GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Marivita geojedonensis DPG-138

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 WP_085637954.1 MGEO_RS12240 ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>NCBI__GCF_002115805.1:WP_085637954.1
          Length = 362

 Score =  199 bits (506), Expect = 8e-56
 Identities = 122/339 (35%), Positives = 184/339 (54%), Gaps = 42/339 (12%)

Query: 10  EAGIFLILIAIVVFLGV------------------TTRE--FLTVENIFTVILNVSFIAI 49
           EA +F+ L+ I++                      T R+   L +  I  VIL VS I I
Sbjct: 24  EANVFIALVLIILIFEALGQILPYMNGQSMLFDFNTNRDGTILNIARIKIVILQVSIIGI 83

Query: 50  MSFGMTMVIITSGIDLSVGSILGAAS-VVMGLLMDEK----------------GLSPFLS 92
           ++ G+T VII+ GIDLS G ++GAA+ +VM     E                  L   + 
Sbjct: 84  IALGVTQVIISGGIDLSSGPLVGAAAMIVMSFAQTELVNGNPNPKAVFGPWSFDLPVIIP 143

Query: 93  VVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGLAYVMSGGWPISPFPESFTVH 152
           +++GLA G   G  NG  I   R+ PFI+TLGM  + RG+A   + G P+S   E +   
Sbjct: 144 ILVGLAFGALIGAINGTFIALTRIPPFIATLGMFLICRGIAQWWTKGQPVSFPTEQYAAL 203

Query: 153 GQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYAIGGNMEASKLVGIKTDRILILVY 212
           G GM+     PV++  ++  +  + +K+TV G+  YAIG N +A+++ GI   R  ILVY
Sbjct: 204 GAGMM-----PVVWFVLLAAVFFVIMKFTVYGKHTYAIGSNEDAARMSGINVKRHKILVY 258

Query: 213 TINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATVIGGTSLSGGEGTILGAFLGAVI 272
            I G LAAFA  +L++    AQ   GQ YEL  IA  VIGG SL+GG G+I+G  LGA++
Sbjct: 259 MIAGMLAAFAAIVLSSKNLTAQAGMGQFYELYAIAMAVIGGVSLTGGRGSIVGTVLGAMV 318

Query: 273 MGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQIRRAK 311
            GV+++G   + + +F+Q + +G +II A+ +DQ R+ +
Sbjct: 319 FGVIQSGFTFIKLDAFYQLMAMGAIIISAVVLDQWRQQR 357


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: 309
Number of extensions: 21
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: 362
Length adjustment: 28
Effective length of query: 285
Effective length of database: 334
Effective search space:    95190
Effective search space used:    95190
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 24 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