GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Tistlia consotensis USBA 355

Align Fructose import permease protein FrcC (characterized)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease

Query= SwissProt::Q9F9B1
         (360 letters)



>NCBI__GCF_900177295.1:WP_085121058.1
          Length = 335

 Score =  166 bits (419), Expect = 1e-45
 Identities = 108/310 (34%), Positives = 166/310 (53%), Gaps = 12/310 (3%)

Query: 49  AVPLIVLVLSLIAFGVI--LGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSV 106
           ++ L +L L+L+   V+  L   F +   +  IL Q  ++GI+    T VILT GIDLSV
Sbjct: 31  SLELRMLGLALVIGAVLSLLSPYFLTESNIFNILDQSVVIGILSIGMTFVILTGGIDLSV 90

Query: 107 GAIMVLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQ 166
           G++  LS +++G     Y  P A  ++ G+  GA  G ++G L+   +L  F+VTLGM  
Sbjct: 91  GSVAGLSGIVLGLALKDYPIPVA--ILLGVLTGAGVGLVSGILIGYFRLAAFVVTLGMMA 148

Query: 167 IVLASNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLN 226
           I  +  +++S    I       ++ +   +   F I   V   G   +     L W  L 
Sbjct: 149 IGRSLAYIFSGQTAISGFPSDLSSIV---YTDVFGIPTNVLFLGFAYL-----LAWGYLT 200

Query: 227 RTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQ 286
            T  GR +YA+G + EAA+ AG+ V    I  Y +SG + A+A    + +I SV P  G 
Sbjct: 201 YTKGGRTIYAIGSNKEAARAAGLGVLFYSILPYVVSGALAAVAITFSVAQILSVDPLTGN 260

Query: 287 FANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLII 346
              +++I AVVIGG SL+GGRGSI+G L G LI+ +   GL L+G  P W    IG +II
Sbjct: 261 GMELDAIAAVVIGGASLYGGRGSIVGTLIGVLIMVMIRNGLNLLGVSPFWQGSAIGSIII 320

Query: 347 IAVAIDQWIR 356
           +A+ +++ +R
Sbjct: 321 MALLVERLVR 330


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: 372
Number of extensions: 25
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: 335
Length adjustment: 29
Effective length of query: 331
Effective length of database: 306
Effective search space:   101286
Effective search space used:   101286
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 Apr 09 2024. 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