GapMind for catabolism of small carbon sources

 

Aligments for a candidate for serP1 in Pseudomonas fluorescens FW300-N2E2

Align Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM) (characterized)
to candidate Pf6N2E2_5459 D-serine/D-alanine/glycine transporter

Query= TCDB::F2HQ25
         (459 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5459
           D-serine/D-alanine/glycine transporter
          Length = 473

 Score =  282 bits (722), Expect = 1e-80
 Identities = 156/430 (36%), Positives = 243/430 (56%), Gaps = 15/430 (3%)

Query: 11  QRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLRTIGEMLY 70
           +R L  RHI+L+A+   IG GLFLG+ K I+M GP+++ +YI+ G+A+   +R +GEM  
Sbjct: 19  KRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMAV 78

Query: 71  NDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQVPLWLIE 130
           ++P   SF  +   Y G   G+ T W+YW + +  C++E+TA+  Y+  W P VP W+  
Sbjct: 79  HNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIWA 138

Query: 131 IVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYSTVLSGKTVH 190
           +  L  +  +N +  + FGE EFWFA+IK+  II M++  + ++A  F    V  G    
Sbjct: 139 LAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALG---- 194

Query: 191 DSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSLPKAINQI 250
               +SN++      P+G    + +LQMVMFA+  +E IG+TA E  NP+K++P AI  +
Sbjct: 195 ----ISNLWTHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSV 250

Query: 251 PVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFVVLTSAASALN 310
             RILLFYVGAL  I++I+ W+ I    SPFVM F+ +GIK AA +INFVV+T+A S+ N
Sbjct: 251 FWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCN 310

Query: 311 SSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAPVLT-LIPQIKN 369
             +FS  R +YSLAQ         F   S  G+P  AL ++ A  LL  +L  L+P+   
Sbjct: 311 GGIFSTGRMLYSLAQNGQAP--AGFATTSANGVPRRALLLSIAALLLGVLLNYLVPE--K 366

Query: 370 AFDFAASCTTNLFLVVYFITLYTYWQYRKSEDYNPKGFLTPKPQITVPFIVAIFAIVFAS 429
            F +  S  T   +  + + L    ++RKS   + +  L  K ++ +  + +  A+ F  
Sbjct: 367 VFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAAL--KYRMWLYPVSSYLALAFLV 424

Query: 430 LFFNADTFYP 439
           L      ++P
Sbjct: 425 LVVGLMAYFP 434


Lambda     K      H
   0.329    0.141    0.434 

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: 648
Number of extensions: 32
Number of successful extensions: 2
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: 459
Length of database: 473
Length adjustment: 33
Effective length of query: 426
Effective length of database: 440
Effective search space:   187440
Effective search space used:   187440
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 (21.8 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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