GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Marinobacter adhaerens HP15

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Marino:GFF3011
          Length = 372

 Score =  201 bits (511), Expect = 3e-56
 Identities = 126/367 (34%), Positives = 200/367 (54%), Gaps = 21/367 (5%)

Query: 1   MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60
           M ++ ++++ K +       L  ++I+I +GE   ++GPSG GK+T M  IAGL+  + G
Sbjct: 1   MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60

Query: 61  ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120
            +  D + +++     + P+DR I MVFQ++ALYP ++  ENIAF L    + K EI + 
Sbjct: 61  SIVLDGKDIST-----MEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQE 115

Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180
           VE VA +L I  ++N  P  LSGGQQQRVA+ RAL + P + L DEP SNLDA++R   R
Sbjct: 116 VERVADLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMR 175

Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240
             +K++  RL  T++ V+HD  +   +ADR+ VL  G+L Q+G P+++YD P ++ VA  
Sbjct: 176 TEIKKLHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGF 235

Query: 241 IGE---------INELEGKVTNE--GVVIGSLRFPV-SVSSDR----AIIGIRPEDVKLS 284
           +G          + + EG +  E  G    S++ PV    +DR     I+GIRPE +   
Sbjct: 236 MGSPAMSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFLADRVGKKVILGIRPEHITQP 295

Query: 285 KDVIKDDSWILVGKGKVKVIGYQGGLFRITITPLDSEEEIFTYSDHPIHSGEEVLVYVRK 344
           +D   D + +  G+  ++V    G      I   D+        +HP+  GE   +    
Sbjct: 296 QDQKNDQTLVAKGEFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPVTWGETAELMFDM 355

Query: 345 DKIKVFE 351
            K+  F+
Sbjct: 356 KKVVFFD 362


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: 302
Number of extensions: 21
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: 372
Length adjustment: 29
Effective length of query: 324
Effective length of database: 343
Effective search space:   111132
Effective search space used:   111132
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