GapMind for catabolism of small carbon sources

 

Alignments 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_RS00280 BWI76_RS00280 ribose ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__Koxy:BWI76_RS00280
          Length = 321

 Score =  228 bits (582), Expect = 1e-64
 Identities = 126/295 (42%), Positives = 190/295 (64%), Gaps = 8/295 (2%)

Query: 15  LILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILGAA 74
           L+LIAIV      +  F TV N+F ++   S  AIM+ GMT+VI+TSGIDLSVGS+L   
Sbjct: 27  LVLIAIV---STMSPNFFTVNNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLALT 83

Query: 75  SVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGLAY 134
             V   ++  + ++  ++V   LA+G   G   G+++ K R+  FI+TL M+ + RG+  
Sbjct: 84  GAVAASIVGIE-VNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLLRGVTM 142

Query: 135 VMSGGWPISP-FPESFTVHGQGMVGP---VPVPVIYMAVIGVIAHIFLKYTVTGRRIYAI 190
           V + G P++  F ++  + G   +G    +P PV  MA++ + A   L +T  GR IYA+
Sbjct: 143 VYTNGSPVNTGFTDNADLFGWFGIGRPLGIPTPVWIMAIVFLAAWYMLHHTRLGRYIYAL 202

Query: 191 GGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATV 250
           GGN  A++L GI  +++ I+VY++ G LA+ AG +  A L  AQP AG GYELD IAA V
Sbjct: 203 GGNEAATRLSGISVNKVKIIVYSLCGMLASLAGIIEVARLSSAQPTAGTGYELDAIAAVV 262

Query: 251 IGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAID 305
           +GGTSL+GG+G I+G  +GA+I+G L NG+ LLGVSS++Q +V  +VI++A+ +D
Sbjct: 263 LGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLVD 317


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: 273
Number of extensions: 17
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: 321
Length adjustment: 27
Effective length of query: 286
Effective length of database: 294
Effective search space:    84084
Effective search space used:    84084
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 (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