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

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources