GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0030 in Ochrobactrum thiophenivorans DSM 7216

Align TM0030, 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_094509497.1 CEV31_RS18995 ABC transporter permease

Query= TCDB::Q9WXN7
         (338 letters)



>NCBI__GCF_002252445.1:WP_094509497.1
          Length = 312

 Score =  165 bits (418), Expect = 1e-45
 Identities = 106/329 (32%), Positives = 172/329 (52%), Gaps = 21/329 (6%)

Query: 7   FKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTLM 66
           F+++LRR + LL      + I F+L R IPG+P   +L       +A P AI      + 
Sbjct: 4   FQFVLRRPLQLLPVLFGISVITFVLVRLIPGDPARVLLG-----TRATPAAIA----NIR 54

Query: 67  EEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAWI 126
            ++GL +P ++QY  F+     G++G SI  Y   V+ LI   I  TL+L++ + I++ +
Sbjct: 55  AQYGLDEPMWLQYLYFLRNIANGEMGKSI-LYKIDVLKLIATRIEPTLMLVICSVILSIL 113

Query: 127 LGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQG 186
           +   L A+AA +     D  + T S      P +WL ++ I LF VKL  LPV G  +  
Sbjct: 114 IAVPLAAIAARQNGKLSDHVIRTVSTFGIGFPPFWLALMLIILFSVKLDLLPVSGYGNT- 172

Query: 187 TIPNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMKDK 246
                    F + L H I+P  +I +S     A  +R  +I  L SD A  +   GM + 
Sbjct: 173 ---------FKEKLAHLILPSLTIALSLSTVLARSLRAAMIQSLNSDVATAARARGMPES 223

Query: 247 RIF-KYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLIQG 305
            +F ++V  NSL+P +  LA+++G ++G  ++ E VF  PG G LL RA+ + DY ++QG
Sbjct: 224 IVFWRHVLPNSLVPTVNLLAVNIGWLIGSTVVVESVFALPGMGQLLVRAIFSRDYMVVQG 283

Query: 306 IFVILIASIYLANFIVDFLYALIDPRIRL 334
           + ++   +  L NF+ D     +DPR++L
Sbjct: 284 VAMVFACATVLVNFMADIATVALDPRVKL 312


Lambda     K      H
   0.329    0.146    0.449 

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: 272
Number of extensions: 15
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: 338
Length of database: 312
Length adjustment: 28
Effective length of query: 310
Effective length of database: 284
Effective search space:    88040
Effective search space used:    88040
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 (21.8 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