GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Caulobacter crescentus NA1000

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Caulo:CCNA_01670
          Length = 339

 Score =  208 bits (529), Expect = 2e-58
 Identities = 123/321 (38%), Positives = 185/321 (57%), Gaps = 21/321 (6%)

Query: 4   IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63
           I +++V K F  G+  AL+ V++ I +GE   +LGPSG+GKTT +R IAGL+ P  G++ 
Sbjct: 3   IAIRSVEKQF--GRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVL 60

Query: 64  FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLT----NMKMSKEEIRK 119
           FD + V            R++G VFQ +AL+ ++T  +NIAF L       K SK EI +
Sbjct: 61  FDGQDVT-----YASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIAR 115

Query: 120 RVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSA 179
           RVEE+ K++++  +   +P +LSGGQ+QRVAL+RAL   PS+LLLDEPF  LDA +R S 
Sbjct: 116 RVEELLKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSL 175

Query: 180 RALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVAS 239
           R  ++ V    GVT + V+HD  +   +ADRV +L  G++ Q+G P+ ++D P +  V  
Sbjct: 176 RRELRRVHDATGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCG 235

Query: 240 LIGEINELEGKVTNEGVVIGSLRFPVSVSSDRAIIG-IRPEDVKLSKDVIKDDSWILVGK 298
            +GE N  +G+V+      G+L  P S   D A    +RP D  L +   +    +L+ +
Sbjct: 236 FVGEANRFDGQVSGGRFKAGALTVPASALKDGAATAYVRPHDFALDEAGFE----VLIER 291

Query: 299 GKVKVIGYQGGLFRITITPLD 319
            +V     QG L  +T    D
Sbjct: 292 AQV-----QGALTAVTALTSD 307


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: 272
Number of extensions: 12
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: 339
Length adjustment: 29
Effective length of query: 324
Effective length of database: 310
Effective search space:   100440
Effective search space used:   100440
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