GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA2 in Caulobacter crescentus NA1000

Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein

Query= uniprot:P70970
         (276 letters)



>FitnessBrowser__Caulo:CCNA_02751
          Length = 332

 Score =  127 bits (319), Expect = 3e-34
 Identities = 77/215 (35%), Positives = 126/215 (58%), Gaps = 5/215 (2%)

Query: 9   ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISL-GSTVIQAGKKNKDL 67
           AL  ++ S+K G    VIG +G+GKSTL++ +NGL  P+ GQ+ + G  V   G     L
Sbjct: 18  ALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQVIVDGDDVAALGVAG--L 75

Query: 68  KKLRKKVGIVFQFPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSEELLD 127
           + LR++VG++FQ   + L  +TV ++++F     G    + + +  E+L+ VGLS     
Sbjct: 76  RALRRRVGMIFQH-FNLLSGKTVAQNVAFPLKLAGRPAAEVKARTAELLERVGLSAHA-G 133

Query: 128 RSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTTI 187
           + P +LSGGQ +RV IA  LA +P+VL+ DE T+ LDP   ++I+D+   L++   LT +
Sbjct: 134 KYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPETTEQILDLIAGLNRELGLTIV 193

Query: 188 LVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFL 222
           L+TH M+      D + V+  G +   G+  ++FL
Sbjct: 194 LITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEVFL 228


Lambda     K      H
   0.318    0.136    0.380 

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: 205
Number of extensions: 10
Number of successful extensions: 4
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: 276
Length of database: 332
Length adjustment: 27
Effective length of query: 249
Effective length of database: 305
Effective search space:    75945
Effective search space used:    75945
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: 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