GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Tistlia consotensis USBA 355

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_085121058.1 B9O00_RS01465 ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>NCBI__GCF_900177295.1:WP_085121058.1
          Length = 335

 Score =  225 bits (574), Expect = 1e-63
 Identities = 127/309 (41%), Positives = 187/309 (60%), Gaps = 2/309 (0%)

Query: 3   KKLFKAREAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSG 62
           K+L  + E  +  + + I   L + +  FLT  NIF ++     I I+S GMT VI+T G
Sbjct: 26  KQLATSLELRMLGLALVIGAVLSLLSPYFLTESNIFNILDQSVVIGILSIGMTFVILTGG 85

Query: 63  IDLSVGSILGAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFIST 122
           IDLSVGS+ G + +V+GL + +  +   +++++G+  G G GL +G+LI   RLA F+ T
Sbjct: 86  IDLSVGSVAGLSGIVLGLALKDYPIP--VAILLGVLTGAGVGLVSGILIGYFRLAAFVVT 143

Query: 123 LGMLSVGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTV 182
           LGM+++GR LAY+ SG   IS FP   +      V  +P  V+++    ++A  +L YT 
Sbjct: 144 LGMMAIGRSLAYIFSGQTAISGFPSDLSSIVYTDVFGIPTNVLFLGFAYLLAWGYLTYTK 203

Query: 183 TGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYE 242
            GR IYAIG N EA++  G+      IL Y ++G LAA A     A +    P  G G E
Sbjct: 204 GGRTIYAIGSNKEAARAAGLGVLFYSILPYVVSGALAAVAITFSVAQILSVDPLTGNGME 263

Query: 243 LDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAI 302
           LD IAA VIGG SL GG G+I+G  +G +IM ++RNG+ LLGVS FWQ   IG +II+A+
Sbjct: 264 LDAIAAVVIGGASLYGGRGSIVGTLIGVLIMVMIRNGLNLLGVSPFWQGSAIGSIIIMAL 323

Query: 303 AIDQIRRAK 311
            ++++ RA+
Sbjct: 324 LVERLVRAR 332


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: 364
Number of extensions: 27
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: 335
Length adjustment: 28
Effective length of query: 285
Effective length of database: 307
Effective search space:    87495
Effective search space used:    87495
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 Apr 09 2024. 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