GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Shewanella oneidensis MR-1

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 203725 SO4655 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__MR1:203725
          Length = 354

 Score =  192 bits (489), Expect = 9e-54
 Identities = 106/290 (36%), Positives = 173/290 (59%), Gaps = 19/290 (6%)

Query: 4   IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63
           I ++ V+K F  G  VA+D+VN+ I+ GE   +LGPSG+GKTT +RIIAGL+   +G   
Sbjct: 3   IHIQQVNKHF--GNFVAVDSVNLEIKTGELTALLGPSGSGKTTLLRIIAGLEQADSG--- 57

Query: 64  FDDRLVASNGKLIVPPE--DRKIGMVFQTWALYPNLTAFENIAFPLT----NMKMSKEEI 117
               +V  NG+ I      +R +G VFQ +AL+ ++T FEN+A+ LT      + SK EI
Sbjct: 58  ----IVKFNGEDITTQHVSERGVGFVFQHYALFKHMTVFENVAYGLTVRPRKTRPSKAEI 113

Query: 118 RKRVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRD 177
            ++V  + K++ +    + +P +LSGGQ+QR+ALARAL  +P +LLLDEPF  LDA++R 
Sbjct: 114 AEKVHSLLKLVQLDWTADRYPSQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRA 173

Query: 178 SARALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQV 237
             R  ++ +   + VT + V+HD  +   +AD++ V+ KG++ Q G PE++YD P +  V
Sbjct: 174 ELRRWLRRLHDEINVTTVFVTHDQEEALEVADKIVVMNKGRIEQQGTPEEVYDTPSNPFV 233

Query: 238 ASLIGEINELEGKVTNEGVVIGSLRFP----VSVSSDRAIIGIRPEDVKL 283
              +G +N    +V +    IG++  P          + +  +RP ++++
Sbjct: 234 YEFLGNVNLFHARVKHGHSTIGNIHIPSPEHAGGEEQQGLAYVRPHEIEV 283


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: 325
Number of extensions: 13
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: 354
Length adjustment: 29
Effective length of query: 324
Effective length of database: 325
Effective search space:   105300
Effective search space used:   105300
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