GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iolD in Caulobacter crescentus NA1000

Align 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (ring-opening) (EC 3.7.1.22) (characterized)
to candidate CCNA_01357 CCNA_01357 myo-inositol catabolism protein IolD

Query= BRENDA::Q9L3I0
         (626 letters)



>lcl|FitnessBrowser__Caulo:CCNA_01357 CCNA_01357 myo-inositol
           catabolism protein IolD
          Length = 614

 Score =  726 bits (1873), Expect = 0.0
 Identities = 368/612 (60%), Positives = 449/612 (73%), Gaps = 2/612 (0%)

Query: 15  IRLTMAQAVAHFLKVQMTIVDGKKVPIFGGVWAIFGHGNVAGIGEALYQVREELTTYRAH 74
           +RLT AQA   +L  Q       +VP F GVWAIFGHGNVAG+GEAL+ VR+ L TYRAH
Sbjct: 4   VRLTAAQATVRWLAAQHVETSDGEVPYFAGVWAIFGHGNVAGLGEALHGVRDVLLTYRAH 63

Query: 75  NEQGMAHAAIAYAKANFRTRFMACTSSIGPGALNMVTAAGVAHVNRIPVLFLPGDVFANR 134
           NEQGMAHAAIA+AK + R R M CT+SIGPGA NMVTAA +AHVNR+PVLFLPGDV+A+R
Sbjct: 64  NEQGMAHAAIAFAKQSRRERAMVCTTSIGPGATNMVTAAALAHVNRLPVLFLPGDVYASR 123

Query: 135 APDPVLQQIEDSATASVSANDAFRSVSRYFDRITRPEQIITALKRAMQVLTDPLDCGPVT 194
            PDPVLQQIED    ++SAN+ F+ VSRYFDRITRPEQI+ AL RA+ V+ DP  CGP T
Sbjct: 124 RPDPVLQQIEDFGDGTISANECFKPVSRYFDRITRPEQILDALPRALAVMLDPATCGPAT 183

Query: 195 LSLCQDVQAEAYDYPESLFAEKVWTTRRPQPDADELANAIALIKASQKPVIVAGGGVLYS 254
           L+ CQDVQAEA+DYP++ FA++VW  R PQPD  EL + + LIKA+++P+IVAGGGVLY+
Sbjct: 184 LAFCQDVQAEAFDYPQAFFAKRVWRIRAPQPDPRELDDLVGLIKAAERPLIVAGGGVLYA 243

Query: 255 QATKELAAFAEAHGIPVVVSQAGKSAINETHPLALGSVGVTGTSAANAIAEETDLVIAVG 314
           +A   LA  A   G+PVV +Q GK ++   HPL LG+VGVTGT+A+ A AE  DLVI +G
Sbjct: 244 RAEAALADLANDAGLPVVETQGGKGSLAWDHPLNLGAVGVTGTTASVAAAEAADLVIGLG 303

Query: 315 TRCQDFTTGSWALFKNDSLKMIGLNIAAYDAVKHDSHPLVADAREGLKALSAGLSGWKAP 374
           TR QDFTTGS ALF  +  K++ +N+A +DA KH +  +V DA   L+AL+  L GW+AP
Sbjct: 304 TRLQDFTTGSRALFGAEGRKLVQVNVAPHDAHKHGATSVVGDALAVLEALAERLDGWRAP 363

Query: 375 AALAEKAAAEKKIWMEAAARAMATTNAALPSDAQVIGAVARTIGGENTTVLCAAGGLPGE 434
            A  ++A +    W      +       LP+DAQV+GAV R    +++ V+CAAGGLPGE
Sbjct: 364 VAWTDQATSGVPAWNAIFDASTRADTRPLPTDAQVLGAVWRA-SSDDSVVVCAAGGLPGE 422

Query: 435 LHKLWPATAPGSYHMEYGFSCMGYEIAGGLGAKMARPERDVVVMVGDGSYMMMNSELATS 494
           LHKLW    PG YH+EYGFSCMGYEIAG +G KMA P+R+V VMVGDGSY+M+NSELATS
Sbjct: 423 LHKLWRTRMPGGYHVEYGFSCMGYEIAGAVGVKMAEPDREVHVMVGDGSYLMLNSELATS 482

Query: 495 VMLGLKLNIIVLDNRGYGCINRLQMGTGGANFNNLLKDSYHEVMPEIDFRAHAESMGAIA 554
           VMLG KL + VLDNRGYGCINRLQ  TGGA FNNLL D+ HE +P+IDF AHA S+GA +
Sbjct: 483 VMLGTKLIVTVLDNRGYGCINRLQAATGGAAFNNLLADTLHETLPDIDFAAHAASLGARS 542

Query: 555 VKVASIAELEQALADSRKNDRTSVFVIDTDPLITTEAGGHWWDVAVPEVSSRSEVNRAHE 614
            KV  ++ LE AL  ++ +DRT V VIDTDP+ TTE GG WWDVAVPEVS R  VN A  
Sbjct: 543 EKVGDLSSLEAALQRAKASDRTYVVVIDTDPMPTTE-GGAWWDVAVPEVSVRPSVNAARA 601

Query: 615 AYVKARAAQRVG 626
            Y      QR G
Sbjct: 602 DYDLKIKQQRTG 613


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: 1052
Number of extensions: 35
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: 626
Length of database: 614
Length adjustment: 37
Effective length of query: 589
Effective length of database: 577
Effective search space:   339853
Effective search space used:   339853
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 Sep 17 2021. 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:

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:

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:

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, or view the source code.

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