Alignments for a candidate for hutI in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Pseudomonas fluorescens FW300-N2E3

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate AO353_12280 AO353_12280 imidazolonepropionase

Query= reanno::pseudo3_N2E3:AO353_12280
         (401 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_12280
          Length = 401

 Score =  794 bits (2051), Expect = 0.0
 Identities = 401/401 (100%), Positives = 401/401 (100%)

Query: 1   MKTLWQHCHVASMAQGTYSIIEDAAIVTSGAHIEWIGPRSELPSGEYLEVHDLAGAWVTP 60
           MKTLWQHCHVASMAQGTYSIIEDAAIVTSGAHIEWIGPRSELPSGEYLEVHDLAGAWVTP
Sbjct: 1   MKTLWQHCHVASMAQGTYSIIEDAAIVTSGAHIEWIGPRSELPSGEYLEVHDLAGAWVTP 60

Query: 61  GLIDCHTHTVFGGNRSGEFEQRLQGVSYAEIAAAGGGIASTVRATRAATEDELFASAKKR 120
           GLIDCHTHTVFGGNRSGEFEQRLQGVSYAEIAAAGGGIASTVRATRAATEDELFASAKKR
Sbjct: 61  GLIDCHTHTVFGGNRSGEFEQRLQGVSYAEIAAAGGGIASTVRATRAATEDELFASAKKR 120

Query: 121 LKSLMRDGVTSIEMKSGYGLDLASERKILRVIRRLGAELPISVRSTCLAAHALPPEYVDR 180
           LKSLMRDGVTSIEMKSGYGLDLASERKILRVIRRLGAELPISVRSTCLAAHALPPEYVDR
Sbjct: 121 LKSLMRDGVTSIEMKSGYGLDLASERKILRVIRRLGAELPISVRSTCLAAHALPPEYVDR 180

Query: 181 ADDYIEHICSEMLPALAAEGLVDAVDAFCEYLAFSPAQVERVFVAAQKLGLPLKLHAEQL 240
           ADDYIEHICSEMLPALAAEGLVDAVDAFCEYLAFSPAQVERVFVAAQKLGLPLKLHAEQL
Sbjct: 181 ADDYIEHICSEMLPALAAEGLVDAVDAFCEYLAFSPAQVERVFVAAQKLGLPLKLHAEQL 240

Query: 241 SSLHGSSLAARYHALSADHLEFMTEEDAIAMAASGTVAVLLPGAFYFLRETQLPPMDALR 300
           SSLHGSSLAARYHALSADHLEFMTEEDAIAMAASGTVAVLLPGAFYFLRETQLPPMDALR
Sbjct: 241 SSLHGSSLAARYHALSADHLEFMTEEDAIAMAASGTVAVLLPGAFYFLRETQLPPMDALR 300

Query: 301 KHGVKIAIASDLNPGTSPALSVRLMLNMACTCFRMTPEEALAGATIHAATALGMERTHGS 360
           KHGVKIAIASDLNPGTSPALSVRLMLNMACTCFRMTPEEALAGATIHAATALGMERTHGS
Sbjct: 301 KHGVKIAIASDLNPGTSPALSVRLMLNMACTCFRMTPEEALAGATIHAATALGMERTHGS 360

Query: 361 LEVGKVADFVAWQIDRPADLSYWLGGDLEKRVVRHGVEVEL 401
           LEVGKVADFVAWQIDRPADLSYWLGGDLEKRVVRHGVEVEL
Sbjct: 361 LEVGKVADFVAWQIDRPADLSYWLGGDLEKRVVRHGVEVEL 401


Lambda     K      H
   0.320    0.133    0.393 

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: 9
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 AO353_12280 AO353_12280 (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.24159.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   1.1e-150  487.7   0.0   1.2e-150  487.4   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12280  AO353_12280 imidazolonepropionas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_12280  AO353_12280 imidazolonepropionase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  487.4   0.0  1.2e-150  1.2e-150       1     375 [.      21     396 ..      21     398 .. 0.99

  Alignments for each domain:
  == domain 1  score: 487.4 bits;  conditional E-value: 1.2e-150
                                     TIGR01224   1 iedaailveegkiaaigqkaalpgeeaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqG 65 
                                                   iedaai+ ++ +i +ig++++lp+ e ++++dl+G  v+PGl+D+HtH vf+g+R+ efe++lqG
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12280  21 IEDAAIVTSGAHIEWIGPRSELPSGEYLEVHDLAGAWVTPGLIDCHTHTVFGGNRSGEFEQRLQG 85 
                                                   58999*9********************************************************** PP

                                     TIGR01224  66 asYleilaeGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLr 130
                                                   +sY+ei+a+GgGi stvratraA e+el+++a++rlk+l+r G+t++E+KsGYGLdl +E k+Lr
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12280  86 VSYAEIAAAGGGIASTVRATRAATEDELFASAKKRLKSLMRDGVTSIEMKSGYGLDLASERKILR 150
                                                   ***************************************************************** PP

                                     TIGR01224 131 vikalkeelpvdvvttflgaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFs 195
                                                   vi++l +elp++v +t+l+aHa+P+e+ ++ d+y+++i++e++p+ a e l++avD+Fce  +Fs
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12280 151 VIRRLGAELPISVRSTCLAAHALPPEYVDRADDYIEHICSEMLPALAAEGLVDAVDAFCEYLAFS 215
                                                   ***************************************************************** PP

                                     TIGR01224 196 veqsrrilkaaqeaGlavklHaeelkalggaelaaklgavsadHleeasdedikalaeagtvavl 260
                                                   ++q++r++ aaq+ Gl++klHae+l++l g++laa+ +a+sadHle +++ed+ a+a++gtvavl
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12280 216 PAQVERVFVAAQKLGLPLKLHAEQLSSLHGSSLAARYHALSADHLEFMTEEDAIAMAASGTVAVL 280
                                                   ***************************************************************** PP

                                     TIGR01224 261 LPgtaflLr.eaapparklidekvivalatDlnPgsspllslqlilslavtllkltaeealaaat 324
                                                   LPg++++Lr ++ pp+++l++++v +a+a+DlnPg+sp ls++l+l++a+t +++t+eeala+at
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12280 281 LPGAFYFLReTQLPPMDALRKHGVKIAIASDLNPGTSPALSVRLMLNMACTCFRMTPEEALAGAT 345
                                                   *********9999**************************************************** PP

                                     TIGR01224 325 vnaAqalglgeekGtleeGkdadlvvlsaesyeeiaYrlgvnvveaviknG 375
                                                   ++aA+alg++ ++G+le Gk ad+v ++++ +++++Y+lg++  + v+ +G
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12280 346 IHAATALGMERTHGSLEVGKVADFVAWQIDRPADLSYWLGGDLEKRVVRHG 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: 12.65
//
[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