GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaD in Sinorhizobium meliloti 1021

Align 3-oxoadipate enol-lactonase (EC 3.1.1.24) (characterized)
to candidate SM_b20579 SM_b20579 beta-ketoadipate enol-lactone hydrolase

Query= BRENDA::Q13KT2
         (263 letters)



>FitnessBrowser__Smeli:SM_b20579
          Length = 268

 Score =  159 bits (403), Expect = 4e-44
 Identities = 93/251 (37%), Positives = 127/251 (50%), Gaps = 2/251 (0%)

Query: 1   MPYAAVNGTELHYRIDGERHGNAPWIVLSNSLGTDLSMWAPQVAALSKHFRVLRYDTRGH 60
           M +  +N   +HYR+ G      P +V  NSLGTD  +W   V  L+  F ++ YD RGH
Sbjct: 1   MQFTRINDVTIHYRVVGAVT-EKPALVFINSLGTDFRIWRDVVLRLAGDFAIVLYDKRGH 59

Query: 61  GHSEAPKGPYTIEQLTGDVLGLMDTLKIARANFCGLSMGGLTGVALAARHADRIERVALC 120
           G S+  + PY+IE    D+ GL+D L + +A  CGLS+GGL   +L  R  D +  + L 
Sbjct: 60  GLSDIGQVPYSIEDHATDLAGLLDRLAVKQAIVCGLSVGGLIAQSLYGRRPDLVRALVLS 119

Query: 121 NTAARIGSPEVWVPRAVKARTEGMHALADAVLPRWFTADYMEREPVVLAMIRDVFVHTDK 180
            TA +IG+ E W  R       G+ A+AD VL RWFT  +   E +     R++ V    
Sbjct: 120 GTAHKIGTVEFWDARITAIEAHGIEAVADGVLERWFTPAFRRPENLAFTGYRNMLVRQPV 179

Query: 181 EGYASNCEAIDAADLRPEAPGIKVPALVISGTHDLAATPAQGRELAQAIAGARY-VELDA 239
            GY   C AI  AD    A  I VP L + G  D +  P   R  A  I GAR+ V   A
Sbjct: 180 PGYVGTCAAIRDADFTEAAGRIAVPVLCVVGDQDGSTPPDLVRSTADLIPGARFEVIRGA 239

Query: 240 SHISNIERADA 250
            HI  +E+ +A
Sbjct: 240 GHIPCVEQPEA 250


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: 203
Number of extensions: 6
Number of successful extensions: 1
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: 268
Length adjustment: 25
Effective length of query: 238
Effective length of database: 243
Effective search space:    57834
Effective search space used:    57834
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 SM_b20579 SM_b20579 (beta-ketoadipate enol-lactone hydrolase)
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.12590.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
     9e-118  378.2   0.0     1e-117  378.0   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SM_b20579  SM_b20579 beta-ketoadipate enol-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b20579  SM_b20579 beta-ketoadipate enol-lactone hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.0   0.0    1e-117    1e-117       1     251 []      10     260 ..      10     260 .. 0.99

  Alignments for each domain:
  == domain 1  score: 378.0 bits;  conditional E-value: 1e-117
                            TIGR02427   1 rlhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedladdvlallD 74 
                                          ++hyr+ ga ++kp+lv+inSLGtd+r+w++v+ +l+ df+++ yDkrGHGlSd++++pysied+a+d+++llD
  lcl|FitnessBrowser__Smeli:SM_b20579  10 TIHYRVVGAVTEKPALVFINSLGTDFRIWRDVVLRLAGDFAIVLYDKRGHGLSDIGQVPYSIEDHATDLAGLLD 83 
                                          59************************************************************************ PP

                            TIGR02427  75 algiekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaavraeGlaaladavlerwFtp 148
                                          +l +++a vcGlS+GGliaq+L+ rrpd+v+alvls ta+kigt e+W+aRi+a++a+G++a+ad+vlerwFtp
  lcl|FitnessBrowser__Smeli:SM_b20579  84 RLAVKQAIVCGLSVGGLIAQSLYGRRPDLVRALVLSGTAHKIGTVEFWDARITAIEAHGIEAVADGVLERWFTP 157
                                          ************************************************************************** PP

                            TIGR02427 149 afreaepaelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlviaGdeDgstPpelvreiadlvpga 222
                                          afr++e+ +++ +rnmlv+qp+ gY++tcaAirdad++e++++iavP+l+++Gd+DgstPp+lvr++adl+pga
  lcl|FitnessBrowser__Smeli:SM_b20579 158 AFRRPENLAFTGYRNMLVRQPVPGYVGTCAAIRDADFTEAAGRIAVPVLCVVGDQDGSTPPDLVRSTADLIPGA 231
                                          ************************************************************************** PP

                            TIGR02427 223 rfaeieeaaHlpnleqpeafaallrdflk 251
                                          rf++i++a+H+p++eqpea++++lr+f++
  lcl|FitnessBrowser__Smeli:SM_b20579 232 RFEVIRGAGHIPCVEQPEALWSVLRRFFR 260
                                          ***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (251 nodes)
Target sequences:                          1  (268 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 8.02
//
[ok]

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