Alignments for a candidate for hutU in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Pseudomonas fluorescens GW456-L13

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate PfGW456L13_326 Urocanate hydratase (EC 4.2.1.49)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_326
         (560 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_326
          Length = 560

 Score = 1139 bits (2945), Expect = 0.0
 Identities = 560/560 (100%), Positives = 560/560 (100%)

Query: 1   VTENKRTKFRDVEIRAARGNKLTAKSWLTEAPLRMLMNNLDPEVAENPKELVVYGGIGRA 60
           VTENKRTKFRDVEIRAARGNKLTAKSWLTEAPLRMLMNNLDPEVAENPKELVVYGGIGRA
Sbjct: 1   VTENKRTKFRDVEIRAARGNKLTAKSWLTEAPLRMLMNNLDPEVAENPKELVVYGGIGRA 60

Query: 61  ARNWECYDKIVESLTNLNDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWASWEHF 120
           ARNWECYDKIVESLTNLNDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWASWEHF
Sbjct: 61  ARNWECYDKIVESLTNLNDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWASWEHF 120

Query: 121 NELDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYNDNLTGKWVLTAGLGGM 180
           NELDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYNDNLTGKWVLTAGLGGM
Sbjct: 121 NELDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYNDNLTGKWVLTAGLGGM 180

Query: 181 GGAQPLAATLAGACSLNIECQQVSIDFRLKSRYVDEQAKDLDDALARIAKYTAEGKAISI 240
           GGAQPLAATLAGACSLNIECQQVSIDFRLKSRYVDEQAKDLDDALARIAKYTAEGKAISI
Sbjct: 181 GGAQPLAATLAGACSLNIECQQVSIDFRLKSRYVDEQAKDLDDALARIAKYTAEGKAISI 240

Query: 241 ALLGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWDEYRARAKTEPAAVIKA 300
           ALLGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWDEYRARAKTEPAAVIKA
Sbjct: 241 ALLGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWDEYRARAKTEPAAVIKA 300

Query: 301 AKQSMAVHVKAMLDFQKQGIPTFDYGNNIRQMAQEEGVENAFDFPGFVPAYIRPLFCRGI 360
           AKQSMAVHVKAMLDFQKQGIPTFDYGNNIRQMAQEEGVENAFDFPGFVPAYIRPLFCRGI
Sbjct: 301 AKQSMAVHVKAMLDFQKQGIPTFDYGNNIRQMAQEEGVENAFDFPGFVPAYIRPLFCRGI 360

Query: 361 GPFRWAALSGNAEDIYKTDAKVKELIPDDAHLHNWLDMARERISFQGLPARICWVGLGLR 420
           GPFRWAALSGNAEDIYKTDAKVKELIPDDAHLHNWLDMARERISFQGLPARICWVGLGLR
Sbjct: 361 GPFRWAALSGNAEDIYKTDAKVKELIPDDAHLHNWLDMARERISFQGLPARICWVGLGLR 420

Query: 421 AKLGLAFNEMVRSGELSAPIVIGRDHLDSGSVSSPNRETESMQDGSDAVSDWPLLNALLN 480
           AKLGLAFNEMVRSGELSAPIVIGRDHLDSGSVSSPNRETESMQDGSDAVSDWPLLNALLN
Sbjct: 421 AKLGLAFNEMVRSGELSAPIVIGRDHLDSGSVSSPNRETESMQDGSDAVSDWPLLNALLN 480

Query: 481 TASGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLHNDPATGVMRHADAGY 540
           TASGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLHNDPATGVMRHADAGY
Sbjct: 481 TASGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLHNDPATGVMRHADAGY 540

Query: 541 QIAIDCAKEQGLNLPMITGK 560
           QIAIDCAKEQGLNLPMITGK
Sbjct: 541 QIAIDCAKEQGLNLPMITGK 560


Lambda     K      H
   0.318    0.134    0.408 

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: 1262
Number of extensions: 45
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: 560
Length of database: 560
Length adjustment: 36
Effective length of query: 524
Effective length of database: 524
Effective search space:   274576
Effective search space used:   274576
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 PfGW456L13_326 (Urocanate hydratase (EC 4.2.1.49))
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.30517.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 1017.8   0.5          0 1017.6   0.5    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_326  Urocanate hydratase (EC 4.2.1.49


