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_RS19635 BWI76_RS19635 galactoside ABC transporter permease MglC

Query= SwissProt::Q9F9B1
         (360 letters)



>FitnessBrowser__Koxy:BWI76_RS19635
          Length = 336

 Score =  172 bits (437), Expect = 9e-48
 Identities = 106/313 (33%), Positives = 167/313 (53%), Gaps = 14/313 (4%)

Query: 52  LIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMV 111
           + V++L L+A  +     F S   ++ IL Q ++  I+      +I+T G DLS G  + 
Sbjct: 18  IYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQVG 77

Query: 112 LSSVIMGQ-----------FTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIV 160
           L++VI              F      P  L ++    +GA+ G ING ++A + + PFI 
Sbjct: 78  LAAVIAATMLQAVDNANKVFPEMATMPIPLVILLVCAIGAVIGLINGIIIAYLNVTPFIT 137

Query: 161 TLGMWQIVLASNFLYSANETIRAQDISANASILQFFGQNF-RIGNAVFTYGVVVMVLLVC 219
           TLG   IV   N LY   + + A  IS   S    F Q F  +G+   +Y     ++ V 
Sbjct: 138 TLGTMIIVYGINSLYY--DFVGASPISGFDSHFSQFAQGFVALGSFRLSYITFYALIAVF 195

Query: 220 LLWYVLNRTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGS 279
            +W + N+T +G+ ++A+G +PEAAK++GVNV   L+ IY LSG+  A  G    GRIGS
Sbjct: 196 FVWILWNKTRFGKNIFAIGGNPEAAKVSGVNVALNLLMIYALSGVFYAFGGLLEAGRIGS 255

Query: 280 VSPTAGQFANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYL 339
            +   G    +++I A V+GG+S  GG G++ G++ G +I  V + GL  +G +P W Y+
Sbjct: 256 ATNNLGFMYELDAIAACVVGGVSFSGGVGTVFGVVTGVIIFTVINYGLTYIGVNPYWQYI 315

Query: 340 LIGLLIIIAVAID 352
           + G +II AVA+D
Sbjct: 316 IKGAIIIFAVALD 328


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: 307
Number of extensions: 11
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: 360
Length of database: 336
Length adjustment: 29
Effective length of query: 331
Effective length of database: 307
Effective search space:   101617
Effective search space used:   101617
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