GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Herbaspirillum seropedicae SmR1

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 HSERO_RS05325 HSERO_RS05325 ribose ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__HerbieS:HSERO_RS05325
          Length = 328

 Score =  246 bits (627), Expect = 7e-70
 Identities = 122/303 (40%), Positives = 189/303 (62%)

Query: 2   WKKLFKAREAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITS 61
           W+ L  +  A     L+ + + +G+ +  F T+ N F V+  VS + I++ GM+ VI+T 
Sbjct: 21  WRSLIHSPLALPLAGLVVVSLLMGLASDNFFTLSNWFNVLRQVSIVGILAVGMSFVILTG 80

Query: 62  GIDLSVGSILGAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFIS 121
           GIDLSVG+ +  A  +   L+   GL   L+++ G+ +    GL NG L+   R+   I 
Sbjct: 81  GIDLSVGAAMALAGTISAGLIVNSGLPAPLALLCGVGLATCIGLLNGALVAWGRMPAIIV 140

Query: 122 TLGMLSVGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYT 181
           TL  + V RG+  + SGG+PIS  P   +  G G +G VPVPVI M ++  +A + L+ T
Sbjct: 141 TLATMGVARGVGLIYSGGYPISGLPGWISWFGVGRIGMVPVPVILMLIVYALAWLLLQRT 200

Query: 182 VTGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGY 241
             GR +YAIGGN  A++L G+KT RI + VY I+GF +  A  +LT  L   QPNAG G+
Sbjct: 201 AFGRHVYAIGGNEMAARLSGVKTTRIKLAVYAISGFTSGLAAIILTGRLMSGQPNAGVGF 260

Query: 242 ELDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIA 301
           ELD IAA V+GGT+++GG G ++G  +GAV++G+L NG+ L+G++ + Q ++ G++I++A
Sbjct: 261 ELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNGLNLMGINPYLQDIIRGVIILLA 320

Query: 302 IAI 304
           I I
Sbjct: 321 IYI 323


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: 357
Number of extensions: 22
Number of successful extensions: 1
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: 328
Length adjustment: 28
Effective length of query: 285
Effective length of database: 300
Effective search space:    85500
Effective search space used:    85500
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