GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Rhodobacter johrii JA192

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_069333385.1 C8J29_RS07090 ABC transporter ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>NCBI__GCF_003046325.1:WP_069333385.1
          Length = 332

 Score =  213 bits (543), Expect = 4e-60
 Identities = 130/354 (36%), Positives = 204/354 (57%), Gaps = 33/354 (9%)

Query: 1   MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60
           M +I ++NV K F  G+ V + +++++IE+GE    +GPSG GK+T +R+IAGL+  S G
Sbjct: 1   MGKITLRNVQKRF--GEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDG 58

Query: 61  ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120
           ++  D R         +PP  R + MVFQ++ALYP++T  +NIAFPL   KM  +EI +R
Sbjct: 59  QIMIDGRDATE-----MPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERR 113

Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180
           V   AKIL++ + L+  P +LSGGQ+QRVA+ RA+V++P+  L DEP SNLDA +R + R
Sbjct: 114 VSNAAKILNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMR 173

Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240
             + E+   L  T++ V+HD  +   +AD++ VL  G++ QVG P  LY NP ++ VA  
Sbjct: 174 LEITELHQSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGF 233

Query: 241 IG--EINELEGKVTNEGVVIGSLRFPVSVSSDRAIIGIRPEDVKLSKDVIKDDSWILVGK 298
           IG  ++N +EG              P +       IGIRPE + LS++     +W    +
Sbjct: 234 IGSPKMNLIEG--------------PEAAKHGATTIGIRPEHIDLSRET---GAW----Q 272

Query: 299 GKVKVIGYQGG--LFRITITPLDSEEEIFTYSDHPIHSGEEVLVYVRKDKIKVF 350
           G+V V  + G      + +  + +   + T  +  +H G+ V +  + DKI  F
Sbjct: 273 GEVGVSEHLGSDTFLHVHVAGMPT-LTVRTGGEFGVHHGDRVWLTPQADKIHRF 325


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: 275
Number of extensions: 10
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: 332
Length adjustment: 29
Effective length of query: 324
Effective length of database: 303
Effective search space:    98172
Effective search space used:    98172
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