GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34240 in Pseudomonas fluorescens FW300-N2C3

Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate AO356_20255 AO356_20255 arabinose ABC transporter permease

Query= uniprot:B2T9V8
         (351 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_20255
          Length = 322

 Score =  152 bits (383), Expect = 2e-41
 Identities = 95/307 (30%), Positives = 160/307 (52%), Gaps = 19/307 (6%)

Query: 43  LLPALALLIV----IGAFISPSFLTKANL-ISVLGASAALALVVLAESLIVLTGKFDLSL 97
           LL A+ + ++    I  F+SP  +    L IS  G +A   L  LA      +G FDLS+
Sbjct: 27  LLAAIGIFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLA------SGHFDLSV 80

Query: 98  ESTVGIAPAVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVIGFINGFLVVRLRLNAFI 157
            S +  A  V A+++    S   G+         A + +G ++G ING ++ +LR+NA I
Sbjct: 81  GSVIACAGVVAAVVMRDTNSVFLGVS--------AALAMGLIVGLINGIVIAKLRVNALI 132

Query: 158 VTLAMLIVLRGMLVGATKGGTLFDMPTSFFALATTIVLGLPLSVWLAAAAFAIAAFMLRY 217
            TLA + ++RG+      G  +     SFF      + G+P+ + +  A F    ++L Y
Sbjct: 133 TTLATMQIVRGLAYIFANGKAVGVSQESFFVFGNGQLFGVPVPILITIACFLFFGWLLNY 192

Query: 218 HRLGRALYAIGGNPEAARAAGIRVERITWGVFVLGSILASVGGLIVTGYVGAINANQGNG 277
              GR   AIGGN EAA  AG+ V+R    +F +  ++ ++ G+I+   + +     G G
Sbjct: 193 TTYGRNTMAIGGNQEAALLAGVNVDRTKIIIFAVHGLIGALAGVILASRMTSGQPMIGQG 252

Query: 278 MIFTVFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLAQVPSFWIQAIYGAIILG 337
              TV +A V+GG+SL GG G +   + GVL+L +++N + L  + +F+   I G+I+L 
Sbjct: 253 FELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLL 312

Query: 338 SLMVARL 344
           ++++ RL
Sbjct: 313 AVVIDRL 319


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: 243
Number of extensions: 7
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 351
Length of database: 322
Length adjustment: 28
Effective length of query: 323
Effective length of database: 294
Effective search space:    94962
Effective search space used:    94962
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 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