GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylH in Collimonas arenae Ter10

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_061535474.1 CAter10_RS19695 ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>NCBI__GCF_001584165.1:WP_061535474.1
          Length = 329

 Score =  176 bits (446), Expect = 7e-49
 Identities = 109/306 (35%), Positives = 164/306 (53%), Gaps = 9/306 (2%)

Query: 12  GIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSIL 71
           G+   L+A+ V     +  FLT+    T+  ++  + +M+ GMT V+I  GIDLSVGS++
Sbjct: 26  GLIGALLAMCVLFSFLSENFLTLATFTTLSNDIPTLVVMAVGMTFVLIIGGIDLSVGSVM 85

Query: 72  GAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRG 131
             A+ V+ + M   G   F + V+ + V    G+  G++    R+  FI +LG+L + RG
Sbjct: 86  ALAASVLSMAMVRWGWPLFGAGVLAVLVASLCGMVTGVISVGWRIPSFIVSLGVLEMARG 145

Query: 132 LAYVMSGGWPISPFPESFTVHGQGMVGPVPV---PVIYMAV-IGVIAHIFLKYTVTGRRI 187
           LAY ++         E       G+  P+ +   P    A+ I +I H+ L  TV GR  
Sbjct: 146 LAYQVTNSRT-----EYIGSAVDGISSPILLGMSPAFLSAILIVIIGHLVLTKTVLGRHW 200

Query: 188 YAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIA 247
             IG N EA +L GI      +LV+ + G LA        + L  A PN G G EL VIA
Sbjct: 201 IGIGTNEEAVRLAGINPRPSKVLVFALMGLLAGVGALFQVSRLEAADPNGGVGMELQVIA 260

Query: 248 ATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQI 307
           A VIGGTSL GG G+++  F+G +I+ VL  G+  +GVS   +++V G+VI+ A+ +D  
Sbjct: 261 AVVIGGTSLMGGRGSVISTFIGVLIISVLEAGLAQVGVSEPMKRIVTGLVIVAAVVLDTY 320

Query: 308 RRAKER 313
           RR  ER
Sbjct: 321 RRRGER 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: 318
Number of extensions: 21
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: 329
Length adjustment: 28
Effective length of query: 285
Effective length of database: 301
Effective search space:    85785
Effective search space used:    85785
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