GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Phaeobacter inhibens BS107

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate GFF776 PGA1_c07900 alpha-glucoside transport ATP-binding protein AglK

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__Phaeo:GFF776
          Length = 363

 Score =  194 bits (493), Expect = 3e-54
 Identities = 118/334 (35%), Positives = 191/334 (57%), Gaps = 33/334 (9%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           M  +++ N++K +  G   V+ + ++++ I  G     +GPSG GK+T LR+IAGLE  +
Sbjct: 1   MANLKLTNVAKTYGGG---VEVLRDINLDIKQGELIVFVGPSGCGKSTLLRMIAGLERIS 57

Query: 61  SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
            G +  DN  ++      + P +RGIAMVFQ++ALYP+MTV DN+AF LK+AK  KD+I+
Sbjct: 58  GGTLEIDNAVMND-----IPPAQRGIAMVFQSYALYPHMTVRDNMAFALKIAKKSKDEID 112

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
             +   ++ L L   L+R PK LSGGQ QR AI R++V+DPKV L DEP SNLDA +R +
Sbjct: 113 AAIDRAAKILQLEPYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVA 172

Query: 181 ARALVRKIQRERKLTTLI-VSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLI 239
            R  + +++     +T+I V+HD  +   +A++  V+ +   AQ+GTP ++Y+ P  + +
Sbjct: 173 TRIEIAQLKEAMPDSTMIYVTHDQVEAMTLASRIVVLADKGIAQVGTPLDLYQRPENEFV 232

Query: 240 ARLTGE--INLIQAKII-----------ENNAIIANLKVPLNNMELKGQSNIVIGLRPDD 286
           A+  G   +NLI   ++               ++A +     +  L     + +G+RP+D
Sbjct: 233 AQFIGSPAMNLIPGTVVATGPRTTVRLTSGEEVVAEIPTTDADQGLA----VNVGVRPED 288

Query: 287 LTLSDT---LLDKYID----MGIVKVKLVSYGAG 313
           L    T   L+D  +D    +G V V  ++ G G
Sbjct: 289 LVEEGTGGALIDSRVDIVEALGEVTVLYIAAGEG 322


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: 303
Number of extensions: 15
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: 363
Length adjustment: 30
Effective length of query: 341
Effective length of database: 333
Effective search space:   113553
Effective search space used:   113553
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