GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Pseudomonas fluorescens FW300-N2E2

Align Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate Pf6N2E2_524 Inositol transport system permease protein

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_524
          Length = 340

 Score =  222 bits (566), Expect = 9e-63
 Identities = 130/320 (40%), Positives = 188/320 (58%), Gaps = 22/320 (6%)

Query: 10  EAGIFLILIAI-VVF--LGVTTRE---FLTVENIFTVILNVSFIAIMSFGMTMVIITSGI 63
           E  IFL+LI I +VF   G   R+    +  + +  +IL VS I +++ G+T VIIT+GI
Sbjct: 23  ELSIFLVLIGIGLVFEMFGWIMRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGI 82

Query: 64  DLSVGSILGAASVVMGLLMDEKG-----------LSPFLSVVIGLAVGVGFGLANGLLIT 112
           DLS GS+L  ++++   L                L  ++ VV GL VG+  G  NG +I 
Sbjct: 83  DLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWIPVVAGLGVGLLAGAINGSIIA 142

Query: 113 KARLAPFISTLGMLSVGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGV 172
              + PFI+TLGM+   RGLA   + G P+S   +S+T  G G +     PVI   V+ V
Sbjct: 143 ITGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGAM-----PVIIFLVVAV 197

Query: 173 IAHIFLKYTVTGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGV 232
           I HI L+YT  G+  YAIGGNM+A++  GI   R L++VY+I G LA  AG + +A    
Sbjct: 198 IFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAGLAGVVASARAAT 257

Query: 233 AQPNAGQGYELDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQV 292
            Q   G  YELD IAA VIGGTSL+GG G I G  +GA+I+GV+ +G   +GV ++ Q +
Sbjct: 258 GQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDI 317

Query: 293 VIGIVIIIAIAIDQIRRAKE 312
           + G++I++A+ IDQ R  ++
Sbjct: 318 IKGLIIVVAVVIDQYRNKRK 337


Lambda     K      H
   0.328    0.145    0.421 

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: 308
Number of extensions: 19
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: 313
Length of database: 340
Length adjustment: 28
Effective length of query: 285
Effective length of database: 312
Effective search space:    88920
Effective search space used:    88920
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: 48 (23.1 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