GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Klebsiella michiganensis M5al

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate BWI76_RS03270 BWI76_RS03270 sugar ABC transporter ATP-binding protein CymD

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__Koxy:BWI76_RS03270
          Length = 376

 Score =  206 bits (525), Expect = 6e-58
 Identities = 119/300 (39%), Positives = 179/300 (59%), Gaps = 22/300 (7%)

Query: 8   NLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGYIYFD 67
           +L KI K+ +   KAV  + + I  G     +GPSG  K+T LR+IAGLE+ + G IY  
Sbjct: 5   SLRKIEKRYENGFKAVHGIDLEIHDGEFMVFVGPSGCAKSTTLRMIAGLEDISGGEIYIG 64

Query: 68  NEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKVKEVS 127
           N  V+      + P+ RGIAMVFQN+ALYP+ TVFDN+AF LK+ K PKD+I+ +V++ +
Sbjct: 65  NRKVND-----LPPKDRGIAMVFQNYALYPHKTVFDNMAFGLKMQKRPKDEIKRRVEDAA 119

Query: 128 EELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARALVRK 187
           E+L ++ +L R PKE+SGGQ QR A+ RA+V+ P V L DEP SNLDA++R S R  + +
Sbjct: 120 EKLEITELLYRKPKEMSGGQRQRVAVGRAIVRKPDVFLFDEPLSNLDAKLRVSMRMKIAQ 179

Query: 188 IQRERK-----LTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARL 242
           + R  K      T + V+HD  +   + ++  V+ +G   Q+ TPT++Y YP    +A  
Sbjct: 180 LHRSLKEEGHPATMIYVTHDQTEALTLGDRICVLNHGNIMQVDTPTDLYNYPNNKFVASF 239

Query: 243 TG--EINLIQAKIIENNAII-------ANLKVP-LNNMELKGQSN--IVIGLRPDDLTLS 290
            G   INLI   I +NN  +         + +P    + L+G  N  +  G+RP+ ++L+
Sbjct: 240 IGSPSINLIDTAIRKNNERLYVEIAPGVEILIPHSKQVLLEGYINKPVCFGIRPEHISLA 299


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: 319
Number of extensions: 16
Number of successful extensions: 3
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: 376
Length adjustment: 30
Effective length of query: 341
Effective length of database: 346
Effective search space:   117986
Effective search space used:   117986
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: 50 (23.9 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