Alignments for a candidate for hutU in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Pseudomonas putida KT2440

Align Urocanate hydratase; Urocanase; Imidazolonepropionate hydrolase; EC 4.2.1.49 (characterized)
to candidate PP_5033 PP_5033 Urocanate hydratase

Query= SwissProt::P25080
         (557 letters)



>FitnessBrowser__Putida:PP_5033
          Length = 557

 Score = 1129 bits (2919), Expect = 0.0
 Identities = 551/557 (98%), Positives = 554/557 (99%)

Query: 1   MTDNNKYRDVEIRAPRGNKLTAKSWLTEAPLRMLMNNLDPQVAENPKELVVYGGIGRAAR 60
           MTDNNKYRDVEIRAPRGNKLTAKSWLTEAPLRMLMNNLDPQVAENPKELVVYGGIGRAAR
Sbjct: 1   MTDNNKYRDVEIRAPRGNKLTAKSWLTEAPLRMLMNNLDPQVAENPKELVVYGGIGRAAR 60

Query: 61  NWECYDKIVETLTRLEDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWANWEHFNE 120
           NW CYDKIVETLTRLEDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWANWEHFNE
Sbjct: 61  NWACYDKIVETLTRLEDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWANWEHFNE 120

Query: 121 LDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYGGTVKAKWVLTAGLGGMGG 180
           LDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYGG++K KWVLTAGLGGMGG
Sbjct: 121 LDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYGGSLKGKWVLTAGLGGMGG 180

Query: 181 AQPLAATLAGACSLNIECQQSRIDFRLETRYVDEQATDLDDALVRIAKYTAEGKAISIAL 240
           AQPLAATLAGACSLNIECQQSRIDFRLETRYVDEQATDLDDAL RIAKYTAEGKAISIAL
Sbjct: 181 AQPLAATLAGACSLNIECQQSRIDFRLETRYVDEQATDLDDALARIAKYTAEGKAISIAL 240

Query: 241 HGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWEQYRDRAQTEPAAVVKAAK 300
           HGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWEQYRDRAQTEPAAVVKAAK
Sbjct: 241 HGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWEQYRDRAQTEPAAVVKAAK 300

Query: 301 QSMAVHVQAMLDFQKQGVPTFDYGNNIRQMAKEEGVANAFDFPGFVPAYIRPLFCRGVGP 360
           QSMAVHVQAMLDFQKQG+PTFDYGNNIRQMAKEEGVANAFDFPGFVPAYIRPLFCRGVGP
Sbjct: 301 QSMAVHVQAMLDFQKQGIPTFDYGNNIRQMAKEEGVANAFDFPGFVPAYIRPLFCRGVGP 360

Query: 361 FRWAALSGEAEDIYKTDAKVKELIPDDAHLHRWLDMARERISFQGLPARICWVGLGLRAK 420
           FRWAALSGEAEDIYKTDAKVKELIPDDAHLHRWLDMARERISFQGLPARICWVGLGLRAK
Sbjct: 361 FRWAALSGEAEDIYKTDAKVKELIPDDAHLHRWLDMARERISFQGLPARICWVGLGLRAK 420

Query: 421 LGLAFNEMVRSGELSAPVVIGRDHLDSGSVSSPNRETEAMRDGSDAVSDWPLLNALLNTA 480
           LGLAFNEMVRSGELSAPVVIGRDHLDSGSVSSPNRETEAMRDGSDAVSDWPLLNALLNTA
Sbjct: 421 LGLAFNEMVRSGELSAPVVIGRDHLDSGSVSSPNRETEAMRDGSDAVSDWPLLNALLNTA 480

Query: 481 GGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLTNDPGTGVMRHADAGYDI 540
           GGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLTNDPGTGVMRHADAGYDI
Sbjct: 481 GGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLTNDPGTGVMRHADAGYDI 540

