GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruG in Azospirillum brasilense Sp245

Align Fructose import permease protein FruG (characterized)
to candidate AZOBR_RS31200 AZOBR_RS31200 sugar ABC transporter permease

Query= SwissProt::Q8G845
         (340 letters)



>FitnessBrowser__azobra:AZOBR_RS31200
          Length = 325

 Score =  207 bits (526), Expect = 4e-58
 Identities = 121/320 (37%), Positives = 181/320 (56%), Gaps = 14/320 (4%)

Query: 21  QMIPTLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGGIDL 80
           + +P L    + ++  ++  A F  +  L  + +L  D+A+L I AV MT  IL+GGIDL
Sbjct: 4   RFLPLLVTSAVLVVGFLLCAAQFPNFASLRVVGNLLTDNAFLGITAVGMTFVILSGGIDL 63

Query: 81  SVGAIVAITAVVGLKLANAG----VPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIAT 136
           SVGA++  T V+   L   G    V AF V    L +   FG   G +I  F M PFI T
Sbjct: 64  SVGAVIGFTTVLLAVLIEQGGWHPVSAFAVA---LAVAGGFGAAMGAVIHVFQMPPFIVT 120

Query: 137 LSTMFLARGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIALVVVV 196
           L+ MF+ARGL  ++STDS+              ++     K++      +GV+ A VV  
Sbjct: 121 LAGMFVARGLGFVLSTDSIPINHPLYAELGDLALRFDGGGKLTLPALLMLGVVAAAVVCA 180

Query: 197 FGYVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIGS 256
                 H TR G  +YA+GG+R SAELMG+PV RT   +Y  S  LA LA IV++   G+
Sbjct: 181 ------HWTRFGANLYALGGNRQSAELMGVPVGRTTVAVYALSGLLAGLAGIVFSLYTGA 234

Query: 257 AKNTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDP-LTSDFGVPAEWTT 315
             +    G ELD + +VVIGGT +TGG+GYV+G+ +G L++ ++   +T D  + + WT 
Sbjct: 235 GYSLAATGVELDTITAVVIGGTQLTGGYGYVIGTFIGVLIQGLIQTYITFDGSLSSWWTK 294

Query: 316 IVIGLMILVFVVLQRAVMAV 335
           I IG+++ VF++LQ+ ++AV
Sbjct: 295 IAIGVLLFVFILLQKGLLAV 314


Lambda     K      H
   0.327    0.142    0.400 

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: 305
Number of extensions: 13
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: 340
Length of database: 325
Length adjustment: 28
Effective length of query: 312
Effective length of database: 297
Effective search space:    92664
Effective search space used:    92664
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