GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Burkholderia phytofirmans PsJN

Align Fructose import permease protein FrcC (characterized)
to candidate BPHYT_RS22740 BPHYT_RS22740 ABC transporter permease

Query= SwissProt::Q9F9B1
         (360 letters)



>FitnessBrowser__BFirm:BPHYT_RS22740
          Length = 328

 Score =  263 bits (672), Expect = 5e-75
 Identities = 137/303 (45%), Positives = 194/303 (64%), Gaps = 6/303 (1%)

Query: 51  PLIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIM 110
           PLI LVL+   F +    +F S   ++LILQQ  +V ++   QTL++LT GIDLS G +M
Sbjct: 26  PLIALVLAC-GFFISQSSRFLSFQNLSLILQQTMVVAVIAIGQTLIVLTGGIDLSCGMVM 84

Query: 111 VLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLA 170
              S+IM +F    G PP L+++CG+G  AL G +NG L+ R+KLP FIVTLG   I  A
Sbjct: 85  AFGSIIMTKFAVTLGVPPVLAILCGVGASALFGALNGVLITRIKLPAFIVTLGTLNIAFA 144

Query: 171 SNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNRTAW 230
              +YS      A+ +S     + F G  F++G A  TYG V+ +L+    W+VL  T  
Sbjct: 145 LTQIYS-----NAESVSNLPDAIMFLGNTFKLGPADVTYGTVLTLLMYLATWFVLRDTVP 199

Query: 231 GRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANI 290
           GR++YA+G++PEAA+L G++  ++L+++Y+L+G I  +A    + R G   P AGQ  N+
Sbjct: 200 GRHLYALGNNPEAARLMGLSSQKILLTVYSLAGAIYGIAALLSVSRTGVGDPQAGQTENL 259

Query: 291 ESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVA 350
           +SITAVV+GG SLFGGRGSI G L GALIVGVF  GL L+G    +  L+ G+L+I+AVA
Sbjct: 260 DSITAVVLGGTSLFGGRGSISGTLLGALIVGVFRNGLTLIGVSSVYQVLITGMLVILAVA 319

Query: 351 IDQ 353
            D+
Sbjct: 320 ADK 322


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: 361
Number of extensions: 21
Number of successful extensions: 2
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: 328
Length adjustment: 29
Effective length of query: 331
Effective length of database: 299
Effective search space:    98969
Effective search space used:    98969
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.

Links

Downloads

Related tools

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