GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_24515
          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:

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