GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Synechococcus elongatus PCC 7942

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate Synpcc7942_0947 Synpcc7942_0947 ATPase

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__SynE:Synpcc7942_0947
          Length = 355

 Score =  188 bits (477), Expect = 2e-52
 Identities = 105/336 (31%), Positives = 194/336 (57%), Gaps = 9/336 (2%)

Query: 9   LSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGYIYFDN 68
           L ++ K     V  V N+S+ +  G    +LGPSG GK+T LRLIAGL++PTSG I+  +
Sbjct: 8   LRQLRKAYSPSVVPVANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTSGSIWLGD 67

Query: 69  EAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKVKEVSE 128
             +++     + P  R +AMVFQ++ALYP++ V  N+   L++ +    +IE ++++V+ 
Sbjct: 68  REITT-----LPPGDRDMAMVFQSYALYPHLNVRQNLTLGLQIRRTSAAEIEQRLQQVAH 122

Query: 129 ELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARALVRKI 188
            L L  +L+R P +LSGGQ QR A+ RALV+ P V LLDEP SNLDA +RE  RA ++ +
Sbjct: 123 NLELDHLLDRRPAQLSGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMKAL 182

Query: 189 QRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLTG--EI 246
             ++    + V+HD  +  +++++  ++  G   Q+ +P  IY+ PA   +A   G   +
Sbjct: 183 FSQQASPVVYVTHDQTEALSLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFIGSPRM 242

Query: 247 NLIQAKIIENNAIIANLKVPLNNMELKGQSNIVIGLRPDDLTLSDTLLDKYIDMGIVKVK 306
           NL+   I    A + +  +P+ +  L  +S ++ GLRP+ L L+   +++ I + +   +
Sbjct: 243 NLLPLPIHSGQAWLGSRALPIPS-HLAARSQVLWGLRPEHLKLATPEVERAIPVQLHLTE 301

Query: 307 LVSYGAGIFKIVVSPITDENIDIIVDAEEPLETGIE 342
            +     +  + ++   +  + +++ +++P+ T ++
Sbjct: 302 NLGM-QRLLTVAIAANPEVRLRLLMPSDQPIPTDLQ 336


Lambda     K      H
   0.317    0.136    0.374 

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: 248
Number of extensions: 11
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: 371
Length of database: 355
Length adjustment: 29
Effective length of query: 342
Effective length of database: 326
Effective search space:   111492
Effective search space used:   111492
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 (21.6 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