GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34240 in Tistlia consotensis USBA 355

Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease

Query= uniprot:B2T9V8
         (351 letters)



>NCBI__GCF_900177295.1:WP_085121058.1
          Length = 335

 Score =  169 bits (428), Expect = 9e-47
 Identities = 109/330 (33%), Positives = 175/330 (53%), Gaps = 15/330 (4%)

Query: 27  RGKRARSELARLRELAL---LPALALLIVIGA---FISPSFLTKANLISVLGASAALALV 80
           R   A  E   L++LA    L  L L +VIGA    +SP FLT++N+ ++L  S  + ++
Sbjct: 14  RSAAAAGEGRLLKQLATSLELRMLGLALVIGAVLSLLSPYFLTESNIFNILDQSVVIGIL 73

Query: 81  VLAESLIVLTGKFDLSLESTVGIAPAVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVI 140
            +  + ++LTG  DLS+ S  G++  V  + +           +P    +L  V+ GA +
Sbjct: 74  SIGMTFVILTGGIDLSVGSVAGLSGIVLGLALK---------DYPIPVAILLGVLTGAGV 124

Query: 141 GFINGFLVVRLRLNAFIVTLAMLIVLRGMLVGATKGGTLFDMPTSFFALATTIVLGLPLS 200
           G ++G L+   RL AF+VTL M+ + R +    +    +   P+   ++  T V G+P +
Sbjct: 125 GLVSGILIGYFRLAAFVVTLGMMAIGRSLAYIFSGQTAISGFPSDLSSIVYTDVFGIPTN 184

Query: 201 VWLAAAAFAIAAFMLRYHRLGRALYAIGGNPEAARAAGIRVERITWGVFVLGSILASVGG 260
           V     A+ +A   L Y + GR +YAIG N EAARAAG+ V   +   +V+   LA+V  
Sbjct: 185 VLFLGFAYLLAWGYLTYTKGGRTIYAIGSNKEAARAAGLGVLFYSILPYVVSGALAAVAI 244

Query: 261 LIVTGYVGAINANQGNGMIFTVFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLA 320
                 + +++   GNGM     AA VIGG SL GG+G++ G L GVL++ +++N L L 
Sbjct: 245 TFSVAQILSVDPLTGNGMELDAIAAVVIGGASLYGGRGSIVGTLIGVLIMVMIRNGLNLL 304

Query: 321 QVPSFWIQAIYGAIILGSLMVARLASGEGQ 350
            V  FW  +  G+II+ +L+V RL     +
Sbjct: 305 GVSPFWQGSAIGSIIIMALLVERLVRARSE 334


Lambda     K      H
   0.326    0.140    0.397 

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: 296
Number of extensions: 23
Number of successful extensions: 3
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: 351
Length of database: 335
Length adjustment: 29
Effective length of query: 322
Effective length of database: 306
Effective search space:    98532
Effective search space used:    98532
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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