GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Gracilibacillus halophilus YIM-C55.5

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_156809555.1 J416_RS08120 ribose ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>NCBI__GCF_000359605.1:WP_156809555.1
          Length = 318

 Score =  203 bits (516), Expect = 5e-57
 Identities = 112/295 (37%), Positives = 179/295 (60%), Gaps = 5/295 (1%)

Query: 12  GIFLILIAIVVFLGVTT---REFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVG 68
           G + ++IA ++   V T     FL ++N   +++ VS I I++ GMT+V+++ GIDLSVG
Sbjct: 19  GEYSVVIAFIIIFIVATIMNDRFLYLDNQINILMQVSTIGIIALGMTVVMLSGGIDLSVG 78

Query: 69  SILGAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSV 128
           S+L    V   + M+  G S F+ V+  L+VG   G+ NGLL++K ++A FI+TLGM++ 
Sbjct: 79  SVLAMVGVFSVMAMNASG-SIFVGVLTALSVGALTGVINGLLVSKGKIASFIATLGMMAA 137

Query: 129 GRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIY 188
            R +A   + G  +S   E FT      +G V +P+I    +  + ++ ++ T  GR +Y
Sbjct: 138 ARSIALYYADGGSMSGEVEGFTAISNTEIGMVDIPIIIFLALTALVYVLMQKTRFGRYVY 197

Query: 189 AIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWL-GVAQPNAGQGYELDVIA 247
           A+G N +A+ L  I+ DRI I VYT    L   A  + T+ L  ++  ++G  YELD IA
Sbjct: 198 ALGSNEKAALLSAIRVDRIKIGVYTFCSLLVGVAAIIETSRLNSISSSSSGNLYELDAIA 257

Query: 248 ATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAI 302
           A +IGGT ++GG+G ++G F G +++GVL N M LL +S   Q +V G++IIIA+
Sbjct: 258 AVIIGGTRMTGGKGKVIGTFFGVLLLGVLNNMMNLLNISPHLQGLVKGLIIIIAV 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: 302
Number of extensions: 14
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
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 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