GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Echinicola vietnamensis KMM 6221, DSM 17526

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>FitnessBrowser__Cola:Echvi_2123
          Length = 318

 Score =  149 bits (376), Expect = 1e-40
 Identities = 88/249 (35%), Positives = 144/249 (57%), Gaps = 9/249 (3%)

Query: 1   MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60
           M+ L++  V+K Y  G    L++  L++  G  + +VG SG GKS+L+  IAGLE  S G
Sbjct: 1   MSYLKVSEVSKRYDAGSL-ALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAG 59

Query: 61  AILVDDADISG----MSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEV 116
            + + D  I      + P   +I ++ Q Y LYP  +V +NIA  L +     A   E  
Sbjct: 60  VVHLGDQKILNPAQKLVPGYDEIQLIHQEYKLYPNSTVEENIARPLLL--YDKAYQKERT 117

Query: 117 ARVSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRT 176
           A + +LL +     +KP QLSGGQQQ+VA+GRAL+  P++ L DEP S+LDA  + ++  
Sbjct: 118 AEILELLSLRAFKDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIE 177

Query: 177 EMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFI 236
           E+K +   L+ T ++VTHD  +A+ + +++ +++ G + Q G  ++++  PA+ +VA   
Sbjct: 178 ELKEIFDALEVTVIFVTHDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLF 237

Query: 237 GSPPMNFIP 245
           G   +N IP
Sbjct: 238 GY--LNLIP 244


Lambda     K      H
   0.319    0.138    0.393 

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: 252
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: 386
Length of database: 318
Length adjustment: 29
Effective length of query: 357
Effective length of database: 289
Effective search space:   103173
Effective search space used:   103173
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