GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Dinoroseobacter shibae DFL-12

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 3608008 Dshi_1416 ABC transporter related (RefSeq)

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Dino:3608008
          Length = 347

 Score =  211 bits (537), Expect = 2e-59
 Identities = 124/312 (39%), Positives = 189/312 (60%), Gaps = 22/312 (7%)

Query: 1   MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60
           M  I + +V K  + G  V +++ ++ I + E   +LGPSG GKTT MR+IAGL+ PS+G
Sbjct: 1   MAEIRLNHVQK--RWGSFVGVEDFHLTIPDREFLVLLGPSGCGKTTTMRMIAGLEEPSSG 58

Query: 61  ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120
           E++  DR+V +     + P+DR + MVFQ++ LYPN+  +ENI FPL   K+ + E   R
Sbjct: 59  EIWIGDRMVNA-----LDPKDRDVAMVFQSYGLYPNMNVYENIRFPLKVRKVPEVEHEAR 113

Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180
           V   + ++++   L+  P  LSGGQ+QRVALARA+V++P++ L+DEP SNLDA++R S R
Sbjct: 114 VMRASAMVELDDFLHRKPAALSGGQRQRVALARAIVREPNVFLMDEPLSNLDAKLRVSTR 173

Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240
           A +K +   L VT + V+HD  +   +ADRV V+  G + QVG P ++YD P +  VAS 
Sbjct: 174 AQIKNLSHELQVTTIYVTHDQIEAMTLADRVVVMSAGVVQQVGTPMEIYDRPANTFVASF 233

Query: 241 IGE--INELEGKVTN-----EGVVIGSLRFPVSVSSDRAIIGIRPEDVKLSKDVIKDDSW 293
           IG   +N +EG VT+     + V I  L    S ++ R  +G R ED +    V+  D  
Sbjct: 234 IGSPAMNLMEGAVTDGTFHGDRVAIAGL----SGAAGRVTLGFRAEDAQ----VVDSDGQ 285

Query: 294 ILVGKGKVKVIG 305
           I      ++++G
Sbjct: 286 IAAPVYSMELLG 297


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: 266
Number of extensions: 15
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: 347
Length adjustment: 29
Effective length of query: 324
Effective length of database: 318
Effective search space:   103032
Effective search space used:   103032
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