GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ascB in Phaeobacter inhibens BS107

Align CAC0385 (EC 3.2.1.86) (characterized)
to candidate GFF770 PGA1_c07840 beta-glucosidase A

Query= CAZy::AAK78365.1
         (469 letters)



>FitnessBrowser__Phaeo:GFF770
          Length = 444

 Score =  262 bits (670), Expect = 1e-74
 Identities = 155/468 (33%), Positives = 242/468 (51%), Gaps = 35/468 (7%)

Query: 3   FPKDFFLGAASASYQVEGAWNEDGKGVSNWDVFTKIPGKTFEGTNGDVAVDHYHRYKEDV 62
           FPKDF  G A+++YQ+EG     G G ++WD F   PG      +G  A DHYHRY ED+
Sbjct: 9   FPKDFLFGTATSAYQIEGH-GFGGAGPTHWDSFAATPGNVVRAEHGQRACDHYHRYAEDL 67

Query: 63  KLMAEMGLDSYRFSVSWPRIIPDGDGEINQKGIEFYNNLIDECLKYGIVPFVTLYHWDMP 122
            L A  G D YRFS SW R++P+G G  N +G++FY+ L D  L+ G+ P VTLYHW++P
Sbjct: 68  DLAAAAGFDCYRFSTSWARVMPEGRGAPNPEGLDFYDRLTDAILERGLKPCVTLYHWELP 127

Query: 123 EVLEKAGGWTNKKTVDAFVKYAKACFEAFGDRVKRWITFNETIVFCSNGYLSGAHPPGIT 182
           + L   GGW N +  + F  YA+      GDR+      NE        +  G H PG+ 
Sbjct: 128 QALADLGGWRNAEIANWFGDYAEVIMGRIGDRMYSAAPINEPWCVGWLSHFLGHHAPGLR 187

Query: 183 GDVKKYFQATHNVFTAHARSVIEYKKLKQYGEIGITHVFSP--AFSVDDKEENKAAAYHA 240
            D++   +A H+V  AH  ++   + ++  G   +  VF+   A  VDD E  + AA   
Sbjct: 188 -DIRATARAMHHVMLAHGTAI---QAMRALGMSNLGGVFNLEWATPVDDSEAAQQAAARY 243

Query: 241 NQYEITWYYDPILKGKYPEYVIKNIEKQGFLPDWTDEELNTLREAAPLNDFIGLNYYQPQ 300
           +     ++      G+YP+  ++ +E    LP    ++  T+   AP+ D+ GLNYY  +
Sbjct: 244 DAIYNGFFLGGAFHGRYPDLALEGLEPH--LPKGWQDDFATI--TAPV-DWCGLNYYTRK 298

Query: 301 RVIKNHDTGEKIERTRENSTGAPGNASFDGFYRTVKMDDKTYTKWGWEISPESLILGLEK 360
           ++    D G             P  A  DG            T+ GWEI P+ L   L +
Sbjct: 299 QIAP--DAGP-----------WPQYAEVDG--------PLPKTQMGWEIYPQGLYDFLTR 337

Query: 361 LKEQY-GDIKIYITENGLGDQDPIIEDEILDMPRIKFIEAHLRAIKEAISRGINLKGYYA 419
               Y GD+ + +TENG+ + D + + ++ D  RI F++ HL A++ AI+ G+ ++GY+ 
Sbjct: 338 TARDYTGDLPLIVTENGMANADVVTKGKVEDAARITFVDDHLDAVRRAIADGVPVQGYFL 397

Query: 420 WSVIDLLSWLNGYKKQYGFIYVDHKHNLDRKKKLSFYWYKKVIEERGK 467
           WS++D   W  GY+K++G ++VD +  L R  K S++  +  +    K
Sbjct: 398 WSLLDNYEWALGYEKRFGLVHVDFE-TLKRTPKASYHALRSALTGASK 444


Lambda     K      H
   0.318    0.138    0.433 

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: 638
Number of extensions: 29
Number of successful extensions: 4
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: 469
Length of database: 444
Length adjustment: 33
Effective length of query: 436
Effective length of database: 411
Effective search space:   179196
Effective search space used:   179196
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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