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.16858.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 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 9.94
//
[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:

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