Alignments for a candidate for uxuB in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for uxuB in Klebsiella michiganensis M5al

Align D-mannonate oxidoreductase (EC 1.1.1.57) (characterized)
to candidate BWI76_RS15490 BWI76_RS15490 mannitol dehydrogenase family protein

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



>FitnessBrowser__Koxy:BWI76_RS15490
          Length = 487

 Score =  551 bits (1419), Expect = e-161
 Identities = 280/473 (59%), Positives = 343/473 (72%), Gaps = 4/473 (0%)

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

Query: 74  KQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEKGYC 133
           KQ LLYTVAE  A++   +++G +K+A+H ++DG E +L  M  PQ AIVSLT+TEKGYC
Sbjct: 71  KQDLLYTVAEMSADAWTARVVGVVKQAMHAQVDGLESVLAKMCEPQVAIVSLTITEKGYC 130

Query: 134 ADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRENGH 193
              ASG+L L++PLI  DL+NP  PKSA G +VEAL  R+  GL AF+VMSCDN+ ENGH
Sbjct: 131 HSPASGELQLDHPLIAADLQNPRQPKSAPGVVVEALARRKAAGLPAFSVMSCDNMPENGH 190

Query: 194 VAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPCAIA 253
           V +  +   A+A D  LA WI  NVTFP TMVDRIVPA T +TL +IA   GV DP A+A
Sbjct: 191 VMRNVICAYARAVDADLAEWITRNVTFPSTMVDRIVPAVTADTLDKIAQLTGVRDPAAVA 250

Query: 254 CEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGGYET 313
           CEPFRQWVIEDNFV GRP W+K GA+ V+DV+PFE MKLRMLNGSHSFLAYLGYL GY+ 
Sbjct: 251 CEPFRQWVIEDNFVAGRPQWEKAGAELVSDVLPFEEMKLRMLNGSHSFLAYLGYLAGYQH 310

Query: 314 IADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQIAMD 373
           I D + +  YR+AA  LM+ EQAPTLS+ +G DL  YA LLIER+SNP+L+HRTWQIAMD
Sbjct: 311 INDCMQDANYRRAAHTLMLAEQAPTLSV-KGVDLARYAGLLIERYSNPALKHRTWQIAMD 369

Query: 374 GSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLAEF-QK 432
           GSQKLPQR+LD +R HL +GG +  LA+GVAGWMRY  GVD+QG AI++ DPML    Q 
Sbjct: 370 GSQKLPQRMLDSIRWHLADGGDFPLLAMGVAGWMRYVSGVDDQGQAIEISDPMLPVITQT 429

Query: 433 INAQYQGADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERGARECVAA 485
           +     G +RV+ALLG+  IF   LP+ + FV AV  AY  L   GA+  VAA
Sbjct: 430 VQNSEDGEERVRALLGIEAIFGLSLPKESRFVNAVVRAYLSLQAHGAKATVAA 482


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: 721
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: 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources