GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Echvi_1871 in Escherichia coli BW25113

Align SSS sodium solute transporter (characterized, see rationale)
to candidate 17739 b3679 predicted transporter (NCBI)

Query= uniprot:L0FZF3
         (547 letters)



>FitnessBrowser__Keio:17739
          Length = 571

 Score =  231 bits (588), Expect = 7e-65
 Identities = 168/558 (30%), Positives = 275/558 (49%), Gaps = 55/558 (9%)

Query: 4   NTLDLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNISAE 63
           N+L ++ FV + LL+    I   + +K      + YFLA ++L    + ASL+ +N+S E
Sbjct: 2   NSLQILSFVGFTLLVAV--ITWWKVRKTDTGSQQGYFLAGRSLKAPVIAASLMLTNLSTE 59

Query: 64  QFIGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGRVRT 123
           Q +G+SG  +  G+++  +E  +A TL+ +A+ FLP YLK GI T+P FL  RYD   R 
Sbjct: 60  QLVGLSGQAYKSGMSVMGWEVTSAVTLIFLALIFLPRYLKRGIATIPDFLEERYDKTTRI 119

Query: 124 VMAIFWLLIYVFVNLTSVLYLGALSLETIMGV----PLTYG------IIGLALFAMVYSI 173
           ++   +L+      L  VLY GAL+L ++  V     +++G      +I L L  ++Y++
Sbjct: 120 IIDFCFLIATGVCFLPIVLYSGALALNSLFHVGESLQISHGAAIWLLVILLGLAGILYAV 179

Query: 174 YGGLKAVAWTDVVQVVFLVAGGLATTYLALSLVGDGDVWEGIGILRKAAPSHFSMIIEKG 233
            GGL+A+A  D +  + LV GGL      L  +G G   +GI  L        + I    
Sbjct: 180 IGGLRAMAVADSINGIGLVIGGLMVPVFGLIAMGKGSFMQGIEQLTTVHAEKLNSI---- 235

Query: 234 EMMIPDGSGGSRDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMV 293
                   GG  D    LP +     G+ +VN  YW  NQ I QR LA+KSL E Q G +
Sbjct: 236 --------GGPTD---PLP-IGAAFTGLILVNTFYWCTNQGIVQRTLASKSLAEGQKGAL 283

Query: 294 FAGFLKLLMPLIVVIPGIAAYVIVQKGADASFIESMTDPVTGLAKSDRAYPTLL-HLLPP 352
               LK+L PL++V+PG+ A+ + Q                 L K+D AYPTL+ ++LP 
Sbjct: 284 LTAVLKMLDPLVLVLPGLIAFHLYQ----------------DLPKADMAYPTLVNNVLPV 327

Query: 353 GLKGLAFAALTAAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFI 412
            + G   A L  A++S+     NS ST+F++ IY+   N+N    + VT+GR       I
Sbjct: 328 PMVGFFGAVLFGAVISTFNGFLNSASTLFSMGIYRRIINQNAEPQQLVTVGRKFGFFIAI 387

Query: 413 IAAIVAPQLRQLDQA-FQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPLS 471
           ++ +VAP +    Q  + ++++  G  +  +  I I GFF+ +  + AA  A  + I   
Sbjct: 388 VSVLVAPWIANAPQGLYSWMKQLNGIYNVPLVTIIIMGFFFPRIPALAAKVAMGIGIISY 447

Query: 472 AAFKVITP-NLPFIDRMGVVFLVLSVLIIAISLYEGKGK--DSKKAIEVDAELFSTSTKF 528
                +   +  F+  +   F +  V+++ I   + +      K A  VD + +      
Sbjct: 448 ITINYLVKFDFHFLYVLACTFCINVVVMLVIGFIKPRATPFTFKDAFAVDMKPWK---NV 504

Query: 529 KVGAVLICGILVALYSVF 546
           K+ ++   GIL A+  V+
Sbjct: 505 KIASI---GILFAMIGVY 519


Lambda     K      H
   0.326    0.140    0.414 

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: 760
Number of extensions: 39
Number of successful extensions: 5
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: 547
Length of database: 571
Length adjustment: 36
Effective length of query: 511
Effective length of database: 535
Effective search space:   273385
Effective search space used:   273385
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 (21.6 bits)
S2: 53 (25.0 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