GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Pseudomonas simiae WCS417

Align Fructose import permease protein FrcC (characterized)
to candidate GFF2674 PS417_13640 ribose ABC transporter permease

Query= SwissProt::Q9F9B1
         (360 letters)



>FitnessBrowser__WCS417:GFF2674
          Length = 325

 Score =  188 bits (477), Expect = 2e-52
 Identities = 112/304 (36%), Positives = 177/304 (58%), Gaps = 11/304 (3%)

Query: 52  LIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMV 111
           L VL+L L+ F  +    F +   +++I QQ ++  ++ A  T VILTAGIDLSVGAI+ 
Sbjct: 25  LPVLILLLVGFA-LASENFLTMQNLSIISQQASVNVVLAAGMTFVILTAGIDLSVGAILA 83

Query: 112 LSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLAS 171
            S+V+  Q +    F     +  G+G G L G +NG L+A M+LPPFIVTLG    +   
Sbjct: 84  ASAVVALQASMSPQFG-MFGIAAGIGFGLLLGLVNGGLIAFMRLPPFIVTLGALTAMRGL 142

Query: 172 NFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNRTAWG 231
             L + ++T+   D+        F G +  +G     + V++ V +V L W++L RT  G
Sbjct: 143 ARLLADDKTVFNPDLP-----FAFIGNDSLLG---VPWLVIIAVAVVALSWFILRRTVMG 194

Query: 232 RYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTA-GQFANI 290
             +Y+VG +PEAA+L+G+ V ++L+ +Y +SG +  L       R+ + +    GQ   +
Sbjct: 195 VQIYSVGGNPEAARLSGIKVWKVLLFVYAMSGALAGLGAVMSASRLFAANGLQLGQSYEL 254

Query: 291 ESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVA 350
           ++I AV++GG S  GG G+I G L GALI+ V + GL L+G    W Y++ G++II AVA
Sbjct: 255 DAIAAVILGGTSFTGGVGTIGGTLIGALIIAVLTNGLVLLGVSDIWQYIIKGIVIIGAVA 314

Query: 351 IDQW 354
           +D++
Sbjct: 315 LDRY 318


Lambda     K      H
   0.327    0.141    0.420 

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: 381
Number of extensions: 25
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 360
Length of database: 325
Length adjustment: 29
Effective length of query: 331
Effective length of database: 296
Effective search space:    97976
Effective search space used:    97976
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