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_RS05645 BWI76_RS05645 fructuronate reductase

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



>FitnessBrowser__Koxy:BWI76_RS05645
          Length = 491

 Score =  875 bits (2260), Expect = 0.0
 Identities = 428/484 (88%), Positives = 449/484 (92%)

Query: 3   TIVDSNLPVARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNLMP 62
           T+ DSNLPV RP+WD SRLESRIVHLGCGAFHRAHQALYTHHLLE++DSDWGICEVNLMP
Sbjct: 4   TLADSNLPVTRPAWDRSRLESRIVHLGCGAFHRAHQALYTHHLLETSDSDWGICEVNLMP 63

Query: 63  GNDRVLIENLKKQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAI 122
           GNDRVLIENLK QQLLYTVAEKGA+STELKIIGSMKEALHPEIDGCEGIL AM RP TAI
Sbjct: 64  GNDRVLIENLKNQQLLYTVAEKGADSTELKIIGSMKEALHPEIDGCEGILRAMTRPHTAI 123

Query: 123 VSLTVTEKGYCADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTV 182
           VSLTVTEKGYC DAASGQLDLNNPLI+HDL NP  PKSAIGYIVEALRLRRE+GL AFTV
Sbjct: 124 VSLTVTEKGYCTDAASGQLDLNNPLIQHDLANPATPKSAIGYIVEALRLRREEGLNAFTV 183

Query: 183 MSCDNVRENGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIAD 242
           MSCDNVRENGHVAKVAVLGLAQARDPQLAAWIE + TFPCTMVDRIVPAATPETLQEIAD
Sbjct: 184 MSCDNVRENGHVAKVAVLGLAQARDPQLAAWIEAHATFPCTMVDRIVPAATPETLQEIAD 243

Query: 243 QLGVYDPCAIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFL 302
           QLGVYDPCAIACEPFRQWVIED+FVNGRP WDKVGAQFV DVVPFEMMKLRMLNGSHSFL
Sbjct: 244 QLGVYDPCAIACEPFRQWVIEDSFVNGRPAWDKVGAQFVEDVVPFEMMKLRMLNGSHSFL 303

Query: 303 AYLGYLGGYETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPS 362
           AYLGYLGGYETIADT+TNPAYRKAA ALMMQEQAPTLSMPEGTDL AYATLLI RFSNPS
Sbjct: 304 AYLGYLGGYETIADTMTNPAYRKAALALMMQEQAPTLSMPEGTDLQAYATLLIARFSNPS 363

Query: 363 LRHRTWQIAMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDV 422
           LRHRTWQIAMDGSQKLPQRLLDP+RLHLQNG  WRHLALGVAGWMRYT G+DEQG  IDV
Sbjct: 364 LRHRTWQIAMDGSQKLPQRLLDPIRLHLQNGSDWRHLALGVAGWMRYTLGIDEQGQPIDV 423

Query: 423 VDPMLAEFQKINAQYQGADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERGAREC 482
           VDP+ AEFQ+IN +YQ A+RV ALL +SGIFA DLP N++FV AVT AYQQL +RGARE 
Sbjct: 424 VDPLQAEFQQINQRYQEAERVPALLAISGIFAHDLPDNSEFVNAVTQAYQQLRKRGARES 483

Query: 483 VAAL 486
           VAA+
Sbjct: 484 VAAV 487


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: 932
Number of extensions: 30
Number of successful extensions: 1
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: 491
Length adjustment: 34
Effective length of query: 452
Effective length of database: 457
Effective search space:   206564
Effective search space used:   206564
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
the source code
instructions for running GapMind on your computer

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