GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araH in Echinicola vietnamensis KMM 6221, DSM 17526

Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components

Query= CharProtDB::CH_014278
         (328 letters)



>FitnessBrowser__Cola:Echvi_1280
          Length = 318

 Score =  194 bits (494), Expect = 2e-54
 Identities = 110/311 (35%), Positives = 170/311 (54%), Gaps = 11/311 (3%)

Query: 24  QYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVAS 83
           ++  L+   +L +  ++    F T  N   +   +S++  ++ GM   + +   DLSV S
Sbjct: 6   KFQSLIALIILCLVLSLLSDRFLTLANGWNVMRQVSVNICISVGMTLVILTAGIDLSVGS 65

Query: 84  VIACAGVTTAVVIN---LTESLWI--------GVAAGLLLGVLCGLVNGFVIAKLKINAL 132
           ++A  G  TA +I      E L +         V  G+ LG   G  NG+ I + K+   
Sbjct: 66  ILALCGAVTASLIKNGIAVEGLNLHIGFAPLGAVILGVGLGFGLGWFNGWTITRFKVPPF 125

Query: 133 ITTLATMQIVRGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLN 192
           + TLA + I RGL  + + G  +    E F  LG   + G+P P+W+T   + +  LL  
Sbjct: 126 VATLAMLTIARGLTMLWTGGFPINGLGEDFAFLGTGWFLGIPMPVWITAVIVALAVLLTK 185

Query: 193 KTTFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSI 252
           KT FGR   AIGGNE AARL+G+ + R K+ ++ ++G ++A+ G+I+ SR+ S QP   I
Sbjct: 186 KTKFGRYVYAIGGNERAARLSGINISRVKMTVYAIAGGLAAVGGMIVTSRLDSAQPNAGI 245

Query: 253 GYELIVISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILL 312
            YEL  I+A V+GG SL GG G I   V G +I+G + N + LLN+SPF Q VV+G ++L
Sbjct: 246 SYELDAIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNGLVLLNVSPFWQQVVKGAVIL 305

Query: 313 AAVIFDRYKQK 323
            AV+ D+   K
Sbjct: 306 LAVVIDKANSK 316


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: 323
Number of extensions: 20
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: 318
Length adjustment: 28
Effective length of query: 300
Effective length of database: 290
Effective search space:    87000
Effective search space used:    87000
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: 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