GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylH in Brucella inopinata BO1

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 WP_008511382.1 BIBO1_RS19480 ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>NCBI__GCF_000182725.1:WP_008511382.1
          Length = 332

 Score =  174 bits (440), Expect = 3e-48
 Identities = 107/317 (33%), Positives = 171/317 (53%), Gaps = 10/317 (3%)

Query: 3   KKLFKAREAGIFLILIAIVVFLGVTTRE---FLTVENIFTVILNVSFIAIMSFGMTMVII 59
           K+L K RE    L+L+ I + +G+ T     F +  N+  +  + S + I++ G   VI+
Sbjct: 2   KQLLKQRE---LLLLVIIALMVGLFTSRAPGFASAHNLANIFNDTSILIIIALGQMAVIL 58

Query: 60  TSGIDLSVGSILGAASVVMGLL-MDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAP 118
           T  IDLSV + L    + + +L     GL   L +V+ + +G   G  NG+L+ K  +  
Sbjct: 59  TKAIDLSVAANLAFTGMAVAMLNATYPGLPLVLLIVLAIGIGAVLGAINGILVWKLNIPA 118

Query: 119 FISTLGMLSVGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFL 178
            + TLG L++ RG+A+V+SGG  ++    +           + +P++    I +IA I++
Sbjct: 119 IVVTLGTLTIYRGMAFVLSGGAWVNAHQMTAPFLNTPRTPFLGLPLLGWTAILIIAFIYV 178

Query: 179 KYTVT--GRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPN 236
             T T  GR +YA GGN  A+   GI   R     + ++G LA   G+L  +   VA  +
Sbjct: 179 LMTRTFFGRALYASGGNPTAAVYTGIDVGRTRFFAFVLSGALAGLCGYLWVSRYAVAYVD 238

Query: 237 AGQGYELDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGI 296
              G+ELD +AA VIGG S  GG GT+ GA LGA+ +GV++N + ++ +S FWQ  + G 
Sbjct: 239 VAAGFELDSVAACVIGGISTLGGIGTVAGAVLGALFLGVIKNALPVIDISPFWQMAISGS 298

Query: 297 VIIIAIAIDQIRRAKER 313
           VII+A+ I   R+ K R
Sbjct: 299 VIILAV-IFNARQEKRR 314


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: 265
Number of extensions: 20
Number of successful extensions: 3
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 24 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