Alignments for a candidate for hutI in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Pseudomonas simiae WCS417

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate GFF345 PS417_01760 imidazolonepropionase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_317
         (401 letters)



>FitnessBrowser__WCS417:GFF345
          Length = 401

 Score =  707 bits (1826), Expect = 0.0
 Identities = 351/398 (88%), Positives = 372/398 (93%)

Query: 1   MKTLWQHCHVATMAQGVYSIIEDAAIVTSGAHIEWIGPRGELPAGEYPAVNDLNGAWVTP 60
           MKTLWQHCHVATMAQG YSIIEDAA+VT+G+ IEWIGPR ++P  +Y  V+DL GAWVTP
Sbjct: 1   MKTLWQHCHVATMAQGNYSIIEDAAMVTAGSLIEWIGPRSQVPTADYAQVHDLQGAWVTP 60

Query: 61  GLIDCHTHTVFGGNRSGEFEQRLQGVSYADIAASGGGIASTVRATRAASEDELFASAAKR 120
           GLIDCHTHTVFGGNRSGEFEQRL+GVSYA+IAA GGGIASTVRATRAA+EDELFASA KR
Sbjct: 61  GLIDCHTHTVFGGNRSGEFEQRLEGVSYAEIAAKGGGIASTVRATRAATEDELFASAHKR 120

Query: 121 LKSLMRDGVTSIEIKSGYGLDLANERKMLRVARRLGAELPVSVRSTCLAAHALPPEYKDR 180
           L+SL+RDGVT++EIKSGYGLDL NERKMLRVARRLG  LPVSVR+TCLAAHALPPEYKDR
Sbjct: 121 LRSLLRDGVTTVEIKSGYGLDLVNERKMLRVARRLGEALPVSVRATCLAAHALPPEYKDR 180

Query: 181 ADDYIDHICADMLPALAAEGLVDAVDAFCEYLAFSPAQVERVFITAQALGLPVKLHAEQL 240
           ADDYIDHIC +MLPALAAEGLVDAVDAFCEYLAFS  QVERVF  AQ LGLPVKLHAEQL
Sbjct: 181 ADDYIDHICVEMLPALAAEGLVDAVDAFCEYLAFSTEQVERVFKVAQQLGLPVKLHAEQL 240

Query: 241 SSLHGSSLAARYHALSADHLEFMTEDDAIAMAKSGTVAVLLPGAFYFLRETQLPPMEALR 300
           SSLHGSSLAARY ALSADHLEFMTEDDAIAMA SGTVAVLLPGAFYFLRETQLPPM+ALR
Sbjct: 241 SSLHGSSLAARYQALSADHLEFMTEDDAIAMAASGTVAVLLPGAFYFLRETQLPPMDALR 300

Query: 301 KHGVKIAIASDLNPGTSPALSLRLMLNMACTCFRMTPEEALAGATIHAATALGMADTHGS 360
           KHGVKIAIASDLNPGTSPALS+RLMLNMACT FRMTPEEALAGAT HAATALGM DTHGS
Sbjct: 301 KHGVKIAIASDLNPGTSPALSVRLMLNMACTLFRMTPEEALAGATQHAATALGMGDTHGS 360

Query: 361 LEVGKVADFVAWQIDRPADLCYWLGGDLEKRVVRHGVE 398
           LE GKVADFVAWQIDRPADL YWLGG+L+KRVVRHGV+
Sbjct: 361 LEAGKVADFVAWQIDRPADLAYWLGGELDKRVVRHGVD 398


Lambda     K      H
   0.320    0.133    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: 605
Number of extensions: 8
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 GFF345 PS417_01760 (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.15602.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   2.7e-150  486.3   0.1   3.4e-150  486.0   0.1    1.0  1  lcl|FitnessBrowser__WCS417:GFF345  PS417_01760 imidazolonepropionas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF345  PS417_01760 imidazolonepropionase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  486.0   0.1  3.4e-150  3.4e-150       2     375 ..      22     396 ..      21     397 .. 0.99

  Alignments for each domain:
  == domain 1  score: 486.0 bits;  conditional E-value: 3.4e-150
                          TIGR01224   2 edaailveegkiaaigqkaalpgeeaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYleilaeGgG 77 
                                        edaa++  +  i +ig+++++p+ + a+++dl+G  v+PGl+D+HtH vf+g+R+ efe++l+G+sY+ei+a+GgG
  lcl|FitnessBrowser__WCS417:GFF345  22 EDAAMVTAGSLIEWIGPRSQVPTADYAQVHDLQGAWVTPGLIDCHTHTVFGGNRSGEFEQRLEGVSYAEIAAKGGG 97 
                                        78889999999***************************************************************** PP

                          TIGR01224  78 ilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkeelpvdvvttflgaHav 153
                                        i stvratraA e+el+++a++rl++llr G+tt+E+KsGYGLdl +E kmLrv+++l e lpv+v +t+l+aHa+
  lcl|FitnessBrowser__WCS417:GFF345  98 IASTVRATRAATEDELFASAHKRLRSLLRDGVTTVEIKSGYGLDLVNERKMLRVARRLGEALPVSVRATCLAAHAL 173
                                        **************************************************************************** PP

                          TIGR01224 154 PkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqeaGlavklHaeelkalggaela 229
                                        P+e++++ d+y+d+i+ e++p+ a e l++avD+Fce  +Fs eq++r++k aq+ Gl+vklHae+l++l g++la
  lcl|FitnessBrowser__WCS417:GFF345 174 PPEYKDRADDYIDHICVEMLPALAAEGLVDAVDAFCEYLAFSTEQVERVFKVAQQLGLPVKLHAEQLSSLHGSSLA 249
                                        **************************************************************************** PP

                          TIGR01224 230 aklgavsadHleeasdedikalaeagtvavlLPgtaflLr.eaapparklidekvivalatDlnPgsspllslqli 304
                                        a+ +a+sadHle ++++d+ a+a++gtvavlLPg++++Lr ++ pp+++l++++v +a+a+DlnPg+sp ls++l+
  lcl|FitnessBrowser__WCS417:GFF345 250 ARYQALSADHLEFMTEDDAIAMAASGTVAVLLPGAFYFLReTQLPPMDALRKHGVKIAIASDLNPGTSPALSVRLM 325
                                        ****************************************9999******************************** PP

                          TIGR01224 305 lslavtllkltaeealaaatvnaAqalglgeekGtleeGkdadlvvlsaesyeeiaYrlgvnvveaviknG 375
                                        l++a+tl+++t+eeala+at +aA+alg+g+++G+le+Gk ad+v ++++ ++++aY+lg++  + v+ +G
  lcl|FitnessBrowser__WCS417:GFF345 326 LNMACTLFRMTPEEALAGATQHAATALGMGDTHGSLEAGKVADFVAWQIDRPADLAYWLGGELDKRVVRHG 396
                                        *************************************************************9999888877 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: 10.66
//
[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