GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0027 in Ochrobactrum thiophenivorans DSM 7216

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 WP_094509482.1 CEV31_RS18940 ABC transporter ATP-binding protein

Query= TCDB::Q9WXN4
         (268 letters)



>NCBI__GCF_002252445.1:WP_094509482.1
          Length = 328

 Score =  179 bits (454), Expect = 7e-50
 Identities = 105/241 (43%), Positives = 148/241 (61%), Gaps = 5/241 (2%)

Query: 19  SKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDI 78
           SK+ + AV ++S ++ + E +S+VGESG GK+T A  I+ L  P+SGEIYFEGK I    
Sbjct: 33  SKQFLHAVNDLSLDLNKGECLSIVGESGCGKSTLALSIVGLQKPSSGEIYFEGKPITGT- 91

Query: 79  KDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLF 138
            +  S +E  +    VFQDPFAS NP   +  +L   + L   K  ++ E    ++E L 
Sbjct: 92  -NEPSRLERAKMAQMVFQDPFASLNPRQTIYTSLAAPLKLHGVK--SRSEVDGRVEEILT 148

Query: 139 RVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLE 198
            VG+ P+    ++PH+ SGGQ+QRI IAR  +L P +IV DEP S +D S R  II LL 
Sbjct: 149 LVGLKPEQAK-RFPHEFSGGQRQRIGIARALLLNPKVIVLDEPVSALDVSIRAQIINLLL 207

Query: 199 ELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSI 258
           EL+E  G S I I+HDL +  ++SD + VM  G+IVE G  D++   PTH YT+ L+ +I
Sbjct: 208 ELKERLGLSYIMISHDLSVVEHMSDRVAVMYFGQIVETGPWDRIFSNPTHPYTRRLISAI 267

Query: 259 P 259
           P
Sbjct: 268 P 268


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: 6
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: 328
Length adjustment: 26
Effective length of query: 242
Effective length of database: 302
Effective search space:    73084
Effective search space used:    73084
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 24 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