Alignments for a candidate for hutI in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Pseudomonas fluorescens GW456-L13

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate PfGW456L13_317 Imidazolonepropionase (EC 3.5.2.7)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_317
         (401 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_317
          Length = 401

 Score =  799 bits (2064), Expect = 0.0
 Identities = 401/401 (100%), Positives = 401/401 (100%)

Query: 1   MKTLWQHCHVATMAQGVYSIIEDAAIVTSGAHIEWIGPRGELPAGEYPAVNDLNGAWVTP 60
           MKTLWQHCHVATMAQGVYSIIEDAAIVTSGAHIEWIGPRGELPAGEYPAVNDLNGAWVTP
Sbjct: 1   MKTLWQHCHVATMAQGVYSIIEDAAIVTSGAHIEWIGPRGELPAGEYPAVNDLNGAWVTP 60

Query: 61  GLIDCHTHTVFGGNRSGEFEQRLQGVSYADIAASGGGIASTVRATRAASEDELFASAAKR 120
           GLIDCHTHTVFGGNRSGEFEQRLQGVSYADIAASGGGIASTVRATRAASEDELFASAAKR
Sbjct: 61  GLIDCHTHTVFGGNRSGEFEQRLQGVSYADIAASGGGIASTVRATRAASEDELFASAAKR 120

Query: 121 LKSLMRDGVTSIEIKSGYGLDLANERKMLRVARRLGAELPVSVRSTCLAAHALPPEYKDR 180
           LKSLMRDGVTSIEIKSGYGLDLANERKMLRVARRLGAELPVSVRSTCLAAHALPPEYKDR
Sbjct: 121 LKSLMRDGVTSIEIKSGYGLDLANERKMLRVARRLGAELPVSVRSTCLAAHALPPEYKDR 180

Query: 181 ADDYIDHICADMLPALAAEGLVDAVDAFCEYLAFSPAQVERVFITAQALGLPVKLHAEQL 240
           ADDYIDHICADMLPALAAEGLVDAVDAFCEYLAFSPAQVERVFITAQALGLPVKLHAEQL
Sbjct: 181 ADDYIDHICADMLPALAAEGLVDAVDAFCEYLAFSPAQVERVFITAQALGLPVKLHAEQL 240

Query: 241 SSLHGSSLAARYHALSADHLEFMTEDDAIAMAKSGTVAVLLPGAFYFLRETQLPPMEALR 300
           SSLHGSSLAARYHALSADHLEFMTEDDAIAMAKSGTVAVLLPGAFYFLRETQLPPMEALR
Sbjct: 241 SSLHGSSLAARYHALSADHLEFMTEDDAIAMAKSGTVAVLLPGAFYFLRETQLPPMEALR 300

Query: 301 KHGVKIAIASDLNPGTSPALSLRLMLNMACTCFRMTPEEALAGATIHAATALGMADTHGS 360
           KHGVKIAIASDLNPGTSPALSLRLMLNMACTCFRMTPEEALAGATIHAATALGMADTHGS
Sbjct: 301 KHGVKIAIASDLNPGTSPALSLRLMLNMACTCFRMTPEEALAGATIHAATALGMADTHGS 360

Query: 361 LEVGKVADFVAWQIDRPADLCYWLGGDLEKRVVRHGVESSL 401
           LEVGKVADFVAWQIDRPADLCYWLGGDLEKRVVRHGVESSL
Sbjct: 361 LEVGKVADFVAWQIDRPADLCYWLGGDLEKRVVRHGVESSL 401


Lambda     K      H
   0.320    0.133    0.399 

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: 677
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate PfGW456L13_317 (Imidazolonepropionase (EC 3.5.2.7))
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.20189.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                              -----------
   1.2e-150  487.4   0.0   1.5e-150  487.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_317  Imidazolonepropionase (EC 3.5.2.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_317  Imidazolonepropionase (EC 3.5.2.7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  487.1   0.0  1.5e-150  1.5e-150       1     375 [.      21     396 ..      21     397 .. 0.99

  Alignments for each domain:
  == domain 1  score: 487.1 bits;  conditional E-value: 1.5e-150
                                              TIGR01224   1 iedaailveegkiaaigqkaalpgeeaakiidleGklvvPGlvDpHtHlvfagdRv 56 
                                                            iedaai+ ++ +i +ig++ +lp+ e   + dl+G  v+PGl+D+HtH vf+g+R+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_317  21 IEDAAIVTSGAHIEWIGPRGELPAGEYPAVNDLNGAWVTPGLIDCHTHTVFGGNRS 76 
                                                            58999*9************************************************* PP

                                              TIGR01224  57 kefelklqGasYleilaeGgGilstvratraAseeellkeaeerlkkllrsGtttl 112
                                                             efe++lqG+sY++i+a+GgGi stvratraAse+el+++a +rlk+l+r G+t++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_317  77 GEFEQRLQGVSYADIAASGGGIASTVRATRAASEDELFASAAKRLKSLMRDGVTSI 132
                                                            ******************************************************** PP

                                              TIGR01224 113 EvKsGYGLdleaElkmLrvikalkeelpvdvvttflgaHavPkevqededeyvdai 168
                                                            E+KsGYGLdl +E kmLrv+++l +elpv+v +t+l+aHa+P+e++++ d+y+d+i
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_317 133 EIKSGYGLDLANERKMLRVARRLGAELPVSVRSTCLAAHALPPEYKDRADDYIDHI 188
                                                            ******************************************************** PP

                                              TIGR01224 169 leelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqeaGlavklHaeelkalg 224
                                                            +++++p+ a e l++avD+Fce  +Fs++q++r++  aq+ Gl+vklHae+l++l 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_317 189 CADMLPALAAEGLVDAVDAFCEYLAFSPAQVERVFITAQALGLPVKLHAEQLSSLH 244
                                                            ******************************************************** PP

                                              TIGR01224 225 gaelaaklgavsadHleeasdedikalaeagtvavlLPgtaflLr.eaapparkli 279
                                                            g++laa+ +a+sadHle ++++d+ a+a++gtvavlLPg++++Lr ++ pp+++l+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_317 245 GSSLAARYHALSADHLEFMTEDDAIAMAKSGTVAVLLPGAFYFLReTQLPPMEALR 300
                                                            *********************************************9999******* PP

                                              TIGR01224 280 dekvivalatDlnPgsspllslqlilslavtllkltaeealaaatvnaAqalglge 335
                                                            +++v +a+a+DlnPg+sp lsl+l+l++a+t +++t+eeala+at++aA+alg+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_317 301 KHGVKIAIASDLNPGTSPALSLRLMLNMACTCFRMTPEEALAGATIHAATALGMAD 356
                                                            ******************************************************** PP

                                              TIGR01224 336 ekGtleeGkdadlvvlsaesyeeiaYrlgvnvveaviknG 375
                                                            ++G+le Gk ad+v ++++ ++++ Y+lg++  + v+ +G
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_317 357 THGSLEVGKVADFVAWQIDRPADLCYWLGGDLEKRVVRHG 396
                                                            *******************************999999887 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.34
//
[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