GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pbgal in Azospirillum brasilense Sp245

Align 6-P-β-galactosidase (Gan1D) (EC 3.2.1.86) (characterized)
to candidate AZOBR_RS16895 AZOBR_RS16895 beta-glucosidase

Query= CAZy::AHL67640.1
         (478 letters)



>FitnessBrowser__azobra:AZOBR_RS16895
          Length = 482

 Score =  302 bits (773), Expect = 2e-86
 Identities = 178/473 (37%), Positives = 240/473 (50%), Gaps = 35/473 (7%)

Query: 6   LKPFPPEFLWGAASAAYQVEGAWNEDGKGLSVWDVFAKQPGRTFKGTNGDVAVDHYHRYQ 65
           L  FP +F+WGA++++YQ+EGA    G+G SVWD F+   G+   G  GDVA DHY+RY 
Sbjct: 37  LAAFPDKFVWGASTSSYQIEGAVTAGGRGPSVWDTFSHSFGKVANGDTGDVACDHYNRYA 96

Query: 66  EDVALMAEMGLKAYRFSVSWSRVFPDGNGAVNEKGLDFYDRLIEELRNHGIEPIVTLYHW 125
           EDV LMA+ G+ AYRFSV+W RV P G G  N +GLDFYDRL + L   GI P   LYHW
Sbjct: 97  EDVDLMAKAGMNAYRFSVAWPRVQPTGTGPANAEGLDFYDRLTDALLAKGIAPWPCLYHW 156

Query: 126 DVPQALMDAYGAWESRRIIDDFDRYAVTLFQRFGDRVKYWVTLNEQNIFISFGYRLGLHP 185
           D+PQAL D  G W +R I   F  YA  +  R GDR K+W  LNE ++   FG+ LG H 
Sbjct: 157 DLPQALQDR-GGWTNRDIAGWFTDYAQLVAARIGDRAKHWTMLNEPSVHAIFGHGLGGHA 215

Query: 186 PGVKDMKRMYEANHIANLANAKVIQSFRHY--VPDGKIGPSFAYSPMYPYDSRPENVLAF 243
           PG+      ++A H  NLA    +++ R        ++G   +  P++P      N  A 
Sbjct: 216 PGMTGKGNYFKAIHHQNLAQGMALKALRAAGGAKGWQLGTVLSLQPVWPVGGLDANYAAS 275

Query: 244 ENAEEFQNHWWMDVYAWGMYPQAAWNYLESQGLEPTVAPGDWELLQAAKPDFMGVNYYQT 303
              +   N   +D    G YP+     L   G  P V  GD E ++    DF+G+NYY  
Sbjct: 276 LMWDAVWNRACLDPLLRGEYPE-----LLRDGFAPLVKAGDLEAIR-QPIDFLGINYYSR 329

Query: 304 TTVEHNPPDGVGEGVMNTTGKKGTSTSSGIPGLFKTVRNPHVDTTNWDWAIDPVGLRIGL 363
               H  PD  G       G    S   G P            TT   W ++P G+   L
Sbjct: 330 M---HQQPDPAG-----LFGTGYGSPPEGTP------------TTGMGWPVEPDGIAEIL 369

Query: 364 RRIANRY-QLPILITENGLGEFDTLEPGDIVNDDYRIDYLRRHVQEIQRAITDGVDVLGY 422
             +   Y   P+ + ENG    +   P   V D+ RI YLRRH+    +A+ +GVD+ G+
Sbjct: 370 IELKQEYGNPPVYVMENGAAYPEQTGPKGFVQDNDRISYLRRHILAGHQALEEGVDLRGW 429

Query: 423 CAWSFTDLLSWLNGYQKRYGFVYVNRDDESEKDLRRIKKKSFYWYQRVIETNG 475
             WS  D   W  GYQ+R+G + V+R     + L R  K S++WY  VI   G
Sbjct: 430 FVWSLLDNFEWAEGYQRRFGLIEVDR-----QTLERRPKASYHWYADVIRKKG 477


Lambda     K      H
   0.320    0.139    0.448 

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: 822
Number of extensions: 50
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: 478
Length of database: 482
Length adjustment: 34
Effective length of query: 444
Effective length of database: 448
Effective search space:   198912
Effective search space used:   198912
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