GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1694 in Escherichia coli BW25113

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 17517 b3456 leucine/isoleucine/valine transporter subunit (NCBI)

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__Keio:17517
          Length = 425

 Score =  236 bits (603), Expect = 6e-67
 Identities = 146/347 (42%), Positives = 200/347 (57%), Gaps = 46/347 (13%)

Query: 13  VALLVLPLILQSF-GNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLF 71
           VALLVL +          V IA L ++Y++L LGLN+VVG +GLL LGY  FYA+GAY F
Sbjct: 94  VALLVLAVAWPFMVSRGTVDIATLTMIYIILGLGLNVVVGLSGLLVLGYGGFYAIGAYTF 153

Query: 72  ALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIV 131
           AL+   +              GL    W  +P+A L+AA  G +LG P L+LRGDYLAIV
Sbjct: 154 ALLNHYY--------------GL--GFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIV 197

Query: 132 TLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINS------ 185
           TLGFGEI+RI L N      +T GP G+ QI    +FGL+  +     G+D  S      
Sbjct: 198 TLGFGEIVRILLLN---NTEITGGPNGISQIPKPTLFGLEFSRTAREGGWDTFSNFFGLK 254

Query: 186 ------VTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLL 239
                 V   Y + L+LVV+S+ +  RL    +GRAW A+REDEIA +++G++ R +KL 
Sbjct: 255 YDPSDRVIFLYLVALLLVVLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLT 314

Query: 240 AFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSA 299
           AF + A+F G +G +F A QGFVSPESF+  ES  ++A+VVLGG+G    VIL A+LL  
Sbjct: 315 AFTISAAFAGFAGTLFAARQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVV 374

Query: 300 LPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWP 346
             E++R              D      L++   M+++M+ RP+GL P
Sbjct: 375 SRELMR--------------DFNEYSMLMLGGLMVLMMIWRPQGLLP 407


Lambda     K      H
   0.328    0.144    0.430 

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: 362
Number of extensions: 19
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: 358
Length of database: 425
Length adjustment: 31
Effective length of query: 327
Effective length of database: 394
Effective search space:   128838
Effective search space used:   128838
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: 50 (23.9 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