Alignments for a candidate for hutU in Lysobacter daejeonensis GH1-9

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Lysobacter daejeonensis GH1-9

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate WP_036139592.1 N800_RS13305 urocanate hydratase

Query= reanno::pseudo6_N2E2:Pf6N2E2_3805
         (562 letters)



>NCBI__GCF_000768355.1:WP_036139592.1
          Length = 554

 Score =  914 bits (2361), Expect = 0.0
 Identities = 438/544 (80%), Positives = 485/544 (89%)

Query: 16  IRAPRGNTLTAKSWLTEAPLRMLMNNLDPEVAENPKELVVYGGIGRAARNWECYDKIVES 75
           IRAPRG   + KSWL+EA  RM+ NNLDP+VAENP ELVVYGGIGRAAR+WE YD I++S
Sbjct: 11  IRAPRGAEKSCKSWLSEAAYRMIQNNLDPDVAENPTELVVYGGIGRAARDWESYDAILKS 70

Query: 76  LTNLNDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWASWEHFNELDAKGLAMYGQ 135
           L  L D+ETLLVQSGKPVGVF TH +APRVLIANSNLVPHWA+WEHFNELD KGL MYGQ
Sbjct: 71  LRELEDNETLLVQSGKPVGVFPTHPDAPRVLIANSNLVPHWATWEHFNELDKKGLMMYGQ 130

Query: 136 MTAGSWIYIGSQGIVQGTYETFVEAGRQHYDSNLKGRWVLTAGLGGMGGAQPLAATLAGA 195
           MTAGSWIYIGSQGIVQGTYETFVE GRQHY  +L G+W+LTAGLGGMGGAQPLAAT+AGA
Sbjct: 131 MTAGSWIYIGSQGIVQGTYETFVEMGRQHYGGDLTGKWILTAGLGGMGGAQPLAATMAGA 190

Query: 196 CSLNIECQQVSIDFRLKTRYVDEQATDLDDALARIEKYTAEGKAISIALCGNAAEILPEM 255
           C L IEC+Q SID RL+TRYVDEQATDLDDALARIEKYTA G+A SIAL GNAAEILPE+
Sbjct: 191 CMLAIECRQSSIDMRLRTRYVDEQATDLDDALARIEKYTAAGEAKSIALLGNAAEILPEL 250

Query: 256 VRRGVRPDMVTDQTSAHDPLNGYLPAGWTWDEYRARAKTEPAAVVKAAKQSMAIHVKAML 315
           VRRGVRPD VTDQTSAHDPL+GYLPAGWT +++  + KTEP  VV+AAK SM +HV+AML
Sbjct: 251 VRRGVRPDAVTDQTSAHDPLHGYLPAGWTLEQWLDKQKTEPQEVVEAAKHSMRVHVEAML 310

Query: 316 AFQKMGVPTFDYGNNIRQMAQEEGVENAFDFPGFVPAYIRPLFCRGIGPFRWAALSGDPQ 375
            F+ MGVPTFDYGNNIRQMA + G ++AFDFPGFVPAY+RPLFCRG+GPFRW ALSGDP+
Sbjct: 311 HFEDMGVPTFDYGNNIRQMAFDMGCKDAFDFPGFVPAYVRPLFCRGVGPFRWVALSGDPE 370

Query: 376 DIYKTDAKVKELIPDDAHLHNWLDMARERISFQGLPARICWVGLGQRAKLGLAFNEMVRS 435
           DI KTDAKVKELIP+D HLH WLDMA ERISFQGLPARICWVGLG R +LGLAFNEMVR+
Sbjct: 371 DIAKTDAKVKELIPNDPHLHKWLDMAHERISFQGLPARICWVGLGDRHRLGLAFNEMVRN 430

Query: 436 GELSAPIVIGRDHLDSGSVASPNRETESMQDGSDAVSDWPLLNALLNTASGATWVSLHHG 495
           GEL AP+VIGRDHLDSGSV+SPNRETESM DGSDAVSDWPLLNA+LN A GATWVSLHHG
Sbjct: 431 GELKAPVVIGRDHLDSGSVSSPNRETESMMDGSDAVSDWPLLNAMLNVAGGATWVSLHHG 490

