GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Lactobacillus silagei IWT126

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_089136363.1 CES79_RS03835 methionine ABC transporter ATP-binding protein

Query= TCDB::Q97UF2
         (371 letters)



>NCBI__GCF_002217945.1:WP_089136363.1
          Length = 345

 Score =  170 bits (430), Expect = 6e-47
 Identities = 91/247 (36%), Positives = 147/247 (59%), Gaps = 2/247 (0%)

Query: 4   IRVENLSKIFKKGKT--EVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTS 61
           I  +++SK FK   T  EV AV +VSI++D G  FGV+G SG GK+T +R+I GLE PT 
Sbjct: 10  IEFKHVSKTFKGTATTKEVHAVHDVSISVDRGEIFGVIGYSGAGKSTLIRMINGLETPTE 69

Query: 62  GYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIEN 121
           G +  DN+ ++  ++  ++  +  I M+FQN+ L    T++ NI  PLKL K+PKD+I+ 
Sbjct: 70  GSVKVDNQDITQLKKEPLAQLRHKIGMIFQNYNLLKTATIYQNITIPLKLEKIPKDEIQQ 129

Query: 122 KVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESA 181
           + ++  + +GL    N YP +LSGGQ QR A+ARAL  +P +LL DE  S LD +   S 
Sbjct: 130 RAEKYLKIVGLWDRRNSYPSQLSGGQSQRVAVARALAHEPTILLSDEATSALDPETTSSI 189

Query: 182 RALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIAR 241
             L++ I ++  LT  I++H+   + +I +K  ++  G   + G   +++  P  ++  +
Sbjct: 190 LDLLKDINQKLGLTIFIITHELDVVKSICDKVAIMEAGNVVEQGRTIDVFTGPKQEVTRQ 249

Query: 242 LTGEINL 248
             G  +L
Sbjct: 250 FLGSNDL 256


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: 274
Number of extensions: 11
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: 371
Length of database: 345
Length adjustment: 29
Effective length of query: 342
Effective length of database: 316
Effective search space:   108072
Effective search space used:   108072
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 24 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