GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylE in Lentibacillus jeotgali Grbi

Align Catechol-2,3-dioxygenase; Catechol-induced ring cleavage extradiol dioxygenase; EC 1.13.11.2 (characterized)
to candidate WP_010529186.1 ON01_RS01220 VOC family protein

Query= SwissProt::P54721
         (285 letters)



>NCBI__GCF_000224785.1:WP_010529186.1
          Length = 284

 Score =  258 bits (659), Expect = 1e-73
 Identities = 130/268 (48%), Positives = 178/268 (66%), Gaps = 5/268 (1%)

Query: 8   THIGYAKLTIRSLERSLQFYCNVIGFQVLKKTDRQAELTADGKRVLLILEENPSAVVLPE 67
           T++G   + +  L+++L FY +VIGF +L++TDR+A LTADGK  LL L + P+A +  E
Sbjct: 11  TYVGEVNINVTDLDQALSFYQHVIGFNILEQTDRKAVLTADGKTPLLTLVQ-PAAPLPKE 69

Query: 68  RSVTGLYHFAILLPDRKELGIALARLIEHGIAIGHGDHAVSEALYLSDPDGNGIEMYADR 127
              +GL+HFAILLP R +L   L  + + G  +G  DH VSEALYL+DPDGNGIE+Y DR
Sbjct: 70  ERTSGLFHFAILLPSRADLSSFLRHIAKAGARLGASDHLVSEALYLNDPDGNGIEVYHDR 129

Query: 128 PRSTWQRDREGNYVMTTTAVDIEGLLEEAGDERKTSLPNDTIIGHIHLHVSDLKEAKAFY 187
           P S W     G   M+T  +D + LL E+  E K  LP +T++GHIHLHV++LK  + FY
Sbjct: 130 PSSEWSWS-NGQVTMSTEPLDADSLLAESDQEWK-GLPEETVMGHIHLHVANLKSTEKFY 187

Query: 188 TDVLGFDIVGNYAGMSALFVSAGGYHHHIGLNIWAGRNAPPKPTNASGLDYYTVVLPHQE 247
            D LGF +V NY G  ALF S GGYHHHIGLNIW G NAP    N++GL++Y+++ P  E
Sbjct: 188 ADGLGFQVVTNYPG--ALFTSTGGYHHHIGLNIWNGENAPVPSDNSAGLNWYSLIFPDNE 245

Query: 248 ELDLVANRVKHAGYSIEETENSFRVKDP 275
             +   N ++ AG SI++  N++ V DP
Sbjct: 246 SREEKVNNLERAGVSIQQENNAYIVNDP 273



 Score = 42.0 bits (97), Expect = 2e-08
 Identities = 29/103 (28%), Positives = 50/103 (48%), Gaps = 6/103 (5%)

Query: 159 ERKTSLPNDTIIGHIHLHVSDLKEAKAFYTDVLGFDIVGNYAGMSALFVSAGGYHHHIGL 218
           E+K      T +G ++++V+DL +A +FY  V+GF+I+       A+  + G       L
Sbjct: 2   EKKFFEKRTTYVGEVNINVTDLDQALSFYQHVIGFNIL-EQTDRKAVLTADG----KTPL 56

Query: 219 NIWAGRNAP-PKPTNASGLDYYTVVLPHQEELDLVANRVKHAG 260
                  AP PK    SGL ++ ++LP + +L      +  AG
Sbjct: 57  LTLVQPAAPLPKEERTSGLFHFAILLPSRADLSSFLRHIAKAG 99



 Score = 37.4 bits (85), Expect = 4e-07
 Identities = 28/119 (23%), Positives = 55/119 (46%), Gaps = 5/119 (4%)

Query: 6   EDTHIGYAKLTIRSLERSLQFYCNVIGFQVLKKTDRQAELTADGKRVLLILE-ENPSAVV 64
           E+T +G+  L + +L+ + +FY + +GFQV+         +  G    + L   N     
Sbjct: 166 EETVMGHIHLHVANLKSTEKFYADGLGFQVVTNYPGALFTSTGGYHHHIGLNIWNGENAP 225

Query: 65  LPERSVTGLYHFAILLPDRKELGIALARLIEHGIAIGHGDHAVSEALYLSDPDGNGIEM 123
           +P  +  GL  ++++ PD +     +  L   G++I       + A  ++DP GN I +
Sbjct: 226 VPSDNSAGLNWYSLIFPDNESREEKVNNLERAGVSI----QQENNAYIVNDPSGNEIHL 280


Lambda     K      H
   0.318    0.137    0.402 

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: 290
Number of extensions: 23
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 285
Length of database: 284
Length adjustment: 26
Effective length of query: 259
Effective length of database: 258
Effective search space:    66822
Effective search space used:    66822
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 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