GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfT in Escherichia coli BW25113

Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate 17810 b3750 ribose ABC transporter permease protein (NCBI)

Query= SwissProt::P39328
         (341 letters)



>FitnessBrowser__Keio:17810
          Length = 321

 Score =  194 bits (494), Expect = 2e-54
 Identities = 120/325 (36%), Positives = 189/325 (58%), Gaps = 15/325 (4%)

Query: 9   TTTPKRRFR--WPTGMPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPV 66
           T + +R F   W      L+ALL+++ + S ++P+F+ +      LF    +IL + +  
Sbjct: 5   TVSGRRYFTKAWLMEQKSLIALLVLIAIVSTLSPNFFTI----NNLF----NILQQTSVN 56

Query: 67  ALLAIGMTLVIATGGIDLSVGAVMAIAGATTAAMTVAGFSLPIVLLSALGTGILAGLWNG 126
           A++A+GMTLVI T GIDLSVG+++A+ GA  A++     +  + + +AL  G   G   G
Sbjct: 57  AIMAVGMTLVILTSGIDLSVGSLLALTGAVAASIVGIEVNALVAVAAALALGAAIGAVTG 116

Query: 127 ILVAILKIQPFVATLILMVAGRGVAQLITAGQIV----TFNSPDLSWFGSGSLLFLPTPV 182
           ++VA  ++Q F+ATL++M+  RGV  + T G  V    T N+    WFG G  L +PTPV
Sbjct: 117 VIVAKGRVQAFIATLVMMLLLRGVTMVYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPV 176

Query: 183 IIAVLTLILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGI 242
            I  +  +  W +   T LG +I A+G N  A + +G+N   I ++ Y L GL A++AGI
Sbjct: 177 WIMGIVFLAAWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGI 236

Query: 243 IVAADIRGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLS 302
           I  A +  A    AG   ELDAI AVV+GG SL GG+  ++ +++GALI+  +N G+ L 
Sbjct: 237 IEVARLSSAQP-TAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLL 295

Query: 303 GFPPEMNQVVKAVVVLCVLIVQSQR 327
           G       +VKAVV+L  ++V +++
Sbjct: 296 GVSSYYQMIVKAVVILLAVLVDNKK 320


Lambda     K      H
   0.327    0.142    0.416 

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: 301
Number of extensions: 18
Number of successful extensions: 3
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: 341
Length of database: 321
Length adjustment: 28
Effective length of query: 313
Effective length of database: 293
Effective search space:    91709
Effective search space used:    91709
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: 49 (23.5 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