GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuB in Sinorhizobium meliloti 1021

Align D-mannonate oxidoreductase (EC 1.1.1.57) (characterized)
to candidate SM_b20749 SM_b20749 D-mannonate oxidoreductase

Query= ecocyc::MANNONOXIDOREDUCT-MONOMER
         (486 letters)



>FitnessBrowser__Smeli:SM_b20749
          Length = 487

 Score =  428 bits (1101), Expect = e-124
 Identities = 243/470 (51%), Positives = 291/470 (61%), Gaps = 7/470 (1%)

Query: 11  VARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNLMPGNDRVLIE 70
           V RP +D   +   IVHLG GAFHRAHQA+YT  LL S D  WGIC V+L     R   +
Sbjct: 15  VKRPHYDLGTVTVGIVHLGIGAFHRAHQAVYTDGLL-SEDPSWGICGVSLRSPETR---D 70

Query: 71  NLKKQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEK 130
            L  Q  LYT+A +  E +EL ++GS+ E L    D  E +L  MA P T IVSLT+TEK
Sbjct: 71  ALHPQDGLYTLAVQDGEGSELSVVGSVVELLCAP-DDPEAVLRRMADPGTRIVSLTITEK 129

Query: 131 GYCADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRE 190
           GYC + A+G LD  +P I HDL NP  P+SAIG+IVEA+  R   G+  FT++SCDN+  
Sbjct: 130 GYCHNPATGTLDEGHPDIVHDLANPARPRSAIGFIVEAISRRVSAGIAPFTLLSCDNLPG 189

Query: 191 NGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPC 250
           NGHV K  V   A+ARDP LAA +  NV  P TMVDRIVPA T      +A  +G+ D  
Sbjct: 190 NGHVLKRIVTQFAEARDPALAA-VVRNVASPSTMVDRIVPATTDSDRSAVASAMGLEDAW 248

Query: 251 AIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGG 310
            I  EPFRQWVIE++F  GRP W+K GA FV DV  FE MKLR+LNGSHS LAYLGYL G
Sbjct: 249 PIMTEPFRQWVIEEDFPLGRPAWEKAGALFVQDVSAFEFMKLRLLNGSHSTLAYLGYLAG 308

Query: 311 YETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQI 370
            ET+AD +           LM  E +PTL    G DL AY   L++RF NP+LRHRTWQI
Sbjct: 309 AETVADAMALAGMEALVEGLMRHEVSPTLPELPGFDLPAYRAELLQRFRNPALRHRTWQI 368

Query: 371 AMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLAEF 430
           AMDGSQKLPQRLL  +R  LQ G  +  LALGVA WMRY +G+DE G  IDV DP  A  
Sbjct: 369 AMDGSQKLPQRLLGSIRDRLQAGAGYDRLALGVAAWMRYARGLDEAGRPIDVRDPHAARI 428

Query: 431 QKINAQYQGADR-VKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERGA 479
             +       DR V A L ++ +F  DLP +A F  A+  A   L   GA
Sbjct: 429 AGLARGIDEPDRIVDAFLTMTDVFGTDLPASAPFRAALIKALDGLLRIGA 478


Lambda     K      H
   0.320    0.135    0.408 

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: 723
Number of extensions: 35
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 486
Length of database: 487
Length adjustment: 34
Effective length of query: 452
Effective length of database: 453
Effective search space:   204756
Effective search space used:   204756
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: 52 (24.6 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