GapMind for catabolism of small carbon sources

 

Alignments for a candidate for boxA in Synechococcus elongatus PCC 7942

Align Benzoyl-CoA oxygenase component A; Benzoyl-CoA 2,3-dioxygenase subunit A; Benzoyl-CoA dioxygenase reductase component; EC 1.14.13.208 (characterized)
to candidate Synpcc7942_0978 Synpcc7942_0978 ferredoxin-NADP oxidoreductase

Query= SwissProt::Q9AIX6
         (414 letters)



>FitnessBrowser__SynE:Synpcc7942_0978
          Length = 403

 Score =  190 bits (483), Expect = 6e-53
 Identities = 115/325 (35%), Positives = 166/325 (51%), Gaps = 16/325 (4%)

Query: 103 GAAELPAEVQQITEVATAGQGGPAMAPWSASHPYVNLYTPANPITATVTGNYRLTAEDAS 162
           GAA L A  +   E A A    PA    SA    VN+Y P  P    V  N  L  E   
Sbjct: 82  GAAPLQAAAE---EPAAAPTPAPAAKKHSAEDVPVNIYRPNKPFVGKVLSNEPLVQEGGI 138

Query: 163 SDIHHIVLDFGTTPFPVLEGQSIGIIPPGVDEKGKPHLLRMYSVASPRDGERPHYNNLSL 222
             + H+  D        +EGQSIGIIP G D+KGKPH LR+YS+AS R G+      +SL
Sbjct: 139 GVVQHLTFDISEGDLRYIEGQSIGIIPDGTDDKGKPHKLRLYSIASTRHGDHVDDKTVSL 198

Query: 223 TVKRVVEDHE-GNPTRGVASNYVCDLKKGDKVQVTGPYGSTYLMPNHPGSSIMMICTGTG 281
            V+++   +E G    GV S ++C LK GD V++TGP G   L+P    ++++M+ TGTG
Sbjct: 199 CVRQLQYQNEAGETINGVCSTFLCGLKPGDDVKITGPVGKEMLLPADTDANVIMMGTGTG 258

Query: 282 SAPMRAMTERRRRRMDR------KEGGELVLFFGARAPEELPYFGPLQKLPKEFID---I 332
            AP RA   R  +  +R      +  G+  L FG      + Y   L+ L  ++ D   +
Sbjct: 259 IAPFRAYLWRMFKDNERAINSEYQFNGKAWLIFGIPTTANILYKEELEALQAQYPDNFRL 318

Query: 333 NFAFSRVPGEP---KRYVQDAIRERADKVFQMLQDDNCYIYICGLKGMEAGVLEAFRDIC 389
            +A SR        + Y+QD + E AD+++ +L+D+  ++YICGL+GME G+ +A     
Sbjct: 319 TYAISREQKNEAGGRMYIQDRVAEHADEIWNLLKDEKTHVYICGLRGMEDGIDQAMTVAA 378

Query: 390 RAKGADWDALRPQLLSKARFHVETY 414
             +   W   +  L    R+HVETY
Sbjct: 379 AKEDVVWSDYQRTLKKAGRWHVETY 403


Lambda     K      H
   0.319    0.136    0.425 

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: 416
Number of extensions: 24
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: 414
Length of database: 403
Length adjustment: 31
Effective length of query: 383
Effective length of database: 372
Effective search space:   142476
Effective search space used:   142476
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 (21.8 bits)
S2: 50 (23.9 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