GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Caulobacter crescentus NA1000

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>FitnessBrowser__Caulo:CCNA_02751
          Length = 332

 Score =  138 bits (347), Expect = 3e-37
 Identities = 79/238 (33%), Positives = 129/238 (54%), Gaps = 5/238 (2%)

Query: 4   LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63
           +  ++V+KTY  G    L  + L +  GE   ++G SG GKSTL+  I GLET S G ++
Sbjct: 2   ITFQDVSKTYAQGGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQVI 61

Query: 64  VDDADIS-----GMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVAR 118
           VD  D++     G+    R + M+FQ + L    +V  N+AF LK+   P AE+    A 
Sbjct: 62  VDGDDVAALGVAGLRALRRRVGMIFQHFNLLSGKTVAQNVAFPLKLAGRPAAEVKARTAE 121

Query: 119 VSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEM 178
           + + + +     + P QLSGGQ+QRV + RALA  PK+ L DE  S LD +   ++   +
Sbjct: 122 LLERVGLSAHAGKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPETTEQILDLI 181

Query: 179 KLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFI 236
             +++ L  T V +TH+      + D+VAV+  G + + G  ++++ +PA+     F+
Sbjct: 182 AGLNRELGLTIVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEVFLHPASDTARRFV 239


Lambda     K      H
   0.319    0.138    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: 318
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: 386
Length of database: 332
Length adjustment: 29
Effective length of query: 357
Effective length of database: 303
Effective search space:   108171
Effective search space used:   108171
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: 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