GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_01357
          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:

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