Alignments for a candidate for hutU in Rhizobium johnstonii 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Rhizobium johnstonii 3841

Align Urocanate hydratase; Urocanase; Imidazolonepropionate hydrolase; EC 4.2.1.49 (characterized)
to candidate WP_011650166.1 RL_RS01900 urocanate hydratase

Query= SwissProt::Q5L084
         (551 letters)



>NCBI__GCF_000009265.1:WP_011650166.1
          Length = 553

 Score =  574 bits (1479), Expect = e-168
 Identities = 283/542 (52%), Positives = 371/542 (68%), Gaps = 4/542 (0%)

Query: 10  PAGTERRAKGWIQEAALRMLNNNLHPDVAERPDELIVYGGIGKAARNWECYEAIVDTLLR 69
           P G E RAKGW QEA LR+L N L   V E PD LIVY  +GKAARNW  +  IV  L  
Sbjct: 14  PGGPELRAKGWRQEALLRLLENVL--SVGEDPDNLIVYAALGKAARNWAAHRGIVKALTE 71

Query: 70  LENDETLLIQSGKPVAVFRTHPDAPRVLIANSNLVPAWATWDHFHELDKKGLIMYGQMTA 129
           +E D+TLLIQSGKP+ + RTH  AP V++AN N+V  WA  + F+EL +KGLI +G +TA
Sbjct: 72  MEEDQTLLIQSGKPIGLVRTHAKAPLVIMANCNIVGQWAKAEVFYELQRKGLICWGGLTA 131

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

Query: 190 AIEVDPARIQRRIDTNYLDTMTDSLDAALEMAKQAKEEKKALSIGLVGNAAEVLPRLVEM 249
            +++DP R ++R    YL  +   LD+AL+M   A ++K+ALS+GLVGNAAEV P +   
Sbjct: 192 CVDIDPERARKRQQIGYLQEIAPDLDSALQMIDAAVKDKRALSVGLVGNAAEVYPEIARR 251

Query: 250 GFVPDVLTDQTSAHDPLNGYIPAGLTLDEAAELRARDPKQYIARAKQSIAAHVRAMLAMQ 309
           G VPD++TDQTSAHD + GY+P G+ LD+   LR     Q +A ++ SI  HV AML  Q
Sbjct: 252 GIVPDIVTDQTSAHDLVYGYVPKGMNLDQVKGLRDDGQGQLMAASRASIVEHVTAMLEFQ 311

Query: 310 KQGAVTFDYGNNIRQVAKDEGVDDAFSFPGFVPAYIRPLFCEGKGPFRWVALSGDPEDIY 369
           K+G+  FD GN IR  AK+ GV +AF  P F  AY+RPLF    GPFRW+ALSG+  DI 
Sbjct: 312 KKGSEVFDNGNLIRTQAKEGGVANAFDIPIFTEAYLRPLFARAIGPFRWMALSGEESDIA 371

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

Query: 430 KAPIVIGRDHLDSGSVASPNRETEGMKDGSDAIADWPILNALLNAVGGASWVSVHHGGGV 489
           K P+   RDHLD+G++A PN  TEGMKDGSDAIADWP+++A++     A  V +H GGG 
Sbjct: 432 KGPVAFSRDHLDAGAMAHPNIMTEGMKDGSDAIADWPLIDAMMLCSSMADLVVIHSGGGG 491

Query: 490 GMGYSIHAGMVIVADGTKEAEKRLERVLTTDPGLGVVRHADAGYELAIRTAKEKGIDMPM 549
             GY    G+ +VADGT +A++RL+  LT D  LGV+R+ADAGYE A+    +K  D+P 
Sbjct: 492 YAGYMTSCGVTVVADGTDDADERLDHALTNDTALGVMRYADAGYEEALDEVAKK--DVPY 549

Query: 550 LK 551
           ++
Sbjct: 550 IR 551


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: 776
Number of extensions: 27
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: 553
Length adjustment: 36
Effective length of query: 515
Effective length of database: 517
Effective search space:   266255
Effective search space used:   266255
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_011650166.1 RL_RS01900 (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.1213420.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-213  695.4   0.9   3.5e-213  695.0   0.9    1.0  1  NCBI__GCF_000009265.1:WP_011650166.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000009265.1:WP_011650166.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  695.0   0.9  3.5e-213  3.5e-213       6     541 ..      14     547 ..      10     550 .. 0.99

