GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Brucella inopinata BO1

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_008510304.1 BIBO1_RS16955 ABC transporter ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>NCBI__GCF_000182725.1:WP_008510304.1
          Length = 353

 Score =  206 bits (523), Expect = 1e-57
 Identities = 116/288 (40%), Positives = 177/288 (61%), Gaps = 15/288 (5%)

Query: 4   IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63
           +  +NV+K F  G   AL N+++ +E G    +LGPSG GKTT +R++AGL+ P++G + 
Sbjct: 9   VTFENVTKKF--GNFTALPNLSLTVEPGTLVTLLGPSGCGKTTTLRLLAGLEHPTSGRIL 66

Query: 64  FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEE 123
              + V +     +P  +R + MVFQ++AL+P++T+ EN+A+ L +    K E R+R EE
Sbjct: 67  IGGKDVTN-----LPANERDVSMVFQSYALFPHMTSLENVAYGLESSGFKKNEARERAEE 121

Query: 124 VAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALV 183
             K++ +  + +  P ELSGGQQQRVA+ARALV +P +LLLDEP SNLDAR+R   R  +
Sbjct: 122 GLKLVGLGGMGHRLPAELSGGQQQRVAVARALVLEPQVLLLDEPLSNLDARLRRRVRTEI 181

Query: 184 KEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGE 243
           +E+Q RLG T + V+HD  +  A++D + V+ +G + Q G P DLY+ P S  +A  +GE
Sbjct: 182 RELQQRLGFTAVYVTHDQDEALAVSDTIIVMKEGGIAQKGSPRDLYETPASAFIADFMGE 241

Query: 244 INELEGKVTN----EGVV-IGSLRFPVSVSSDR---AIIGIRPEDVKL 283
            N +  +V +    E V+ +  L   V   + R   A + IRP  V L
Sbjct: 242 ANVVPCEVISAEDGEAVIRVAGLTHRVPARNARPGPAQLAIRPNAVTL 289


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: 285
Number of extensions: 10
Number of successful extensions: 2
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: 353
Length adjustment: 29
Effective length of query: 324
Effective length of database: 324
Effective search space:   104976
Effective search space used:   104976
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 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