GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Caulobacter crescentus NA1000

Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP

Query= uniprot:A0A0C4Y7K0
         (337 letters)



>FitnessBrowser__Caulo:CCNA_00904
          Length = 332

 Score =  219 bits (559), Expect = 6e-62
 Identities = 130/302 (43%), Positives = 181/302 (59%), Gaps = 6/302 (1%)

Query: 39  LVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSILSISAV 98
           L+LL   F    E F   +N   I  + SI  ++A GMTFVIL GGID++VGS+L+ +++
Sbjct: 32  LLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAFASI 91

Query: 99  VAMLVSLM-----PQLGMLSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVRGL 153
            A  V        P   ++++  + L GL  G V G  V ++ +P FIVTLG +T  RG 
Sbjct: 92  AAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGA 151

Query: 154 ARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGG 213
             L+ +   I   +  + + G+GE+L +P  V+I   V A     LR T  G Q+YAVGG
Sbjct: 152 TLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQVYAVGG 211

Query: 214 NAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVIL 273
           NAEAARLSG+ V  +   VYA+ G LAGL G + SARL +A  +  G  YEL  IA+V++
Sbjct: 212 NAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAV-AGTGYELRVIASVVI 270

Query: 274 GGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDSYRRKG 333
           GG S  GG+G + GT++GAL+I VLSNGLV+L V+   Q ++ GL+I+ AVA D Y R  
Sbjct: 271 GGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFDHYARTH 330

Query: 334 SA 335
            A
Sbjct: 331 KA 332


Lambda     K      H
   0.325    0.141    0.409 

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: 384
Number of extensions: 24
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: 337
Length of database: 332
Length adjustment: 28
Effective length of query: 309
Effective length of database: 304
Effective search space:    93936
Effective search space used:    93936
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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