Alignments for a candidate for hutI in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Pseudomonas putida KT2440

Align imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate PP_5030 PP_5030 Imidazolonepropionase

Query= metacyc::MONOMER-11617
         (401 letters)



>FitnessBrowser__Putida:PP_5030
          Length = 401

 Score =  781 bits (2017), Expect = 0.0
 Identities = 390/401 (97%), Positives = 397/401 (99%)

Query: 1   MRTVWQHCHVATMAEGRYSAIEDAAIVTSAGLIEWIGPRAELAPVDADRTVDLGGAWITP 60
           MRT+WQHCHVATMA+GRYSAIEDAAIVTSAGLIEWIGPRAELAPV+ADRTVDLGGAW+TP
Sbjct: 1   MRTLWQHCHVATMADGRYSAIEDAAIVTSAGLIEWIGPRAELAPVEADRTVDLGGAWVTP 60

Query: 61  GLIDCHTHAVFGGNRSGEFEQRLQGVSYAEIAAQGGGIASTVRATRAASEDELFASARQR 120
           GLIDCHTHAVFGGNRSGEFEQRLQGVSYAEIAAQGGGIASTVRATRAASEDELFASA QR
Sbjct: 61  GLIDCHTHAVFGGNRSGEFEQRLQGVSYAEIAAQGGGIASTVRATRAASEDELFASAHQR 120

Query: 121 VQALMRDGVTTLEIKSGYGLDLANERKMLRVARRLADELPLAVRATCLAAHALPPEYAGR 180
           VQALMRDGVTTLEIKSGYGLDLANERKMLRVARRLADELPL VRATCLAAHALPPEYAGR
Sbjct: 121 VQALMRDGVTTLEIKSGYGLDLANERKMLRVARRLADELPLTVRATCLAAHALPPEYAGR 180

Query: 181 ADDYIAHICDEMLPALAAEGLVDAVDAFCEHLAFSPAQVERLFIKARELGLPVKLHAEQL 240
           ADDYIAHICDEMLPALA EGLVDAVDAFCEHLAFSPAQVERLFIKARELGLPVKLHAEQL
Sbjct: 181 ADDYIAHICDEMLPALAGEGLVDAVDAFCEHLAFSPAQVERLFIKARELGLPVKLHAEQL 240

Query: 241 SSLHGSSLAARYQALSADHLEFMTEEDAIAMAAAGTVAVLLPGAFYFLRETQLPPMDALR 300
           SSLHGSSLAARYQALSADHLEFMTEEDA+AMA+AGTVAVLLPGAFYFLRETQLPPMDALR
Sbjct: 241 SSLHGSSLAARYQALSADHLEFMTEEDAVAMASAGTVAVLLPGAFYFLRETQLPPMDALR 300

Query: 301 RHGVKIALASDLNPGTSPGLSLRLMLNMGCTCFRMTPEEALAGVTVHAATALGLGDSHGS 360
           RHGVKIALASDLNPGTSPGLSLRLMLNMGCTCFRMTPEEALAGVTVHAATALGLGDSHGS
Sbjct: 301 RHGVKIALASDLNPGTSPGLSLRLMLNMGCTCFRMTPEEALAGVTVHAATALGLGDSHGS 360

Query: 361 LEVGKVADFVAWQIERPADLAYWLGGDLPKRVVRKGHEISN 401
           L+VGKVADFVAWQIERPADLAYWLGGDLPKRVVR GHEISN
Sbjct: 361 LQVGKVADFVAWQIERPADLAYWLGGDLPKRVVRMGHEISN 401


Lambda     K      H
   0.321    0.134    0.400 

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: 699
Number of extensions: 11
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: 401
Length of database: 401
Length adjustment: 31
Effective length of query: 370
Effective length of database: 370
Effective search space:   136900
Effective search space used:   136900
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate PP_5030 PP_5030 (Imidazolonepropionase)
to HMM TIGR01224 (hutI: imidazolonepropionase (EC 3.5.2.7))

# 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/TIGR01224.hmm
# target sequence database:        /tmp/gapView.5373.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01224  [M=377]
Accession:   TIGR01224
Description: hutI: imidazolonepropionase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.4e-153  497.2   0.0   1.6e-153  497.0   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_5030  PP_5030 Imidazolonepropionase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_5030  PP_5030 Imidazolonepropionase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  497.0   0.0  1.6e-153  1.6e-153       1     375 [.      21     396 ..      21     398 .. 0.99

  Alignments for each domain:
  == domain 1  score: 497.0 bits;  conditional E-value: 1.6e-153
                           TIGR01224   1 iedaailveegkiaaigqkaalpgeeaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYleilaeG 75 
                                         iedaai+ + g i +ig++a+l++ ea++++dl+G  v+PGl+D+HtH+vf+g+R+ efe++lqG+sY+ei+a+G
  lcl|FitnessBrowser__Putida:PP_5030  21 IEDAAIVTSAGLIEWIGPRAELAPVEADRTVDLGGAWVTPGLIDCHTHAVFGGNRSGEFEQRLQGVSYAEIAAQG 95 
                                         589999999****************************************************************** PP

                           TIGR01224  76 gGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkeelpvdvvttflga 150
                                         gGi stvratraAse+el+++a++r++ l+r G+ttlE+KsGYGLdl +E kmLrv+++l++elp+ v +t+l+a
  lcl|FitnessBrowser__Putida:PP_5030  96 GGIASTVRATRAASEDELFASAHQRVQALMRDGVTTLEIKSGYGLDLANERKMLRVARRLADELPLTVRATCLAA 170
                                         *************************************************************************** PP

                           TIGR01224 151 HavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqeaGlavklHaeelkalgg 225
                                         Ha+P+e+ ++ d+y+++i++e++p+ a e l++avD+Fce+ +Fs++q++r++ +a+e Gl+vklHae+l++l g
  lcl|FitnessBrowser__Putida:PP_5030 171 HALPPEYAGRADDYIAHICDEMLPALAGEGLVDAVDAFCEHLAFSPAQVERLFIKARELGLPVKLHAEQLSSLHG 245
                                         *************************************************************************** PP

                           TIGR01224 226 aelaaklgavsadHleeasdedikalaeagtvavlLPgtaflLr.eaapparklidekvivalatDlnPgsspll 299
                                         ++laa+ +a+sadHle +++ed+ a+a agtvavlLPg++++Lr ++ pp+++l+ ++v +ala+DlnPg+sp l
  lcl|FitnessBrowser__Putida:PP_5030 246 SSLAARYQALSADHLEFMTEEDAVAMASAGTVAVLLPGAFYFLReTQLPPMDALRRHGVKIALASDLNPGTSPGL 320
                                         ********************************************9999*************************** PP

                           TIGR01224 300 slqlilslavtllkltaeealaaatvnaAqalglgeekGtleeGkdadlvvlsaesyeeiaYrlgvnvveavikn 374
                                         sl+l+l++++t +++t+eeala++tv+aA+alglg+++G+l+ Gk ad+v +++e ++++aY+lg++  + v+  
  lcl|FitnessBrowser__Putida:PP_5030 321 SLRLMLNMGCTCFRMTPEEALAGVTVHAATALGLGDSHGSLQVGKVADFVAWQIERPADLAYWLGGDLPKRVVRM 395
                                         **********************************************************************99988 PP

                           TIGR01224 375 G 375
                                         G
  lcl|FitnessBrowser__Putida:PP_5030 396 G 396
                                         8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (401 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.26
//
[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