GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaD in Ruegeria conchae TW15

Align 3-oxoadipate enol-lactonase (EC 3.1.1.24) (characterized)
to candidate WP_010437977.1 G7G_RS0102510 3-oxoadipate enol-lactonase

Query= BRENDA::Q13KT2
         (263 letters)



>NCBI__GCF_000192475.1:WP_010437977.1
          Length = 262

 Score =  176 bits (446), Expect = 4e-49
 Identities = 98/262 (37%), Positives = 144/262 (54%), Gaps = 5/262 (1%)

Query: 1   MPYAAVNGTELHYRIDGERHGNAPWIVLSNSLGTDLSMWAPQVAALSKHFRVLRYDTRGH 60
           M  A +    LHYRIDG+  G AP IV +NSLGTD+ +W P +  L K  R++R+D RGH
Sbjct: 1   MRIANLKDVSLHYRIDGDVDG-AP-IVFANSLGTDMRLWDPIIPFLPKGLRIIRFDKRGH 58

Query: 61  GHSEAPKGPYTIEQLTGDVLGLMDTLKIARANFCGLSMGGLTGVALAARHADRIERVALC 120
           G S  P  PY++  L  D   L+D L++    F GLS+GG+    LA +  D++  + L 
Sbjct: 59  GLSSQPAAPYSMGSLIRDAEQLLDHLEVKDCVFVGLSIGGMIAQGLAVKRMDQVRALVLS 118

Query: 121 NTAARIGSPEVWVPRAVKARTEGMHALADAVLPRWFTADYMEREPVVLAMIRDVFVHTDK 180
           NTAA+IG+P++W  R    R  G+ ALADA + RWF+  +       + + R++ V    
Sbjct: 119 NTAAKIGTPKIWHDRMAAVRAGGIEALADATMERWFSKHFQSGPE--MPLWRNMMVRQPV 176

Query: 181 EGYASNCEAIDAADLRPEAPGIKVPALVISGTHDLAATPAQGRELAQAIAGARYVEL-DA 239
           EGY   C AI   D      G+++P L I+G+ D +  P   RE    I G+R+  +  A
Sbjct: 177 EGYLGCCAAISGTDFYTPTSGLQLPTLGIAGSEDGSTPPDLVRETVDLIPGSRFALIRRA 236

Query: 240 SHISNIERADAFTKTVVDFLTE 261
            H+  +ER   + + + DFL E
Sbjct: 237 GHLPCVERPREYAELLGDFLIE 258


Lambda     K      H
   0.320    0.134    0.402 

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: 210
Number of extensions: 10
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: 263
Length of database: 262
Length adjustment: 25
Effective length of query: 238
Effective length of database: 237
Effective search space:    56406
Effective search space used:    56406
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate WP_010437977.1 G7G_RS0102510 (3-oxoadipate enol-lactonase)
to HMM TIGR02427 (pcaD: 3-oxoadipate enol-lactonase (EC 3.1.1.24))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02427.hmm
# target sequence database:        /tmp/gapView.2435451.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02427  [M=251]
Accession:   TIGR02427
Description: protocat_pcaD: 3-oxoadipate enol-lactonase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.4e-102  326.5   0.0   6.2e-102  326.3   0.0    1.0  1  NCBI__GCF_000192475.1:WP_010437977.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000192475.1:WP_010437977.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.3   0.0  6.2e-102  6.2e-102       2     250 ..      11     256 ..      10     257 .. 0.98

  Alignments for each domain:
  == domain 1  score: 326.3 bits;  conditional E-value: 6.2e-102
                             TIGR02427   2 lhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedladdvlallD 74 
                                           lhyr++g+ +++p +v+ nSLGtd+rlwd++++ l k +r++r+DkrGHGlS+ p++pys++ l +d  +llD
  NCBI__GCF_000192475.1:WP_010437977.1  11 LHYRIDGDVDGAP-IVFANSLGTDMRLWDPIIPFLPKGLRIIRFDKRGHGLSSQPAAPYSMGSLIRDAEQLLD 82 
                                           9********8888.9********************************************************** PP

                             TIGR02427  75 algiekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaavraeGlaaladavlerwFt 147
                                           +l++++ +++GlS+GG+iaq+La++r d+v+alvlsntaakigt+++W++R+aavra G++alada++erwF+
  NCBI__GCF_000192475.1:WP_010437977.1  83 HLEVKDCVFVGLSIGGMIAQGLAVKRMDQVRALVLSNTAAKIGTPKIWHDRMAAVRAGGIEALADATMERWFS 155
                                           ************************************************************************* PP

                             TIGR02427 148 pafreaepaelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlviaGdeDgstPpelvreiadlvp 220
                                           ++f+  +  e+ l+rnm+v+qp+egY ++caAi  +d+++ ++ +++Ptl iaG+eDgstPp+lvre++dl+p
  NCBI__GCF_000192475.1:WP_010437977.1 156 KHFQ--SGPEMPLWRNMMVRQPVEGYLGCCAAISGTDFYTPTSGLQLPTLGIAGSEDGSTPPDLVRETVDLIP 226
                                           ***9..566778************************************************************* PP

                             TIGR02427 221 garfaeieeaaHlpnleqpeafaallrdfl 250
                                           g+rfa i+ a+Hlp++e+p ++a+ll dfl
  NCBI__GCF_000192475.1:WP_010437977.1 227 GSRFALIRRAGHLPCVERPREYAELLGDFL 256
                                           ****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (251 nodes)
Target sequences:                          1  (262 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 19.12
//
[ok]

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