GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lysP in Pseudomonas fluorescens FW300-N1B4

Align The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized)
to candidate Pf1N1B4_1639 transport permease protein of gamma-aminobutyrate

Query= TCDB::K7VV21
         (488 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1639 transport permease
           protein of gamma-aminobutyrate
          Length = 464

 Score =  294 bits (752), Expect = 5e-84
 Identities = 161/434 (37%), Positives = 255/434 (58%), Gaps = 18/434 (4%)

Query: 4   SSNSTTEMQVKRGLKSRHVSMIALGGTIGTGLFLTSGDVIHTAGPFGALTAYVLIGAMVY 63
           SS+ ++   +++GLK RHV+M+++ G IG GLF+ SG  I  AGP   L AY   GA+V 
Sbjct: 2   SSSQSSSNGLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGP-AVLLAYAAAGALVV 60

Query: 64  FLMTSLGEMATYLPTSGSFSDYGTRYVDPAFGFALGWNYWLNWAITVAVDLTAVALCIKF 123
            +M  LGEMA   P +GSFS Y  R +    GF +GW YW  W + + ++  A A  +  
Sbjct: 61  LVMRMLGEMAVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHA 120

Query: 124 WLPDVPSWIFSLIALIIVFSINALSVKTFGETEYWLSAIKITVVVLFLIIGFLSIFGIMG 183
           W P+V  W F+L+  +++ + N  SVK +GE E+W + +K+  ++ F+ +G L+IFG + 
Sbjct: 121 WFPNVAIWAFTLVITLLLTATNLFSVKNYGEFEFWFALVKVIAIIGFIGLGILAIFGFL- 179

Query: 184 GHIDVAKNLSVGNHGFVGGLGSFTTG-GGILGVLLVAGFSFQGTELLGITAGEAENPEKS 242
                   +S  +H F    G    G G +LG +L   FSF GTE++ I A E++NP + 
Sbjct: 180 ----PTSQVSGVSHLF-DTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQ 234

Query: 243 IPKAMNSIFWRILVFYILSIFVMAAIIPFTDPHLVGGNSAAQSPFTIVFERVGFSIAASI 302
           I KA NS+ WRI +FY++SIF++ A++P+ DP L     A+   +  V ER+G   A  I
Sbjct: 235 ISKATNSVIWRIGLFYLVSIFIVVALVPWNDPIL-----ASVGSYQTVLERMGIPNAKLI 289

Query: 303 MNAVVLTSVVSAANSGMYASTRMLYSLAKDGGAPTIFSKTSKNGIPFIALLATTAVALL- 361
           ++ VVL +V S  NS +Y ++RM++SL K G AP +  +T+ +G P+ A++ +TA A L 
Sbjct: 290 VDIVVLVAVTSCLNSALYTASRMMFSLGKRGDAPAVSQRTNSSGTPYWAVMLSTAAAFLA 349

Query: 362 TFLTSIYGVSFFTFLVSASGLTGFIAWIGIAISHFRFRRAYVAQGKDVKKLPYHAKLFPF 421
            F   +   + F FL+++SG    + ++ IAIS  R R+  +A+G   +K+ +   LFP 
Sbjct: 350 VFANYVAPAAVFEFLLASSGAIALLVYLVIAISQLRMRKQRMARG---EKIAFSMWLFP- 405

Query: 422 GPILALIMTVLVTL 435
           G   A+I+ ++  L
Sbjct: 406 GLTYAVIVFIVAAL 419


Lambda     K      H
   0.326    0.141    0.425 

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: 541
Number of extensions: 30
Number of successful extensions: 6
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: 488
Length of database: 464
Length adjustment: 33
Effective length of query: 455
Effective length of database: 431
Effective search space:   196105
Effective search space used:   196105
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: 51 (24.3 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