GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_04205 in Pseudomonas putida KT2440

Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate PP_1710 PP_1710 MFS transporter, phthalate permease family

Query= reanno::WCS417:GFF828
         (454 letters)



>FitnessBrowser__Putida:PP_1710
          Length = 446

 Score =  358 bits (920), Expect = e-103
 Identities = 171/432 (39%), Positives = 258/432 (59%), Gaps = 12/432 (2%)

Query: 6   PTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQI 65
           PT  R+ +L +L + T INY DR  I+IA   + KDLG+D V +G IFSAF W Y    +
Sbjct: 24  PTRRRWFMLSLLLVATIINYVDRVNISIAAPFMAKDLGLDKVEMGLIFSAFAWTYALALV 83

Query: 66  PGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPSFP 125
           P G++ DRFGS+  Y +S+ +WS  TV QG    F       +LF LR  VG  EAP+FP
Sbjct: 84  PAGFIADRFGSRLTYGVSLISWSAVTVAQGLASGFA------SLFGLRLAVGAMEAPAFP 137

Query: 126 GNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGIIF 185
            N+R V  WFP  ERG AS+I+   QY  T LF   + W+  ++ W+HVF   G++GI+F
Sbjct: 138 ANSRAVTVWFPARERGMASSIYVCGQYLGTALFTGALLWLATTYDWRHVFYSTGLVGILF 197

Query: 186 SLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLLTNRM 245
            ++WL +   P     +++ E  +I   G +V   Q++ +        W  + +L   R 
Sbjct: 198 GVVWLVLYRDPLNCKKVSKEELAYIENGGGLVKSSQERTRFD------WRQVAELFRYRQ 251

Query: 246 MLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGVISD 305
           +  + LG++      YFFLTWFP YL+++R +T++K G  A +P I   +G +L G++SD
Sbjct: 252 VWAICLGKFASTSALYFFLTWFPTYLIEERQLTLIKVGIFAVMPFIGATVGILLAGIVSD 311

Query: 306 YLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALGWAVV 365
            L+RKG+SL+FARK P++ G ++  SIV  N+ D   + +  + LAFF +G+ +  WA V
Sbjct: 312 LLIRKGYSLSFARKLPLVVGSMLGMSIVLVNFTDSNVLCIAVLTLAFFAQGIASSSWAAV 371

Query: 366 SDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVFSYL 425
           S+ +PK++ GL+GG+ +   N+  I TPIVIG I+  +GSF  A  F+G  AL+   SY 
Sbjct: 372 SEVAPKELIGLTGGITSLAANIGGIVTPIVIGAIVHASGSFAMAFWFIGGVALMGTLSYS 431

Query: 426 VIVGPIKRVVLK 437
           +++G + R+ LK
Sbjct: 432 LLLGKLYRIELK 443


Lambda     K      H
   0.327    0.142    0.444 

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: 595
Number of extensions: 29
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: 454
Length of database: 446
Length adjustment: 33
Effective length of query: 421
Effective length of database: 413
Effective search space:   173873
Effective search space used:   173873
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