GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Klebsiella michiganensis M5al

Align Fructose import permease protein FrcC (characterized)
to candidate BWI76_RS00280 BWI76_RS00280 ribose ABC transporter permease

Query= SwissProt::Q9F9B1
         (360 letters)



>FitnessBrowser__Koxy:BWI76_RS00280
          Length = 321

 Score =  179 bits (454), Expect = 9e-50
 Identities = 100/300 (33%), Positives = 170/300 (56%), Gaps = 5/300 (1%)

Query: 53  IVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMVL 112
           ++ +L LIA    +   FF+   +  ILQQ ++  I+    TLVILT+GIDLSVG+++ L
Sbjct: 23  LIALLVLIAIVSTMSPNFFTVNNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLAL 82

Query: 113 SSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLASN 172
           +  +             ++V   L +GA  G + G +VA+ ++  FI TL M  ++    
Sbjct: 83  TGAVAASIV-GIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLLRGVT 141

Query: 173 FLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNRTAWGR 232
            +Y+    +     + NA +  +FG    +G       V +M ++    WY+L+ T  GR
Sbjct: 142 MVYTNGSPVNT-GFTDNADLFGWFGIGRPLG---IPTPVWIMAIVFLAAWYMLHHTRLGR 197

Query: 233 YVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANIES 292
           Y+YA+G +  A +L+G++V ++ I +Y+L G++ +LAG   + R+ S  PTAG    +++
Sbjct: 198 YIYALGGNEAATRLSGISVNKVKIIVYSLCGMLASLAGIIEVARLSSAQPTAGTGYELDA 257

Query: 293 ITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVAID 352
           I AVV+GG SL GG+G I+G L GALI+G  + GL L+G    +  ++  ++I++AV +D
Sbjct: 258 IAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLVD 317


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: 343
Number of extensions: 23
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: 360
Length of database: 321
Length adjustment: 28
Effective length of query: 332
Effective length of database: 293
Effective search space:    97276
Effective search space used:    97276
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