GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proP in Escherichia coli BW25113

Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate 16092 b1981 shikimate transporter (NCBI)

Query= SwissProt::Q47421
         (501 letters)



>FitnessBrowser__Keio:16092
          Length = 438

 Score =  231 bits (589), Expect = 4e-65
 Identities = 138/426 (32%), Positives = 224/426 (52%), Gaps = 15/426 (3%)

Query: 23  RLRKAITAAALGNAMEWFDFGVYGFVA-YALGQVFFPGADPGVQMIAALATFSVPFLIRP 81
           R R+A   +  G  ++W+DF +YG  A     + FFP   P +  +AA ATF V FL RP
Sbjct: 19  RARRAALGSFAGAVVDWYDFLLYGITAALVFNREFFPQVSPAMGTLAAFATFGVGFLFRP 78

Query: 82  LGGVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFS 141
           LGGV FG  GD+ GR+++L +T+ +M I+T  IG++PS+  IG WAPILL+  +  QGF+
Sbjct: 79  LGGVIFGHFGDRLGRKRMLMLTVWMMGIATALIGILPSFSTIGWWAPILLVTLRAIQGFA 138

Query: 142 VGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGW 201
           VGGE+ GA++   E +P  K+ F  S +  G   G +L  G+V LIS +  ++ FL+WGW
Sbjct: 139 VGGEWGGAALLSVESAPKNKKAFYSSGVQVGYGVGLLLSTGLVSLISMMTTDEQFLSWGW 198

Query: 202 RLPFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWKS 261
           R+PF  ++ L L  L++R+ +EE+  F       EQ       A   +   E    H  +
Sbjct: 199 RIPFLFSIVLVLGALWVRNGMEESAEF-------EQQQHYQAAAKKRIPVIEALLRHPGA 251

Query: 262 LLVCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAIMIGML--FVQPVMGLL 319
            L  I L +   +T Y++  +  +Y + ++       + + I +++G L     P    L
Sbjct: 252 FLKIIALRLCELLTMYIVTAFALNYSTQNMGLPRE--LFLNIGLLVGGLSCLTIPCFAWL 309

Query: 320 SDRFGRKPFVVIGSVAMFFLAVPSFMLINS-DIIGLIFLGLLMLAVILNAFTGVMASTLP 378
           +DRFGR+   + G++     A P FM + +  I  ++F  +++  +  +    V      
Sbjct: 310 ADRFGRRRVYITGTLIGTLSAFPFFMALEAQSIFWIVFFSIMLANIAHDMVVCVQQPMFT 369

Query: 379 ALFPTHIRYSALASAFNI-SVLIAGLTPTVAAWLVE-SSQNLYMPAYYLMVIAVIGLLTG 436
            +F    RYS     + + SV+  G TP +AA L+   + N +  A YL+   +I  +T 
Sbjct: 370 EMFGASYRYSGAGVGYQVASVVGGGFTPFIAAALITYFAGNWHSVAIYLLAGCLISAMTA 429

Query: 437 LFMKET 442
           L MK++
Sbjct: 430 LLMKDS 435


Lambda     K      H
   0.327    0.142    0.427 

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: 521
Number of extensions: 28
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: 501
Length of database: 438
Length adjustment: 33
Effective length of query: 468
Effective length of database: 405
Effective search space:   189540
Effective search space used:   189540
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