GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Klebsiella michiganensis M5al

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 BWI76_RS07245 BWI76_RS07245 ABC transporter

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__Koxy:BWI76_RS07245
          Length = 343

 Score =  227 bits (579), Expect = 3e-64
 Identities = 132/321 (41%), Positives = 194/321 (60%), Gaps = 22/321 (6%)

Query: 9   REAGIFLILIAIVV---FLGVTTRE---FLTVENIFTVILNVSFIAIMSFGMTMVIITSG 62
           ++ GIF++++ I +     G   R+    L    +  ++L V+ I I++ G+T VIIT+G
Sbjct: 27  KDTGIFIVMLVIALTFEIAGWYVRDQSFLLNTNRLILIVLQVAIIGIIAVGVTQVIITTG 86

Query: 63  IDLSVGSILGAASVVMG-LLMDEKGLSP-FLSVV-------IGLAVGVGF--GLANGLLI 111
           IDLS GS++  A+VV   L      LSP F S+V       IG  +GVG   GL NG L+
Sbjct: 87  IDLSSGSVIALAAVVAASLAQTSDSLSPMFPSLVNMPAIIPIGAGIGVGLLCGLTNGFLV 146

Query: 112 TKARLAPFISTLGMLSVGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIG 171
           T+  + PFI+TLGM+   RGLA   + G PIS   +SFT  GQG +     PVI   V+ 
Sbjct: 147 TRTGIPPFIATLGMMVSARGLAQYYTQGNPISFLSDSFTAIGQGAM-----PVIIFFVVA 201

Query: 172 VIAHIFLKYTVTGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLG 231
            + HI LK+T  G+ +YAIGGNM ++K+ GI  ++ L++VY I G L+  AG +L A + 
Sbjct: 202 AVFHIALKHTRYGKYVYAIGGNMTSAKVSGINVNKYLVIVYAIAGALSGLAGVVLAARVS 261

Query: 232 VAQPNAGQGYELDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQ 291
             Q + G  YELD IAA VIGG+SL GG G I G  +GA+I+G++++G   +GV ++ Q 
Sbjct: 262 SGQSSMGMSYELDAIAAAVIGGSSLMGGVGRITGTLIGAMILGLIKSGFTFVGVDAYVQD 321

Query: 292 VVIGIVIIIAIAIDQIRRAKE 312
           ++ GI+I+ A+ ID  R  K+
Sbjct: 322 IIKGIIIVAAVTIDMRRNRKK 342


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: 306
Number of extensions: 17
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: 343
Length adjustment: 28
Effective length of query: 285
Effective length of database: 315
Effective search space:    89775
Effective search space used:    89775
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