Alignments for a candidate for hutI in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Phaeobacter inhibens BS107

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate GFF3580 PGA1_c36350 imidazolonepropionase HutI

Query= reanno::Phaeo:GFF3580
         (404 letters)



>FitnessBrowser__Phaeo:GFF3580
          Length = 404

 Score =  808 bits (2087), Expect = 0.0
 Identities = 404/404 (100%), Positives = 404/404 (100%)

Query: 1   MGDTDSYLICDATLATMTGSDPAYGLVPDGLIVVQNGWIRWCGSEAQLPKDYSDWPRVSM 60
           MGDTDSYLICDATLATMTGSDPAYGLVPDGLIVVQNGWIRWCGSEAQLPKDYSDWPRVSM
Sbjct: 1   MGDTDSYLICDATLATMTGSDPAYGLVPDGLIVVQNGWIRWCGSEAQLPKDYSDWPRVSM 60

Query: 61  GGRLVTPGLIDCHTHIVFGGNRAMEFEMRLNGASYEDVARAGGGIVSTVSATRTASLEDL 120
           GGRLVTPGLIDCHTHIVFGGNRAMEFEMRLNGASYEDVARAGGGIVSTVSATRTASLEDL
Sbjct: 61  GGRLVTPGLIDCHTHIVFGGNRAMEFEMRLNGASYEDVARAGGGIVSTVSATRTASLEDL 120

Query: 121 VQGALPRLDALIAEGATVVEVKSGYGLDRETELNMLRAARRLAVLRSVTVNTTFLGAHAT 180
           VQGALPRLDALIAEGATVVEVKSGYGLDRETELNMLRAARRLAVLRSVTVNTTFLGAHAT
Sbjct: 121 VQGALPRLDALIAEGATVVEVKSGYGLDRETELNMLRAARRLAVLRSVTVNTTFLGAHAT 180

Query: 181 PGEYKGRDDAYIDEVCIPALRAAHAEGLVDAVDGFCENIAFAPAQIERVFKAARELGLPV 240
           PGEYKGRDDAYIDEVCIPALRAAHAEGLVDAVDGFCENIAFAPAQIERVFKAARELGLPV
Sbjct: 181 PGEYKGRDDAYIDEVCIPALRAAHAEGLVDAVDGFCENIAFAPAQIERVFKAARELGLPV 240

Query: 241 KLHAEQLSHQGGTALSAQYGALSVDHVEYATEDDAKMMAAAGSVAVILPGAFYTIREIQA 300
           KLHAEQLSHQGGTALSAQYGALSVDHVEYATEDDAKMMAAAGSVAVILPGAFYTIREIQA
Sbjct: 241 KLHAEQLSHQGGTALSAQYGALSVDHVEYATEDDAKMMAAAGSVAVILPGAFYTIREIQA 300

Query: 301 PPIEHFRSHGVPMALATDCNPGSSPLTSLLLTMNMGCTLFRMTPEEALAGVTRNAASALG 360
           PPIEHFRSHGVPMALATDCNPGSSPLTSLLLTMNMGCTLFRMTPEEALAGVTRNAASALG
Sbjct: 301 PPIEHFRSHGVPMALATDCNPGSSPLTSLLLTMNMGCTLFRMTPEEALAGVTRNAASALG 360

Query: 361 LTDRGQISAGMRADLAVWDVETPGELAYRIGFNPLYTRIYEGNQ 404
           LTDRGQISAGMRADLAVWDVETPGELAYRIGFNPLYTRIYEGNQ
Sbjct: 361 LTDRGQISAGMRADLAVWDVETPGELAYRIGFNPLYTRIYEGNQ 404


Lambda     K      H
   0.319    0.135    0.401 

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: 628
Number of extensions: 19
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: 404
Length of database: 404
Length adjustment: 31
Effective length of query: 373
Effective length of database: 373
Effective search space:   139129
Effective search space used:   139129
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 GFF3580 PGA1_c36350 (imidazolonepropionase HutI)
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.8685.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-140  454.4   0.0   1.5e-140  454.2   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3580  PGA1_c36350 imidazolonepropionas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3580  PGA1_c36350 imidazolonepropionase HutI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  454.2   0.0  1.5e-140  1.5e-140       3     376 ..      29     403 ..      27     404 .] 0.98

  Alignments for each domain:
  == domain 1  score: 454.2 bits;  conditional E-value: 1.5e-140
                          TIGR01224   3 daailveegkiaaigqkaalpge.eaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYleilaeGgG 77 
                                        d+ i+v++g i + g++a+lp    +   ++++G+lv+PGl+D+HtH+vf+g+R+ efe++l+GasY++++++GgG
  lcl|FitnessBrowser__Phaeo:GFF3580  29 DGLIVVQNGWIRWCGSEAQLPKDySDWPRVSMGGRLVTPGLIDCHTHIVFGGNRAMEFEMRLNGASYEDVARAGGG 104
                                        67899**************9986488899*********************************************** PP

                          TIGR01224  78 ilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkeelpvdvvttflgaHav 153
                                        i+stv atr As e+l++ a +rl+ l+++G+t +EvKsGYGLd e+El mLr++++l+  + v v ttflgaHa 
  lcl|FitnessBrowser__Phaeo:GFF3580 105 IVSTVSATRTASLEDLVQGALPRLDALIAEGATVVEVKSGYGLDRETELNMLRAARRLAVLRSVTVNTTFLGAHAT 180
                                        **************************************************************************** PP

                          TIGR01224 154 PkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqeaGlavklHaeelkalggaela 229
                                        P e+++++d+y+d+++   +++++ e l++avD Fce+ +F ++q +r++kaa+e Gl+vklHae+l++ gg++l+
  lcl|FitnessBrowser__Phaeo:GFF3580 181 PGEYKGRDDAYIDEVCIPALRAAHAEGLVDAVDGFCENIAFAPAQIERVFKAARELGLPVKLHAEQLSHQGGTALS 256
                                        **************************************************************************** PP

                          TIGR01224 230 aklgavsadHleeasdedikalaeagtvavlLPgtaflLr.eaapparklidekvivalatDlnPgsspllslqli 304
                                        a+ ga+s+dH+e+a+++d+k +a+ag+vav+LPg+++++r  +app+++++ ++v++alatD nPgsspl+sl l 
  lcl|FitnessBrowser__Phaeo:GFF3580 257 AQYGALSVDHVEYATEDDAKMMAAAGSVAVILPGAFYTIReIQAPPIEHFRSHGVPMALATDCNPGSSPLTSLLLT 332
                                        ****************************************899********************************* PP

                          TIGR01224 305 lslavtllkltaeealaaatvnaAqalglgeekGtleeGkdadlvvlsaesyeeiaYrlgvnvveaviknGe 376
                                        +++++tl+++t+eeala++t naA+algl++ +G++++G +adl+v+++e + e+aYr+g n + ++i +G+
  lcl|FitnessBrowser__Phaeo:GFF3580 333 MNMGCTLFRMTPEEALAGVTRNAASALGLTD-RGQISAGMRADLAVWDVETPGELAYRIGFNPLYTRIYEGN 403
                                        ******************************9.************************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (404 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: 10.95
//
[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