GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natC in Burkholderia phytofirmans PsJN

Align NatC aka SLL0146, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate BPHYT_RS31745 BPHYT_RS31745 ABC transporter ATP-binding protein

Query= TCDB::P74455
         (372 letters)



>FitnessBrowser__BFirm:BPHYT_RS31745
          Length = 389

 Score = 78.6 bits (192), Expect = 3e-19
 Identities = 46/118 (38%), Positives = 64/118 (54%), Gaps = 17/118 (14%)

Query: 5   YLIFLITSAATYGIFALGLNLQWGFAGLINFGHVAFMTLGAYATTLLSLRGL-------- 56
           Y + ++  A  Y + ALGLN+  GFAGL++ G++AF  +GAY   LL+   L        
Sbjct: 47  YGVRVLDFAMLYVMLALGLNIVVGFAGLLDLGYIAFYAVGAYTAALLTSPHLAAHFEWIG 106

Query: 57  ---------PIPLAVLVGMGLAMALGLLIGTSTLRLREDYLAIVTIGVSELIRLIANN 105
                    P    + V M LA   G+ +G  TLRLR DYLAIVT+G  E++R+  NN
Sbjct: 107 HMWPSGFHAPYWFVMPVAMVLAAIAGICLGAPTLRLRGDYLAIVTLGFGEIVRIFMNN 164



 Score = 67.8 bits (164), Expect = 5e-16
 Identities = 54/188 (28%), Positives = 84/188 (44%), Gaps = 15/188 (7%)

Query: 189 LTAYVPGVVSLYNYSGKAGLMLLALTLLALTY------AGLEFWV-----HSPWGRILKA 237
           +T   P  V+ +N S     +    T + + Y      + L  WV     HS  GR   A
Sbjct: 178 ITGVAPVTVAGFNLSETHAFLGFQFTTVYMYYYVFVLCSLLVVWVCTRLQHSRIGRAWAA 237

Query: 238 IREDEEIPRALGKNVFWYKLQAFMGGGAIAGLAGALFAWQLTSIYPSNFDTLLTFNAWII 297
           IREDE   +A+G N    KL AF  G +  GL+GA+FA     + P +F    +      
Sbjct: 238 IREDEIAAKAMGINTRNVKLLAFAMGASFGGLSGAMFAGFQGFVSPESFTLWESVTVLAC 297

Query: 298 VVLGGAGSNAGTVLGTIIFWAYDSLTRFLLP--QIAFLDQ--SQAGALRVMVIGLILMVL 353
           VVLGG G   G + G ++      + R  +   Q A           +R ++ GL ++++
Sbjct: 298 VVLGGMGHIPGVIFGAVLLAILPEILRSTMTPLQNAIFGHVIVDTEVIRQLLYGLAMVII 357

Query: 354 MVWRPQGI 361
           M+ RP+G+
Sbjct: 358 MLRRPEGL 365


Lambda     K      H
   0.327    0.143    0.442 

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: 305
Number of extensions: 11
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 372
Length of database: 389
Length adjustment: 30
Effective length of query: 342
Effective length of database: 359
Effective search space:   122778
Effective search space used:   122778
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 (21.7 bits)
S2: 50 (23.9 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