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.25108.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: 8.95
//
[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