GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20255 AO356_20255
           arabinose ABC transporter permease
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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