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_326  Urocanate hydratase (EC 4.2.1.49)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1017.6   0.5         0         0       2     545 .]      13     556 ..      12     556 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1017.6 bits;  conditional E-value: 0
                                              TIGR01228   2 eiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafd 57 
                                                            eira+rG++l+ak+w +ea+lr+lmnnldpevae+p+elvvyGG+G+aarnwe++d
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_326  13 EIRAARGNKLTAKSWLTEAPLRMLMNNLDPEVAENPKELVVYGGIGRAARNWECYD 68 
                                                            79****************************************************** PP

                                              TIGR01228  58 kiveelkrleddetllvqsGkpvgvfkthekaprvliansnlvpkwadwekfeele 113
                                                            kive+l++l+ddetllvqsGkpvgvfkth++aprvliansnlvp+wa+we+f+el+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_326  69 KIVESLTNLNDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWASWEHFNELD 124
                                                            ******************************************************** PP

                                              TIGR01228 114 akGlimyGqmtaGswiyiGtqGilqGtyetlaelarkhfggslkgklvltaGlGgm 169
                                                            akGl+myGqmtaGswiyiG+qGi+qGtyet++e++r+h+ ++l gk+vltaGlGgm
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_326 125 AKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYNDNLTGKWVLTAGLGGM 180
                                                            ******************************************************** PP

                                              TIGR01228 170 GGaqplavtlneavsiavevdeeridkrletkyldektddldealaraeeakaeGk 225
                                                            GGaqpla+tl++a+s+++e+++  id+rl+++y+de+++dld+alar+++++aeGk
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_326 181 GGAQPLAATLAGACSLNIECQQVSIDFRLKSRYVDEQAKDLDDALARIAKYTAEGK 236
                                                            ******************************************************** PP

                                              TIGR01228 226 alsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadklrde 281
                                                            a+si+llGnaae+l+el++rgv+pd+vtdqtsahd+l+Gy+p+g+t+++++ ++++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_326 237 AISIALLGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWDEYRARAKT 292
                                                            ******************************************************** PP

                                              TIGR01228 282 epeeyvkaakaslakhvrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfv 337
                                                            ep++++kaak+s+a+hv+a+l++qk+G  tfdyGnnirq+a+eeGve+afdfpGfv
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_326 293 EPAAVIKAAKQSMAVHVKAMLDFQKQGIPTFDYGNNIRQMAQEEGVENAFDFPGFV 348
                                                            ******************************************************** PP

                                              TIGR01228 338 payirdlfceGkGpfrwvalsGdpadiyrtdkavkelfpedeelhrwidlakekva 393
                                                            payir+lfc+G Gpfrw+alsG+++diy+td++vkel+p+d++lh+w+d+a+e+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_326 349 PAYIRPLFCRGIGPFRWAALSGNAEDIYKTDAKVKELIPDDAHLHNWLDMARERIS 404
                                                            ******************************************************** PP

                                              TIGR01228 394 fqGlparicwlgygereklalainelvrsGelkapvvigrdhldaGsvaspnrete 449
                                                            fqGlparicw+g+g r+kl+la+ne+vrsGel+ap+vigrdhld+Gsv+spnrete
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_326 405 FQGLPARICWVGLGLRAKLGLAFNEMVRSGELSAPIVIGRDHLDSGSVSSPNRETE 460
                                                            ******************************************************** PP

                                              TIGR01228 450 amkdGsdavadwpllnallntaaGaswvslhhGGGvglGfslhaglvivadGtdea 505
                                                            +m+dGsdav+dwpllnallnta+Ga+wvslhhGGGvg+Gfs+h+g+viv+dGtdea
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_326 461 SMQDGSDAVSDWPLLNALLNTASGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEA 516
                                                            ******************************************************** PP

                                              TIGR01228 506 aerlkrvltadpGlGvirhadaGyesaldvakeqgldlpm 545
                                                            aer++rvl +dp +Gv+rhadaGy+ a+d+akeqgl+lpm
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_326 517 AERIARVLHNDPATGVMRHADAGYQIAIDCAKEQGLNLPM 556
                                                            ***************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (560 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.91
//
[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