Alignments for a candidate for hutI in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Pseudomonas benzenivorans DSM 8628

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate WP_090440933.1 BLS63_RS05530 imidazolonepropionase

Query= reanno::pseudo6_N2E2:Pf6N2E2_3798
         (400 letters)



>NCBI__GCF_900100495.1:WP_090440933.1
          Length = 402

 Score =  630 bits (1625), Expect = 0.0
 Identities = 312/399 (78%), Positives = 356/399 (89%)

Query: 1   MKTLWQNCHAATMAQGVYSIIEDAAIVTQGKHIQWIGPRAELPTGDYPAVNDLKGAWVTP 60
           M+ LW NCHAATMA G YSIIEDAA++++G+ I+WIGPRAELP G+     DL GAW+TP
Sbjct: 1   MQRLWLNCHAATMAGGRYSIIEDAALLSRGQLIEWIGPRAELPAGEPAETIDLGGAWLTP 60

Query: 61  GLIDCHTHTVFGGNRSGEFEQRLQGVSYAEIAAAGGGIASTVRATRAASEDELFASAAKR 120
           GLIDCHTH VFGG+RS EFEQRL+G SYAEIAAAGGGIASTVRATRAASEDEL ASA +R
Sbjct: 61  GLIDCHTHLVFGGDRSSEFEQRLEGASYAEIAAAGGGIASTVRATRAASEDELLASALQR 120

Query: 121 LGSLMRDGVTTVEIKSGYGLDLASERKILRVIRRLGAELPVSVRSTCLAAHALPPEYKDR 180
              L+R+GVT++E+KSGYGLDLASERK+LRV RRLG  LP++VRSTCLAAHALPPE+  R
Sbjct: 121 ARQLLREGVTSLEVKSGYGLDLASERKMLRVARRLGELLPLTVRSTCLAAHALPPEFAGR 180

Query: 181 ADDYIEHICSEMLPALAAEGLVDAVDAFCEYLAFSPAQVERVFITAQQLGLPVKLHAEQL 240
           AD YIE +C E+LPALA EGLVDAVDAFCE+L FSPAQVERVF  A +LGLPVKLHAEQL
Sbjct: 181 ADAYIELVCGEILPALAGEGLVDAVDAFCEHLGFSPAQVERVFQAASELGLPVKLHAEQL 240

Query: 241 SSLHGSSLAARYQALSADHLEFMTEDDAKAMAASGTVAVLLPGAFYFLRETQLPPMEALR 300
           SSLHG+SLAARY+ALSADHLE+M EDDA+AMAA+G+VAVLLPGAFY LRET++PP+E LR
Sbjct: 241 SSLHGASLAARYRALSADHLEYMDEDDARAMAAAGSVAVLLPGAFYLLRETRVPPIELLR 300

Query: 301 KHGVKIAVASDLNPGTSPALSLRLMLNMACTCFRMTPEEALAGVTIHAAQALGMAQTHGS 360
           +HGV +AVASDLNPGTSPALSLRLMLNMACT FR+TPEEALAGVT+HAA+ALG++ +HGS
Sbjct: 301 RHGVAMAVASDLNPGTSPALSLRLMLNMACTSFRLTPEEALAGVTLHAARALGLSASHGS 360

Query: 361 LEAGKVADFVAWHIDRPADLAYWLGGDLEKRVVRHGVEI 399
           LEAGKVADFVAW I RPA+LAYWLGGDL KRV+RHG EI
Sbjct: 361 LEAGKVADFVAWQIRRPAELAYWLGGDLPKRVIRHGEEI 399


Lambda     K      H
   0.320    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: 594
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: 400
Length of database: 402
Length adjustment: 31
Effective length of query: 369
Effective length of database: 371
Effective search space:   136899
Effective search space used:   136899
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 WP_090440933.1 BLS63_RS05530 (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.30614.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-153  496.4   0.0   2.8e-153  496.1   0.0    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090440933.1  BLS63_RS05530 imidazolonepropion


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090440933.1  BLS63_RS05530 imidazolonepropionase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  496.1   0.0  2.8e-153  2.8e-153       1     376 [.      21     397 ..      21     398 .. 0.99

  Alignments for each domain:
  == domain 1  score: 496.1 bits;  conditional E-value: 2.8e-153
                                 TIGR01224   1 iedaailveegkiaaigqkaalpgeeaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYl 69 
                                               iedaa+l +++ i +ig++a+lp+ e a++idl+G   +PGl+D+HtHlvf+gdR++efe++l+GasY+
  lcl|NCBI__GCF_900100495.1:WP_090440933.1  21 IEDAALLSRGQLIEWIGPRAELPAGEPAETIDLGGAWLTPGLIDCHTHLVFGGDRSSEFEQRLEGASYA 89 
                                               5899999************************************************************** PP

                                 TIGR01224  70 eilaeGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkee 138
                                               ei+a+GgGi stvratraAse+ell++a +r+++llr+G+t+lEvKsGYGLdl +E kmLrv+++l e 
  lcl|NCBI__GCF_900100495.1:WP_090440933.1  90 EIAAAGGGIASTVRATRAASEDELLASALQRARQLLREGVTSLEVKSGYGLDLASERKMLRVARRLGEL 158
                                               ********************************************************************* PP

                                 TIGR01224 139 lpvdvvttflgaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaq 207
                                               lp+ v +t+l+aHa+P+e+ ++ d+y++ ++ e++p+ a e l++avD+Fce+ +Fs++q++r+++aa 
  lcl|NCBI__GCF_900100495.1:WP_090440933.1 159 LPLTVRSTCLAAHALPPEFAGRADAYIELVCGEILPALAGEGLVDAVDAFCEHLGFSPAQVERVFQAAS 227
                                               ********************************************************************* PP

                                 TIGR01224 208 eaGlavklHaeelkalggaelaaklgavsadHleeasdedikalaeagtvavlLPgtaflLr.eaappa 275
                                               e Gl+vklHae+l++l ga+laa+ +a+sadHle+++++d++a+a+ag+vavlLPg+++lLr +  pp+
  lcl|NCBI__GCF_900100495.1:WP_090440933.1 228 ELGLPVKLHAEQLSSLHGASLAARYRALSADHLEYMDEDDARAMAAAGSVAVLLPGAFYLLReTRVPPI 296
                                               **************************************************************8889*** PP

                                 TIGR01224 276 rklidekvivalatDlnPgsspllslqlilslavtllkltaeealaaatvnaAqalglgeekGtleeGk 344
                                               + l+ ++v +a+a+DlnPg+sp lsl+l+l++a+t ++lt+eeala++t++aA algl++++G+le+Gk
  lcl|NCBI__GCF_900100495.1:WP_090440933.1 297 ELLRRHGVAMAVASDLNPGTSPALSLRLMLNMACTSFRLTPEEALAGVTLHAARALGLSASHGSLEAGK 365
                                               ********************************************************************* PP

                                 TIGR01224 345 dadlvvlsaesyeeiaYrlgvnvveaviknGe 376
                                                ad+v ++++ ++e+aY+lg++  + vi +Ge
  lcl|NCBI__GCF_900100495.1:WP_090440933.1 366 VADFVAWQIRRPAELAYWLGGDLPKRVIRHGE 397
                                               ****************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (402 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: 7.42
//
[ok]

This GapMind analysis is from Sep 24 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