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

GapMind for catabolism of small carbon sources

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

Align Urocanate hydratase; Urocanase; Imidazolonepropionate hydrolase; EC 4.2.1.49 (characterized)
to candidate 199294 SO0097 urocanate hydratase (NCBI ptt file)

Query= SwissProt::P25080
         (557 letters)



>FitnessBrowser__MR1:199294
          Length = 556

 Score =  872 bits (2253), Expect = 0.0
 Identities = 419/544 (77%), Positives = 467/544 (85%)

Query: 12  IRAPRGNKLTAKSWLTEAPLRMLMNNLDPQVAENPKELVVYGGIGRAARNWECYDKIVET 71
           I AP G++L+ KSWLTEAP+RMLMNNL P VAE P++LVVYGGIGRAAR+W+CYDKI+E 
Sbjct: 11  IIAPHGSQLSCKSWLTEAPMRMLMNNLHPDVAERPEDLVVYGGIGRAARDWDCYDKIIEV 70

Query: 72  LTRLEDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWANWEHFNELDAKGLAMYGQ 131
           L RLEDDETLLVQSGKPVGVF+TH++APRVLIANSNLVPHWANWEHFNELD +GLAMYGQ
Sbjct: 71  LKRLEDDETLLVQSGKPVGVFRTHADAPRVLIANSNLVPHWANWEHFNELDKQGLAMYGQ 130

Query: 132 MTAGSWIYIGSQGIVQGTYETFVEAGRQHYGGTVKAKWVLTAGLGGMGGAQPLAATLAGA 191
           MTAGSWIYIG+QGIVQGTYETFV   +QH+GG  K KW+LT GLGGMGGAQ LA T+AG 
Sbjct: 131 MTAGSWIYIGTQGIVQGTYETFVSVAKQHFGGISKGKWILTGGLGGMGGAQTLAGTMAGF 190

Query: 192 CSLNIECQQSRIDFRLETRYVDEQATDLDDALVRIAKYTAEGKAISIALHGNAAEILPEL 251
             L  E  ++RIDFRL TRYVD++AT LD+AL  I      GK +S+ L  NAA++  EL
Sbjct: 191 SVLACEVDETRIDFRLRTRYVDKKATSLDEALAMIEAANQAGKPVSVGLLANAADVFAEL 250

Query: 252 VKRGVRPDMVTDQTSAHDPLNGYLPAGWTWEQYRDRAQTEPAAVVKAAKQSMAVHVQAML 311
           VKRG+ PD+VTDQTSAHDPLNGYLP GWT  Q  D  +T+ AAVVKAAK SMAV VQAML
Sbjct: 251 VKRGITPDVVTDQTSAHDPLNGYLPQGWTMAQAADMRKTDEAAVVKAAKASMAVQVQAML 310

Query: 312 DFQKQGVPTFDYGNNIRQMAKEEGVANAFDFPGFVPAYIRPLFCRGVGPFRWAALSGEAE 371
           D Q  G  T DYGNNIRQMA E GV NAFDFPGFVPAYIRPLFC G+GPFRW ALSG+ E
Sbjct: 311 DLQAAGAATLDYGNNIRQMAFETGVKNAFDFPGFVPAYIRPLFCEGIGPFRWVALSGDPE 370

Query: 372 DIYKTDAKVKELIPDDAHLHRWLDMARERISFQGLPARICWVGLGLRAKLGLAFNEMVRS 431
           DIYKTDAKVKELIPD+ HLH WLDMARERI+FQGLPARICWVGL  RA+L  AFNEMV++
Sbjct: 371 DIYKTDAKVKELIPDNPHLHNWLDMARERIAFQGLPARICWVGLKDRARLAQAFNEMVKN 430

Query: 432 GELSAPVVIGRDHLDSGSVSSPNRETEAMRDGSDAVSDWPLLNALLNTAGGATWVSLHHG 491
           GELSAP+VIGRDHLDSGSV+SPNRETE+M DGSDAVSDWPLLNALLNTA GATWVSLHHG
Sbjct: 431 GELSAPIVIGRDHLDSGSVASPNRETESMLDGSDAVSDWPLLNALLNTASGATWVSLHHG 490

Query: 492 GGVGMGFSQHSGMVIVCDGTDEAAERIARVLTNDPGTGVMRHADAGYDIAIDCAKEQGLD 551
           GGVGMGFSQHSG+VIVCDGT+ AA+R+ RVL NDP TGVMRHADAGY+IA +CAKEQGLD
Sbjct: 491 GGVGMGFSQHSGVVIVCDGTETAAKRVGRVLWNDPATGVMRHADAGYEIAKNCAKEQGLD 550

Query: 552 LPMI 555
           LPM+
Sbjct: 551 LPML 554


Lambda     K      H
   0.318    0.135    0.413 

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: 1075
Number of extensions: 49
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: 557
Length of database: 556
Length adjustment: 36
Effective length of query: 521
Effective length of database: 520
Effective search space:   270920
Effective search space used:   270920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate 199294 SO0097 (urocanate hydratase (NCBI ptt file))
to HMM TIGR01228 (hutU: urocanate hydratase (EC 4.2.1.49))

