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_4824 Oligopeptide transport ATP-binding protein OppF (TC 3.A.1.5.1)

Query= TCDB::Q9WXN4
         (268 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4824
          Length = 295

 Score =  172 bits (436), Expect = 7e-48
 Identities = 97/262 (37%), Positives = 156/262 (59%), Gaps = 9/262 (3%)

Query: 4   LVVKNLTKIFSLG----FFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRL 59
           L VK+L + ++L     F     ++A+  VSF +     + +VGESGSGK+T A++++ L
Sbjct: 14  LQVKDLVREYTLPREHLFRPPGTVQALNGVSFSIAAGRSLGVVGESGSGKSTLARLVMAL 73

Query: 60  LPPTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLL 119
             PT+G +   G+++ +     E L + RR    VFQDP+ S +P   VER + + +   
Sbjct: 74  DAPTAGTVELLGRNLHQ--LPAEQLRQARRDFQMVFQDPYGSLDPRQTVERIVTEPLQA- 130

Query: 120 ENKPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVAD 179
               + + E  E   + L +VG+   D LGKYPH+ SGGQ+QRI IAR  I RP LIVAD
Sbjct: 131 -QGQTTRAEQREQAAQVLSQVGLRTND-LGKYPHEFSGGQRQRIAIARALITRPRLIVAD 188

Query: 180 EPTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHP 239
           EP S +D S +  ++ L+++L+++ G + + I+HDL +  ++ D + V+  G IVERG P
Sbjct: 189 EPVSALDVSVQAQVLNLMQDLQQQFGITYMLISHDLAVVNHLCDEVVVLYQGRIVERGSP 248

Query: 240 DKVVLEPTHEYTKLLVGSIPKL 261
            ++     H YT+ LVG++P++
Sbjct: 249 GELFRNAQHPYTQSLVGAVPQV 270


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: 181
Number of extensions: 4
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: 295
Length adjustment: 26
Effective length of query: 242
Effective length of database: 269
Effective search space:    65098
Effective search space used:    65098
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: 47 (22.7 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