GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruF in Klebsiella michiganensis M5al

Align Fructose import permease protein FruF (characterized)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease

Query= SwissProt::Q8G846
         (356 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS14865 BWI76_RS14865 ribose ABC
           transporter permease
          Length = 339

 Score =  172 bits (435), Expect = 2e-47
 Identities = 106/325 (32%), Positives = 176/325 (54%), Gaps = 11/325 (3%)

Query: 23  WSIVAFILLVIICTIFQHDFLALSWNSNTGGLAGPLITMLQESARYLMIATGMTLVISTA 82
           W  V  ++++++  I    F A ++N         L+ + +  +   ++A GMT VI T+
Sbjct: 22  WDRVGILIVLLVLLILMSTF-APNFNR-----VDNLLNIARSISVNAILAAGMTFVILTS 75

Query: 83  GIDLSVGSVMAVAGAAAMQTLSNGMNVWLSILIALAVGLAIGCVNGALVSFLGLQPFITT 142
           GIDLSVGS++AV+G  ++     G+   L+IL  + VG   G +NG L ++L L PFI T
Sbjct: 76  GIDLSVGSIVAVSGVVSVVAAMAGIPAPLAILAGVGVGALCGLLNGVLTAYLALAPFIVT 135

Query: 143 LIMMLAGRGMAKVITSGENTDASAVAGNEPLKWFANGFILGIPANFVIAVIIVILVGLLC 202
           L  M   RGMA  IT G+   +S+++  E      NG+++GIP   +I +++ +L   + 
Sbjct: 136 LGTMTFLRGMAYTITEGQPIVSSSLSFRE----LGNGYLIGIPIPVIIMLVVYLLAWFIL 191

Query: 203 RKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFATASVMRVDVVKT 262
            +T  G  I AVG N +A+R+ G++ K++L  VY I+G  A +AG+   A V+       
Sbjct: 192 ERTRFGRHIYAVGGNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQPT-A 250

Query: 263 GQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLGVNAEATPAFFAVV 322
           G   E+ AI AVV+GGTSL GG+  + G+ +G++I+ ++   +I L V          +V
Sbjct: 251 GTGYELDAIAAVVLGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSVPFFTQLLIKGIV 310

Query: 323 VIVICVMQAPKIHNLSANMKRKRAL 347
           +I+   +   K H       RK+ +
Sbjct: 311 IILAVAIDGLKQHPELFTFWRKKEI 335


Lambda     K      H
   0.325    0.136    0.384 

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: 14
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: 356
Length of database: 339
Length adjustment: 29
Effective length of query: 327
Effective length of database: 310
Effective search space:   101370
Effective search space used:   101370
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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