GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SM_b20929
          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.

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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