GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Azospirillum brasilense Sp245

Align Fructose import permease protein FrcC (characterized)
to candidate AZOBR_RS27940 AZOBR_RS27940 ABC transporter permease

Query= SwissProt::Q9F9B1
         (360 letters)



>FitnessBrowser__azobra:AZOBR_RS27940
          Length = 329

 Score =  135 bits (341), Expect = 1e-36
 Identities = 97/311 (31%), Positives = 157/311 (50%), Gaps = 14/311 (4%)

Query: 51  PLIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIM 110
           P + L  +LI  G I+   F S   +  +L + A +GI+    T VI   GIDLSVG++ 
Sbjct: 19  PFLALA-ALIVLGTIVNPVFLSPGNIGNVLTRTAFIGIIAVGATFVITAGGIDLSVGSLA 77

Query: 111 VLSS----VIMGQF--TFRYGFPPAL-SVICGLGVGALCGYINGTLVARMKLPPFIVTLG 163
             +S    V+M     +   G P  L  V+  LG+G + G +NG LV + ++  FIVTLG
Sbjct: 78  AFASGVMIVVMNALVGSMGAGLPVILIGVLVALGLGLVAGLVNGLLVTKGRMEAFIVTLG 137

Query: 164 MWQIVLASNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWY 223
              I   S   Y A+       +S N+ I   +   +  G    +Y ++   ++  +   
Sbjct: 138 TMGI-FRSLVTYIAD----GGTLSLNSEIRTIYRPVYYGGVFGISYPILAFAVVALIGAL 192

Query: 224 VLNRTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPT 283
           ++ RT +GRY  A+G   + A+ + +NV R+ +  + L G+  A+A    + R+GS S T
Sbjct: 193 IMYRTRFGRYCAAIGSSEDVARYSAINVDRVKLLAFVLQGICVAIAVVIYVPRLGSASAT 252

Query: 284 AGQFANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLI-G 342
            G    +E+I AV+IGG  L GG G I G + GA+++ +    L L G    +    I G
Sbjct: 253 TGLLWELEAIAAVIIGGTMLKGGYGRIWGTVVGAVMLTLIDNILNLTGAISVYLNGTIQG 312

Query: 343 LLIIIAVAIDQ 353
           ++II+AV + +
Sbjct: 313 VIIIVAVLLQR 323


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: 366
Number of extensions: 29
Number of successful extensions: 4
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: 329
Length adjustment: 29
Effective length of query: 331
Effective length of database: 300
Effective search space:    99300
Effective search space used:    99300
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