GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglC in Klebsiella michiganensis M5al

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 BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS14865 BWI76_RS14865 ribose ABC
           transporter permease
          Length = 339

 Score =  246 bits (629), Expect = 4e-70
 Identities = 133/301 (44%), Positives = 194/301 (64%), Gaps = 1/301 (0%)

Query: 12  GIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSIL 71
           GI ++L+ +++ +      F  V+N+  +  ++S  AI++ GMT VI+TSGIDLSVGSI+
Sbjct: 26  GILIVLLVLLILMSTFAPNFNRVDNLLNIARSISVNAILAAGMTFVILTSGIDLSVGSIV 85

Query: 72  GAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRG 131
            A S V+ ++    G+   L+++ G+ VG   GL NG+L     LAPFI TLG ++  RG
Sbjct: 86  -AVSGVVSVVAAMAGIPAPLAILAGVGVGALCGLLNGVLTAYLALAPFIVTLGTMTFLRG 144

Query: 132 LAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYAIG 191
           +AY ++ G PI     SF   G G +  +P+PVI M V+ ++A   L+ T  GR IYA+G
Sbjct: 145 MAYTITEGQPIVSSSLSFRELGNGYLIGIPIPVIIMLVVYLLAWFILERTRFGRHIYAVG 204

Query: 192 GNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATVI 251
           GN +A++L G++  R+L  VY I G  A  AG +  A +  AQP AG GYELD IAA V+
Sbjct: 205 GNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQPTAGTGYELDAIAAVVL 264

Query: 252 GGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQIRRAK 311
           GGTSL+GG G I+G  +G++I+GVL  G+ILL V  F Q ++ GIVII+A+AID +++  
Sbjct: 265 GGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSVPFFTQLLIKGIVIILAVAIDGLKQHP 324

Query: 312 E 312
           E
Sbjct: 325 E 325


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: 316
Number of extensions: 16
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: 339
Length adjustment: 28
Effective length of query: 285
Effective length of database: 311
Effective search space:    88635
Effective search space used:    88635
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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