GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__Cola:Echvi_1280
          Length = 318

 Score =  257 bits (657), Expect = 2e-73
 Identities = 141/302 (46%), Positives = 193/302 (63%), Gaps = 10/302 (3%)

Query: 15  LILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILGAA 74
           + LI + + L + +  FLT+ N + V+  VS    +S GMT+VI+T+GIDLSVGSIL   
Sbjct: 11  IALIILCLVLSLLSDRFLTLANGWNVMRQVSVNICISVGMTLVILTAGIDLSVGSILALC 70

Query: 75  SVVMGLLMDEK----------GLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLG 124
             V   L+             G +P  +V++G+ +G G G  NG  IT+ ++ PF++TL 
Sbjct: 71  GAVTASLIKNGIAVEGLNLHIGFAPLGAVILGVGLGFGLGWFNGWTITRFKVPPFVATLA 130

Query: 125 MLSVGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTG 184
           ML++ RGL  + +GG+PI+   E F   G G    +P+PV   AVI  +A +  K T  G
Sbjct: 131 MLTIARGLTMLWTGGFPINGLGEDFAFLGTGWFLGIPMPVWITAVIVALAVLLTKKTKFG 190

Query: 185 RRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELD 244
           R +YAIGGN  A++L GI   R+ + VY I G LAA  G ++T+ L  AQPNAG  YELD
Sbjct: 191 RYVYAIGGNERAARLSGINISRVKMTVYAIAGGLAAVGGMIVTSRLDSAQPNAGISYELD 250

Query: 245 VIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAI 304
            IAA VIGGTSLSGG+GTI+GA LG +I+GVL NG++LL VS FWQQVV G VI++A+ I
Sbjct: 251 AIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNGLVLLNVSPFWQQVVKGAVILLAVVI 310

Query: 305 DQ 306
           D+
Sbjct: 311 DK 312


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: 330
Number of extensions: 19
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: 313
Length of database: 318
Length adjustment: 27
Effective length of query: 286
Effective length of database: 291
Effective search space:    83226
Effective search space used:    83226
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