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 (EC 4.2.1.49) (characterized)
to candidate WP_003548647.1 RL_RS30795 urocanate hydratase

Query= reanno::Smeli:SM_b21163
         (557 letters)



>NCBI__GCF_000009265.1:WP_003548647.1
          Length = 557

 Score = 1089 bits (2817), Expect = 0.0
 Identities = 517/556 (92%), Positives = 544/556 (97%)

Query: 1   MNNPRHNIREVRSPRGTEISAKSWLTEAPLRMLMNNLDPDVAENPHELVVYGGIGRAART 60
           MNNPRHNIREVR+PRG +++AKSW+TEAPLRMLMNNLDPDVAENP+ELVVYGGIGRAART
Sbjct: 1   MNNPRHNIREVRAPRGNDLNAKSWMTEAPLRMLMNNLDPDVAENPNELVVYGGIGRAART 60

Query: 61  WADFDRIVASLKDLNEDETLLVQSGKPVGVFRTHKDAPRVLIANSNLVPHWATWDHFNEL 120
           W DFDRIVA+LK L E+ETL+VQSGKPVGVFRTHKDAPRVLIANSNLVPHWATWDHFNEL
Sbjct: 61  WEDFDRIVATLKTLTEEETLVVQSGKPVGVFRTHKDAPRVLIANSNLVPHWATWDHFNEL 120

Query: 121 DKKGLAMYGQMTAGSWIYIGTQGIVQGTYETFVEAGRQHYGGSLKGKWILTGGLGGMGGA 180
           DKKGLAMYGQMTAGSWIYIGTQGIVQGTYETFVEAGRQHYGG+LKGKWILTGGLGGMGGA
Sbjct: 121 DKKGLAMYGQMTAGSWIYIGTQGIVQGTYETFVEAGRQHYGGNLKGKWILTGGLGGMGGA 180

Query: 181 QPLAAVMAGACCLAVECNPDSIDFRLRTRYLDEKAETLEEAMEMIERWTKAGEPKSVGLL 240
           QPLAAVMAGACCLAVECNPDSIDFRLRTRY+D KAETL+EA+EMI+RWTKAGE KSVGLL
Sbjct: 181 QPLAAVMAGACCLAVECNPDSIDFRLRTRYVDAKAETLDEALEMIDRWTKAGEAKSVGLL 240

Query: 241 GNAAEILPEMVRRGIRPDMVTDQTSAHDPINGYLPKGWTMAEWKAKRESDPKAVEKAARA 300
           GNAAEILPEMVRRGIRPD+VTDQTSAHDPINGYLPKGWTM EWKAKRESDPKAVEKAARA
Sbjct: 241 GNAAEILPEMVRRGIRPDIVTDQTSAHDPINGYLPKGWTMGEWKAKRESDPKAVEKAARA 300

Query: 301 SMRDHVEAMLAFWDSGVPTLDYGNNIRQVAKDEGLERAFDFPGFVPAYIRPLFCRGIGPF 360
           SMR+HVEAM+AFW++GVPTLDYGNNIRQVAKDEGLE AF FPGFVPAYIRPLFCRGIGPF
Sbjct: 301 SMREHVEAMIAFWNAGVPTLDYGNNIRQVAKDEGLENAFAFPGFVPAYIRPLFCRGIGPF 360

Query: 361 RWAALSGDPEDIYRTDRKVKELLPDNKHLHNWLDMARERIAFQGLPARICWVGLGDRHRL 420
           RWAALSGDPEDIY+TD KVKELLPDNKHLH+WLDMARERIAFQGLPARICWVGLGDRH+L
Sbjct: 361 RWAALSGDPEDIYKTDAKVKELLPDNKHLHHWLDMARERIAFQGLPARICWVGLGDRHKL 420

Query: 421 GLAFNEMVRSGELKAPIVIGRDHLDSGSVASPNRETEAMKDGSDAVSDWPLLNALLNTAS 480
           GLAFNEMVR+GEL APIVIGRDHLDSGSVASPNRETEAMKDGSDAVSDWPLLNALLNTAS
Sbjct: 421 GLAFNEMVRTGELSAPIVIGRDHLDSGSVASPNRETEAMKDGSDAVSDWPLLNALLNTAS 480

Query: 481 GATWVSLHHGGGVGMGFSQHSGMVICCDGTDDAARRIERVLWNDPATGVMRHADAGYDIA 540
           GATWVSLHHGGGVGMGFSQHSGMVIC DGTDDAARR+ERVLWNDPATGVMRHADAGY+IA
Sbjct: 481 GATWVSLHHGGGVGMGFSQHSGMVICADGTDDAARRLERVLWNDPATGVMRHADAGYEIA 540

