Alignments for a candidate for iolD in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolD in Klebsiella michiganensis M5al

Align 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (ring-opening) (EC 3.7.1.22) (characterized)
to candidate BWI76_RS03090 BWI76_RS03090 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase

Query= BRENDA::P42415
         (637 letters)



>FitnessBrowser__Koxy:BWI76_RS03090
          Length = 646

 Score =  707 bits (1826), Expect = 0.0
 Identities = 348/644 (54%), Positives = 466/644 (72%), Gaps = 10/644 (1%)

Query: 4   KIRLTTAQALIKFLNQQYIHVDGKEEPFVEGIFTIFGHGNVLGIGQALEQDAGHLKVYQG 63
           K+RLT AQAL+KFL+ QY+ VDG+E  FV+GIF IFGHGNVLG+GQALEQD+G ++VYQG
Sbjct: 3   KLRLTMAQALVKFLDNQYLEVDGEEHKFVKGIFAIFGHGNVLGMGQALEQDSGEMRVYQG 62

Query: 64  KNEQGMAHAAMAYSKQMLRRKIYAVSTSVGPGAANLVAAAGTALANNIPVLLIPADTFAT 123
           +NEQGMAH A  +++Q LRR+I A ++S+GPGAAN++ AA TA AN IP+LL+P D FAT
Sbjct: 63  RNEQGMAHVATGFARQSLRRQIIACTSSIGPGAANMITAAATATANRIPLLLLPGDVFAT 122

Query: 124 RQPDPVLQQMEQEYSAAITTNDALKPVSRYWDRITRPEQLMSSLLRAFEVMTDPAKAGPA 183
           RQPDPVLQQ+EQ +  +ITTNDA + VS+YWDRITRPEQLMS+ + A  V+TDPA+ G  
Sbjct: 123 RQPDPVLQQIEQSHDLSITTNDAFRAVSKYWDRITRPEQLMSACINAMRVLTDPAETGAV 182

Query: 184 TICISQDVEGEAYDFDESFFVKRVHYIDRMQPSERELQGAAELIKSSKKPVILVGGGAKY 243
           T+C+ QDV+GEA+D+ ESFF +RVH +DR   S  +L  A   IK+S+KP+I+ GGG KY
Sbjct: 183 TLCLPQDVQGEAWDYPESFFTRRVHRLDRRPASAAQLADAVAAIKASRKPLIVCGGGVKY 242

Query: 244 SGARDELVAISEAYNIPLVETQAGKSTVEADFANNLGGMGITGTLAANKAARQADLIIGI 303
           SGA + L   +E Y +P  ETQAGK +V +    N+GG+G TG LAAN  A++ADL+IG+
Sbjct: 243 SGAGEALTRFAERYGVPFAETQAGKGSVVSSHPYNVGGVGETGCLAANLLAKEADLVIGL 302

Query: 304 GTRYTDFATSSKTAFDFDKAKFLNINVSRMQAYKLDAFQVVADAKVTLGKLHGLLEG--Y 361
           GTR++DF TSSK  F     +FLNINVS   A+KLD   ++ADA+  L  L G L G  +
Sbjct: 303 GTRFSDFTTSSKWIFQHPGVRFLNINVSNFDAWKLDGIPMLADAREALTALDGALSGESW 362

Query: 362 ESEFGTTIRELKDEWLAERERLSKVTFKREAFDPEIKNHFSQE-VLNEYADALNTELPQT 420
           ++ +G  I  ++   L E +R+ +  ++  AF PEI +H  +E V  E+    ++ L Q+
Sbjct: 363 QAGWGEQIESVQSRQLKETQRVYQAVWQETAFVPEIDDHLDRESVYREFRQITDSTLTQS 422

Query: 421 TALLTINETIPEDSVIICSAGSLPGDLQRLWHSNVPNTYHLEYGYSCMGYEVSGTLGLKL 480
           + L  +NET+P D+VI+ +AGSLPGDLQR+W +   NTYH+EYGYSCMGYEVS  LG+KL
Sbjct: 423 SVLGVLNETLPADAVIVAAAGSLPGDLQRVWRNRAANTYHVEYGYSCMGYEVSAALGVKL 482

Query: 481 AHPDREVYSIVGDGSFLMLHSELITAIQYNKKINVLLFDNSGFGCINNLQMDHGSGSYYC 540
           A P  EVYS+VGDGSF+MLHSEL+T++Q   KIN++L DN   GCINNLQM+HG  S+  
Sbjct: 483 AQPQSEVYSLVGDGSFMMLHSELVTSLQERAKINIVLLDNMANGCINNLQMEHGMDSFGT 542

Query: 541 EFR---TDDNQ----ILNVDYAKVAEGYGAKTYRANTVEELKAALEDAKKQDVSTLIEMK 593
           EFR    +  Q    ++ VD+A VA GYG KT+R  T+EEL+ AL+ A+++ VSTLI++K
Sbjct: 543 EFRFRCAESGQLQGGLVPVDFATVAAGYGCKTWRVTTLEELRHALDAARRETVSTLIDIK 602

Query: 594 VLPKTMTDGYDSWWHVGVAEVSEQESVQKAYEAKEKKLESAKQY 637
           VLPKTM   Y SWW+VGVA+ +  E ++K  +   +K   A+ Y
Sbjct: 603 VLPKTMVHKYGSWWNVGVAQSALSERIRKVAQMINEKRAQARDY 646


Lambda     K      H
   0.316    0.132    0.375 

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: 990
Number of extensions: 23
Number of successful extensions: 3
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: 637
Length of database: 646
Length adjustment: 38
Effective length of query: 599
Effective length of database: 608
Effective search space:   364192
Effective search space used:   364192
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 (21.6 bits)
S2: 54 (25.4 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