GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0030 in Magnetospirillum magneticum AMB-1

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_050750808.1 AMB_RS09975 ABC transporter permease

Query= TCDB::Q9WXN7
         (338 letters)



>NCBI__GCF_000009985.1:WP_050750808.1
          Length = 299

 Score =  154 bits (388), Expect = 4e-42
 Identities = 96/307 (31%), Positives = 161/307 (52%), Gaps = 15/307 (4%)

Query: 27  IVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTLMEEFGLGKPWYVQYFEFITKA 86
           +V+ L   +PG+P+  +++G  R+     +A+R     L   +GL +PW  ++  ++ + 
Sbjct: 4   VVYGLMGLMPGDPIDLMIAGDPRLTPE--DAVR-----LKVLYGLDRPWTERWLRWLGQV 56

Query: 87  LRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAWILGNSLGALAAYKRNTWIDKG 146
           L+G+LG S   Y R V+D + P +  + +L+L A  ++  L   LG LA+ +    +D+ 
Sbjct: 57  LQGELGYS-RLYARPVLDAMAPALGNSALLMLSAMALSLSLAIPLGILASLRPGGLVDRL 115

Query: 147 VLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQGTIPNLSWSFFVDVLKHYIMP 206
           V   +     +P +WLG++ I +F V LGWLP  G  S G           D L+H ++P
Sbjct: 116 VNLAAFASVSVPVFWLGLMLIVVFAVSLGWLPAGGVESVGD------GGPTDRLRHMVLP 169

Query: 207 FASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMKDKRI-FKYVFRNSLLPQITGLA 265
            +++ ++ +G     MR  +I E G+DY   +   G    RI  ++  RN+LLP  T +A
Sbjct: 170 VSALALAGIGQATRHMRAAMIGEAGADYIRTARAKGCGPARIVLRHQLRNALLPITTIIA 229

Query: 266 LSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLIQGIFVILIASIYLANFIVDFLY 325
           L  GG+  GALITE VF +PG G L++ A+   D+ L     ++  A     + + D  Y
Sbjct: 230 LEFGGLFSGALITETVFAWPGMGRLIYEAVMGNDFNLALSGLLLATAMTLAGSILADMAY 289

Query: 326 ALIDPRI 332
             +DPRI
Sbjct: 290 QRLDPRI 296


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: 4
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: 299
Length adjustment: 27
Effective length of query: 311
Effective length of database: 272
Effective search space:    84592
Effective search space used:    84592
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 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