GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Echinicola vietnamensis KMM 6221, DSM 17526

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components

Query= uniprot:D8IPI1
         (406 letters)



>FitnessBrowser__Cola:Echvi_2123
          Length = 318

 Score =  149 bits (375), Expect = 1e-40
 Identities = 85/241 (35%), Positives = 138/241 (57%), Gaps = 8/241 (3%)

Query: 1   MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60
           M+ +    ++K Y  G   L    L +  G  V ++G SG GKS++LR+IAGLE  S G 
Sbjct: 1   MSYLKVSEVSKRYDAGSLALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGV 60

Query: 61  LRIGGTVVNDLPARER-----NVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRV 115
           + +G   + + PA++       + ++ Q Y LYP+ +V +NIA  L  L    A    R 
Sbjct: 61  VHLGDQKILN-PAQKLVPGYDEIQLIHQEYKLYPNSTVEENIARPL--LLYDKAYQKERT 117

Query: 116 REVAALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRG 175
            E+  LL+L A  ++KPR +SGGQQQ+ AI RA+   P V L DEP S+LDA  +  L  
Sbjct: 118 AEILELLSLRAFKDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIE 177

Query: 176 DIKRLHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFI 235
           ++K +   L  T ++VTHD  +A+ +++ ++++Q G+++Q G+  E++R P + + A   
Sbjct: 178 ELKEIFDALEVTVIFVTHDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLF 237

Query: 236 G 236
           G
Sbjct: 238 G 238


Lambda     K      H
   0.321    0.137    0.403 

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: 221
Number of extensions: 11
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: 406
Length of database: 318
Length adjustment: 29
Effective length of query: 377
Effective length of database: 289
Effective search space:   108953
Effective search space used:   108953
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 (21.8 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