GapMind for catabolism of small carbon sources

 

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

Align L-tyrosine transporter (characterized)
to candidate Pf6N2E2_5459 D-serine/D-alanine/glycine transporter

Query= reanno::pseudo5_N2C3_1:AO356_18530
         (471 letters)



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

 Score =  407 bits (1046), Expect = e-118
 Identities = 201/456 (44%), Positives = 288/456 (63%), Gaps = 12/456 (2%)

Query: 3   GQNSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMI 62
           G+ +  G LKR L  RHI+L+ALG  IG GLFLGSA  ++ AGP+++L Y I G    +I
Sbjct: 10  GETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVI 69

Query: 63  MRQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWA 122
           MR LGEM V  PVAGSFS +A  Y G  AGFL+GWN W L+++  ++E+TAV  Y+  W 
Sbjct: 70  MRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWF 129

Query: 123 PDIPTWVSAAAFFILINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGHG-- 180
           PD+P W+ A A  + + +INL  VK FGE EFWFA+IK+V I+ M+  G  ++  G G  
Sbjct: 130 PDVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGND 189

Query: 181 GPQASVTNLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240
           G    ++NLW+HGGF PNGV G++M++ ++MF++ G+EM+G TA EA  P+  IP AI  
Sbjct: 190 GVALGISNLWTHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGS 249

Query: 241 VIYRILIFYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSNTAAHILNFV 300
           V +RIL+FY+GAL V+LS+ PW+ +            GSPFV  F  LG  TAA I+NFV
Sbjct: 250 VFWRILLFYVGALFVILSIYPWNEI---------GTQGSPFVMTFERLGIKTAAGIINFV 300

Query: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALSRIDKRGVPVRSILASAAVTLVAVLLN 360
           V+TAALS  N G +   RML  +A+ G AP   +     GVP R++L S A  L+ VLLN
Sbjct: 301 VITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFATTSANGVPRRALLLSIAALLLGVLLN 360

Query: 361 YLVPQHALELLMSLVVATLVINWAMISYSHFKFRQHMNQTQQTPLFKALW-YPYGNYICL 419
           YLVP+     + S+     +  W MI  +  KFR+ ++ +++  L   +W YP  +Y+ L
Sbjct: 361 YLVPEKVFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLAL 420

Query: 420 AFVVFILGVMLLIPGIQISVYAIPVWVVFMWVCYVI 455
           AF+V ++G+M   P  ++++Y  P ++V + V + +
Sbjct: 421 AFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFYV 456


Lambda     K      H
   0.327    0.139    0.432 

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: 666
Number of extensions: 32
Number of successful extensions: 4
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: 471
Length of database: 473
Length adjustment: 33
Effective length of query: 438
Effective length of database: 440
Effective search space:   192720
Effective search space used:   192720
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: 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