GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate 8502259 DvMF_2969 ABC transporter related (RefSeq)

Query= reanno::Dino:3607124
         (338 letters)



>FitnessBrowser__Miya:8502259
          Length = 418

 Score =  216 bits (549), Expect = 1e-60
 Identities = 120/292 (41%), Positives = 168/292 (57%), Gaps = 22/292 (7%)

Query: 2   AGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIE 61
           A + + ++ K +    A+ D++ ++E G F   +GPSGCGK+TLLR +AG E   SG I 
Sbjct: 27  ADLSVTRLVKRFEKFTAVNDVSFEVEQGRFFSILGPSGCGKTTLLRMIAGFESPDSGVIA 86

Query: 62  IGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVL 121
           I GRD+  + P  R + ++FQ  AL+P M+V EN+ FG+K  G        R+ +    +
Sbjct: 87  IRGRDMAGIAPNRRPVNLIFQHLALFPMMSVAENVAFGLKRRGMAGGEISRRVQDVLERV 146

Query: 122 QLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHK 181
            L  Y  + P QLSGGQ+QRVAI R +V  P+V L DEPL  LD KLR QM+VEL+ L  
Sbjct: 147 GLPGYGVKMPAQLSGGQKQRVAIARCLVLEPAVLLLDEPLGALDLKLREQMKVELKTLQA 206

Query: 182 QLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIG-----S 236
           ++G T +Y+THDQ EA+ M+D + V+N GR EQV +P +LY +P S FVA F+G     S
Sbjct: 207 EVGTTFVYITHDQSEALVMSDHVAVMNAGRFEQVDTPRNLYRRPASAFVAGFVGETNVWS 266

Query: 237 PAMNVFSSDVGLQDISLDASAAF---------------VGCRPEHIEIVPDG 273
             +   + D GL  +  D  A F               +  RPE + I PDG
Sbjct: 267 GTLEEATGDAGL--VRTDEGAVFRARVAAGLAKGTRVDMFIRPEAVLIDPDG 316


Lambda     K      H
   0.320    0.139    0.396 

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: 376
Number of extensions: 18
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: 338
Length of database: 418
Length adjustment: 30
Effective length of query: 308
Effective length of database: 388
Effective search space:   119504
Effective search space used:   119504
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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