GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Pseudovibrio axinellae Ad2

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_068000560.1 PsAD2_RS00560 ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>NCBI__GCF_001623255.1:WP_068000560.1
          Length = 332

 Score =  235 bits (599), Expect = 1e-66
 Identities = 131/302 (43%), Positives = 180/302 (59%), Gaps = 4/302 (1%)

Query: 11  AGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSI 70
           AGI L L+A+++F  + T  FLT  NI  ++  V+   I++ GMT VI+  GIDLSVGS+
Sbjct: 25  AGIGLALLALILFFSIFTEHFLTANNITNILTQVTINLILAVGMTFVILIGGIDLSVGSV 84

Query: 71  LGAASVVMGLLMDEKGLSPF----LSVVIGLAVGVGFGLANGLLITKARLAPFISTLGML 126
           +  ASV+ G  +   GL PF    L+V+   AVGV  G  NG +  +  L  FI TLGML
Sbjct: 85  MAFASVIAGKAITLAGLGPFEAIVLAVIAATAVGVVCGAINGTITARWSLPSFIITLGML 144

Query: 127 SVGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRR 186
           ++ RG A   S    I  FP +F   G  M   VPV  +    +  IA   L +TV GR 
Sbjct: 145 NIARGAALQASNAQTIYSFPLAFEDFGSAMFYGVPVVFMVALALVFIAWFILNFTVFGRL 204

Query: 187 IYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVI 246
           +Y IG N EA +L G    R  I  +TI G  A  A  +  A L ++ P AG G+EL+ I
Sbjct: 205 LYGIGNNEEAVRLAGHSVYRYKIAAFTICGLTAGIAAVVYMARLNISSPIAGIGFELNAI 264

Query: 247 AATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQ 306
           AA +IGGTSL+GG G+++G  +GA I+GVL NG+IL+G+S F +Q++ G+VIIIA+ +D 
Sbjct: 265 AAVIIGGTSLNGGRGSVIGTLIGAFIIGVLANGLILIGLSDFMRQMITGVVIIIAVILDY 324

Query: 307 IR 308
            R
Sbjct: 325 YR 326


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: 303
Number of extensions: 9
Number of successful extensions: 2
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: 332
Length adjustment: 28
Effective length of query: 285
Effective length of database: 304
Effective search space:    86640
Effective search space used:    86640
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 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