Alignments for a candidate for iolD in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolD in Sinorhizobium meliloti 1021

Align 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (ring-opening) (EC 3.7.1.22) (characterized)
to candidate SMc01166 SMc01166 malonic semialdehyde oxidative decarboxylase

Query= BRENDA::Q9L3I0
         (626 letters)



>FitnessBrowser__Smeli:SMc01166
          Length = 617

 Score =  909 bits (2349), Expect = 0.0
 Identities = 443/614 (72%), Positives = 518/614 (84%)

Query: 13  KTIRLTMAQAVAHFLKVQMTIVDGKKVPIFGGVWAIFGHGNVAGIGEALYQVREELTTYR 72
           KT+RLTMAQAVA FL  QMTI+DG++VPIFGGV+AIFGHGNVAG+GEALY VRE L TYR
Sbjct: 4   KTVRLTMAQAVARFLTRQMTIIDGERVPIFGGVFAIFGHGNVAGVGEALYGVRETLPTYR 63

Query: 73  AHNEQGMAHAAIAYAKANFRTRFMACTSSIGPGALNMVTAAGVAHVNRIPVLFLPGDVFA 132
           A NEQGMA+AAIA+AKA+FR RFMACT+SIGPGALNMVT+A +AHVNR+PVL LPGDVFA
Sbjct: 64  AQNEQGMANAAIAFAKASFRRRFMACTTSIGPGALNMVTSAALAHVNRLPVLLLPGDVFA 123

Query: 133 NRAPDPVLQQIEDSATASVSANDAFRSVSRYFDRITRPEQIITALKRAMQVLTDPLDCGP 192
           NR PDPVLQQ+E     ++SAND F+ VSRYFDRITRPEQII AL+RAMQVLTDP DCGP
Sbjct: 124 NRRPDPVLQQVESFGDGTISANDCFKPVSRYFDRITRPEQIIPALRRAMQVLTDPADCGP 183

Query: 193 VTLSLCQDVQAEAYDYPESLFAEKVWTTRRPQPDADELANAIALIKASQKPVIVAGGGVL 252
           VTLSLCQDVQAEAYDYPES F EKVW  RR +PD DELA+AI  +++++KP+I+AGGGVL
Sbjct: 184 VTLSLCQDVQAEAYDYPESFFDEKVWVPRRIEPDLDELASAIEALRSAKKPIIIAGGGVL 243

Query: 253 YSQATKELAAFAEAHGIPVVVSQAGKSAINETHPLALGSVGVTGTSAANAIAEETDLVIA 312
           YS+A+ ELAAFAE HGIPVV +QAGKSA+  +HPL +GSVGVTGTSA+NA+AEE D+V+A
Sbjct: 244 YSEASAELAAFAEKHGIPVVETQAGKSALPHSHPLNMGSVGVTGTSASNALAEEADVVLA 303

Query: 313 VGTRCQDFTTGSWALFKNDSLKMIGLNIAAYDAVKHDSHPLVADAREGLKALSAGLSGWK 372
           VG+R QDFTTGSWALFKN++LK+IGLN+ A+DA KH+  PL++DAR GL  +S GL  +K
Sbjct: 304 VGSRLQDFTTGSWALFKNEALKIIGLNVQAFDAGKHEGQPLISDARAGLNRISGGLGSYK 363

Query: 373 APAALAEKAAAEKKIWMEAAARAMATTNAALPSDAQVIGAVARTIGGENTTVLCAAGGLP 432
           A +A  E+A A K  W+ AA RA ATTNAALPSDAQVIGAV R  GG  TT++CAAGGLP
Sbjct: 364 ADSAWTERAKAGKAEWLAAAERATATTNAALPSDAQVIGAVQRARGGRKTTLVCAAGGLP 423

Query: 433 GELHKLWPATAPGSYHMEYGFSCMGYEIAGGLGAKMARPERDVVVMVGDGSYMMMNSELA 492
           GELHKLW A  PG YHMEYGFS MGYE+AGGLG K+A+P+ DV+VMVGDGSYMM+NSE+A
Sbjct: 424 GELHKLWQAEEPGGYHMEYGFSTMGYEVAGGLGVKLAKPDSDVIVMVGDGSYMMLNSEIA 483

Query: 493 TSVMLGLKLNIIVLDNRGYGCINRLQMGTGGANFNNLLKDSYHEVMPEIDFRAHAESMGA 552
           +S+MLG K  +++LDN GYGCINRLQMGTGGANFNNLLKD++H  +P+IDF AHA +MGA
Sbjct: 484 SSIMLGAKFTVVLLDNAGYGCINRLQMGTGGANFNNLLKDTHHVELPQIDFAAHAAAMGA 543

Query: 553 IAVKVASIAELEQALADSRKNDRTSVFVIDTDPLITTEAGGHWWDVAVPEVSSRSEVNRA 612
           +  KV SI ELE ALA++    RT+V VIDTDPLITTEAGGHWWDVAVPEVS R +V  A
Sbjct: 544 VTRKVGSIPELEAALAETADEVRTTVIVIDTDPLITTEAGGHWWDVAVPEVSDRDQVKAA 603

Query: 613 HEAYVKARAAQRVG 626
            E Y KA  AQR G
Sbjct: 604 REGYEKALQAQRFG 617


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: 1114
Number of extensions: 35
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: 626
Length of database: 617
Length adjustment: 37
Effective length of query: 589
Effective length of database: 580
Effective search space:   341620
Effective search space used:   341620
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: 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