GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1747 in Pseudomonas fluorescens FW300-N2E2

Align TM1747, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate Pf6N2E2_3423 Putative glutathione transporter, permease component

Query= TCDB::Q9X269
         (341 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3423
          Length = 315

 Score =  170 bits (430), Expect = 5e-47
 Identities = 100/320 (31%), Positives = 165/320 (51%), Gaps = 17/320 (5%)

Query: 26  KFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKGF 85
           +F+L R L +   +  + +IT+VL+   PG+       R  +   +TP+       L   
Sbjct: 7   RFILSRPLQLLPVLFGISMITFVLVRSIPGD-----PARALLGSRSTPE------ALIRI 55

Query: 86  EERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFAL 145
             +YGL+ PLW Q   +LK  +    G S       ++ LI  +   T  L L S+L AL
Sbjct: 56  RAQYGLDQPLWMQYFYFLKNLLKGDLGQSLLYKVDALQ-LISTRIEPTLFLVLGSVLLAL 114

Query: 146 VVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSG---- 201
           ++ VPL  +AA  K  W D+     +  G+ +P++ + + LIL+ S+ LG  P SG    
Sbjct: 115 LIAVPLATVAARNKGGWQDHLIRLFTTAGLGMPAFWLGIMLILLLSVQLGLFPVSGYGRT 174

Query: 202 -WEGIRTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTVIMKHALR 260
            W+ +   +LP + +AL   A + R  R S+L  L  D    A A+G  +R +  +H L 
Sbjct: 175 AWDKLHHMVLPCLTIALALSAVLVRNLRASMLMELQADHATAARARGLSERAIFRRHVLP 234

Query: 261 PSMIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTSTFILALTV 320
            S++P V ++   + +L+ GTV +E++F IPG+GQL      TRDY ++     +LAL  
Sbjct: 235 NSLVPAVNLLAVNIGWLISGTVVIESLFAIPGIGQLLVRGIFTRDYMVVQGVAMVLALAT 294

Query: 321 MIMNLIVDVLYAILDPRIKL 340
           + +N + DVL  ++DPR+ +
Sbjct: 295 VTVNFLADVLTVMIDPRVNM 314


Lambda     K      H
   0.328    0.143    0.429 

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: 257
Number of extensions: 13
Number of successful extensions: 4
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: 341
Length of database: 315
Length adjustment: 28
Effective length of query: 313
Effective length of database: 287
Effective search space:    89831
Effective search space used:    89831
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: 49 (23.5 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