Alignments for a candidate for hutU in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Pseudomonas fluorescens FW300-N1B4

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate Pf1N1B4_1587 Urocanate hydratase (EC 4.2.1.49)

Query= reanno::pseudo1_N1B4:Pf1N1B4_1587
         (560 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1587
          Length = 560

 Score = 1142 bits (2955), Expect = 0.0
 Identities = 560/560 (100%), Positives = 560/560 (100%)

Query: 1   VTDNKPTKYRNVEIRAARGNKLTAKSWLTEAPLRMLMNNLDPEVAENPKELVVYGGIGRA 60
           VTDNKPTKYRNVEIRAARGNKLTAKSWLTEAPLRMLMNNLDPEVAENPKELVVYGGIGRA
Sbjct: 1   VTDNKPTKYRNVEIRAARGNKLTAKSWLTEAPLRMLMNNLDPEVAENPKELVVYGGIGRA 60

Query: 61  ARNWECYDKIVESLTNLNDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWANWEHF 120
           ARNWECYDKIVESLTNLNDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWANWEHF
Sbjct: 61  ARNWECYDKIVESLTNLNDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWANWEHF 120

Query: 121 NELDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYNDDLKGRWVLTAGLGGM 180
           NELDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYNDDLKGRWVLTAGLGGM
Sbjct: 121 NELDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYNDDLKGRWVLTAGLGGM 180

Query: 181 GGAQPLAATLAGACSLNIECQQVSIDFRLNSRYVDEQATDLDDALARIAKYTKEGKAISI 240
           GGAQPLAATLAGACSLNIECQQVSIDFRLNSRYVDEQATDLDDALARIAKYTKEGKAISI
Sbjct: 181 GGAQPLAATLAGACSLNIECQQVSIDFRLNSRYVDEQATDLDDALARIAKYTKEGKAISI 240

Query: 241 ALLGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWEEYRARAKTEPAAVVKA 300
           ALLGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWEEYRARAKTEPAAVVKA
Sbjct: 241 ALLGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWEEYRARAKTEPAAVVKA 300

Query: 301 AKQSMAVHVKAMLDFQKMGIPTFDYGNNIRQMAQEEGVENAFDFPGFVPAYIRPLFCRGI 360
           AKQSMAVHVKAMLDFQKMGIPTFDYGNNIRQMAQEEGVENAFDFPGFVPAYIRPLFCRGI
Sbjct: 301 AKQSMAVHVKAMLDFQKMGIPTFDYGNNIRQMAQEEGVENAFDFPGFVPAYIRPLFCRGI 360

Query: 361 GPFRWAALSGDPQDIYKTDAKVKELIPDDAHLHNWLDMARERISFQGLPARICWVGLGLR 420
           GPFRWAALSGDPQDIYKTDAKVKELIPDDAHLHNWLDMARERISFQGLPARICWVGLGLR
Sbjct: 361 GPFRWAALSGDPQDIYKTDAKVKELIPDDAHLHNWLDMARERISFQGLPARICWVGLGLR 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    0.411 

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: 1290
Number of extensions: 49
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 Pf1N1B4_1587 (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.6401.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 1021.5   0.3          0 1021.3   0.3    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1587  Urocanate hydratase (EC 4.2.1.49


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1587  Urocanate hydratase (EC 4.2.1.49)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1021.3   0.3         0         0       2     545 .]      13     556 ..      12     556 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1021.3 bits;  conditional E-value: 0
                                      TIGR01228   2 eiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkr 65 
                                                    eira+rG++l+ak+w +ea+lr+lmnnldpevae+p+elvvyGG+G+aarnwe++dkive+l++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1587  13 EIRAARGNKLTAKSWLTEAPLRMLMNNLDPEVAENPKELVVYGGIGRAARNWECYDKIVESLTN 76 
                                                    79************************************************************** PP

                                      TIGR01228  66 leddetllvqsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswi 129
                                                    l+ddetllvqsGkpvgvfkth++aprvliansnlvp+wa+we+f+el+akGl+myGqmtaGswi
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1587  77 LNDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWANWEHFNELDAKGLAMYGQMTAGSWI 140
                                                    **************************************************************** PP

                                      TIGR01228 130 yiGtqGilqGtyetlaelarkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeer 193
                                                    yiG+qGi+qGtyet++e++r+h+ ++lkg++vltaGlGgmGGaqpla+tl++a+s+++e+++  
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1587 141 YIGSQGIVQGTYETFVEAGRQHYNDDLKGRWVLTAGLGGMGGAQPLAATLAGACSLNIECQQVS 204
                                                    **************************************************************** PP

                                      TIGR01228 194 idkrletkyldektddldealaraeeakaeGkalsigllGnaaevleellergvvpdvvtdqts 257
                                                    id+rl+++y+de+++dld+alar++++++eGka+si+llGnaae+l+el++rgv+pd+vtdqts
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1587 205 IDFRLNSRYVDEQATDLDDALARIAKYTKEGKAISIALLGNAAEILPELVKRGVRPDMVTDQTS 268
                                                    **************************************************************** PP

                                      TIGR01228 258 ahdellGyipegytvedadklrdeepeeyvkaakaslakhvrallalqkkGavtfdyGnnirqv 321
                                                    ahd+l+Gy+p+g+t+e+++ ++++ep+++vkaak+s+a+hv+a+l++qk G  tfdyGnnirq+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1587 269 AHDPLNGYLPAGWTWEEYRARAKTEPAAVVKAAKQSMAVHVKAMLDFQKMGIPTFDYGNNIRQM 332
                                                    **************************************************************** PP

                                      TIGR01228 322 akeeGvedafdfpGfvpayirdlfceGkGpfrwvalsGdpadiyrtdkavkelfpedeelhrwi 385
                                                    a+eeGve+afdfpGfvpayir+lfc+G Gpfrw+alsGdp+diy+td++vkel+p+d++lh+w+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1587 333 AQEEGVENAFDFPGFVPAYIRPLFCRGIGPFRWAALSGDPQDIYKTDAKVKELIPDDAHLHNWL 396
                                                    **************************************************************** PP

                                      TIGR01228 386 dlakekvafqGlparicwlgygereklalainelvrsGelkapvvigrdhldaGsvaspnrete 449
                                                    d+a+e+++fqGlparicw+g+g r+kl+la+ne+vrsGel+ap+vigrdhld+Gsv+spnrete
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1587 397 DMARERISFQGLPARICWVGLGLRAKLGLAFNEMVRSGELSAPIVIGRDHLDSGSVSSPNRETE 460
                                                    **************************************************************** PP

                                      TIGR01228 450 amkdGsdavadwpllnallntaaGaswvslhhGGGvglGfslhaglvivadGtdeaaerlkrvl 513
                                                    +m+dGsdav+dwpllnallnta+Ga+wvslhhGGGvg+Gfs+h+g+viv+dGtdeaaer++rvl
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1587 461 SMQDGSDAVSDWPLLNALLNTASGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVL 524
                                                    **************************************************************** PP

                                      TIGR01228 514 tadpGlGvirhadaGyesaldvakeqgldlpm 545
                                                     +dp +Gv+rhadaGy+ a+d+akeqgl+lpm
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1587 525 HNDPATGVMRHADAGYQIAIDCAKEQGLNLPM 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.27
//
[ok]

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

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Candidates (tab-delimited)
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 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