Query: 541 AIDCAKEQGLDLPMITG 557
           AIDCAKEQGLDLPMITG
Sbjct: 541 AIDCAKEQGLDLPMITG 557


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: 1254
Number of extensions: 43
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate PP_5033 PP_5033 (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.15802.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
          0 1048.0   0.5          0 1047.8   0.5    1.0  1  lcl|FitnessBrowser__Putida:PP_5033  PP_5033 Urocanate hydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_5033  PP_5033 Urocanate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1047.8   0.5         0         0       2     545 .]      11     554 ..      10     554 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1047.8 bits;  conditional E-value: 0
                           TIGR01228   2 eiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddetllvqs 76 
                                         eiraprG++l+ak+w +ea+lr+lmnnldp+vae+p+elvvyGG+G+aarnw ++dkive+l+rleddetllvqs
  lcl|FitnessBrowser__Putida:PP_5033  11 EIRAPRGNKLTAKSWLTEAPLRMLMNNLDPQVAENPKELVVYGGIGRAARNWACYDKIVETLTRLEDDETLLVQS 85 
                                         79************************************************************************* PP

                           TIGR01228  77 GkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGtyetlaelarkh 151
                                         Gkpvgvfkth++aprvliansnlvp+wa+we+f+el+akGl+myGqmtaGswiyiG+qGi+qGtyet++e++r+h
  lcl|FitnessBrowser__Putida:PP_5033  86 GKPVGVFKTHSNAPRVLIANSNLVPHWANWEHFNELDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQH 160
                                         *************************************************************************** PP

                           TIGR01228 152 fggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddldealaraeeakaeGka 226
                                         +ggslkgk+vltaGlGgmGGaqpla+tl++a+s+++e++++rid+rlet+y+de+++dld+alar+++++aeGka
  lcl|FitnessBrowser__Putida:PP_5033 161 YGGSLKGKWVLTAGLGGMGGAQPLAATLAGACSLNIECQQSRIDFRLETRYVDEQATDLDDALARIAKYTAEGKA 235
                                         *************************************************************************** PP

                           TIGR01228 227 lsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadklrdeepeeyvkaakaslakhvral 301
                                         +si+l+Gnaae+l+el++rgv+pd+vtdqtsahd+l+Gy+p+g+t+e++++++++ep+++vkaak+s+a+hv+a+
  lcl|FitnessBrowser__Putida:PP_5033 236 ISIALHGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWEQYRDRAQTEPAAVVKAAKQSMAVHVQAM 310
                                         *************************************************************************** PP

                           TIGR01228 302 lalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfceGkGpfrwvalsGdpadiyrtdkavkelfp 376
                                         l++qk+G  tfdyGnnirq+akeeGv++afdfpGfvpayir+lfc+G Gpfrw+alsG+++diy+td++vkel+p
  lcl|FitnessBrowser__Putida:PP_5033 311 LDFQKQGIPTFDYGNNIRQMAKEEGVANAFDFPGFVPAYIRPLFCRGVGPFRWAALSGEAEDIYKTDAKVKELIP 385
                                         *************************************************************************** PP

                           TIGR01228 377 edeelhrwidlakekvafqGlparicwlgygereklalainelvrsGelkapvvigrdhldaGsvaspnreteam 451
                                         +d++lhrw+d+a+e+++fqGlparicw+g+g r+kl+la+ne+vrsGel+apvvigrdhld+Gsv+spnreteam
  lcl|FitnessBrowser__Putida:PP_5033 386 DDAHLHRWLDMARERISFQGLPARICWVGLGLRAKLGLAFNEMVRSGELSAPVVIGRDHLDSGSVSSPNRETEAM 460
                                         *************************************************************************** PP

                           TIGR01228 452 kdGsdavadwpllnallntaaGaswvslhhGGGvglGfslhaglvivadGtdeaaerlkrvltadpGlGvirhad 526
                                         +dGsdav+dwpllnallnta+Ga+wvslhhGGGvg+Gfs+h+g+viv+dGtdeaaer++rvlt+dpG+Gv+rhad
  lcl|FitnessBrowser__Putida:PP_5033 461 RDGSDAVSDWPLLNALLNTAGGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLTNDPGTGVMRHAD 535
                                         *************************************************************************** PP

                           TIGR01228 527 aGyesaldvakeqgldlpm 545
                                         aGy+ a+d+akeqgldlpm
  lcl|FitnessBrowser__Putida:PP_5033 536 AGYDIAIDCAKEQGLDLPM 554
                                         ******************8 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 9.72
//
[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:

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