GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bglF in Megamonas funiformis YIT 11815

Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate WP_008539247.1 HMPREF9454_RS08705 PTS transporter subunit EIIC

Query= TCDB::P08722
         (625 letters)



>NCBI__GCF_000245775.1:WP_008539247.1
          Length = 362

 Score =  272 bits (696), Expect = 2e-77
 Identities = 137/349 (39%), Positives = 215/349 (61%), Gaps = 6/349 (1%)

Query: 95  NLLNRFVYVISGIFTPLIGLMAATGILKGMLALALTFQWTTEQSGTYLILFSASDALFWF 154
           +++N  +  I+GIF P++ L++A GILKG++A+ +      ++S  YL+L + +D+LF+F
Sbjct: 10  SMINTIIDGIAGIFLPIVSLLSAAGILKGIIAVLIATDVLIKESDNYLVLNAMTDSLFYF 69

Query: 155 FPIILGYTAGKRFGGNPFTAMVIGGALVHPLILTAFENGQKADALGLDFLGIPVTLLNYS 214
            P++L YT+ K+FG NPFTA+VI G  ++P +    E+GQ      ++F  IP+  + Y 
Sbjct: 70  LPMLLAYTSAKKFGANPFTAVVIAGIFLYPSLNHILESGQT-----VEFFHIPLKGVTYH 124

Query: 215 SSVIPIIFSAWLCSILERRLNAWLPSAIKNFFTPLLCLMVITPVTFLLVGPLSTWISELI 274
           SSVIPII ++ L + +E+ LN   P  +K F TPLLC++ +  VT  L GP+   I + +
Sbjct: 125 SSVIPIILASALLTFVEKFLNKIFPDMVKGFLTPLLCIIFVGFVTLFLFGPIGMVIGDFL 184

Query: 275 AAGYLWLYQAVPAFAGAVMGGFWQIFVMFGLHWGLVPLCINNFTVLGYDTMIPLLMPAIM 334
           A  Y ++Y+  P  +GA++G   Q  V+FG HW  + + +NN  VLG DT++ L+ PA+ 
Sbjct: 185 ANIYEYIYKFSPIISGALLGTVIQPMVIFGFHWSFILIGMNNIAVLGSDTVLALMGPAVF 244

Query: 335 AQVGAALGVFLCERDAQKKVVAGSAALTSLFGITEPAVYGVNLPRKYPFVIACISGALGA 394
           AQ GA L VFL  +D + K +  S+ L++LFGITEP ++GVNLPRK P +  CI G +G 
Sbjct: 245 AQAGAGLAVFLKSKDTKFKSICASSILSALFGITEPIMFGVNLPRKKPMIAVCIGGGIGG 304

Query: 395 TIIGYAQTKVYSFGLPSIFTFMQTIPSTGIDFTVWASVIGGVIAIGCAF 443
            I GY+  K  +F  PS+ + +      G    + + VI  +IA   A+
Sbjct: 305 AIAGYSGAKAIAFAFPSLAS-LPVFYGDGFLLYILSDVIAAIIAFIIAY 352


Lambda     K      H
   0.324    0.141    0.427 

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: 668
Number of extensions: 30
Number of successful extensions: 2
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: 625
Length of database: 362
Length adjustment: 33
Effective length of query: 592
Effective length of database: 329
Effective search space:   194768
Effective search space used:   194768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 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