GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0027 in Acidovorax sp. GW101-3H11

Align TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate Ac3H11_2052 Putative glutathione transporter, ATP-binding component

Query= TCDB::Q9WXN4
         (268 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2052
          Length = 345

 Score =  172 bits (435), Expect = 1e-47
 Identities = 91/243 (37%), Positives = 151/243 (62%), Gaps = 9/243 (3%)

Query: 23  IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRE 82
           + AV  VSFE+++ + ++LVGESG GK+T A++++ L  PT G + F+ +D     K ++
Sbjct: 48  LHAVDGVSFEIEKGKTLALVGESGCGKSTVARLLVGLYEPTRGGLTFDNQDAHAAFKGKD 107

Query: 83  SLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAI---SLLENKPSNKKEALELIKESLFR 139
           +    RR++  +FQDP+AS NP + VE  + + +    L+ +K   K    EL+K     
Sbjct: 108 AQA-MRRRIQMIFQDPYASLNPRWLVEDIIGEPLREHGLITDKAELKARVGELLKS---- 162

Query: 140 VGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEE 199
           VG+ P D++ KYPHQ SGGQ+QRI IAR     P  +V DEPTS +D S +  ++ ++++
Sbjct: 163 VGLSPLDMV-KYPHQFSGGQRQRISIARALATEPEFLVCDEPTSALDVSVQAQVLNIMKD 221

Query: 200 LREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSIP 259
           L+ E+  + +FI+H+L +  +VSD + VM  G +VE     ++   P H YT++L+ +IP
Sbjct: 222 LQRERQLTYLFISHNLAVVRHVSDQVGVMYLGRLVELADKHQLFNSPRHPYTRMLLDAIP 281

Query: 260 KLY 262
           K++
Sbjct: 282 KMH 284


Lambda     K      H
   0.319    0.139    0.397 

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: 237
Number of extensions: 9
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: 268
Length of database: 345
Length adjustment: 27
Effective length of query: 241
Effective length of database: 318
Effective search space:    76638
Effective search space used:    76638
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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