Alignments for a candidate for hutI in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Sphingomonas koreensis DSMZ 15582

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate Ga0059261_3964 Ga0059261_3964 imidazolonepropionase (EC 3.5.2.7)

Query= reanno::Korea:Ga0059261_3964
         (395 letters)



>FitnessBrowser__Korea:Ga0059261_3964
          Length = 395

 Score =  783 bits (2022), Expect = 0.0
 Identities = 395/395 (100%), Positives = 395/395 (100%)

Query: 1   MAIPADTLWRNARLATMTGDGLGIVEQGAIAATGGTISYIGPDSDAPDAAEIVDCQGRWI 60
           MAIPADTLWRNARLATMTGDGLGIVEQGAIAATGGTISYIGPDSDAPDAAEIVDCQGRWI
Sbjct: 1   MAIPADTLWRNARLATMTGDGLGIVEQGAIAATGGTISYIGPDSDAPDAAEIVDCQGRWI 60

Query: 61  TPGLVDCHTHLVHAGNRAREFEARLEGATYEEIARAGGGILSTVTATRAASEDELIASAL 120
           TPGLVDCHTHLVHAGNRAREFEARLEGATYEEIARAGGGILSTVTATRAASEDELIASAL
Sbjct: 61  TPGLVDCHTHLVHAGNRAREFEARLEGATYEEIARAGGGILSTVTATRAASEDELIASAL 120

Query: 121 PRLDQLIAEGVTTVEIKSGYGLTLDDELKMLRAARSLGEARNVHIRTTLLAAHAVPPEYK 180
           PRLDQLIAEGVTTVEIKSGYGLTLDDELKMLRAARSLGEARNVHIRTTLLAAHAVPPEYK
Sbjct: 121 PRLDQLIAEGVTTVEIKSGYGLTLDDELKMLRAARSLGEARNVHIRTTLLAAHAVPPEYK 180

Query: 181 GDADGYVDLVCETIIPAAIGHADAVDAFCEGIGFSPEQTDRVLAAAVAHGLPVKLHAEQL 240
           GDADGYVDLVCETIIPAAIGHADAVDAFCEGIGFSPEQTDRVLAAAVAHGLPVKLHAEQL
Sbjct: 181 GDADGYVDLVCETIIPAAIGHADAVDAFCEGIGFSPEQTDRVLAAAVAHGLPVKLHAEQL 240

Query: 241 SNLHGAALAAHHNALSADHLEHLDEAGIAAMAASGTVATLLPGAFYFTREEHRPPIAALR 300
           SNLHGAALAAHHNALSADHLEHLDEAGIAAMAASGTVATLLPGAFYFTREEHRPPIAALR
Sbjct: 241 SNLHGAALAAHHNALSADHLEHLDEAGIAAMAASGTVATLLPGAFYFTREEHRPPIAALR 300

Query: 301 AAGVPIALATDCNPGTSPMASILLAANMGATFFRLTVTECLRGITVNGARALGLRTGTLE 360
           AAGVPIALATDCNPGTSPMASILLAANMGATFFRLTVTECLRGITVNGARALGLRTGTLE
Sbjct: 301 AAGVPIALATDCNPGTSPMASILLAANMGATFFRLTVTECLRGITVNGARALGLRTGTLE 360

Query: 361 PGGPADLAIWNVTDLAELVYRIGANPLHSRIYAGT 395
           PGGPADLAIWNVTDLAELVYRIGANPLHSRIYAGT
Sbjct: 361 PGGPADLAIWNVTDLAELVYRIGANPLHSRIYAGT 395


Lambda     K      H
   0.318    0.134    0.396 

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: 715
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: 395
Length of database: 395
Length adjustment: 31
Effective length of query: 364
Effective length of database: 364
Effective search space:   132496
Effective search space used:   132496
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate Ga0059261_3964 Ga0059261_3964 (imidazolonepropionase (EC 3.5.2.7))
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.16645.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-142  459.3   1.4   4.9e-142  459.1   1.4    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_3964  Ga0059261_3964 imidazolonepropio


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3964  Ga0059261_3964 imidazolonepropionase (EC 3.5.2.7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.1   1.4  4.9e-142  4.9e-142       2     376 ..      26     395 .]      25     395 .] 0.99

  Alignments for each domain:
  == domain 1  score: 459.1 bits;  conditional E-value: 4.9e-142
                                 TIGR01224   2 edaailveegkiaaigqkaalpgeeaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYle 70 
                                               e++ai+ ++g i++ig+ +++p   aa+i+d++G+ ++PGlvD+HtHlv+ag+R++efe++l+Ga+Y+e
  lcl|FitnessBrowser__Korea:Ga0059261_3964  26 EQGAIAATGGTISYIGPDSDAPD--AAEIVDCQGRWITPGLVDCHTHLVHAGNRAREFEARLEGATYEE 92 
                                               7899*************999988..******************************************** PP

                                 TIGR01224  71 ilaeGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkeel 139
                                               i+++GgGilstv atraAse+el+++a +rl++l+++G+tt+E+KsGYGL+l++ElkmLr++++l e +
  lcl|FitnessBrowser__Korea:Ga0059261_3964  93 IARAGGGILSTVTATRAASEDELIASALPRLDQLIAEGVTTVEIKSGYGLTLDDELKMLRAARSLGEAR 161
                                               ********************************************************************* PP

                                 TIGR01224 140 pvdvvttflgaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqe 208
                                               +v++ tt+l+aHavP+e+++d d yvd ++e++ip++     a+avD+Fce  +Fs+eq+ r+l+aa +
  lcl|FitnessBrowser__Korea:Ga0059261_3964 162 NVHIRTTLLAAHAVPPEYKGDADGYVDLVCETIIPAAIG--HADAVDAFCEGIGFSPEQTDRVLAAAVA 228
                                               ***********************************9988..5*************************** PP

                                 TIGR01224 209 aGlavklHaeelkalggaelaaklgavsadHleeasdedikalaeagtvavlLPgtaflLr.eaappar 276
                                               +Gl+vklHae+l++l ga+laa+ +a+sadHle++++++i+a+a++gtva+lLPg++++ r e+ pp+ 
  lcl|FitnessBrowser__Korea:Ga0059261_3964 229 HGLPVKLHAEQLSNLHGAALAAHHNALSADHLEHLDEAGIAAMAASGTVATLLPGAFYFTReEHRPPIA 297
                                               ************************************************************98999**** PP

                                 TIGR01224 277 klidekvivalatDlnPgsspllslqlilslavtllkltaeealaaatvnaAqalglgeekGtleeGkd 345
                                               +l++++v++alatD nPg+sp++s+ l+ ++++t ++lt  e l+++tvn A algl    Gtle G  
  lcl|FitnessBrowser__Korea:Ga0059261_3964 298 ALRAAGVPIALATDCNPGTSPMASILLAANMGATFFRLTVTECLRGITVNGARALGLRT--GTLEPGGP 364
                                               ********************************************************987..******** PP

                                 TIGR01224 346 adlvvlsaesyeeiaYrlgvnvveaviknGe 376
                                               adl+++++++ +e+ Yr+g+n ++ +i +G+
  lcl|FitnessBrowser__Korea:Ga0059261_3964 365 ADLAIWNVTDLAELVYRIGANPLHSRIYAGT 395
                                               ***************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (395 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: 8.88
//
[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