GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araH in Caulobacter crescentus NA1000

Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP

Query= CharProtDB::CH_014278
         (328 letters)



>FitnessBrowser__Caulo:CCNA_00904
          Length = 332

 Score =  160 bits (406), Expect = 3e-44
 Identities = 95/303 (31%), Positives = 161/303 (53%), Gaps = 6/303 (1%)

Query: 29  VVFAVLFIAC-AIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVASVIAC 87
           ++F +L +A        F T  N   +   +S+ G++A GM F +  G  D++V S++A 
Sbjct: 29  ILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAF 88

Query: 88  AGVTTAVVINLT----ESLW-IGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQIV 142
           A +  A V+        + W I +    L+G+  G V G  +  L + A I TL  M + 
Sbjct: 89  ASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVW 148

Query: 143 RGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRNTLA 202
           RG   +++DG  +   ++++   G      LP P+ +         + L  T +GR   A
Sbjct: 149 RGATLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQVYA 208

Query: 203 IGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVISAC 262
           +GGN EAARL+GV V      ++ + G ++ ++G +L++R+ S + +   GYEL VI++ 
Sbjct: 209 VGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIASV 268

Query: 263 VLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIFDRYKQ 322
           V+GG SL GG G +   V G L++G + N + +L+++ + Q VV GLI++AAV FD Y +
Sbjct: 269 VIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFDHYAR 328

Query: 323 KAK 325
             K
Sbjct: 329 THK 331


Lambda     K      H
   0.327    0.141    0.414 

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: 327
Number of extensions: 22
Number of successful extensions: 1
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: 328
Length of database: 332
Length adjustment: 28
Effective length of query: 300
Effective length of database: 304
Effective search space:    91200
Effective search space used:    91200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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