GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolD in Rhodococcus qingshengii djl-6-2

Align 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (ring-opening) (EC 3.7.1.22) (characterized)
to candidate WP_050654910.1 C1M55_RS10190 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (decyclizing)

Query= BRENDA::Q9L3I0
         (626 letters)



>NCBI__GCF_002893965.1:WP_050654910.1
          Length = 651

 Score =  520 bits (1340), Expect = e-152
 Identities = 279/636 (43%), Positives = 393/636 (61%), Gaps = 23/636 (3%)

Query: 7   REDPMGKTIRLTMAQAVAHFLKVQMTIVDGKKVPIFGGVWAIFGHGNVAGIGEALYQV-- 64
           R++P   T+ LT++QAV  FL  Q T  DG++  +F G + IFGHGNVAG+G+AL Q   
Sbjct: 14  RDEP---TVYLTVSQAVVRFLANQYTERDGQRTKLFAGCFGIFGHGNVAGLGQALLQAEI 70

Query: 65  ------REELTTY-RAHNEQGMAHAAIAYAKANFRTRFMACTSSIGPGALNMVTAAGVAH 117
                 RE    Y    NEQ M H+A+A+A+   R +  A +SS+GPGA NM+T A +A 
Sbjct: 71  QDLDAGREPTLPYVLGRNEQAMVHSAVAHARMKDRLQTWAVSSSVGPGATNMITGAALAT 130

Query: 118 VNRIPVLFLPGDVFANRAPDPVLQQIEDSATASVSANDAFRSVSRYFDRITRPEQIITAL 177
           +NR+PVL LP D FA RA  PVLQ++E  ++  V+ NDAF+ VSRYFDR+ RPEQ+ +AL
Sbjct: 131 INRLPVLLLPADTFATRASAPVLQELELPSSGDVTVNDAFKPVSRYFDRVWRPEQLPSAL 190

Query: 178 KRAMQVLTDPLDCGPVTLSLCQDVQAEAYDYPESLFAEKVWTTRRPQPDADELANAIALI 237
              M+VLTDP++ G VT+++ QDVQAEA+D+PES FAE+VW   RP P+   +  A A+I
Sbjct: 191 LAGMRVLTDPVETGAVTIAIPQDVQAEAFDWPESFFAERVWHVARPLPERSVIERAAAII 250

Query: 238 KASQKPVIVAGGGVLYSQATKELAAFAEAHGIPVVVSQAGKSAINETHPLALGSVGVTGT 297
           ++++KP+IVAGGGV+YSQAT  LAAF    GIPV  SQAGK ++   HP ++G+VG TGT
Sbjct: 251 RSARKPLIVAGGGVIYSQATDSLAAFCAQTGIPVGQSQAGKGSLVYDHPQSVGAVGSTGT 310

Query: 298 SAANAIAEETDLVIAVGTRCQDFTTGSWALFKNDSLKMIGLNIAAYDAVKHDSHPLVADA 357
           +AANA+A E D+VI +GTR  DFT+ S   F N  ++ + +N+A+ D+VK     +VADA
Sbjct: 311 TAANALATEADVVIGIGTRYSDFTSASRTAFTNPDVRFVNINVASLDSVKQGGVSVVADA 370

Query: 358 REGLKALSAGLSGWKAPAALAEKAAAEKKIW---MEAAARAMATTNAALPSDAQVIGAVA 414
           RE L AL+  L+ ++     A +     + W   +E+             +  QVIG V 
Sbjct: 371 REALDALALALNDYRVDEEYASRIGDLARDWDAIVESVYNPAEPAADGSLNQNQVIGLV- 429

Query: 415 RTIGGENTTVLCAAGGLPGELHKLWPATAPGSYHMEYGFSCMGYEIAGGLGAKMARPERD 474
            T+      V+CAAG +PG+LHKLW       YH+EYG+SCMGYE+AGGLG +MA P+RD
Sbjct: 430 NTLSDPRDVVVCAAGSMPGDLHKLWRTRDSKGYHVEYGYSCMGYEVAGGLGVRMACPDRD 489

Query: 475 VVVMVGDGSYMMMNSELATSVMLGLKLNIIVLDNRGYGCINRLQMGTGGANFNNLLKDSY 534
           V VMVGDGSY+MM +EL T+V   LK+ ++++ N G+  I  L    G   F    +   
Sbjct: 490 VFVMVGDGSYLMMATELVTAVQERLKVIVVLVQNHGFASIGSLSESLGSQRFGTQYRYRS 549

Query: 535 HE------VMPEIDFRAHAESMGAIAVKVASIAELEQALADSRKNDRTSVFVIDTDPLIT 588
           ++      V+P +D  A+A S+G   ++  + AE   A+  ++ +D ++V  ++TDPLI 
Sbjct: 550 NDGRLDGGVLP-VDLAANAASLGVDVIRANTAAEFADAIKVAKASDTSTVIHVETDPLIG 608

Query: 589 TEAGGHWWDVAVPEVSSRSEVNRAHEAYVKARAAQR 624
                 WWDV V   S      +A   Y   +  QR
Sbjct: 609 APDSESWWDVPVSATSELESTKKARTTYESWKKIQR 644


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: 940
Number of extensions: 35
Number of successful extensions: 4
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: 651
Length adjustment: 38
Effective length of query: 588
Effective length of database: 613
Effective search space:   360444
Effective search space used:   360444
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 24 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