Alignments for a candidate for hutI in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Pseudomonas fluorescens FW300-N1B4

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate Pf1N1B4_1579 Imidazolonepropionase (EC 3.5.2.7)

Query= reanno::pseudo1_N1B4:Pf1N1B4_1579
         (401 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1579
          Length = 401

 Score =  799 bits (2063), Expect = 0.0
 Identities = 401/401 (100%), Positives = 401/401 (100%)

Query: 1   MKTLWQHCHVATMAQGAYSIIEDAAIVTSGAHIEWIGPRGELPPGEYPAVNDLNGAWVTP 60
           MKTLWQHCHVATMAQGAYSIIEDAAIVTSGAHIEWIGPRGELPPGEYPAVNDLNGAWVTP
Sbjct: 1   MKTLWQHCHVATMAQGAYSIIEDAAIVTSGAHIEWIGPRGELPPGEYPAVNDLNGAWVTP 60

Query: 61  GLIDCHTHTVFGGNRSGEFEQRLQGVSYAEIAAAGGGIASTVRATRAASEDELFASAAKR 120
           GLIDCHTHTVFGGNRSGEFEQRLQGVSYAEIAAAGGGIASTVRATRAASEDELFASAAKR
Sbjct: 61  GLIDCHTHTVFGGNRSGEFEQRLQGVSYAEIAAAGGGIASTVRATRAASEDELFASAAKR 120

Query: 121 LKSLMRDGVTSIEIKSGYGLDLANERKMLRVVRRLGAELPVSVRSTCLAAHALPPEYTDR 180
           LKSLMRDGVTSIEIKSGYGLDLANERKMLRVVRRLGAELPVSVRSTCLAAHALPPEYTDR
Sbjct: 121 LKSLMRDGVTSIEIKSGYGLDLANERKMLRVVRRLGAELPVSVRSTCLAAHALPPEYTDR 180

Query: 181 ADAYIDHICTEMLPALAAEGLVDAVDAFCEYLGFSPEQVERVFVAAQNLGLPVKLHAEQL 240
           ADAYIDHICTEMLPALAAEGLVDAVDAFCEYLGFSPEQVERVFVAAQNLGLPVKLHAEQL
Sbjct: 181 ADAYIDHICTEMLPALAAEGLVDAVDAFCEYLGFSPEQVERVFVAAQNLGLPVKLHAEQL 240

Query: 241 SSLHGSSLAARYHALSADHLEFMTEDDAIAMAKSGTVAVLLPGAFYFLRETQLPPMEALR 300
           SSLHGSSLAARYHALSADHLEFMTEDDAIAMAKSGTVAVLLPGAFYFLRETQLPPMEALR
Sbjct: 241 SSLHGSSLAARYHALSADHLEFMTEDDAIAMAKSGTVAVLLPGAFYFLRETQLPPMEALR 300

Query: 301 KHGVKIAIASDLNPGTSPALSLRLMLNMACTCFRMTPEEALAGATIHAATALGMAETHGS 360
           KHGVKIAIASDLNPGTSPALSLRLMLNMACTCFRMTPEEALAGATIHAATALGMAETHGS
Sbjct: 301 KHGVKIAIASDLNPGTSPALSLRLMLNMACTCFRMTPEEALAGATIHAATALGMAETHGS 360

Query: 361 LEAGKVADFVAWQIDRPADLSYWLGGDLEKRVVRHGVETSV 401
           LEAGKVADFVAWQIDRPADLSYWLGGDLEKRVVRHGVETSV
Sbjct: 361 LEAGKVADFVAWQIDRPADLSYWLGGDLEKRVVRHGVETSV 401


Lambda     K      H
   0.319    0.133    0.395 

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: 697
Number of extensions: 12
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 Pf1N1B4_1579 (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.11332.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-151  490.7   0.0   1.4e-151  490.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1579  Imidazolonepropionase (EC 3.5.2.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1579  Imidazolonepropionase (EC 3.5.2.7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  490.5   0.0  1.4e-151  1.4e-151       1     375 [.      21     396 ..      21     398 .. 0.99

  Alignments for each domain:
  == domain 1  score: 490.5 bits;  conditional E-value: 1.4e-151
                                      TIGR01224   1 iedaailveegkiaaigqkaalpgeeaakiidleGklvvPGlvDpHtHlvfagdRvkefelklq 64 
                                                    iedaai+ ++ +i +ig++ +lp+ e   + dl+G  v+PGl+D+HtH vf+g+R+ efe++lq
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1579  21 IEDAAIVTSGAHIEWIGPRGELPPGEYPAVNDLNGAWVTPGLIDCHTHTVFGGNRSGEFEQRLQ 84 
                                                    58999*9********************************************************* PP

                                      TIGR01224  65 GasYleilaeGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkm 128
                                                    G+sY+ei+a+GgGi stvratraAse+el+++a +rlk+l+r G+t++E+KsGYGLdl +E km
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1579  85 GVSYAEIAAAGGGIASTVRATRAASEDELFASAAKRLKSLMRDGVTSIEIKSGYGLDLANERKM 148
                                                    **************************************************************** PP

                                      TIGR01224 129 LrvikalkeelpvdvvttflgaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekg 192
                                                    Lrv+++l +elpv+v +t+l+aHa+P+e++++ d+y+d+i+ e++p+ a e l++avD+Fce  
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1579 149 LRVVRRLGAELPVSVRSTCLAAHALPPEYTDRADAYIDHICTEMLPALAAEGLVDAVDAFCEYL 212
                                                    **************************************************************** PP

                                      TIGR01224 193 vFsveqsrrilkaaqeaGlavklHaeelkalggaelaaklgavsadHleeasdedikalaeagt 256
                                                    +Fs+eq++r++ aaq+ Gl+vklHae+l++l g++laa+ +a+sadHle ++++d+ a+a++gt
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1579 213 GFSPEQVERVFVAAQNLGLPVKLHAEQLSSLHGSSLAARYHALSADHLEFMTEDDAIAMAKSGT 276
                                                    **************************************************************** PP

                                      TIGR01224 257 vavlLPgtaflLr.eaapparklidekvivalatDlnPgsspllslqlilslavtllkltaeea 319
                                                    vavlLPg++++Lr ++ pp+++l++++v +a+a+DlnPg+sp lsl+l+l++a+t +++t+eea
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1579 277 VAVLLPGAFYFLReTQLPPMEALRKHGVKIAIASDLNPGTSPALSLRLMLNMACTCFRMTPEEA 340
                                                    *************9999*********************************************** PP

                                      TIGR01224 320 laaatvnaAqalglgeekGtleeGkdadlvvlsaesyeeiaYrlgvnvveaviknG 375
                                                    la+at++aA+alg++e++G+le+Gk ad+v ++++ +++++Y+lg++  + v+ +G
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1579 341 LAGATIHAATALGMAETHGSLEAGKVADFVAWQIDRPADLSYWLGGDLEKRVVRHG 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: 00:00:00.01
# Mc/sec: 9.38
//
[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