# 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/TIGR01228.hmm
# target sequence database:        /tmp/gapView.30551.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01228  [M=545]
Accession:   TIGR01228
Description: hutU: urocanate hydratase
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-297  972.0   1.5     5e-297  971.8   1.5    1.0  1  lcl|FitnessBrowser__MR1:199294  SO0097 urocanate hydratase (NCBI


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199294  SO0097 urocanate hydratase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  971.8   1.5    5e-297    5e-297       2     545 .]      10     553 ..       9     553 .. 1.00

  Alignments for each domain:
  == domain 1  score: 971.8 bits;  conditional E-value: 5e-297
                       TIGR01228   2 eiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddetllvqsGkpv 80 
                                      i ap+G++l++k+w +ea++r+lmnnl p+vae pe+lvvyGG+G+aar+w+++dki+e lkrleddetllvqsGkpv
  lcl|FitnessBrowser__MR1:199294  10 RIIAPHGSQLSCKSWLTEAPMRMLMNNLHPDVAERPEDLVVYGGIGRAARDWDCYDKIIEVLKRLEDDETLLVQSGKPV 88 
                                     5789*************************************************************************** PP

                       TIGR01228  81 gvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGtyetlaelarkhfggslkgk 159
                                     gvf+th +aprvliansnlvp+wa+we+f+el+++Gl+myGqmtaGswiyiGtqGi+qGtyet++++a++hfgg  kgk
  lcl|FitnessBrowser__MR1:199294  89 GVFRTHADAPRVLIANSNLVPHWANWEHFNELDKQGLAMYGQMTAGSWIYIGTQGIVQGTYETFVSVAKQHFGGISKGK 167
                                     ******************************************************************************* PP

                       TIGR01228 160 lvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddldealaraeeakaeGkalsigllGnaaev 238
                                     ++lt GlGgmGGaq la t+++ +++a evde+rid+rl+t+y+d+k+++ldeala++e+a+++Gk++s+gll naa+v
  lcl|FitnessBrowser__MR1:199294 168 WILTGGLGGMGGAQTLAGTMAGFSVLACEVDETRIDFRLRTRYVDKKATSLDEALAMIEAANQAGKPVSVGLLANAADV 246
                                     ******************************************************************************* PP

                       TIGR01228 239 leellergvvpdvvtdqtsahdellGyipegytvedadklrdeepeeyvkaakaslakhvrallalqkkGavtfdyGnn 317
                                     + el++rg++pdvvtdqtsahd+l+Gy+p+g+t+++a+++r+++++++vkaakas+a++v+a+l+lq +Ga t+dyGnn
  lcl|FitnessBrowser__MR1:199294 247 FAELVKRGITPDVVTDQTSAHDPLNGYLPQGWTMAQAADMRKTDEAAVVKAAKASMAVQVQAMLDLQAAGAATLDYGNN 325
                                     ******************************************************************************* PP

                       TIGR01228 318 irqvakeeGvedafdfpGfvpayirdlfceGkGpfrwvalsGdpadiyrtdkavkelfpedeelhrwidlakekvafqG 396
                                     irq+a+e+Gv++afdfpGfvpayir+lfceG GpfrwvalsGdp+diy+td++vkel+p++ +lh+w+d+a+e++afqG
  lcl|FitnessBrowser__MR1:199294 326 IRQMAFETGVKNAFDFPGFVPAYIRPLFCEGIGPFRWVALSGDPEDIYKTDAKVKELIPDNPHLHNWLDMARERIAFQG 404
                                     ******************************************************************************* PP

                       TIGR01228 397 lparicwlgygereklalainelvrsGelkapvvigrdhldaGsvaspnreteamkdGsdavadwpllnallntaaGas 475
                                     lparicw+g+++r++la a+ne+v++Gel+ap+vigrdhld+Gsvaspnrete+m dGsdav+dwpllnallnta+Ga+
  lcl|FitnessBrowser__MR1:199294 405 LPARICWVGLKDRARLAQAFNEMVKNGELSAPIVIGRDHLDSGSVASPNRETESMLDGSDAVSDWPLLNALLNTASGAT 483
                                     ******************************************************************************* PP

                       TIGR01228 476 wvslhhGGGvglGfslhaglvivadGtdeaaerlkrvltadpGlGvirhadaGyesaldvakeqgldlpm 545
                                     wvslhhGGGvg+Gfs+h+g+viv+dGt++aa+r+ rvl +dp +Gv+rhadaGye a ++akeqgldlpm
  lcl|FitnessBrowser__MR1:199294 484 WVSLHHGGGVGMGFSQHSGVVIVCDGTETAAKRVGRVLWNDPATGVMRHADAGYEIAKNCAKEQGLDLPM 553
                                     *********************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (556 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.52
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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