Aligments for a candidate for sglS in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Aligments for a candidate for sglS in Escherichia coli BW25113

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

Query= uniprot:L0FZF3
         (547 letters)



>lcl|FitnessBrowser__Keio:17739 b3679 predicted transporter (NCBI)
          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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources