GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuB in Escherichia coli BW25113

Align D-mannonate oxidoreductase (EC 1.1.1.57) (characterized)
to candidate 15664 b1542 predicted mannonate dehydrogenase (NCBI)

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



>FitnessBrowser__Keio:15664
          Length = 486

 Score =  531 bits (1369), Expect = e-155
 Identities = 274/472 (58%), Positives = 336/472 (71%), Gaps = 4/472 (0%)

Query: 14  PSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNLMPGNDRVLIENLK 73
           P +D + L  RIVHLG GAFHRAHQ +Y   L     SDWG  EVNL+ G  +  I +L+
Sbjct: 13  PVYDLNNLAPRIVHLGFGAFHRAHQGVYADILATEHFSDWGYYEVNLIGGEQQ--IADLQ 70

Query: 74  KQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEKGYC 133
           +Q  LYTVAE  A+    +++G +K+ALH +IDG E +L AM  PQ AIVSLT+TEKGY 
Sbjct: 71  QQDNLYTVAEMSADVWTARVVGVVKKALHVQIDGLETVLAAMCEPQIAIVSLTITEKGYF 130

Query: 134 ADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRENGH 193
              A+GQL L++P++  D++NP  PK+A G IVEAL  R+  GL AFTVMSCDN+ ENGH
Sbjct: 131 HSPATGQLMLDHPMVAADVQNPHQPKTATGVIVEALARRKAAGLPAFTVMSCDNMPENGH 190

Query: 194 VAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPCAIA 253
           V +  V   AQA D +LA WIE+NVTFP TMVDRIVPA T +TL +I    GV DP  +A
Sbjct: 191 VMRDVVTSYAQAVDVKLAQWIEDNVTFPSTMVDRIVPAVTEDTLAKIEQLTGVRDPAGVA 250

Query: 254 CEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGGYET 313
           CEPFRQWVIEDNFV GRP+W+K GA+ V+DV+P+E MKLRMLNGSHSFLAYLGYL GY+ 
Sbjct: 251 CEPFRQWVIEDNFVAGRPEWEKAGAELVSDVLPYEEMKLRMLNGSHSFLAYLGYLAGYQH 310

Query: 314 IADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQIAMD 373
           I D + +  YR AA+ LM+QEQAPTL + +G DL  YA  LI R+SNP+LRHRTWQIAMD
Sbjct: 311 INDCMEDEHYRYAAYGLMLQEQAPTLKV-QGVDLQDYANRLIARYSNPALRHRTWQIAMD 369

Query: 374 GSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLAEFQK- 432
           GSQKLPQR+LD VR HL +   +  LALGVAGWMRY  GVDEQGN I++ DP+L   QK 
Sbjct: 370 GSQKLPQRMLDSVRWHLAHDSKFDLLALGVAGWMRYVGGVDEQGNPIEISDPLLPVIQKA 429

Query: 433 INAQYQGADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERGARECVA 484
           + +  +G  RV++LL +  IF DDLP N+ F   VT  Y  L   GA+  VA
Sbjct: 430 VQSSAEGKARVQSLLAIKAIFGDDLPDNSLFTARVTETYLSLLAHGAKATVA 481


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: 703
Number of extensions: 25
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: 486
Length of database: 486
Length adjustment: 34
Effective length of query: 452
Effective length of database: 452
Effective search space:   204304
Effective search space used:   204304
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