GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Caulobacter crescentus NA1000

Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein

Query= TCDB::P31134
         (377 letters)



>FitnessBrowser__Caulo:CCNA_02751
          Length = 332

 Score =  171 bits (433), Expect = 3e-47
 Identities = 94/264 (35%), Positives = 157/264 (59%), Gaps = 19/264 (7%)

Query: 19  LLEIRNLTKSY--DGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQI 76
           ++  ++++K+Y   G  A+  VSL++  GE+F ++GASG GKSTL+R++ G E PSAGQ+
Sbjct: 1   MITFQDVSKTYAQGGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQV 60

Query: 77  MLDGVDLSQVP-----PYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVN 131
           ++DG D++ +         R + M+FQ + L    TV QN+AF LK    P AE+ +R  
Sbjct: 61  IVDGDDVAALGVAGLRALRRRVGMIFQHFNLLSGKTVAQNVAFPLKLAGRPAAEVKARTA 120

Query: 132 EMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLE 191
           E+L  V +   A + P QLSGGQ+QRV +AR+LA  PK+LL DE   ALD +  +++   
Sbjct: 121 ELLERVGLSAHAGKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPETTEQILDL 180

Query: 192 VVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIG 251
           +  +   +G+T V++TH+ +    +  R+A+++ G+ V+ G  EE++ HP +  +  F+ 
Sbjct: 181 IAGLNRELGLTIVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEVFLHPASDTARRFV- 239

Query: 252 SVNVFEGVLKERQEDGLVLDSPGL 275
                      R+ +G V  +PG+
Sbjct: 240 -----------REAEGDVTAAPGV 252


Lambda     K      H
   0.321    0.137    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: 314
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: 377
Length of database: 332
Length adjustment: 29
Effective length of query: 348
Effective length of database: 303
Effective search space:   105444
Effective search space used:   105444
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