GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08240 in Escherichia coli BW25113

Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate 17517 b3456 leucine/isoleucine/valine transporter subunit (NCBI)

Query= uniprot:G8ALI9
         (505 letters)



>FitnessBrowser__Keio:17517
          Length = 425

 Score =  369 bits (947), Expect = e-106
 Identities = 191/330 (57%), Positives = 248/330 (75%), Gaps = 7/330 (2%)

Query: 156 VVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYA 215
           +V+A+A+PF  +  R  +DI  L + YI+LG GLN+VVGL+GLL LGY  FYA+GAY++A
Sbjct: 97  LVLAVAWPF--MVSRGTVDIATLTMIYIILGLGLNVVVGLSGLLVLGYGGFYAIGAYTFA 154

Query: 216 LLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILINWYQ 275
           LL HY+G  FW CLP+AG +AA +G LLGFPVLRLRGDY AIVTLGFGEI+RI+L+N  +
Sbjct: 155 LLNHYYGLGFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIVRILLLNNTE 214

Query: 276 FTGGPNGISGIPRPSFFGIADFTRTPAE-GTAAFHEMFGLEFSPLHRIIFLYYLILVLAL 334
            TGGPNGIS IP+P+ FG+ +F+RT  E G   F   FGL++ P  R+IFL YL+ +L +
Sbjct: 215 ITGGPNGISQIPKPTLFGL-EFSRTAREGGWDTFSNFFGLKYDPSDRVIFL-YLVALLLV 272

Query: 335 VVNLFTM-RVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFFAT 393
           V++LF + R+ ++PLGRAWEALRED+IAC SLG++   +KL AF I+A F GFAG+ FA 
Sbjct: 273 VLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFAGFAGTLFAA 332

Query: 394 RQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELADYRMLAFGM 453
           RQGF+SPESFTF ESA +LAIVVLGGMGSQ  V++AA L++   E  R+  +Y ML  G 
Sbjct: 333 RQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMRDFNEYSMLMLGG 392

Query: 454 GMVLIMLWRPRGLLAHRDPTI-LLHGRPKG 482
            MVL+M+WRP+GLL    P + L +G  KG
Sbjct: 393 LMVLMMIWRPQGLLPMTRPQLKLKNGAAKG 422


Lambda     K      H
   0.329    0.144    0.438 

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: 597
Number of extensions: 32
Number of successful extensions: 2
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: 505
Length of database: 425
Length adjustment: 33
Effective length of query: 472
Effective length of database: 392
Effective search space:   185024
Effective search space used:   185024
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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