GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Shewanella sp. ANA-3

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate 7023042 Shewana3_0280 ABC transporter related (RefSeq)

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



>FitnessBrowser__ANA3:7023042
          Length = 367

 Score =  145 bits (367), Expect = 1e-39
 Identities = 90/235 (38%), Positives = 135/235 (57%), Gaps = 16/235 (6%)

Query: 29  GEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIGG------RDVTTVEPADRDLAMVFQ 82
           GE +  VGPSG GK+TLLR +AGL    +G I  G       +  T + P  R +  + Q
Sbjct: 29  GEVLAVVGPSGGGKTTLLRMIAGLNHPDAGSIVFGETLWFDHQSRTALTPQQRHIGYMPQ 88

Query: 83  SYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQ---LEDYLDRKPGQLSGGQR 139
            + L+P++T  EN+     V G +   + ERIA A   L+   L    DR P  LSGGQR
Sbjct: 89  HFGLFPNLTALENV-----VAGLDHIPKSERIARAKDWLERVNLHGLPDRLPMHLSGGQR 143

Query: 140 QRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQLGATMIYVTHDQVEAMT 199
           QRVA+ RA+ + PSV L DEP S +D + R ++ +EL  L +QL   +I VTHD  EA+ 
Sbjct: 144 QRVALARALAREPSVLLLDEPFSAVDRETRERLYLELARLKEQLLCPVIMVTHDLNEALL 203

Query: 200 MADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMNVFSSDVGLQDISLD 254
           +AD ++++++G++ Q G+P ++  +P +  VA  +G    N+F  +V  QD + D
Sbjct: 204 LADSMILISQGQMLQQGAPFEVLSRPRNEAVARQMG--LRNIFDGEVVFQDRTKD 256


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: 264
Number of extensions: 7
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: 338
Length of database: 367
Length adjustment: 29
Effective length of query: 309
Effective length of database: 338
Effective search space:   104442
Effective search space used:   104442
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: 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