GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutI in Pseudomonas putida KT2440

Align imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate PP_5030 PP_5030 Imidazolonepropionase

Query= metacyc::MONOMER-11617
         (401 letters)



>FitnessBrowser__Putida:PP_5030
          Length = 401

 Score =  781 bits (2017), Expect = 0.0
 Identities = 390/401 (97%), Positives = 397/401 (99%)

Query: 1   MRTVWQHCHVATMAEGRYSAIEDAAIVTSAGLIEWIGPRAELAPVDADRTVDLGGAWITP 60
           MRT+WQHCHVATMA+GRYSAIEDAAIVTSAGLIEWIGPRAELAPV+ADRTVDLGGAW+TP
Sbjct: 1   MRTLWQHCHVATMADGRYSAIEDAAIVTSAGLIEWIGPRAELAPVEADRTVDLGGAWVTP 60

Query: 61  GLIDCHTHAVFGGNRSGEFEQRLQGVSYAEIAAQGGGIASTVRATRAASEDELFASARQR 120
           GLIDCHTHAVFGGNRSGEFEQRLQGVSYAEIAAQGGGIASTVRATRAASEDELFASA QR
Sbjct: 61  GLIDCHTHAVFGGNRSGEFEQRLQGVSYAEIAAQGGGIASTVRATRAASEDELFASAHQR 120

Query: 121 VQALMRDGVTTLEIKSGYGLDLANERKMLRVARRLADELPLAVRATCLAAHALPPEYAGR 180
           VQALMRDGVTTLEIKSGYGLDLANERKMLRVARRLADELPL VRATCLAAHALPPEYAGR
Sbjct: 121 VQALMRDGVTTLEIKSGYGLDLANERKMLRVARRLADELPLTVRATCLAAHALPPEYAGR 180

Query: 181 ADDYIAHICDEMLPALAAEGLVDAVDAFCEHLAFSPAQVERLFIKARELGLPVKLHAEQL 240
           ADDYIAHICDEMLPALA EGLVDAVDAFCEHLAFSPAQVERLFIKARELGLPVKLHAEQL
Sbjct: 181 ADDYIAHICDEMLPALAGEGLVDAVDAFCEHLAFSPAQVERLFIKARELGLPVKLHAEQL 240

Query: 241 SSLHGSSLAARYQALSADHLEFMTEEDAIAMAAAGTVAVLLPGAFYFLRETQLPPMDALR 300
           SSLHGSSLAARYQALSADHLEFMTEEDA+AMA+AGTVAVLLPGAFYFLRETQLPPMDALR
Sbjct: 241 SSLHGSSLAARYQALSADHLEFMTEEDAVAMASAGTVAVLLPGAFYFLRETQLPPMDALR 300

Query: 301 RHGVKIALASDLNPGTSPGLSLRLMLNMGCTCFRMTPEEALAGVTVHAATALGLGDSHGS 360
           RHGVKIALASDLNPGTSPGLSLRLMLNMGCTCFRMTPEEALAGVTVHAATALGLGDSHGS
Sbjct: 301 RHGVKIALASDLNPGTSPGLSLRLMLNMGCTCFRMTPEEALAGVTVHAATALGLGDSHGS 360

Query: 361 LEVGKVADFVAWQIERPADLAYWLGGDLPKRVVRKGHEISN 401
           L+VGKVADFVAWQIERPADLAYWLGGDLPKRVVR GHEISN
Sbjct: 361 LQVGKVADFVAWQIERPADLAYWLGGDLPKRVVRMGHEISN 401


Lambda     K      H
   0.321    0.134    0.400 

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: 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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate PP_5030 PP_5030 (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.26839.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.4e-153  497.2   0.0   1.6e-153  497.0   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_5030  PP_5030 Imidazolonepropionase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_5030  PP_5030 Imidazolonepropionase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  497.0   0.0  1.6e-153  1.6e-153       1     375 [.      21     396 ..      21     398 .. 0.99

  Alignments for each domain:
  == domain 1  score: 497.0 bits;  conditional E-value: 1.6e-153
                           TIGR01224   1 iedaailveegkiaaigqkaalpgeeaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYleilaeG 75 
                                         iedaai+ + g i +ig++a+l++ ea++++dl+G  v+PGl+D+HtH+vf+g+R+ efe++lqG+sY+ei+a+G
  lcl|FitnessBrowser__Putida:PP_5030  21 IEDAAIVTSAGLIEWIGPRAELAPVEADRTVDLGGAWVTPGLIDCHTHAVFGGNRSGEFEQRLQGVSYAEIAAQG 95 
                                         589999999****************************************************************** PP

                           TIGR01224  76 gGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkeelpvdvvttflga 150
                                         gGi stvratraAse+el+++a++r++ l+r G+ttlE+KsGYGLdl +E kmLrv+++l++elp+ v +t+l+a
  lcl|FitnessBrowser__Putida:PP_5030  96 GGIASTVRATRAASEDELFASAHQRVQALMRDGVTTLEIKSGYGLDLANERKMLRVARRLADELPLTVRATCLAA 170
                                         *************************************************************************** PP

                           TIGR01224 151 HavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqeaGlavklHaeelkalgg 225
                                         Ha+P+e+ ++ d+y+++i++e++p+ a e l++avD+Fce+ +Fs++q++r++ +a+e Gl+vklHae+l++l g
  lcl|FitnessBrowser__Putida:PP_5030 171 HALPPEYAGRADDYIAHICDEMLPALAGEGLVDAVDAFCEHLAFSPAQVERLFIKARELGLPVKLHAEQLSSLHG 245
                                         *************************************************************************** PP

                           TIGR01224 226 aelaaklgavsadHleeasdedikalaeagtvavlLPgtaflLr.eaapparklidekvivalatDlnPgsspll 299
                                         ++laa+ +a+sadHle +++ed+ a+a agtvavlLPg++++Lr ++ pp+++l+ ++v +ala+DlnPg+sp l
  lcl|FitnessBrowser__Putida:PP_5030 246 SSLAARYQALSADHLEFMTEEDAVAMASAGTVAVLLPGAFYFLReTQLPPMDALRRHGVKIALASDLNPGTSPGL 320
                                         ********************************************9999*************************** PP

                           TIGR01224 300 slqlilslavtllkltaeealaaatvnaAqalglgeekGtleeGkdadlvvlsaesyeeiaYrlgvnvveavikn 374
                                         sl+l+l++++t +++t+eeala++tv+aA+alglg+++G+l+ Gk ad+v +++e ++++aY+lg++  + v+  
  lcl|FitnessBrowser__Putida:PP_5030 321 SLRLMLNMGCTCFRMTPEEALAGVTVHAATALGLGDSHGSLQVGKVADFVAWQIERPADLAYWLGGDLPKRVVRM 395
                                         **********************************************************************99988 PP

                           TIGR01224 375 G 375
                                         G
  lcl|FitnessBrowser__Putida:PP_5030 396 G 396
                                         8 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.47
//
[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