Alignments for a candidate for arcA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcA in Pseudomonas putida KT2440

Align arginine deiminase (EC 3.5.3.6) (characterized)
to candidate PP_1001 PP_1001 arginine deiminase

Query= BRENDA::A7LKB0
         (417 letters)



>FitnessBrowser__Putida:PP_1001
          Length = 417

 Score =  825 bits (2132), Expect = 0.0
 Identities = 401/417 (96%), Positives = 410/417 (98%)

Query: 1   MSAEKQKYGVHSEAGKLRKVMVCAPGLAHKRLTPSNCDELLFDDVIWVDQAKRDHFDFVT 60
           MSAEKQKYGVHSEAGKLRKVMVCAPGLAHKRLTPSNCDELLFDDVIWVDQAKRDHFDFVT
Sbjct: 1   MSAEKQKYGVHSEAGKLRKVMVCAPGLAHKRLTPSNCDELLFDDVIWVDQAKRDHFDFVT 60

Query: 61  KMRERGVDVLEMHNLLTDIVQNPEALKWILDRKITPDTVGVGLTNEVRSWLEGQEPRHLA 120
           KMRERGVDVLEMHNLLTDIVQN EALKWILDRKITPDTVGVGLTNEVRSWLEG EPRHLA
Sbjct: 61  KMRERGVDVLEMHNLLTDIVQNKEALKWILDRKITPDTVGVGLTNEVRSWLEGLEPRHLA 120

Query: 121 EFLIGGVAGQDLPESEGASVVKMYNDYLGHSSFILPPLPNTQFTRDTTCWIYGGVTLNPM 180
           EFLIGGVAGQDLP+SEGA VVKMYNDYLGHSSFILPPLPNTQFTRDTTCWIYGGVTLNPM
Sbjct: 121 EFLIGGVAGQDLPQSEGADVVKMYNDYLGHSSFILPPLPNTQFTRDTTCWIYGGVTLNPM 180

Query: 181 YWPARRQETLLTTAIYKFHPEFTKADFQVWYGDPDQEHGQATLEGGDVMPIGKGIVLIGM 240
           YWPARRQETLLTTAIYKFH EFT+ADFQVWYGDPD++HG ATLEGGDVMPIG GIVLIGM
Sbjct: 181 YWPARRQETLLTTAIYKFHKEFTEADFQVWYGDPDKDHGNATLEGGDVMPIGNGIVLIGM 240

Query: 241 GERTSRQAIGQLAQNLFAKGAVEQVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVRE 300
           GERTSRQAIGQLAQNLFAKGAV++VIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVV+E
Sbjct: 241 GERTSRQAIGQLAQNLFAKGAVKEVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVKE 300

Query: 301 IVPFIIRPDESKPYGMDVRRENKSFIEVVGEQLGVKLRVVETGGNSFAAEREQWDDGNNV 360
           IVPFIIRPDESKPYGMDVRR NKSFIEVVGEQLGV+LRVVETGGNSFAAEREQWDDGNNV
Sbjct: 301 IVPFIIRPDESKPYGMDVRRINKSFIEVVGEQLGVQLRVVETGGNSFAAEREQWDDGNNV 360

Query: 361 VALEPGVVIGYDRNTYTNTLLRKAGIEVITISAGELGRGRGGGHCMTCPIVRDPINY 417
           VA+EPGVVIGYDRNTYTNTLLRKAGIEVITISAGELGRGRGGGHCMTCPIVRDPINY
Sbjct: 361 VAIEPGVVIGYDRNTYTNTLLRKAGIEVITISAGELGRGRGGGHCMTCPIVRDPINY 417


Lambda     K      H
   0.320    0.139    0.424 

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: 749
Number of extensions: 17
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: 417
Length of database: 417
Length adjustment: 31
Effective length of query: 386
Effective length of database: 386
Effective search space:   148996
Effective search space used:   148996
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: 50 (23.9 bits)

Align candidate PP_1001 PP_1001 (arginine deiminase)
to HMM TIGR01078 (arcA: arginine deiminase (EC 3.5.3.6))

