Aligments for a candidate for hutI in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Aligments for a candidate for hutI in Pseudomonas fluorescens FW300-N2C3

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate AO356_09595 AO356_09595 imidazolonepropionase

Query= reanno::pseudo5_N2C3_1:AO356_09595
         (400 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09595 AO356_09595
           imidazolonepropionase
          Length = 400

 Score =  798 bits (2061), Expect = 0.0
 Identities = 400/400 (100%), Positives = 400/400 (100%)

Query: 1   MKTLWQNCHAATMAQGVYSIIEDAAIVTQGEHIHWIGPRAELPMGDYPAVNDLKGAWVTP 60
           MKTLWQNCHAATMAQGVYSIIEDAAIVTQGEHIHWIGPRAELPMGDYPAVNDLKGAWVTP
Sbjct: 1   MKTLWQNCHAATMAQGVYSIIEDAAIVTQGEHIHWIGPRAELPMGDYPAVNDLKGAWVTP 60

Query: 61  GLIDCHTHTVFGGNRSGEFEQRLQGVSYAEIAAAGGGIASTVRATRAASEDELFASAAKR 120
           GLIDCHTHTVFGGNRSGEFEQRLQGVSYAEIAAAGGGIASTVRATRAASEDELFASAAKR
Sbjct: 61  GLIDCHTHTVFGGNRSGEFEQRLQGVSYAEIAAAGGGIASTVRATRAASEDELFASAAKR 120

Query: 121 LKGLMHDGVTTVEIKSGYGLDLASERKILRVIRRLGAELPVSVRSTCLAAHALPPEYKDR 180
           LKGLMHDGVTTVEIKSGYGLDLASERKILRVIRRLGAELPVSVRSTCLAAHALPPEYKDR
Sbjct: 121 LKGLMHDGVTTVEIKSGYGLDLASERKILRVIRRLGAELPVSVRSTCLAAHALPPEYKDR 180

Query: 181 ADDYIEHICTEMLPALAAEGLVDAVDAFCEYLAFSPAQVERVFITARQLGLPVKLHAEQL 240
           ADDYIEHICTEMLPALAAEGLVDAVDAFCEYLAFSPAQVERVFITARQLGLPVKLHAEQL
Sbjct: 181 ADDYIEHICTEMLPALAAEGLVDAVDAFCEYLAFSPAQVERVFITARQLGLPVKLHAEQL 240

Query: 241 SSLHGSSLAARYQALSADHLEFMTEDDAKAMAASGTVAVLLPGAFYFLRETQLPPMDALR 300
           SSLHGSSLAARYQALSADHLEFMTEDDAKAMAASGTVAVLLPGAFYFLRETQLPPMDALR
Sbjct: 241 SSLHGSSLAARYQALSADHLEFMTEDDAKAMAASGTVAVLLPGAFYFLRETQLPPMDALR 300

Query: 301 KHGVKIAVASDLNPGTSPALSLRLMLNMACTCFRMTPEEALAGATIHAAQALGMAQTHGS 360
           KHGVKIAVASDLNPGTSPALSLRLMLNMACTCFRMTPEEALAGATIHAAQALGMAQTHGS
Sbjct: 301 KHGVKIAVASDLNPGTSPALSLRLMLNMACTCFRMTPEEALAGATIHAAQALGMAQTHGS 360

Query: 361 LEVGKVADFVAWHIDRPADLAYWLGGDLEKRVVRHGVEID 400
           LEVGKVADFVAWHIDRPADLAYWLGGDLEKRVVRHGVEID
Sbjct: 361 LEVGKVADFVAWHIDRPADLAYWLGGDLEKRVVRHGVEID 400


Lambda     K      H
   0.320    0.134    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: 699
Number of extensions: 15
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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 AO356_09595 AO356_09595 (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.13215.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   3.8e-150  485.8   0.1   4.4e-150  485.6   0.1    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09595  AO356_09595 imidazolonepropionas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09595  AO356_09595 imidazolonepropionase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  485.6   0.1  4.4e-150  4.4e-150       1     375 [.      21     396 ..      21     398 .. 0.99

  Alignments for each domain:
  == domain 1  score: 485.6 bits;  conditional E-value: 4.4e-150
                                       TIGR01224   1 iedaailveegkiaaigqkaalpgeeaakiidleGklvvPGlvDpHtHlvfagdRvkefelkl 63 
                                                     iedaai+ ++++i +ig++a+lp  +   + dl+G  v+PGl+D+HtH vf+g+R+ efe++l
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09595  21 IEDAAIVTQGEHIHWIGPRAELPMGDYPAVNDLKGAWVTPGLIDCHTHTVFGGNRSGEFEQRL 83 
                                                     5899********************99999********************************** PP

                                       TIGR01224  64 qGasYleilaeGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaEl 126
                                                     qG+sY+ei+a+GgGi stvratraAse+el+++a +rlk l+  G+tt+E+KsGYGLdl +E 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09595  84 QGVSYAEIAAAGGGIASTVRATRAASEDELFASAAKRLKGLMHDGVTTVEIKSGYGLDLASER 146
                                                     *************************************************************** PP

                                       TIGR01224 127 kmLrvikalkeelpvdvvttflgaHavPkevqededeyvdaileelipkvaeeklaeavDvFc 189
                                                     k+Lrvi++l +elpv+v +t+l+aHa+P+e++++ d+y+++i+ e++p+ a e l++avD+Fc
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09595 147 KILRVIRRLGAELPVSVRSTCLAAHALPPEYKDRADDYIEHICTEMLPALAAEGLVDAVDAFC 209
                                                     *************************************************************** PP

                                       TIGR01224 190 ekgvFsveqsrrilkaaqeaGlavklHaeelkalggaelaaklgavsadHleeasdedikala 252
                                                     e  +Fs++q++r++  a++ Gl+vklHae+l++l g++laa+ +a+sadHle ++++d+ka+a
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09595 210 EYLAFSPAQVERVFITARQLGLPVKLHAEQLSSLHGSSLAARYQALSADHLEFMTEDDAKAMA 272
                                                     *************************************************************** PP

                                       TIGR01224 253 eagtvavlLPgtaflLr.eaapparklidekvivalatDlnPgsspllslqlilslavtllkl 314
                                                     ++gtvavlLPg++++Lr ++ pp+++l++++v +a+a+DlnPg+sp lsl+l+l++a+t +++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09595 273 ASGTVAVLLPGAFYFLReTQLPPMDALRKHGVKIAVASDLNPGTSPALSLRLMLNMACTCFRM 335
                                                     *****************9999****************************************** PP

                                       TIGR01224 315 taeealaaatvnaAqalglgeekGtleeGkdadlvvlsaesyeeiaYrlgvnvveaviknG 375
                                                     t+eeala+at++aAqalg+++++G+le Gk ad+v ++++ ++++aY+lg++  + v+ +G
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09595 336 TPEEALAGATIHAAQALGMAQTHGSLEVGKVADFVAWHIDRPADLAYWLGGDLEKRVVRHG 396
                                                     ****************************************************999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (400 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: 8.03
//
[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, or view the source code.

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