Alignments for a candidate for hutI in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Shewanella oneidensis MR-1

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate 199292 SO0095 imidazolonepropionase (NCBI ptt file)

Query= reanno::MR1:199292
         (408 letters)



>FitnessBrowser__MR1:199292
          Length = 408

 Score =  814 bits (2103), Expect = 0.0
 Identities = 408/408 (100%), Positives = 408/408 (100%)

Query: 1   MSWDQVWIDVNVATMDPSISAPYGAITHAAIAVKDGKIAWLGPRSELPAFDVLSIPVYRG 60
           MSWDQVWIDVNVATMDPSISAPYGAITHAAIAVKDGKIAWLGPRSELPAFDVLSIPVYRG
Sbjct: 1   MSWDQVWIDVNVATMDPSISAPYGAITHAAIAVKDGKIAWLGPRSELPAFDVLSIPVYRG 60

Query: 61  KGGWITPGLIDAHTHLVFAGNRANEFELRLKGATYEEIARAGGGIISTVNACREADEAAL 120
           KGGWITPGLIDAHTHLVFAGNRANEFELRLKGATYEEIARAGGGIISTVNACREADEAAL
Sbjct: 61  KGGWITPGLIDAHTHLVFAGNRANEFELRLKGATYEEIARAGGGIISTVNACREADEAAL 120

Query: 121 FELGRQRLNALAKEGVTTVEIKSGYGLDTETELKILRVARELGKHHHVDVKTTFLGAHAV 180
           FELGRQRLNALAKEGVTTVEIKSGYGLDTETELKILRVARELGKHHHVDVKTTFLGAHAV
Sbjct: 121 FELGRQRLNALAKEGVTTVEIKSGYGLDTETELKILRVARELGKHHHVDVKTTFLGAHAV 180

Query: 181 PPEYKGNSDGYVDLIINKMLPAVIKENLADAVDVFCENIAFNLEQTERVLSAAKAAGLQV 240
           PPEYKGNSDGYVDLIINKMLPAVIKENLADAVDVFCENIAFNLEQTERVLSAAKAAGLQV
Sbjct: 181 PPEYKGNSDGYVDLIINKMLPAVIKENLADAVDVFCENIAFNLEQTERVLSAAKAAGLQV 240

Query: 241 KLHAEQLSNMGGSELAARLGAKSVDHIEYLDEAGVKALSESGTCAVLLPGAFYFLRETQK 300
           KLHAEQLSNMGGSELAARLGAKSVDHIEYLDEAGVKALSESGTCAVLLPGAFYFLRETQK
Sbjct: 241 KLHAEQLSNMGGSELAARLGAKSVDHIEYLDEAGVKALSESGTCAVLLPGAFYFLRETQK 300

Query: 301 PPIDLLRQYGVPMVLASDFNPGSFPICSTLLMLNMGCTLFRLTPEEALAGLTLNAAKALG 360
           PPIDLLRQYGVPMVLASDFNPGSFPICSTLLMLNMGCTLFRLTPEEALAGLTLNAAKALG
Sbjct: 301 PPIDLLRQYGVPMVLASDFNPGSFPICSTLLMLNMGCTLFRLTPEEALAGLTLNAAKALG 360

Query: 361 IEDKVGSLVVGKQADFCLWNIATPAQLAYSYGVNPCKDVVKNGKLVHQ 408
           IEDKVGSLVVGKQADFCLWNIATPAQLAYSYGVNPCKDVVKNGKLVHQ
Sbjct: 361 IEDKVGSLVVGKQADFCLWNIATPAQLAYSYGVNPCKDVVKNGKLVHQ 408


Lambda     K      H
   0.319    0.136    0.402 

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: 728
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: 408
Length of database: 408
Length adjustment: 31
Effective length of query: 377
Effective length of database: 377
Effective search space:   142129
Effective search space used:   142129
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 199292 SO0095 (imidazolonepropionase (NCBI ptt file))
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.8927.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.8e-152  492.4   0.0   4.4e-152  492.2   0.0    1.0  1  lcl|FitnessBrowser__MR1:199292  SO0095 imidazolonepropionase (NC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199292  SO0095 imidazolonepropionase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  492.2   0.0  4.4e-152  4.4e-152       3     376 ..      28     404 ..      26     405 .. 0.98

  Alignments for each domain:
  == domain 1  score: 492.2 bits;  conditional E-value: 4.4e-152
                       TIGR01224   3 daailveegkiaaigqkaalpgeeaakiidl..eGklvvPGlvDpHtHlvfagdRvkefelklqGasYleilaeGgGil 79 
                                     +aai+v++gkia++g++++lp+ + + i  +  +G+ ++PGl+D+HtHlvfag+R++efel+l+Ga+Y+ei+++GgGi+
  lcl|FitnessBrowser__MR1:199292  28 HAAIAVKDGKIAWLGPRSELPAFDVLSIPVYrgKGGWITPGLIDAHTHLVFAGNRANEFELRLKGATYEEIARAGGGII 106
                                     689*******************987776655226789****************************************** PP

                       TIGR01224  80 stvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkeelpvdvvttflgaHavPkevq 158
                                     stv+a r+A+e++l++  ++rl+ l ++G+tt+E+KsGYGLd+e+Elk+Lrv+++l ++++vdv+ttflgaHavP+e++
  lcl|FitnessBrowser__MR1:199292 107 STVNACREADEAALFELGRQRLNALAKEGVTTVEIKSGYGLDTETELKILRVARELGKHHHVDVKTTFLGAHAVPPEYK 185
                                     ******************************************************************************* PP

                       TIGR01224 159 ededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqeaGlavklHaeelkalggaelaaklgavsa 237
                                     +++d yvd i+++++p+v +e+la+avDvFce+ +F+ eq++r+l+aa++aGl+vklHae+l+++gg+elaa+lga s+
  lcl|FitnessBrowser__MR1:199292 186 GNSDGYVDLIINKMLPAVIKENLADAVDVFCENIAFNLEQTERVLSAAKAAGLQVKLHAEQLSNMGGSELAARLGAKSV 264
                                     ******************************************************************************* PP

                       TIGR01224 238 dHleeasdedikalaeagtvavlLPgtaflLr.eaapparklidekvivalatDlnPgsspllslqlilslavtllklt 315
                                     dH+e+++++++kal e+gt avlLPg++++Lr +++pp++ l++++v++ la+D+nPgs p+ s+ l+l++++tl++lt
  lcl|FitnessBrowser__MR1:199292 265 DHIEYLDEAGVKALSESGTCAVLLPGAFYFLReTQKPPIDLLRQYGVPMVLASDFNPGSFPICSTLLMLNMGCTLFRLT 343
                                     ********************************999******************************************** PP

                       TIGR01224 316 aeealaaatvnaAqalglgeekGtleeGkdadlvvlsaesyeeiaYrlgvnvveaviknGe 376
                                     +eeala+ t+naA+alg +++ G+l  Gk+ad+ ++++  ++++aY +gvn  + v+knG+
  lcl|FitnessBrowser__MR1:199292 344 PEEALAGLTLNAAKALGIEDKVGSLVVGKQADFCLWNIATPAQLAYSYGVNPCKDVVKNGK 404
                                     ************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (408 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: 7.35
//
[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