GapMind for catabolism of small carbon sources

 

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

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components

Query= uniprot:D4GP38
         (383 letters)



>FitnessBrowser__Cola:Echvi_2123
          Length = 318

 Score =  163 bits (412), Expect = 7e-45
 Identities = 90/250 (36%), Positives = 154/250 (61%), Gaps = 10/250 (4%)

Query: 1   MGQIQLTDLTKRF-GDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGD 59
           M  +++++++KR+   ++A++D SL +     + +VG SG GKS+ LR++AGLE  ++G 
Sbjct: 1   MSYLKVSEVSKRYDAGSLALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGV 60

Query: 60  IYIGGDHM----NYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERV 115
           +++G   +       VP   +I ++ Q+Y LYP+ TV +NI   L     Y  A + ER 
Sbjct: 61  VHLGDQKILNPAQKLVPGYDEIQLIHQEYKLYPNSTVEENIARPLLL---YDKAYQKERT 117

Query: 116 VEVAETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 175
            E+ E L +    D+KP +LSGGQQQ+VA+GRA+  +PEV L+DEP S+LDA  + ++  
Sbjct: 118 AEILELLSLRAFKDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIE 177

Query: 176 ELQNLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFI 235
           EL+ + D L VT ++VTH+  +A+ M++ + ++  G+L Q  +  E + +P + +VA   
Sbjct: 178 ELKEIFDALEVTVIFVTHDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLF 237

Query: 236 GEPMINLVRG 245
           G   +NL+ G
Sbjct: 238 G--YLNLIPG 245


Lambda     K      H
   0.317    0.135    0.386 

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: 237
Number of extensions: 8
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: 383
Length of database: 318
Length adjustment: 29
Effective length of query: 354
Effective length of database: 289
Effective search space:   102306
Effective search space used:   102306
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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