GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Acidovorax sp. GW101-3H11

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate Ac3H11_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4785
          Length = 334

 Score =  203 bits (517), Expect = 5e-57
 Identities = 126/357 (35%), Positives = 201/357 (56%), Gaps = 36/357 (10%)

Query: 1   MVRIIVKNVSKVFKKGKVV--ALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPS 58
           M  + ++N++K +  G      +  VN  +++GE   I+GPSG GK+T +R++AGL+  S
Sbjct: 1   MASLSLRNITKRYGHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEIS 60

Query: 59  TGELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIR 118
            GEL   DR+V       + P  R I MVFQ +ALYP++T FEN+A+ L   K+ K+EI+
Sbjct: 61  GGELRIGDRVVND-----LEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAKVPKDEIK 115

Query: 119 KRVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDS 178
            RV++ AKIL++ H+L   PRELSGGQ+QRVA+ RA+V+ P + L DEP SNLDA++R  
Sbjct: 116 ARVDKAAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQ 175

Query: 179 ARALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVA 238
            R  ++++   LG+T L V+HD  +   +A R+ V+  G + Q G PE++Y  P +  VA
Sbjct: 176 TRLEIQKLHRELGITSLFVTHDQVEAMTLAQRMIVMNAGNMEQFGTPEEVYHTPATTFVA 235

Query: 239 SLIGE--INELEGKVTNEGVVIGSLRFPVSVSSDRAIIGIRPEDVKLSKDVIKDDSWILV 296
           S IG   +N L+      G   G+            I+GIRPE +      ++ + W + 
Sbjct: 236 SFIGSPPMNLLKNA---PGAQPGT------------ILGIRPEHLD-----VRSEGWAVT 275

Query: 297 GKGKVKVIGYQGGLFRITITPLDSEEEIFTYSD--HPIHSGEEVLVYVRKDKIKVFE 351
            +  V+++G +    R+    ++ E+ I    +  H       + V  R D++  F+
Sbjct: 276 VE-TVELLGAE----RLIYGRINGEQVIVRVEEGTHSPEPDSVIHVQPRADRLHAFD 327


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: 298
Number of extensions: 18
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: 334
Length adjustment: 29
Effective length of query: 324
Effective length of database: 305
Effective search space:    98820
Effective search space used:    98820
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