GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ascB in Caulobacter crescentus NA1000

Align 6-P-β-galactosidase (Gan1D) (EC 3.2.1.86) (characterized)
to candidate CCNA_02220 CCNA_02220 beta-glucosidase

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



>FitnessBrowser__Caulo:CCNA_02220
          Length = 482

 Score =  271 bits (694), Expect = 3e-77
 Identities = 170/472 (36%), Positives = 231/472 (48%), Gaps = 40/472 (8%)

Query: 7   KPFPPEFLWGAASAAYQVEGAWNEDGKGLSVWDVFAKQPGRTFKGTNGDVAVDHYHRYQE 66
           + FP +F+WG A+AA+Q EG+   DG+G S+WDVF + PG    G     A D Y RYQ+
Sbjct: 39  RQFPKDFVWGVATAAFQTEGSQTADGRGPSIWDVFERVPGHVKNGDTAADATDSYRRYQD 98

Query: 67  DVALMAEMGLKAYRFSVSWSRVFPDGNGAVNEKGLDFYDRLIEELRNHGIEPIVTLYHWD 126
           DV L+A   L AYRFS+SWSR+ P G GAVN  GLD Y RL++ L   GI P  TL+HWD
Sbjct: 99  DVDLIAGASLSAYRFSMSWSRILPTGAGAVNAAGLDHYSRLVDALLAKGITPYATLFHWD 158

Query: 127 VPQALMDAYGAWESRRIIDDFDRYAVTLFQRFGDRVKYWVTLNEQNIFISFGYRLGLHPP 186
           +PQ L D  G W +R        YA  + +R GDR+K ++ LNE  +   FG+ LG H P
Sbjct: 159 LPQGLQDK-GGWANRDTAQRLADYARAVVERLGDRLKNYIILNEAAVHTVFGHVLGDHAP 217

Query: 187 GVKDMKRMYEANHIANLANAKVIQSFRHYVPDGKIGPSFAYSPMYPYDSRPE--NVLAFE 244
           G+KD   +    H  NL     IQ+ R    D  +G + A  P  P        N LA +
Sbjct: 218 GLKDAALLGPVTHHMNLGQGLAIQALRAARSDLSVGTTMALQPCRPAGGPLAFWNRLASD 277

Query: 245 NAEEFQNHWWMDVYAWGMYPQAAWNYLESQGLEPTVAPGDWELLQAAKP-DFMGVNYYQT 303
             +E  N  W+D    G YP+A       + L+  V  GD  L    +P DF+GVNYY  
Sbjct: 278 GLDEIWNLAWLDPLFKGTYPKAM-----EEPLKGVVRDGD--LKTTRQPVDFLGVNYYAP 330

Query: 304 TTVEHNPPDGVGEGVMNTTGKKGTSTSSGIPGLFKTVRNPH-VDTTNWDWAIDPVGLRIG 362
             V                           P        P+  +   +   IDP GL   
Sbjct: 331 AYVR---------------------LDLSAPSKIAAAAAPNSAEQDAFGRHIDPSGLFEV 369

Query: 363 LRRIANRYQLP-ILITENGLGEFDTLEPGDIVNDDYRIDYLRRHVQEIQRAITDGVDVLG 421
           L R+   Y  P +L+TENG  +  +  P  I++D +RI YLRRH++ +  A   G DV G
Sbjct: 370 LDRVRREYGAPKMLVTENGCSDPFSSGPA-ILDDTFRIKYLRRHLEAVLAAREAGCDVRG 428

Query: 422 YCAWSFTDLLSWLNGYQKRYGFVYVNRDDESEKDLRRIKKKSFYWYQRVIET 473
           Y  W+  D   W  GY  ++G   +          RRI K S+ W++ + +T
Sbjct: 429 YFEWTLIDNFEWDLGYTSKFGITTMEAASG-----RRIPKASYGWFKALAQT 475


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: 746
Number of extensions: 42
Number of successful extensions: 7
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