GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglC in Pseudomonas fluorescens FW300-N2E3

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 AO353_21390 AO353_21390 ABC transporter

Query= TCDB::G4FGN4
         (313 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_21390 AO353_21390 ABC
           transporter
          Length = 340

 Score =  223 bits (568), Expect = 5e-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  ELSIFLVLIGIGLVFEMFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGI 82

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

Query: 113 KARLAPFISTLGMLSVGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGV 172
              + PFI+TLGM+   RGLA   + G P+S   +S+T  G G +     PVI   V+ V
Sbjct: 143 VTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGAM-----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+IA+ IDQ R  ++
Sbjct: 318 IKGLIIVIAVVIDQYRNKRK 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: 311
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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