GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgl in Escherichia coli BW25113

Align 6-P-β-glucosidase (AscB) (EC 3.2.1.21|3.2.1.86) (characterized)
to candidate 16800 b2716 cryptic 6-phospho-beta-glucosidase (NCBI)

Query= CAZy::AAT45375.1
         (476 letters)



>FitnessBrowser__Keio:16800
          Length = 474

 Score =  835 bits (2156), Expect = 0.0
 Identities = 390/472 (82%), Positives = 431/472 (91%)

Query: 4   STFPNGFLWGGAIAANQAEGAYLEGGKGLTTVDMIPHGVNRAAGETGARTAFALREDEFY 63
           S FP  FLWGGA+AANQ+EGA+ EG KGLTTVDMIPHG +R A + G    F LR+DEFY
Sbjct: 2   SVFPESFLWGGALAANQSEGAFREGDKGLTTVDMIPHGEHRMAVKLGLEKRFQLRDDEFY 61

Query: 64  PSHQAIDFYHRYKEDIALMAEMGFTVFRTSIAWSRLYPNGDELTPNAEGIAFYRDMFAEC 123
           PSH+A DFYHRYKEDIALMAEMGF VFRTSIAWSRL+P GDE+TPN +GIAFYR +F EC
Sbjct: 62  PSHEATDFYHRYKEDIALMAEMGFKVFRTSIAWSRLFPQGDEITPNQQGIAFYRSVFEEC 121

Query: 124 KKYNIEPLVTLCHFDVPMHLVTEYGSWRNRKMVEFFARYARTCFEAFDGLVKYWLTFNEI 183
           KKY IEPLVTLCHFDVPMHLVTEYGSWRNRK+VEFF+RYARTCFEAFDGLVKYWLTFNEI
Sbjct: 122 KKYGIEPLVTLCHFDVPMHLVTEYGSWRNRKLVEFFSRYARTCFEAFDGLVKYWLTFNEI 181

Query: 184 NILLHSPFSGAGLVFADGENQEQVKYQAAHHELVASALATKIAHEVNPENQVGCMLAGGN 243
           NI+LHSPFSGAGLVF +GENQ+QVKYQAAHH+LVASALATKIAHEVNP+NQVGCMLAGGN
Sbjct: 182 NIMLHSPFSGAGLVFEEGENQDQVKYQAAHHQLVASALATKIAHEVNPQNQVGCMLAGGN 241

Query: 244 FYPWSCKPEDVWAALNKYRENLFFIDVQARGTYPAYTGRLFKEKGITIASEPGDDEILKN 303
           FYP+SCKPEDVWAAL K RENLFFIDVQARGTYPAY+ R+F+EKG+TI   PGDDEILKN
Sbjct: 242 FYPYSCKPEDVWAALEKDRENLFFIDVQARGTYPAYSARVFREKGVTINKAPGDDEILKN 301

Query: 304 TVDFVSFSYYASRCASADMNEHNSSAANIVKSLKNPHIKASEWGWGIDPLGLRITMNMMY 363
           TVDFVSFSYYASRCASA+MN +NSSAAN+VKSL+NP+++ S+WGWGIDPLGLRITMNMMY
Sbjct: 302 TVDFVSFSYYASRCASAEMNANNSSAANVVKSLRNPYLQVSDWGWGIDPLGLRITMNMMY 361

Query: 364 DRYQKPLFLVENGLGAKDEINAQGEIDDDYRISYLREHISAMADAIGDGIPVIGYTSWGC 423
           DRYQKPLFLVENGLGAKDE  A GEI+DDYRISYLREHI AM +AI DGIP++GYT+WGC
Sbjct: 362 DRYQKPLFLVENGLGAKDEFAANGEINDDYRISYLREHIRAMGEAIADGIPLMGYTTWGC 421

Query: 424 IDLVAASTGEMSKRYGFIYVDRDDRGEGTLARKKKKSFYWYKKVIASNGADL 475
           IDLV+ASTGEMSKRYGF++VDRDD G GTL R +KKSF+WYKKVIASNG DL
Sbjct: 422 IDLVSASTGEMSKRYGFVFVDRDDAGNGTLTRTRKKSFWWYKKVIASNGEDL 473


Lambda     K      H
   0.320    0.136    0.422 

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: 893
Number of extensions: 28
Number of successful extensions: 1
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: 476
Length of database: 474
Length adjustment: 33
Effective length of query: 443
Effective length of database: 441
Effective search space:   195363
Effective search space used:   195363
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: 51 (24.3 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