GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylH in Sinorhizobium meliloti 1021

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 SM_b20929 SM_b20929 sugar uptake ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>lcl|FitnessBrowser__Smeli:SM_b20929 SM_b20929 sugar uptake ABC
           transporter permease
          Length = 332

 Score =  225 bits (573), Expect = 1e-63
 Identities = 127/323 (39%), Positives = 190/323 (58%), Gaps = 20/323 (6%)

Query: 2   WKKLFKAREAGIFLILIAIVV---FLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVI 58
           W     A +A  F +L+A+++   FL + T  F T +N++ +  N +F+AI++ GMT+VI
Sbjct: 16  WLSFLLASQA--FWVLVAVILACLFLSIATDSFATAKNLYNITRNFTFVAIIALGMTLVI 73

Query: 59  ITSGIDLSVGSILGAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLA----NGLLITKA 114
           IT GIDLSVGS+L   S+V+ ++M          + +G+A  +G  L     NG++I   
Sbjct: 74  ITGGIDLSVGSVLCLCSMVLAVVMHAG-----YGIEVGIAASIGTALVAGAFNGVMIAYL 128

Query: 115 RLAPFISTLGMLSVGRGLAYVMSGGWPISPF-PESFTVHGQG----MVGPVPVPVIYMAV 169
              PF+ TLGMLS+ R LA V S    +  F P+  T+   G     +G +  PV+YM V
Sbjct: 129 GFPPFVITLGMLSIARSLAMVASNNTVVFEFGPDHDTLLALGGGAWFLG-IANPVLYMIV 187

Query: 170 IGVIAHIFLKYTVTGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAW 229
           + ++    L++T  GR ++AIGGN  A+ L G+   RI + VY I+   A  AG + T W
Sbjct: 188 LALLTGFVLRWTKFGRYVFAIGGNEHAATLTGVPVRRIKVAVYMISALAAGIAGIIQTGW 247

Query: 230 LGVAQPNAGQGYELDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFW 289
           LG    N G G EL VIAA VIGG +L+GG GT  GA +GA ++ V+RN + LLG+++FW
Sbjct: 248 LGAVTTNIGAGMELQVIAAAVIGGANLAGGAGTASGALIGAALIEVIRNSLGLLGINAFW 307

Query: 290 QQVVIGIVIIIAIAIDQIRRAKE 312
           Q   IG  I++A+  D+IR  ++
Sbjct: 308 QGAFIGGAIVLAVLFDRIRNFRQ 330


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: 295
Number of extensions: 21
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: 332
Length adjustment: 28
Effective length of query: 285
Effective length of database: 304
Effective search space:    86640
Effective search space used:    86640
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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