA+LSGGQ+QRV I RA+   PK+ L DE  S LD          IA L+R L  T
Sbjct: 132 AGKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPETTEQILDLIAGLNRELGLT 191

Query: 203 MIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMNFIEAAK 262
           ++ +TH+      + D++ VL+AGR+ + G+  E++  PA+     F+   + +   A  
Sbjct: 192 IVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEVFLHPASDTARRFVREAEGDVTAAPG 251

Query: 263 LG 264
           +G
Sbjct: 252 VG 253


Lambda     K      H
   0.320    0.137    0.393 

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: 296
Number of extensions: 10
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: 352
Length of database: 332
Length adjustment: 29
Effective length of query: 323
Effective length of database: 303
Effective search space:    97869
Effective search space used:    97869
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