Alignments for a candidate for iolD in Methylobacterium nodulans ORS 2060

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolD in Methylobacterium nodulans ORS 2060

Align 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (ring-opening) (EC 3.7.1.22) (characterized)
to candidate WP_012631041.1 MNOD_RS38625 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (decyclizing)

Query= BRENDA::Q9L3I0
         (626 letters)



>NCBI__GCF_000022085.1:WP_012631041.1
          Length = 612

 Score =  699 bits (1803), Expect = 0.0
 Identities = 366/618 (59%), Positives = 439/618 (71%), Gaps = 13/618 (2%)

Query: 11  MGKTIRLTMAQAVAHFLKVQMTIVDGKKVPIFGGVWAIFGHGNVAGIGEALYQVREELTT 70
           M  T+RLT AQ +  +L VQMT  +G++     GVWAIFGHGNVAGIGEAL ++ + L T
Sbjct: 1   MMTTVRLTAAQTMMRWLSVQMT-EEGER--FIEGVWAIFGHGNVAGIGEALEKIGDALPT 57

Query: 71  YRAHNEQGMAHAAIAYAKANFRTRFMACTSSIGPGALNMVTAAGVAHVNRIPVLFLPGDV 130
           +R  NEQ MAHAAIAYAK   R + MA TSSIGPGA NMVTAA +AHVNR+PVL +PGDV
Sbjct: 58  WRGQNEQTMAHAAIAYAKTKRRRKAMAVTSSIGPGATNMVTAAALAHVNRLPVLLIPGDV 117

Query: 131 FANRAPDPVLQQIEDSATASVSANDAFRSVSRYFDRITRPEQIITALKRAMQVLTDPLDC 190
           FANR PDPVLQQIED    +VSAND FR VSRYFDRITRPE ++TAL RA+QV+TDP  C
Sbjct: 118 FANRRPDPVLQQIEDFDDGTVSANDCFRPVSRYFDRITRPEHLLTALPRALQVMTDPAQC 177

Query: 191 GPVTLSLCQDVQAEAYDYPESLFAEKVWTTRRPQPDADELANAIALIKASQKPVIVAGGG 250
           GPVTL+ CQDVQAEAYD+PE+ FA KVW  RRP+PD  ELA  I +I+A+QKPVIV+GGG
Sbjct: 178 GPVTLAFCQDVQAEAYDWPEAFFAPKVWHIRRPEPDRRELAAVIEMIRAAQKPVIVSGGG 237

Query: 251 VLYSQATKELAAFAEAHGIPVVVSQAGKSAINETHPLALGSVGVTGTSAANAIAEETDLV 310
           VLYS A ++LAAFAE H IPVV +QAGK A++  HPL  GS GVTG+  AN I  E DL+
Sbjct: 238 VLYSGADQDLAAFAEKHNIPVVETQAGKGALDWQHPLNFGSPGVTGSDCANRICAEADLI 297

Query: 311 IAVGTRCQDFTTGSWALFKNDSLKMIGLNIAAYDAVKHDSHPLVADAREGLKALSAGLSG 370
           I  GTR QDFTTGSWA F+N   K++ +N+  YDA KH + PLVADA+  L A++AGL G
Sbjct: 298 IGAGTRFQDFTTGSWAAFRNPQRKLVSVNLTGYDAAKHSAVPLVADAKIALTAITAGLEG 357

Query: 371 WKAPAALAEKAAAEKKIWMEAAARAMATTNAA----LPSDAQVIGAVARTIGGENTTVLC 426
            +     A   A+ +  W +AA R MA         LP+DAQV+GAV R   G +T V+C
Sbjct: 358 HR----FAGPDASLRTAWFKAADRVMAAPQGENPNDLPTDAQVVGAVQR-YAGADTVVMC 412

Query: 427 AAGGLPGELHKLWPATAPGSYHMEYGFSCMGYEIAGGLGAKMARPERDVVVMVGDGSYMM 486
           AAG +PG L  LW A APG YHMEYG+SCMGYE+AG +G  +A PE++V+  VGDGSYMM
Sbjct: 413 AAGTMPGALQVLWRA-APGGYHMEYGYSCMGYEVAGAMGIALAVPEKEVICFVGDGSYMM 471

Query: 487 MNSELATSVMLGLKLNIIVLDNRGYGCINRLQMGTGGANFNNLLKDSYHEVMPEIDFRAH 546
            NSELAT+ M+ +   I++ DNRGYGCINRLQ+  GGA FNN+  DS H+  PEIDF AH
Sbjct: 472 ANSELATAAMMHVPFTIVLTDNRGYGCINRLQIECGGAPFNNMYVDSRHKTFPEIDFVAH 531

Query: 547 AESMGAIAVKVASIAELEQALADSRKNDRTSVFVIDTDPLITTEAGGHWWDVAVPEVSSR 606
           A +MGA AVKVA IA LE  LA  R      V +IDT+   +   GG WWDVAVPEV + 
Sbjct: 532 ARAMGAEAVKVAGIAGLEAELARPRDRKVPRVILIDTEAESSLGVGGAWWDVAVPEVGTT 591

Query: 607 SEVNRAHEAYVKARAAQR 624
             +  A E Y    A QR
Sbjct: 592 EALRAARERYDSHAAFQR 609


Lambda     K      H
   0.318    0.131    0.382 

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: 1020
Number of extensions: 37
Number of successful extensions: 5
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: 626
Length of database: 612
Length adjustment: 37
Effective length of query: 589
Effective length of database: 575
Effective search space:   338675
Effective search space used:   338675
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. 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:

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 2024 update 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