GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Klebsiella michiganensis M5al

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate BWI76_RS14600 BWI76_RS14600 ABC transporter ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__Koxy:BWI76_RS14600
          Length = 260

 Score =  194 bits (494), Expect = 1e-54
 Identities = 111/248 (44%), Positives = 154/248 (62%), Gaps = 4/248 (1%)

Query: 12  LVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQ 71
           + K YG + +L   + +L PGE+L ++GDNGAGKS++ K +SGAV P  G IR++G+  Q
Sbjct: 16  ITKTYGSIRSLRGVNLELAPGEVLGLVGDNGAGKSTLTKVLSGAVIPSGGTIRIDGEQQQ 75

Query: 72  FRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQAR 131
           F +P ++R+  IE VYQ+L+L   + +A N+F+GRE  K  ++G  F  LD A M   AR
Sbjct: 76  FANPADSRRCHIEMVYQDLSLCDTVDVAGNLFMGREPMK-SVLGIPF--LDEAKMHADAR 132

Query: 132 AKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVL 191
             L  LG+ +I +    V  LSGGQRQ +A+ARAAAF  KV+IMDEPTAAL V E   VL
Sbjct: 133 EMLKGLGI-SIPDTRLLVRNLSGGQRQAIAIARAAAFDPKVLIMDEPTAALAVAEVEAVL 191

Query: 192 ELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTGAK 251
           ELI  V  RG+ ++LI+H +  +F V DRI +   G  +      D ++SD V  + G K
Sbjct: 192 ELIRRVSARGVSVILITHRLQDLFLVCDRIMVMYEGTNVADRRVADTSLSDIVNLIVGEK 251

Query: 252 EPPREAIA 259
              R A A
Sbjct: 252 FTARSAAA 259


Lambda     K      H
   0.321    0.136    0.383 

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: 180
Number of extensions: 6
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: 260
Length of database: 260
Length adjustment: 24
Effective length of query: 236
Effective length of database: 236
Effective search space:    55696
Effective search space used:    55696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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