GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylH in Pseudomonas fluorescens FW300-N2C3

Align D-xylose ABC transporter, permease protein (characterized)
to candidate AO356_28515 AO356_28515 sugar ABC transporter permease

Query= CharProtDB::CH_024441
         (393 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28515
          Length = 378

 Score =  374 bits (959), Expect = e-108
 Identities = 186/363 (51%), Positives = 260/363 (71%)

Query: 28  QVFVMIAAIIAIMLFFTWTTDGAYLSARNVSNLLRQTAITGILAVGMVFVIISAEIDLSV 87
           ++  ++ A+  I LFF+W T+G +++ RN+SNLLRQ +ITGILA GMV VIIS EIDLSV
Sbjct: 12  KMLALVIAVALIWLFFSWQTEGGFVTPRNLSNLLRQMSITGILACGMVLVIISGEIDLSV 71

Query: 88  GSMMGLLGGVAAICDVWLGWPLPLTIIVTLVLGLLLGAWNGWWVAYRKVPSFIVTLAGML 147
           GS++GLLGG+AAI DV    PL   + +  + GL++G  NG+  AY ++PSFIV L GML
Sbjct: 72  GSLLGLLGGLAAILDVVYHVPLLANLSLVALCGLVIGLGNGYMTAYLRIPSFIVGLGGML 131

Query: 148 AFRGILIGITNGTTVSPTSAAMSQIGQSYLPASTGFIIGALGLMAFVGWQWRGRMRRQAL 207
           AFRG+L+G+T GTT++P S  +  +GQ YLP + G  +G L     +   W+ R  R   
Sbjct: 132 AFRGVLLGVTGGTTIAPVSPELVYVGQGYLPHTVGTGLGILLFALTLFLTWKQRRNRALH 191

Query: 208 GLQSPASTAVVGRQALTAIIVLGAIWLLNDYRGVPTPVLLLTLLLLGGMFMATRTAFGRR 267
           GL + +    V R  +   ++ G ++ LN Y G+P PVLLL +LL    ++ ++T FGRR
Sbjct: 192 GLAAHSLVRDVLRVVVIGAVLAGFVYTLNSYDGIPVPVLLLLILLGVFSYVTSQTVFGRR 251

Query: 268 IYAIGGNLEAARLSGINVERTKLAVFAINGLMVAIAGLILSSRLGAGSPSAGNIAELDAI 327
           +Y++G N+EA RLSGINV+  KL +F I G+M A+AG++ ++RL AGSPSAGN+ ELDAI
Sbjct: 252 VYSVGSNMEATRLSGINVQAVKLWIFGIMGVMCALAGVVNTARLAAGSPSAGNMGELDAI 311

Query: 328 AACVIGGTSLAGGVGSVAGAVMGAFIMASLDNGMSMMDVPTFWQYIVKGAILLLAVWMDS 387
           AAC IGGTS+ GG G+V GA++GA ++ SLDNGMSM+DV ++WQ IVKG+IL+LAVW+D 
Sbjct: 312 AACFIGGTSMRGGSGTVYGALLGALVITSLDNGMSMLDVDSYWQMIVKGSILVLAVWVDV 371

Query: 388 ATK 390
           +T+
Sbjct: 372 STR 374


Lambda     K      H
   0.325    0.138    0.415 

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: 432
Number of extensions: 9
Number of successful extensions: 1
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: 393
Length of database: 378
Length adjustment: 30
Effective length of query: 363
Effective length of database: 348
Effective search space:   126324
Effective search space used:   126324
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 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