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.5002.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: 00:00:00.02
# Mc/sec: 11.94
//
[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