GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutU in Rhodobacter viridis JA737

Align Urocanate hydratase; Urocanase; Imidazolonepropionate hydrolase; EC 4.2.1.49 (characterized)
to candidate WP_110805607.1 C8J30_RS09465 urocanate hydratase

Query= SwissProt::Q5L084
         (551 letters)



>NCBI__GCF_003217355.1:WP_110805607.1
          Length = 552

 Score =  569 bits (1466), Expect = e-166
 Identities = 279/536 (52%), Positives = 365/536 (68%), Gaps = 2/536 (0%)

Query: 10  PAGTERRAKGWIQEAALRMLNNNLHPDVAERPDELIVYGGIGKAARNWECYEAIVDTLLR 69
           P+G + RAK W  E  LR+L N L   V E P++LIVY  +GKAARNW  + AIV +L  
Sbjct: 14  PSGPDLRAKNWRAEGLLRLLENVL--SVGEAPEKLIVYAALGKAARNWPAHAAIVKSLTE 71

Query: 70  LENDETLLIQSGKPVAVFRTHPDAPRVLIANSNLVPAWATWDHFHELDKKGLIMYGQMTA 129
           +E DETL+IQSGKPV + +TH  AP V++AN N+V  WA  + F++L++KGLI +G +TA
Sbjct: 72  IEEDETLIIQSGKPVGILKTHAGAPMVIMANCNIVGQWAKAEVFYDLERKGLICWGGLTA 131

Query: 130 GSWIYIGSQGIVQGTYETFAEVARQHFGGTLAGTITLTAGLGGMGGAQPLAVTMNGGVCL 189
           G+W YIGSQG++QGTYE F  +A + F  +LAG   LTAGLGGMGGAQPLA  M G   L
Sbjct: 132 GAWQYIGSQGVIQGTYEIFMRIAERRFNSSLAGRFILTAGLGGMGGAQPLAGRMAGAAIL 191

Query: 190 AIEVDPARIQRRIDTNYLDTMTDSLDAALEMAKQAKEEKKALSIGLVGNAAEVLPRLVEM 249
            ++VD AR + R +  +LD +   LD+AL M   A+ E +A S+ L+GNAAE+ P +   
Sbjct: 192 CVDVDEARAKMRQEIGFLDAIAPDLDSALAMIDAARAEGRATSVALIGNAAEIYPEIAAR 251

Query: 250 GFVPDVLTDQTSAHDPLNGYIPAGLTLDEAAELRARDPKQYIARAKQSIAAHVRAMLAMQ 309
           G  PD++TDQTSAHD + GY+PAG  L     LR ++P++ I   + SIAAHV AML  Q
Sbjct: 252 GITPDIVTDQTSAHDLVYGYVPAGYDLPRVRRLREQNPEELIEAGRASIAAHVSAMLEFQ 311

Query: 310 KQGAVTFDYGNNIRQVAKDEGVDDAFSFPGFVPAYIRPLFCEGKGPFRWVALSGDPEDIY 369
            +GA  FD GN IR  AK  GV++AF  P F  AY+RPLFC   GPFRW+ALSGDPEDI 
Sbjct: 312 SRGAEVFDNGNLIRTQAKQGGVENAFDIPIFTEAYLRPLFCRAIGPFRWMALSGDPEDIR 371

Query: 370 KTDEVILREFSDNERLCHWIRMAQKRIKFQGLPARICWLGYGERAKFGKIINDMVAKGEL 429
           + D+++L+ F DN+ + +WIR+A++ + F+GLPARI WLG+GER      +N MVA GEL
Sbjct: 372 RIDDLVLKMFPDNQIVTNWIRLARENVPFEGLPARIAWLGHGERTDLAVAVNRMVASGEL 431

Query: 430 KAPIVIGRDHLDSGSVASPNRETEGMKDGSDAIADWPILNALLNAVGGASWVSVHHGGGV 489
             P+   RDHLD+G +A PN  TE M+DGSDAIADWP+L+A+     GA  V+VH GGG 
Sbjct: 432 AGPVAFSRDHLDAGGMAHPNIMTEKMRDGSDAIADWPLLDAMTLCASGADLVTVHSGGGG 491

Query: 490 GMGYSIHAGMVIVADGTKEAEKRLERVLTTDPGLGVVRHADAGYELAIRTAKEKGI 545
             GY   AG+ IVA+G+  AE RL   LT D  LGV+R+ADAGY  A+  A +K +
Sbjct: 492 YAGYMTSAGVTIVAEGSAAAETRLRLALTNDTALGVIRYADAGYADALDEAAQKAV 547