Query: 541 VDCAREKGLRLPGILG 556
           +DCA+EKGLRLPGILG
Sbjct: 541 IDCAKEKGLRLPGILG 556


Lambda     K      H
   0.319    0.137    0.431 

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: 1270
Number of extensions: 40
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: 557
Length adjustment: 36
Effective length of query: 521
Effective length of database: 521
Effective search space:   271441
Effective search space used:   271441
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_003548647.1 RL_RS30795 (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.706844.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.9e-299  978.4   0.2   5.7e-299  978.2   0.2    1.0  1  NCBI__GCF_000009265.1:WP_003548647.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000009265.1:WP_003548647.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  978.2   0.2  5.7e-299  5.7e-299       1     544 [.       9     552 ..       9     553 .. 1.00

  Alignments for each domain:
  == domain 1  score: 978.2 bits;  conditional E-value: 5.7e-299
                             TIGR01228   1 keiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddetll 73 
                                           +e+raprG++l+ak+w++ea+lr+lmnnldp+vae+p+elvvyGG+G+aar we fd+iv++lk+l ++etl+
  NCBI__GCF_000009265.1:WP_003548647.1   9 REVRAPRGNDLNAKSWMTEAPLRMLMNNLDPDVAENPNELVVYGGIGRAARTWEDFDRIVATLKTLTEEETLV 81 
                                           689********************************************************************** PP

                             TIGR01228  74 vqsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGtyetlae 146
                                           vqsGkpvgvf+th++aprvliansnlvp+wa+w++f+el++kGl+myGqmtaGswiyiGtqGi+qGtyet++e
  NCBI__GCF_000009265.1:WP_003548647.1  82 VQSGKPVGVFRTHKDAPRVLIANSNLVPHWATWDHFNELDKKGLAMYGQMTAGSWIYIGTQGIVQGTYETFVE 154
                                           ************************************************************************* PP

                             TIGR01228 147 larkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddldealaraee 219
                                           ++r+h+gg+lkgk++lt GlGgmGGaqpla+ +++a+++ave++++ id+rl+t+y+d k++ ldeal+++++
  NCBI__GCF_000009265.1:WP_003548647.1 155 AGRQHYGGNLKGKWILTGGLGGMGGAQPLAAVMAGACCLAVECNPDSIDFRLRTRYVDAKAETLDEALEMIDR 227
                                           ************************************************************************* PP

                             TIGR01228 220 akaeGkalsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadklrdeepeeyvkaaka 292
                                            +++G+a+s+gllGnaae+l+e+++rg++pd+vtdqtsahd+++Gy+p+g+t+ + +  r+ +p+++ kaa+a
  NCBI__GCF_000009265.1:WP_003548647.1 228 WTKAGEAKSVGLLGNAAEILPEMVRRGIRPDIVTDQTSAHDPINGYLPKGWTMGEWKAKRESDPKAVEKAARA 300
                                           ************************************************************************* PP

                             TIGR01228 293 slakhvrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfceGkGpfrwvalsGdpadiy 365
                                           s+ +hv+a++a+ ++G+ t+dyGnnirqvak+eG+e+af fpGfvpayir+lfc+G Gpfrw+alsGdp+diy
  NCBI__GCF_000009265.1:WP_003548647.1 301 SMREHVEAMIAFWNAGVPTLDYGNNIRQVAKDEGLENAFAFPGFVPAYIRPLFCRGIGPFRWAALSGDPEDIY 373
                                           ************************************************************************* PP

                             TIGR01228 366 rtdkavkelfpedeelhrwidlakekvafqGlparicwlgygereklalainelvrsGelkapvvigrdhlda 438
                                           +td++vkel+p++++lh+w+d+a+e++afqGlparicw+g+g+r+kl+la+ne+vr+Gel+ap+vigrdhld+
  NCBI__GCF_000009265.1:WP_003548647.1 374 KTDAKVKELLPDNKHLHHWLDMARERIAFQGLPARICWVGLGDRHKLGLAFNEMVRTGELSAPIVIGRDHLDS 446
                                           ************************************************************************* PP

                             TIGR01228 439 GsvaspnreteamkdGsdavadwpllnallntaaGaswvslhhGGGvglGfslhaglvivadGtdeaaerlkr 511
                                           GsvaspnreteamkdGsdav+dwpllnallnta+Ga+wvslhhGGGvg+Gfs+h+g+vi adGtd+aa+rl+r
  NCBI__GCF_000009265.1:WP_003548647.1 447 GSVASPNRETEAMKDGSDAVSDWPLLNALLNTASGATWVSLHHGGGVGMGFSQHSGMVICADGTDDAARRLER 519
                                           ************************************************************************* PP

                             TIGR01228 512 vltadpGlGvirhadaGyesaldvakeqgldlp 544
                                           vl +dp +Gv+rhadaGye a+d+ake+gl+lp
  NCBI__GCF_000009265.1:WP_003548647.1 520 VLWNDPATGVMRHADAGYEIAIDCAKEKGLRLP 552
                                           *******************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (557 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: 26.33
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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

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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