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.3198.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: 9.99
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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