  Alignments for each domain:
  == domain 1  score: 695.0 bits;  conditional E-value: 3.5e-213
                             TIGR01228   6 prGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddetllvqsGk 78 
                                           p G el akgw+qea lrll+n l   v edp++l+vy   Gkaarnw a+  iv+ l+ +e+d+tll+qsGk
  NCBI__GCF_000009265.1:WP_011650166.1  14 PGGPELRAKGWRQEALLRLLENVL--SVGEDPDNLIVYAALGKAARNWAAHRGIVKALTEMEEDQTLLIQSGK 84 
                                           7899*******************9..69********************************************* PP

                             TIGR01228  79 pvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGtyetlaelarkh 151
                                           p+g+++th kap v++an+n+v++wa+ e+f el++kGli +G +taG+w yiG+qG++qGtye +  +a ++
  NCBI__GCF_000009265.1:WP_011650166.1  85 PIGLVRTHAKAPLVIMANCNIVGQWAKAEVFYELQRKGLICWGGLTAGAWQYIGSQGVIQGTYEIFMRIAERR 157
                                           ************************************************************************* PP

                             TIGR01228 152 fggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddldealaraeeakaeG 224
                                           fgg+l g++vltaGlGgmGGaqpla ++++a+ + v++d+er +kr +  yl+e + dld al+++++a ++ 
  NCBI__GCF_000009265.1:WP_011650166.1 158 FGGDLLGRFVLTAGLGGMGGAQPLAGRMAGAAILCVDIDPERARKRQQIGYLQEIAPDLDSALQMIDAAVKDK 230
                                           ************************************************************************* PP

                             TIGR01228 225 kalsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadklrdeepeeyvkaakaslakh 297
                                           +als+gl Gnaaev++e+ +rg+vpd+vtdqtsahd + Gy+p+g+ +++ + lrd+ + + + a++as+++h
  NCBI__GCF_000009265.1:WP_011650166.1 231 RALSVGLVGNAAEVYPEIARRGIVPDIVTDQTSAHDLVYGYVPKGMNLDQVKGLRDDGQGQLMAASRASIVEH 303
                                           ************************************************************************* PP

                             TIGR01228 298 vrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfceGkGpfrwvalsGdpadiyrtdka 370
                                           v a+l++qkkG+ +fd Gn ir++ake Gv++afd+p f  ay+r+lf++  Gpfrw+alsG+  di r+d+ 
  NCBI__GCF_000009265.1:WP_011650166.1 304 VTAMLEFQKKGSEVFDNGNLIRTQAKEGGVANAFDIPIFTEAYLRPLFARAIGPFRWMALSGEESDIARIDDL 376
                                           ************************************************************************* PP

                             TIGR01228 371 vkelfpedeelhrwidlakekvafqGlparicwlgygereklalainelvrsGelkapvvigrdhldaGsvas 443
                                           ++e+fp+++ +++wi la+e+v f+Glpari wlg+ger  la ++n lv sGelk pv+ +rdhldaG++a 
  NCBI__GCF_000009265.1:WP_011650166.1 377 LLEMFPDNKIITNWIRLAREHVPFEGLPARIAWLGHGERTALARRVNALVASGELKGPVAFSRDHLDAGAMAH 449
                                           ************************************************************************* PP

                             TIGR01228 444 pnreteamkdGsdavadwpllnallntaaGaswvslhhGGGvglGfslhaglvivadGtdeaaerlkrvltad 516
                                           pn  te mkdGsda+adwpl++a++   + a++v +h GGG   G+   +g+ +vadGtd+a+erl  +lt+d
  NCBI__GCF_000009265.1:WP_011650166.1 450 PNIMTEGMKDGSDAIADWPLIDAMMLCSSMADLVVIHSGGGGYAGYMTSCGVTVVADGTDDADERLDHALTND 522
                                           ************************************************************************* PP

                             TIGR01228 517 pGlGvirhadaGyesaldvakeqgl 541
                                             lGv+r+adaGye+ald++ ++++
  NCBI__GCF_000009265.1:WP_011650166.1 523 TALGVMRYADAGYEEALDEVAKKDV 547
                                           ******************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (553 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 38.43
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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