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.31640.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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.86
//
[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:

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:

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:

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:

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