Lambda     K      H
   0.319    0.136    0.411 

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: 771
Number of extensions: 28
Number of successful extensions: 2
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: 551
Length of database: 552
Length adjustment: 36
Effective length of query: 515
Effective length of database: 516
Effective search space:   265740
Effective search space used:   265740
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_110805607.1 C8J30_RS09465 (urocanate hydratase)
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.174199.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-215  702.6   0.9   2.3e-215  702.2   0.9    1.0  1  NCBI__GCF_003217355.1:WP_110805607.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003217355.1:WP_110805607.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  702.2   0.9  2.3e-215  2.3e-215       6     540 ..      14     546 ..      10     549 .. 0.99

  Alignments for each domain:
  == domain 1  score: 702.2 bits;  conditional E-value: 2.3e-215
                             TIGR01228   6 prGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddetllvqsGk 78 
                                           p G +l ak w+ e  lrll+n l   v e pe+l+vy   Gkaarnw a+ +iv++l+ +e+detl++qsGk
  NCBI__GCF_003217355.1:WP_110805607.1  14 PSGPDLRAKNWRAEGLLRLLENVL--SVGEAPEKLIVYAALGKAARNWPAHAAIVKSLTEIEEDETLIIQSGK 84 
                                           89*********************9..69********************************************* PP

                             TIGR01228  79 pvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGtyetlaelarkh 151
                                           pvg++kth  ap v++an+n+v++wa+ e+f +le+kGli +G +taG+w yiG+qG++qGtye +  +a ++
  NCBI__GCF_003217355.1:WP_110805607.1  85 PVGILKTHAGAPMVIMANCNIVGQWAKAEVFYDLERKGLICWGGLTAGAWQYIGSQGVIQGTYEIFMRIAERR 157
                                           ************************************************************************* PP

                             TIGR01228 152 fggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddldealaraeeakaeG 224
                                           f  sl g+++ltaGlGgmGGaqpla ++++a+ + v+vde+r + r e  +ld  + dld ala++++a+aeG
  NCBI__GCF_003217355.1:WP_110805607.1 158 FNSSLAGRFILTAGLGGMGGAQPLAGRMAGAAILCVDVDEARAKMRQEIGFLDAIAPDLDSALAMIDAARAEG 230
                                           ************************************************************************* PP

                             TIGR01228 225 kalsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadklrdeepeeyvkaakaslakh 297
                                           +a+s++l Gnaae+++e+  rg++pd+vtdqtsahd + Gy+p+gy +   ++lr+++pee ++a +as+a+h
  NCBI__GCF_003217355.1:WP_110805607.1 231 RATSVALIGNAAEIYPEIAARGITPDIVTDQTSAHDLVYGYVPAGYDLPRVRRLREQNPEELIEAGRASIAAH 303
                                           ************************************************************************* PP

                             TIGR01228 298 vrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfceGkGpfrwvalsGdpadiyrtdka 370
                                           v a+l++q++Ga +fd Gn ir++ak+ Gve+afd+p f  ay+r+lfc+  Gpfrw+alsGdp+di r+d+ 
  NCBI__GCF_003217355.1:WP_110805607.1 304 VSAMLEFQSRGAEVFDNGNLIRTQAKQGGVENAFDIPIFTEAYLRPLFCRAIGPFRWMALSGDPEDIRRIDDL 376
                                           ************************************************************************* PP

                             TIGR01228 371 vkelfpedeelhrwidlakekvafqGlparicwlgygereklalainelvrsGelkapvvigrdhldaGsvas 443
                                           v+++fp+++ +++wi la+e+v f+Glpari wlg+ger  la+a+n +v sGel  pv+ +rdhldaG +a 
  NCBI__GCF_003217355.1:WP_110805607.1 377 VLKMFPDNQIVTNWIRLARENVPFEGLPARIAWLGHGERTDLAVAVNRMVASGELAGPVAFSRDHLDAGGMAH 449
                                           ************************************************************************* PP

                             TIGR01228 444 pnreteamkdGsdavadwpllnallntaaGaswvslhhGGGvglGfslhaglvivadGtdeaaerlkrvltad 516
                                           pn  te+m+dGsda+adwpll+a+   a+Ga++v++h GGG   G+   ag+ iva+G+ +a+ rl+ +lt+d
  NCBI__GCF_003217355.1:WP_110805607.1 450 PNIMTEKMRDGSDAIADWPLLDAMTLCASGADLVTVHSGGGGYAGYMTSAGVTIVAEGSAAAETRLRLALTND 522
                                           ************************************************************************* PP

                             TIGR01228 517 pGlGvirhadaGyesaldvakeqg 540
                                             lGvir+adaGy++ald+a ++ 
  NCBI__GCF_003217355.1:WP_110805607.1 523 TALGVIRYADAGYADALDEAAQKA 546
                                           ******************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (552 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 36.10
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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:

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