GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ascB in Marivita geojedonensis DPG-138

Align 6-P-β-galactosidase (Gan1D) (EC 3.2.1.86) (characterized)
to candidate WP_085638906.1 MGEO_RS13930 beta-glucosidase

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



>NCBI__GCF_002115805.1:WP_085638906.1
          Length = 442

 Score =  272 bits (696), Expect = 1e-77
 Identities = 173/462 (37%), Positives = 237/462 (51%), Gaps = 42/462 (9%)

Query: 9   FPPEFLWGAASAAYQVEGAWNEDGKGLSVWDVFAKQPGRTFKGTNGDVAVDHYHRYQEDV 68
           FP +FL+G A+++YQ+EG     G G + WD FA  PG   +  NGD+A DHYHR++ED+
Sbjct: 9   FPDDFLFGTATSSYQIEGH-AFGGAGKTHWDTFAATPGNVVRAENGDLACDHYHRFEEDL 67

Query: 69  ALMAEMGLKAYRFSVSWSRVFPDGNGAVNEKGLDFYDRLIEELRNHGIEPIVTLYHWDVP 128
            L+   GL AYRFS SW+RV PDG GA N +GLDFYDRL + +   G++P  TLYHW++P
Sbjct: 68  DLVKAAGLDAYRFSTSWARVMPDGRGAPNPEGLDFYDRLTDAMLERGLKPCATLYHWELP 127

Query: 129 QALMDAYGAWESRRIIDDFDRYAVTLFQRFGDRVKYWVTLNEQNIFISFGYRLGLHPPGV 188
            AL D  G W +  +   F  +A  +  R GDR+     +NE        + LG H PG+
Sbjct: 128 VALAD-LGGWRNPDLPKWFGDFAEVIMGRIGDRMFSVAPINEPWCVGWLSHFLGHHAPGL 186

Query: 189 KDMKRMYEANHIANLANAKVIQSFRHYVPDGKIGPSFAYSPMYPYDSRPENVLAFENAEE 248
           +D++    A H    A+   IQ  R  +  G +G  F      P D   E   A    + 
Sbjct: 187 RDIRATAHAMHHVLKAHGTAIQVMRG-LGMGNLGGVFNMEWATPADDSAEAQQAAALYDG 245

Query: 249 FQNHWWMDVYAWGMYPQAAWNYLESQGLEPTVAPG---DWELLQAAKPDFMGVNYYQTTT 305
           + NH++M     G YP    N +E  GLEP +  G   D+ ++QA   D+ G+NYY    
Sbjct: 246 YYNHFFMSGVFKGEYPA---NVME--GLEPHMPKGWQEDFGIIQAPL-DWCGINYYTRKI 299

Query: 306 VEHNPPDGVGEGVMNTTGKKGTSTSSGIPGLFKTVRNPHVDTTNWDWAIDPVGLRIGLRR 365
           +   P DG         G                     +  T  DW I P GL   L R
Sbjct: 300 IA--PDDGAWPSHHEVEGP--------------------LPKTFMDWEIYPDGLYNFLTR 337

Query: 366 IANRY--QLPILITENGLGEFDTLEPGDIVNDDYRIDYLRRHVQEIQRAITDGVDVLGYC 423
            A  Y   LP+ +TENG+   D +E G +V+D +RIDYL +HV  +QRA+ DG  V GY 
Sbjct: 338 TAREYTGDLPLYVTENGMAAPDVIENG-VVDDPHRIDYLNQHVAAVQRALADGAPVKGYF 396

Query: 424 AWSFTDLLSWLNGYQKRYGFVYVNRDDESEKDLRRIKKKSFY 465
            WS  D   W  GY+KR+G V+V+ D      L R  K S++
Sbjct: 397 IWSLMDNYEWSLGYEKRFGLVHVDFD-----TLDRTPKSSYH 433


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: 805
Number of extensions: 64
Number of successful extensions: 6
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: 442
Length adjustment: 33
Effective length of query: 445
Effective length of database: 409
Effective search space:   182005
Effective search space used:   182005
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 24 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