GapMind for catabolism of small carbon sources

 

Alignments for a candidate for susB in Oscillibacter ruminantium GH1

Align alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate WP_040660580.1 ON16_RS06835 alpha-amylase

Query= BRENDA::P21517
         (604 letters)



>NCBI__GCF_000307265.1:WP_040660580.1
          Length = 623

 Score =  218 bits (554), Expect = 8e-61
 Identities = 176/569 (30%), Positives = 249/569 (43%), Gaps = 94/569 (16%)

Query: 82  KLLWHDRQRW-------------FTPQGFSRMPPARLEQFAVDVPDIGPQWAADQIFYQI 128
           +LLW+  + W             +   GF    PA  +    D     P+W  + I YQI
Sbjct: 82  ELLWYHFRFWREDGSGCDLDGSGYRSDGF----PADWQLTVYDDSHPTPRWFGEGITYQI 137

Query: 129 FPDRFAR-SLPREAEQDHVYYHHAAGQEIILRDWDEPVTAQAGGSTFYGGDLDGISEKLP 187
           FPDRF R S+P  A        H   ++    DW    T       F+GG L GI+ +L 
Sbjct: 138 FPDRFCRLSVPDPAGMVGDRMVHENWEDT--PDWRPDETGAVRNRDFFGGSLQGIASRLA 195

Query: 188 YLKKLGVTALYLNPVFKAPSVHKYDTEDYRHVDPQFGGDGALLRLRHNTQQLGMRLVLDG 247
            L++L VT LYL PVF++ S H+Y+T DY  +DP  G +     L    +  G+R++LDG
Sbjct: 196 ELEQLHVTTLYLCPVFESASNHRYNTADYTKIDPMLGTEEDFRFLCAQAETHGIRVILDG 255

Query: 248 VFNHSGDSHAWFDRHN-RGTGGACHNPESPWRDWYSF---SDDGTALDWLGYASLPKLDY 303
           VFNH+G +  +F+      T GA  + +SP+ +WY+F    DD  A  W G  +LP ++ 
Sbjct: 256 VFNHTGSNSVYFNAEGFYPTVGAAQSQDSPYFNWYTFHPWPDDYEA--WWGIRTLPAVNE 313

Query: 304 QSESLVNEIYRGEDSIVRHWLKAPWNMDGWRLDVVHMLGEAGGARNNMQHVAGITEAAKE 363
            S S    I  GE+S++R WL+A     GWRLDV   L +        + +A +  A   
Sbjct: 314 SSASYGAFIADGENSVIRRWLRA--GASGWRLDVADELPD--------EFLARLRSAVDT 363

Query: 364 TQPEAYIVGEHFGDA---------RQWLQADVEDAAMNYRGFTFPLWGFLANTDISYDPQ 414
            +P + ++GE + D          R++L        MNY   T  L  +L         Q
Sbjct: 364 AKPGSILLGEVWEDGSNKIAYSKRRKYLLGSETHGLMNYPFRTAAL-AYL---------Q 413

Query: 415 QIDAQTCMAWMDNYRAGLSHQQQLRMFNQLDSHDTARFKTLLG----------------- 457
             DA + +  M+  R            N L +HDTAR  T+LG                 
Sbjct: 414 GGDACSFVQAMETIRENYPPPAFYSAMNFLGTHDTARILTVLGAPTVPESKAERADFLLS 473

Query: 458 -----RDIARLPLAVVWLFTWPGVPCIYYGDEVGLDGKNDPFCRKPFPWQVEKQDTALFA 512
                  +A L +A   L+ +PG P IYYGDE G++G  DPF R  +PW   K+D AL A
Sbjct: 474 PNQRTEGLALLRVAAALLYAFPGSPMIYYGDEAGMEGWEDPFNRGTYPW--GKEDQALRA 531

Query: 513 LYQRMIALRKKSQALRHGGCQVLYAEDNVVVFVRVLNQQRVLVAINRGEACEVVLPASPF 572
            Y R+  LR    +LR G  + LYA  + + F R    +      N G          P 
Sbjct: 532 FYVRLGQLRHSRVSLRRGDIRYLYAAGSGLAFSRSWEDETTTAVFNAGR--------EPL 583

Query: 573 LNAVQWQCKEGHGQLT-------DGILAL 594
              V W        LT       DG+L L
Sbjct: 584 TMEVPWVFSAARDFLTGRAFSPVDGVLKL 612


Lambda     K      H
   0.322    0.138    0.451 

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: 1199
Number of extensions: 79
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: 604
Length of database: 623
Length adjustment: 37
Effective length of query: 567
Effective length of database: 586
Effective search space:   332262
Effective search space used:   332262
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 (21.9 bits)
S2: 53 (25.0 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