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_3391 PP_3391 putative Tartrate MFS transporter

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



>FitnessBrowser__Putida:PP_3391
          Length = 438

 Score =  265 bits (676), Expect = 3e-75
 Identities = 145/403 (35%), Positives = 222/403 (55%), Gaps = 3/403 (0%)

Query: 20  KLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLIM 79
           ++MPL II ++ S+ DR NI+ AK  +  +LG+S AAYGL A +FF+ Y L E+PS+L +
Sbjct: 29  RIMPLAIICFLFSYFDRINISFAKTQMQQELGLSDAAYGLAASMFFVGYVLFEVPSSLGL 88

Query: 80  HKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFNR 139
            + GA  WI RIMV+WGL +AA+ F   + + Y LR L+G+ EAG  P ++ YL  WF R
Sbjct: 89  KRYGAPAWICRIMVSWGLATAALVFAYTQYTLYFLRFLIGVMEAGFGPAILFYLACWFPR 148

Query: 140 EQRARATGYFLLGVCFANIIGGP-VGAALMRMDGMLGWHGWQWMFMLEGLPAVAFAWVVW 198
           +  A+  G + L V  A  +GGP  G  L  MDG+LG  GW W+F++ GLP V    +V 
Sbjct: 149 KHLAKMNGLWFLAVPLAGAVGGPAAGFLLGTMDGVLGLAGWHWLFLMSGLPCVLLGLLVL 208

Query: 199 RKLPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWLTPQILLAIFVYFCHQI 258
            KL      A WLS EE   + + +AQ+        G   +  LT ++ +  F+Y+  + 
Sbjct: 209 WKLDRDIEAAKWLSREEKDLLAENLAQDKRTAKPILGSIWRVLLTREVAIMAFIYYVVKT 268

Query: 259 TIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGRCRRLLVTGL 318
             Y + F++P +I   G    + VG+L++LP+  A +G +L+ R +   G  +R LV  L
Sbjct: 269 ASYGLNFWMPHLIKSSGVQDMLWVGVLSALPYAVACIGMVLLTRHSDRTGERKRYLVYCL 328

Query: 319 LTMALGLGIASV--SGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLGFVNA 376
           L  A+G  +A +    P   +    L+    F+   I +  P S   G+A+A G   +N+
Sbjct: 329 LAAAVGYLLACLFSDSPFAMMTALVLATAGTFIAIPIFWTIPQSTFSGLAIATGTAAINS 388

Query: 377 CGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALR 419
            G L G V P ++G I   T +   G+  IA +++VA L  +R
Sbjct: 389 VGQLSGIVAPVMVGKINDLTDSTYMGMLSIAPLILVACLVVMR 431


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: 508
Number of extensions: 26
Number of successful extensions: 3
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: 438
Length adjustment: 32
Effective length of query: 406
Effective length of database: 406
Effective search space:   164836
Effective search space used:   164836
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