Alignments for a candidate for iolD in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolD in Herbaspirillum seropedicae SmR1

Align 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (ring-opening) (EC 3.7.1.22) (characterized)
to candidate HSERO_RS12130 HSERO_RS12130 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase

Query= BRENDA::Q9L3I0
         (626 letters)



>FitnessBrowser__HerbieS:HSERO_RS12130
          Length = 625

 Score =  678 bits (1749), Expect = 0.0
 Identities = 352/618 (56%), Positives = 439/618 (71%), Gaps = 8/618 (1%)

Query: 14  TIRLTMAQAVAHFLKVQMTIVDGKKVPIFGGVWAIFGHGNVAGIGEALYQVREELTTYRA 73
           T+RLTMAQA+  +L           +P+FGGV++IFGHGNVAG+GEALYQ R  L TYRA
Sbjct: 10  TLRLTMAQALVRYLDALRIQTPQGVLPLFGGVFSIFGHGNVAGMGEALYQYRATLPTYRA 69

Query: 74  HNEQGMAHAAIAYAKANFRTRFMACTSSIGPGALNMVTAAGVAHVNRIPVLFLPGDVFAN 133
           HNEQ MAH+AIAYAKA+ R R MA T+SIGPGA N++TAA +AHVNR+PVL LPGDVF +
Sbjct: 70  HNEQAMAHSAIAYAKAHLRQRMMAVTTSIGPGATNLLTAAALAHVNRLPVLLLPGDVFVS 129

Query: 134 RAPDPVLQQIEDSATASVSANDAFRSVSRYFDRITRPEQIITALKRAMQVLTDPLDCGPV 193
           R PDPVLQQ+ED     +S NDAFR +SR FDRI  PEQ++TAL RA+QVLTDP  CGPV
Sbjct: 130 RRPDPVLQQLEDFNDPGLSVNDAFRPLSRMFDRICYPEQLLTALPRAIQVLTDPAQCGPV 189

Query: 194 TLSLCQDVQAEAYDYPESLFAEKVWTTRRPQPDADELANAIALIKASQKPVIVAGGGVLY 253
           TL+L QDVQ  AYDYP   F+ +V   R   P A EL +A+AL++ +++P+++AGGGVLY
Sbjct: 190 TLALPQDVQTMAYDYPLDFFSPRVIVPRAQAPAAQELEDAVALLRQARQPLLIAGGGVLY 249

Query: 254 SQATKELAAFAEAHGIPVVVSQAGKSAINETHPLALGSVGVTGTSAANAIAEETDLVIAV 313
             A + L  FAE HG+PV  +QAGKSA+  +H L +G++GVTG+ AANA+A+E D+VIAV
Sbjct: 250 GNACEHLRRFAEQHGVPVAETQAGKSALPWSHALQMGAIGVTGSPAANALAQEADVVIAV 309

Query: 314 GTRCQDFTTGSWALFKNDSLKMIGLNIAAYDAVKHDSHPLVADAREGLKALSAGLSGWKA 373
           GTR QDFTTGS  LF     +++ LN+ A DA K     L ADA  GL+ALS  L GW++
Sbjct: 310 GTRLQDFTTGSHTLFA--QARLLNLNVNAMDAHKWRGLALQADAGLGLEALSHALEGWRS 367

Query: 374 PAALAEKAAAEKKIWMEAAAR--AMATTNAALPSDAQVIGAVARTIGG--ENTTVLCAAG 429
                 +A    + W E  A+      T   LP D +VIGA+ R++        V+CAAG
Sbjct: 368 APEWHARAHTLAQDWRERVAQITGQTDTGGRLPYDGEVIGAIQRSVADSPSQDIVVCAAG 427

Query: 430 GLPGELHKLWPATAPGSYHMEYGFSCMGYEIAGGLGAKMARPERDVVVMVGDGSYMMMNS 489
            LP ELHKLW A  PG+YH+EYG+SCMGYE+AGGLG K+A+P+R+V+V+VGDGSY+MMNS
Sbjct: 428 TLPAELHKLWRAGRPGAYHVEYGYSCMGYEVAGGLGVKLAQPQREVIVIVGDGSYLMMNS 487

Query: 490 ELATSVMLGLKLNIIVLDNRGYGCINRLQMGTGGANFNNLLKDSYH--EVMPEIDFRAHA 547
           ELATSVMLG KL ++VLDNRGYGCINRLQ   GGA FNN+L D        P IDF AHA
Sbjct: 488 ELATSVMLGAKLIVVVLDNRGYGCINRLQQACGGAPFNNMLADCLQAGPGAPAIDFAAHA 547

Query: 548 ESMGAIAVKVASIAELEQALADSRKNDRTSVFVIDTDPLITTEAGGHWWDVAVPEVSSRS 607
            S+GA+   V +I ELE AL  +R  DR+ +  IDTD   TT+ GG WW+VAVPEVS RS
Sbjct: 548 RSLGALGENVKTITELEAALQRARAADRSYLVCIDTDASRTTDDGGCWWEVAVPEVSPRS 607

Query: 608 EVNRAHEAYVKARAAQRV 625
           +V +A   Y +AR AQ V
Sbjct: 608 QVQQARSQYEQARQAQSV 625


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: 1027
Number of extensions: 42
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: 625
Length adjustment: 38
Effective length of query: 588
Effective length of database: 587
Effective search space:   345156
Effective search space used:   345156
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