Alignments for a candidate for praD in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for praD in Cupriavidus basilensis 4G11

Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate RR42_RS32640 RR42_RS32640 4-oxalocrotonate decarboxylase

Query= metacyc::MONOMER-14737
         (262 letters)



>FitnessBrowser__Cup4G11:RR42_RS32640
          Length = 262

 Score =  370 bits (950), Expect = e-107
 Identities = 180/262 (68%), Positives = 216/262 (82%)

Query: 1   MKLDKNTLAQLAEHLENAELKAHDVTKITDDHPDMDWDDAYAIQDLIRARKESRGHKTLG 60
           M L ++T  QLAEHLE AEL    V KITD HP+MDW+DAYAIQD IRARK++RG +  G
Sbjct: 1   MNLTQDTTRQLAEHLETAELNREPVRKITDTHPEMDWEDAYAIQDAIRARKQARGTRIAG 60

Query: 61  LKCGLTSYAKMKQMGVDTPVFGFVSDYMACAEGSDIKTSELIHPKVEAEICVVTKAPLKG 120
           LK GLTS+AKM+QMGV  PV+GF++DY AC +G  I T+ LIHPKVEAEI  V K PLKG
Sbjct: 61  LKMGLTSFAKMRQMGVTDPVYGFLTDYGACMDGGAIDTASLIHPKVEAEIAFVLKHPLKG 120

Query: 121 PGCHVGAVMAAIDFVIPGVEIIDSRYRDFKFDLKSVIADNTSASRFVIGGRARRVEDLDL 180
           PGCH+G V+AA DFV+P VE+IDSRY +F+FDLKSVIADNTS++RFV+GG  R  E +DL
Sbjct: 121 PGCHIGDVLAATDFVLPAVEVIDSRYENFRFDLKSVIADNTSSARFVVGGTHRSAEGIDL 180

Query: 181 RTLGVVLEKNGQIVAMAAGAAVMGHPAAAIAALANHLGARGQEIPTGSFIMTGGVTEAIA 240
           + LGVVLEKNG++VA AAGAAV+GHPA+++A LAN LGARG+E+P G+FIMTGGVTEAIA
Sbjct: 181 KNLGVVLEKNGEVVATAAGAAVLGHPASSVAMLANMLGARGRELPAGTFIMTGGVTEAIA 240

Query: 241 VQAGDSVNVRFQDLGTVGMRFV 262
           V AGDS+ VR+Q LGTV MRFV
Sbjct: 241 VAAGDSITVRYQHLGTVSMRFV 262


Lambda     K      H
   0.320    0.135    0.391 

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: 241
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: 262
Length of database: 262
Length adjustment: 25
Effective length of query: 237
Effective length of database: 237
Effective search space:    56169
Effective search space used:    56169
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 RR42_RS32640 RR42_RS32640 (4-oxalocrotonate decarboxylase)
to HMM TIGR03218 (dmpH: 4-oxalocrotonate decarboxylase (EC 4.1.1.77))

# 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/TIGR03218.hmm
# target sequence database:        /tmp/gapView.7991.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03218  [M=263]
Accession:   TIGR03218
Description: catechol_dmpH: 4-oxalocrotonate decarboxylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.8e-141  454.1   0.6   7.6e-141  454.0   0.6    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS32640  RR42_RS32640 4-oxalocrotonate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS32640  RR42_RS32640 4-oxalocrotonate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  454.0   0.6  7.6e-141  7.6e-141       3     263 .]       1     261 [.       1     261 [. 1.00

  Alignments for each domain:
  == domain 1  score: 454.0 bits;  conditional E-value: 7.6e-141
                                 TIGR03218   3 ltltreqiealaehvenaeleareitkitdeyPdldfadaydiqaeirrrklarGakvvGlkaGltska 71 
                                               ++lt+++  +laeh+e ael+ + + kitd +P++d++day+iq++ir+rk+arG+++ Glk+Glts+a
  lcl|FitnessBrowser__Cup4G11:RR42_RS32640   1 MNLTQDTTRQLAEHLETAELNREPVRKITDTHPEMDWEDAYAIQDAIRARKQARGTRIAGLKMGLTSFA 69 
                                               689****************************************************************** PP

                                 TIGR03218  72 kmkqmGvetpvfGfladyfsvpdggeiktselihPkveaeiafvlkaelkgpgchigdvlaatdfvlpa 140
                                               km+qmGv++pv+Gfl+dy +  dgg+i+t  lihPkveaeiafvlk++lkgpgchigdvlaatdfvlpa
  lcl|FitnessBrowser__Cup4G11:RR42_RS32640  70 KMRQMGVTDPVYGFLTDYGACMDGGAIDTASLIHPKVEAEIAFVLKHPLKGPGCHIGDVLAATDFVLPA 138
                                               ********************************************************************* PP

                                 TIGR03218 141 vevidsrykdfkfdlksvvadnassarfvtGgraaavedldlrtlGvvleknGevvalgagaavlGhpa 209
                                               vevidsry++f+fdlksv+adn+ssarfv+Gg  ++ e++dl++lGvvleknGevva++agaavlGhpa
  lcl|FitnessBrowser__Cup4G11:RR42_RS32640 139 VEVIDSRYENFRFDLKSVIADNTSSARFVVGGTHRSAEGIDLKNLGVVLEKNGEVVATAAGAAVLGHPA 207
                                               ********************************************************************* PP

                                 TIGR03218 210 aavamlanllaergeeiPaGslilsggiteavavaaGdsvtvrvqelgsvslrf 263
                                               ++vamlan+l++rg+e+PaG++i++gg+tea+avaaGds+tvr+q+lg+vs+rf
  lcl|FitnessBrowser__Cup4G11:RR42_RS32640 208 SSVAMLANMLGARGRELPAGTFIMTGGVTEAIAVAAGDSITVRYQHLGTVSMRF 261
                                               *****************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.30
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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