Alignments for a candidate for pcaD in Sinorhizobium meliloti 1021

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.24293.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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.05
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources