GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-transport in Pseudomonas putida KT2440

Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate PP_2830 PP_2830 Major facilitator family transporter

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



>FitnessBrowser__Putida:PP_2830
          Length = 450

 Score =  578 bits (1491), Expect = e-170
 Identities = 285/421 (67%), Positives = 341/421 (80%), Gaps = 1/421 (0%)

Query: 5   PSARTPQALNKLMFVKLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLF 64
           P+    Q LN L+  KLMPLLI+ Y++SFLDRTNIALAK  + +DLG+SAAAYGLGAGLF
Sbjct: 29  PATTHEQRLNGLLLRKLMPLLIVVYVMSFLDRTNIALAKASMGIDLGLSAAAYGLGAGLF 88

Query: 65  FLTYALSEIPSNLIMHKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAG 124
           FLTYAL+E+PSNLIMH+VGARFWI RIM+TWGL+SA MAFVQGETSFY++RLLLG+AEAG
Sbjct: 89  FLTYALAEVPSNLIMHRVGARFWITRIMITWGLLSAGMAFVQGETSFYIMRLLLGVAEAG 148

Query: 125 LFPGVMLYLTYWFNREQRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFM 184
           LFPGVMLYLTYWF+REQRARATGYFLLGVC ANI+ GP+G AL+ +DG+LGWHGWQW+F+
Sbjct: 149 LFPGVMLYLTYWFDREQRARATGYFLLGVCVANILSGPLGGALLELDGVLGWHGWQWLFV 208

Query: 185 LEGLPAVAFAWVVWRKLPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWLTP 244
           LEGLPAVA A+VVW+KLPD P+ APWL+A +A+ IE+R+A E +  A +     + +   
Sbjct: 209 LEGLPAVALAYVVWKKLPDGPASAPWLTAADAQDIERRLAAE-QAAAPQQSKLGQMFRDR 267

Query: 245 QILLAIFVYFCHQITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFA 304
           QI LAI VYF HQITIYTVIFFLP II  Y  LS   VGLLT++PWIAAA+GA  +PR A
Sbjct: 268 QIWLAIAVYFVHQITIYTVIFFLPGIIGTYAALSPFQVGLLTAVPWIAAAIGAATLPRLA 327

Query: 305 TTPGRCRRLLVTGLLTMALGLGIASVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKG 364
           T+P RCR LL  GLLTMA GL +AS++     L+GF L+A+M FVVQSIIF++P+SRL G
Sbjct: 328 TSPRRCRTLLFLGLLTMAAGLLLASLTNSFIGLIGFSLTALMLFVVQSIIFVFPSSRLSG 387

Query: 365 VALAGGLGFVNACGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRLRMGH 424
            ALA GL FV  CGL GGFVGPSVMG+IEQ+TG+  NGL +IA +LV AAL + RLR G 
Sbjct: 388 SALAAGLAFVTTCGLFGGFVGPSVMGLIEQTTGSTRNGLWIIAALLVCAALVSTRLRQGQ 447

Query: 425 E 425
           E
Sbjct: 448 E 448


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: 668
Number of extensions: 29
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: 438
Length of database: 450
Length adjustment: 32
Effective length of query: 406
Effective length of database: 418
Effective search space:   169708
Effective search space used:   169708
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