Alignments for a candidate for hutI in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Dyella japonica UNC79MFTsu3.2

Align imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate N515DRAFT_0142 N515DRAFT_0142 imidazolonepropionase

Query= metacyc::MONOMER-11617
         (401 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0142
          Length = 410

 Score =  466 bits (1200), Expect = e-136
 Identities = 244/395 (61%), Positives = 291/395 (73%), Gaps = 7/395 (1%)

Query: 10  VATMAEGR-YSAIEDAAIVTSAGLIEWIGPRAELAPVDADRTV----DLGGAWITPGLID 64
           +AT   G+ Y  IED A+  + G I WIGPRA+L P DA         L GA +TPGL+D
Sbjct: 15  LATFDGGQPYGLIEDGALAMAGGRIAWIGPRAQL-PADAQARAASVEHLDGALVTPGLVD 73

Query: 65  CHTHAVFGGNRSGEFEQRLQGVSYAEIAAQGGGIASTVRATRAASEDELFASARQRVQAL 124
           CHTH VFGG+R+ EF+ RL G SY EIA  GGGIASTV+ATR A EDELF  A  R +AL
Sbjct: 74  CHTHLVFGGDRAHEFDLRLNGASYEEIARAGGGIASTVKATREADEDELFTQALPRARAL 133

Query: 125 MRDGVTTLEIKSGYGLDLANERKMLRVARRLADELPLAVRATCLAAHALPPEYAGRADDY 184
           + DGVTTLEIKSGYGL+L +ER+MLRVARRL + L + VR + L  HALP EY    D Y
Sbjct: 134 LADGVTTLEIKSGYGLELESERRMLRVARRLGEALGIGVRTSFLGLHALPAEYREDRDGY 193

Query: 185 IAHICDEMLPALAAEGLVDAVDAFCEHLAFSPAQVERLFIKARELGLPVKLHAEQLSSLH 244
           +A +CD +LPALAAEGLVDAVDAFCE + F+  +  R+F +AR LGLPVKLHAEQLS+L 
Sbjct: 194 VALVCDRILPALAAEGLVDAVDAFCEGIGFTREETRRVFERARSLGLPVKLHAEQLSNLE 253

Query: 245 GSSLAARYQALSADHLEFMTEEDAIAMAAAGTVAVLLPGAFYFLRETQLPPMDALRRHGV 304
           G++L A Y  LSADHLE+++E+   AMAA GTVAVLLPGAFY LRET+LPP+ ALR HGV
Sbjct: 254 GAALVAEYDGLSADHLEYLSEDGVRAMAAKGTVAVLLPGAFYALRETKLPPIAALREHGV 313

Query: 305 KIALASDLNPGTSPGLSLRLMLNMGCTCFRMTPEEALAGVTVHAATALGLGDSHGSLEVG 364
            +A+A+D NPGTSP LSLRL   M CT FR+TPEEAL GVTVHAA ALGL D  G+L VG
Sbjct: 314 AMAVATDCNPGTSPLLSLRLAAGMACTLFRLTPEEALRGVTVHAARALGL-DDRGTLAVG 372

Query: 365 KVADFVAWQIERPADLAYWLGGDLPKRVVRKGHEI 399
           + AD V WQ++RPA+L YW+GG L + V   G  I
Sbjct: 373 QRADLVVWQVQRPAELCYWIGGGLVRAVYCGGRRI 407


Lambda     K      H
   0.321    0.134    0.400 

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: 538
Number of extensions: 18
Number of successful extensions: 4
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: 410
Length adjustment: 31
Effective length of query: 370
Effective length of database: 379
Effective search space:   140230
Effective search space used:   140230
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate N515DRAFT_0142 N515DRAFT_0142 (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.25906.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-145  470.0   0.0   2.8e-145  469.8   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0142  N515DRAFT_0142 imidazolonepropio


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0142  N515DRAFT_0142 imidazolonepropionase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.8   0.0  2.8e-145  2.8e-145       1     375 [.      27     404 ..      27     406 .. 0.98

  Alignments for each domain:
  == domain 1  score: 469.8 bits;  conditional E-value: 2.8e-145
                                    TIGR01224   1 iedaailveegkiaaigqkaalpge...eaakiidleGklvvPGlvDpHtHlvfagdRvkefelkl 63 
                                                  ied+a+++ +g+ia+ig++a+lp+     aa +  l+G lv+PGlvD+HtHlvf+gdR++ef+l+l
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0142  27 IEDGALAMAGGRIAWIGPRAQLPADaqaRAASVEHLDGALVTPGLVDCHTHLVFGGDRAHEFDLRL 92 
                                                  5899****************99998444566677789***************************** PP

                                    TIGR01224  64 qGasYleilaeGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmL 129
                                                  +GasY+ei+++GgGi stv+atr+A+e+el+ +a +r++ ll+ G+ttlE+KsGYGL+le+E +mL
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0142  93 NGASYEEIARAGGGIASTVKATREADEDELFTQALPRARALLADGVTTLEIKSGYGLELESERRML 158
                                                  ****************************************************************** PP

                                    TIGR01224 130 rvikalkeelpvdvvttflgaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFs 195
                                                  rv+++l e l + v t flg Ha+P e++ed d yv+ +++ ++p+ a e l++avD+Fce  +F+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0142 159 RVARRLGEALGIGVRTSFLGLHALPAEYREDRDGYVALVCDRILPALAAEGLVDAVDAFCEGIGFT 224
                                                  ****************************************************************** PP

                                    TIGR01224 196 veqsrrilkaaqeaGlavklHaeelkalggaelaaklgavsadHleeasdedikalaeagtvavlL 261
                                                   e++rr++++a+  Gl+vklHae+l++l ga+l a+ +++sadHle++s+++++a+a+ gtvavlL
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0142 225 REETRRVFERARSLGLPVKLHAEQLSNLEGAALVAEYDGLSADHLEYLSEDGVRAMAAKGTVAVLL 290
                                                  ****************************************************************** PP

                                    TIGR01224 262 PgtaflLr.eaapparklidekvivalatDlnPgsspllslqlilslavtllkltaeealaaatvn 326
                                                  Pg++++Lr ++ pp+ +l++++v +a+atD nPg+spllsl+l+  +a+tl++lt+eeal+++tv+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0142 291 PGAFYALReTKLPPIAALREHGVAMAVATDCNPGTSPLLSLRLAAGMACTLFRLTPEEALRGVTVH 356
                                                  ********8889****************************************************** PP

                                    TIGR01224 327 aAqalglgeekGtleeGkdadlvvlsaesyeeiaYrlgvnvveaviknG 375
                                                  aA algl + +Gtl+ G++adlvv++++ ++e+ Y++g+  v av+  G
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0142 357 AARALGLDD-RGTLAVGQRADLVVWQVQRPAELCYWIGGGLVRAVYCGG 404
                                                  *******98.**********************************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (410 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: 11.15
//
[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