# 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/TIGR01078.hmm
# target sequence database:        /tmp/gapView.27703.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01078  [M=408]
Accession:   TIGR01078
Description: arcA: arginine deiminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.4e-169  547.7   0.0   8.4e-169  547.5   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_1001  PP_1001 arginine deiminase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_1001  PP_1001 arginine deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  547.5   0.0  8.4e-169  8.4e-169       3     408 .]      10     415 ..       8     415 .. 0.99

  Alignments for each domain:
  == domain 1  score: 547.5 bits;  conditional E-value: 8.4e-169
                           TIGR01078   3 vysEiGkLkkvllhrPgkelenltPsnldelLFddilavedakkeHdeFveklrdngvevllledLlaEtlaase 77 
                                         v+sE+GkL+kv+++ Pg ++++ltPsn+delLFdd+++v++ak++H +Fv+k+r++gv+vl++++Ll++ +++ e
  lcl|FitnessBrowser__Putida:PP_1001  10 VHSEAGKLRKVMVCAPGLAHKRLTPSNCDELLFDDVIWVDQAKRDHFDFVTKMRERGVDVLEMHNLLTDIVQNKE 84 
                                         99************************************************************************* PP

                           TIGR01078  78 akeklldealeeaeilgeelkkelreylksletrelvekllaGvakeelpeeedselslvdlevegdsefvidPl 152
                                         a +++ld++++ +  +g +l++e+r++l+ le+r+l+e l++Gva ++lp++e +++ +++  + g+s+f+++Pl
  lcl|FitnessBrowser__Putida:PP_1001  85 ALKWILDRKITPDT-VGVGLTNEVRSWLEGLEPRHLAEFLIGGVAGQDLPQSEGADVVKMYNDYLGHSSFILPPL 158
                                         *************9.9*********************************************************** PP

                           TIGR01078 153 PnllFtRDpsasigngvtlnkmalkaRqrEtlftelifkhHpkfanaevevyyd....rsekaslEGGDvlvlsk 223
                                         Pn++FtRD++++i++gvtln+m+++aR++Etl+t++i+k+H +f++a+++v+y+    ++ +a+lEGGDv+ +++
  lcl|FitnessBrowser__Putida:PP_1001 159 PNTQFTRDTTCWIYGGVTLNPMYWPARRQETLLTTAIYKFHKEFTEADFQVWYGdpdkDHGNATLEGGDVMPIGN 233
                                         *****************************************************999988999************* PP

                           TIGR01078 224 dvlviGiseRtsaqsveklakslfkneaefkkvlaiklpkkralmHLDtvltmvDkdkftvfpevekelkafsiy 298
                                         ++++iG++eRts+q++++la++lf++ +++k+v+++ lpk+ra+mHLDtv++++D+d +tvfpev+ke+++f i+
  lcl|FitnessBrowser__Putida:PP_1001 234 GIVLIGMGERTSRQAIGQLAQNLFAK-GAVKEVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVKEIVPFIIR 307
                                         **************************.************************************************ PP

                           TIGR01078 299 sltkgneekikveekakleevlaealgvkklkliktgGgdsveaeREqwnDgnnvlaiaPGvvvaYeRnvvtnal 373
                                          ++++++++  ++ ++++ ev+ e+lg  +l++++tg g+s++aeREqw+Dgnnv+ai+PGvv++Y+Rn++tn+l
  lcl|FitnessBrowser__Putida:PP_1001 308 PDESKPYGMDVRRINKSFIEVVGEQLG-VQLRVVETG-GNSFAAEREQWDDGNNVVAIEPGVVIGYDRNTYTNTL 380
                                         ***************************.58******9.9************************************ PP

                           TIGR01078 374 lekaGikvltiagseLsrGrGgprCmsmplvRddi 408
                                         l+kaGi+v+ti++ eL+rGrGg++Cm++p+vRd+i
  lcl|FitnessBrowser__Putida:PP_1001 381 LRKAGIEVITISAGELGRGRGGGHCMTCPIVRDPI 415
                                         ********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (408 nodes)
Target sequences:                          1  (417 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: 00:00:00.01
# Mc/sec: 9.28
//
[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