GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Rhizobium freirei PRF 81

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_004129777.1 RHSP_RS32465 ribose ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>NCBI__GCF_000359745.1:WP_004129777.1
          Length = 320

 Score =  253 bits (646), Expect = 4e-72
 Identities = 133/302 (44%), Positives = 187/302 (61%), Gaps = 1/302 (0%)

Query: 9   REAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVG 68
           R+  I L+   IV F     + F+T  N   ++   S   I++ G+T VI+T GIDLSVG
Sbjct: 19  RQFSIVLVFFLIVAFFAFANQYFMTWLNWLNLVRQSSINGILAIGVTFVILTKGIDLSVG 78

Query: 69  SILGAASVVMGLLMDEKGLSPFL-SVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLS 127
           S++  A ++   L+ E      L  +  GLA G G GL NG+L+   ++ PF+ TLGMLS
Sbjct: 79  SVMALAGMIAASLVTETNEQFVLFGIFAGLAAGAGLGLVNGVLVAAVKVPPFVVTLGMLS 138

Query: 128 VGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRI 187
           V RGL  + S G PI    + F   G G +  +PVP++ + V+ +I    L YT  GR +
Sbjct: 139 VARGLTLIFSEGRPIPNLSDPFKWIGSGQIMYIPVPIVILFVVFLIGWTVLNYTTFGRYV 198

Query: 188 YAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIA 247
           YA+GGN +A++  GI T  I+   Y I+G LA  AG +LTA    A P AG GYELD IA
Sbjct: 199 YAVGGNEKAARTSGISTKVIVGATYVISGLLAGLAGLVLTARTTAALPQAGIGYELDAIA 258

Query: 248 ATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQI 307
           A VIGGTSL+GG G++LG  +GA+I+G + NGM L+GVSS++QQV+ G +I++A+  DQI
Sbjct: 259 AVVIGGTSLAGGRGSLLGTLIGALIIGTINNGMDLMGVSSYYQQVLKGTIIVVAVIADQI 318

Query: 308 RR 309
           R+
Sbjct: 319 RK 320


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: 307
Number of extensions: 15
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: 320
Length adjustment: 27
Effective length of query: 286
Effective length of database: 293
Effective search space:    83798
Effective search space used:    83798
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