GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Caulobacter crescentus NA1000

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate CCNA_03714 CCNA_03714 ABC transporter ATP-binding protein

Query= TCDB::Q8DQH7
         (236 letters)



>FitnessBrowser__Caulo:CCNA_03714
          Length = 252

 Score =  130 bits (328), Expect = 2e-35
 Identities = 75/237 (31%), Positives = 130/237 (54%), Gaps = 4/237 (1%)

Query: 1   MSVLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKI 60
           M  L V+++   +G    V++VS  +  GEV  L+G NGAGKTT    ++GL+    G I
Sbjct: 8   MDGLFVDSVGKSFGDRPVVKNVSLRLKRGEVAGLLGPNGAGKTTCFYMVTGLIAADYGAI 67

Query: 61  EFLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVF 120
              G+ I   P  +    G+  +P+   +F G+TV +N+ M     + R+  +A  ++V 
Sbjct: 68  YLDGENITAQPMFQRARLGVGYLPQEASIFRGMTVEQNV-MAVVEMRERDPRKAR-EQVT 125

Query: 121 SRFP--RLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDI 178
           S     R+   +   A  LSGGE++ + + RAL S P  +LLDEP  G+ P+ I +I ++
Sbjct: 126 SILEELRITHIRKSPAVALSGGERRRVEIARALASEPSFMLLDEPFAGIDPLAIADIREV 185

Query: 179 IQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235
           I  ++ +G  +L+ + N  + L I DR  ++  G+++  G+ +E+  + EV++ YLG
Sbjct: 186 IGYLKGRGIGILITDHNVRETLDIIDRASIIHAGEVLFEGSPREIVENPEVKRVYLG 242


Lambda     K      H
   0.315    0.134    0.358 

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: 132
Number of extensions: 6
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: 236
Length of database: 252
Length adjustment: 24
Effective length of query: 212
Effective length of database: 228
Effective search space:    48336
Effective search space used:    48336
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: 42 (22.0 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