GapMind for catabolism of small carbon sources

 

Aligments for a candidate for deoxyribonate-transport in Pseudomonas fluorescens FW300-N2E3

Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate AO353_24515 AO353_24515 MFS transporter permease

Query= reanno::WCS417:GFF1429
         (438 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_24515 AO353_24515 MFS
           transporter permease
          Length = 432

 Score =  295 bits (755), Expect = 2e-84
 Identities = 159/409 (38%), Positives = 236/409 (57%), Gaps = 14/409 (3%)

Query: 20  KLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLIM 79
           +LMP L++ Y+ ++LDR N+  AK  +  DL +S   YGLGAG+FF+ Y L E+PSN+I+
Sbjct: 23  RLMPFLMLCYLCAYLDRVNVGFAKLQMMNDLALSETVYGLGAGMFFIGYFLCEVPSNIIL 82

Query: 80  HKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFNR 139
           HKVGAR WIARIM+TWG++SA  AFV+    FY LR LLGIAEAGL PG++LYLTYWF  
Sbjct: 83  HKVGARVWIARIMITWGIVSALFAFVETAWQFYALRFLLGIAEAGLAPGLLLYLTYWFPS 142

Query: 140 EQRARATGYFLLGVCFANIIGGPVGAALM-RMDGMLGWHGWQWMFMLEGLPAVAFAWVVW 198
            +RAR T  + + +  + ++GGP+   +M    GM GW GWQWMF+LE +P V    +V 
Sbjct: 143 YRRARMTVLWFIAIPLSGMVGGPLSGWIMNHFAGMHGWAGWQWMFVLEAVPTVLIGLLVL 202

Query: 199 RKLPDRPSKAPWLSAEEARGIEQRIAQE-----TEEGAGEGGHSLKNWLTPQILLAIFVY 253
             L D   +A WL  +E   I + +A++     T    GE     + WL   I      Y
Sbjct: 203 SYLKDGVHQASWLDDDEKALISRELAEDDQQKVTHASVGEFIRDRRLWLLAGI------Y 256

Query: 254 FCHQITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGRCRRL 313
           FC  +  Y + F+LP+++   G  + + +G L+SLP++ A    L   R        R  
Sbjct: 257 FCVVMGQYAITFWLPTLVRNAGVSNPLHIGFLSSLPYLCAIAAMLYAGRSGDKHRERRWH 316

Query: 314 LVTGLLTMALGLGIASVSG--PVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGL 371
           L+  ++  A+GL +A++ G   + S+L  CL+A       S+ ++ P + L GV+ A G+
Sbjct: 317 LIVPMIAGAIGLSLAALMGGNVLLSILSLCLAASGILSATSMFWMLPTTLLGGVSAAAGI 376

Query: 372 GFVNACGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRL 420
             VN+   L GF  P ++G +   TG++  G+ +I  VL+  A   LR+
Sbjct: 377 AAVNSFANLAGFCSPYLIGWVTTQTGSSAIGMYLITGVLLFGATLVLRI 425


Lambda     K      H
   0.327    0.141    0.438 

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: 565
Number of extensions: 30
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: 438
Length of database: 432
Length adjustment: 32
Effective length of query: 406
Effective length of database: 400
Effective search space:   162400
Effective search space used:   162400
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 (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