GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Pseudomonas simiae WCS417

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 GFF2674 PS417_13640 ribose ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__WCS417:GFF2674
          Length = 325

 Score =  212 bits (539), Expect = 1e-59
 Identities = 128/310 (41%), Positives = 187/310 (60%), Gaps = 10/310 (3%)

Query: 9   REAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVG 68
           R  G+  +LI ++V   + +  FLT++N+  +    S   +++ GMT VI+T+GIDLSVG
Sbjct: 20  RTVGMLPVLILLLVGFALASENFLTMQNLSIISQQASVNVVLAAGMTFVILTAGIDLSVG 79

Query: 69  SILGAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGL----ANGLLITKARLAPFISTLG 124
           +IL AAS V+ L   +  +SP   +  G+A G+GFGL     NG LI   RL PFI TLG
Sbjct: 80  AIL-AASAVVAL---QASMSPQFGM-FGIAAGIGFGLLLGLVNGGLIAFMRLPPFIVTLG 134

Query: 125 MLSVGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTG 184
            L+  RGLA +++    +      F   G   +  VP  VI    +  ++   L+ TV G
Sbjct: 135 ALTAMRGLARLLADDKTVFNPDLPFAFIGNDSLLGVPWLVIIAVAVVALSWFILRRTVMG 194

Query: 185 RRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQP-NAGQGYEL 243
            +IY++GGN EA++L GIK  ++L+ VY ++G LA     +  + L  A     GQ YEL
Sbjct: 195 VQIYSVGGNPEAARLSGIKVWKVLLFVYAMSGALAGLGAVMSASRLFAANGLQLGQSYEL 254

Query: 244 DVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIA 303
           D IAA ++GGTS +GG GTI G  +GA+I+ VL NG++LLGVS  WQ ++ GIVII A+A
Sbjct: 255 DAIAAVILGGTSFTGGVGTIGGTLIGALIIAVLTNGLVLLGVSDIWQYIIKGIVIIGAVA 314

Query: 304 IDQIRRAKER 313
           +D+ R++  R
Sbjct: 315 LDRYRQSGAR 324


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: 319
Number of extensions: 19
Number of successful extensions: 5
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: 325
Length adjustment: 28
Effective length of query: 285
Effective length of database: 297
Effective search space:    84645
Effective search space used:    84645
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.

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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