GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Dyella japonica UNC79MFTsu3.2

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4212
          Length = 364

 Score =  197 bits (501), Expect = 4e-55
 Identities = 116/301 (38%), Positives = 174/301 (57%), Gaps = 21/301 (6%)

Query: 1   MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60
           M ++ +  + KV+  G V  +   +  I +GE   ++GPSG GKTT +R+IAGL+  S G
Sbjct: 1   MAKVRLDKLRKVYPNGHV-GVAEASFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGG 59

Query: 61  ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120
            L   +R+V       + P+DR I MVFQ +ALYP++T  EN+ F L      K EI +R
Sbjct: 60  TLSIGERVVND-----IAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERR 114

Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180
           V E A++L++   L+  P  LSGGQ+QRVAL RALV+DP + LLDEP SNLDA++R S R
Sbjct: 115 VAEAARMLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMR 174

Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240
             +  +  RL  T++ V+HD  +   +  R+ VL  G + Q+  P +LYD P ++ VA  
Sbjct: 175 VEIARIHQRLKATMVYVTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGF 234

Query: 241 IGE--INELEGKVTNEG----------VVIGSLRFPVSVSSDR---AIIGIRPEDVKLSK 285
           +G   +N L G +  +G          +V+G L    ++ + R    ++G+RPED+ L  
Sbjct: 235 LGSPAMNLLRGILYRDGGWKLAMPQGELVLGELPQGAALEAWRDRDIVVGLRPEDLLLCA 294

Query: 286 D 286
           D
Sbjct: 295 D 295


Lambda     K      H
   0.319    0.139    0.390 

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: 305
Number of extensions: 11
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: 353
Length of database: 364
Length adjustment: 29
Effective length of query: 324
Effective length of database: 335
Effective search space:   108540
Effective search space used:   108540
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 (21.7 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