Query: 496 GGVGMGFSQHSGMVIVCDGTDEAAERIARVLHNDPGTGVMRHADAGYQIAIDCAKEQGLN 555
           GGVGMG+SQHSG+VIVCDG++ A +R+ARVL NDPGTGVMRHADAGY+IA  CAKEQGL 
Sbjct: 491 GGVGMGYSQHSGVVIVCDGSEAADQRLARVLWNDPGTGVMRHADAGYEIAKQCAKEQGLK 550

Query: 556 LPMI 559
           LPM+
Sbjct: 551 LPML 554


Lambda     K      H
   0.318    0.134    0.412 

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: 1166
Number of extensions: 44
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: 562
Length of database: 554
Length adjustment: 36
Effective length of query: 526
Effective length of database: 518
Effective search space:   272468
Effective search space used:   272468
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 WP_036139592.1 N800_RS13305 (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.4089871.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-298  976.6   0.1   1.9e-298  976.4   0.1    1.0  1  NCBI__GCF_000768355.1:WP_036139592.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000768355.1:WP_036139592.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  976.4   0.1  1.9e-298  1.9e-298       1     545 []       9     553 ..       9     553 .. 1.00

  Alignments for each domain:
  == domain 1  score: 976.4 bits;  conditional E-value: 1.9e-298
                             TIGR01228   1 keiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddetll 73 
                                           ++iraprG e+++k+w  eaa r+++nnldp+vae+p elvvyGG+G+aar+we++d+i+++l+ led+etll
  NCBI__GCF_000768355.1:WP_036139592.1   9 RTIRAPRGAEKSCKSWLSEAAYRMIQNNLDPDVAENPTELVVYGGIGRAARDWESYDAILKSLRELEDNETLL 81 
                                           689********************************************************************** PP

                             TIGR01228  74 vqsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGtyetlae 146
                                           vqsGkpvgvf th +aprvliansnlvp+wa+we+f+el++kGl+myGqmtaGswiyiG+qGi+qGtyet++e
  NCBI__GCF_000768355.1:WP_036139592.1  82 VQSGKPVGVFPTHPDAPRVLIANSNLVPHWATWEHFNELDKKGLMMYGQMTAGSWIYIGSQGIVQGTYETFVE 154
                                           ************************************************************************* PP

                             TIGR01228 147 larkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddldealaraee 219
                                           ++r+h+gg+l gk++ltaGlGgmGGaqpla+t+++a+++a+e+ ++ id rl+t+y+de+++dld+alar+e+
  NCBI__GCF_000768355.1:WP_036139592.1 155 MGRQHYGGDLTGKWILTAGLGGMGGAQPLAATMAGACMLAIECRQSSIDMRLRTRYVDEQATDLDDALARIEK 227
                                           ************************************************************************* PP

                             TIGR01228 220 akaeGkalsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadklrdeepeeyvkaaka 292
                                           ++a+G+a+si+llGnaae+l+el++rgv+pd vtdqtsahd+l Gy+p+g+t+e+  + +++ep+e+v+aak+
  NCBI__GCF_000768355.1:WP_036139592.1 228 YTAAGEAKSIALLGNAAEILPELVRRGVRPDAVTDQTSAHDPLHGYLPAGWTLEQWLDKQKTEPQEVVEAAKH 300
                                           ************************************************************************* PP

                             TIGR01228 293 slakhvrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfceGkGpfrwvalsGdpadiy 365
                                           s+ +hv+a+l++++ G+ tfdyGnnirq+a++ G +dafdfpGfvpay+r+lfc+G GpfrwvalsGdp+di 
  NCBI__GCF_000768355.1:WP_036139592.1 301 SMRVHVEAMLHFEDMGVPTFDYGNNIRQMAFDMGCKDAFDFPGFVPAYVRPLFCRGVGPFRWVALSGDPEDIA 373
                                           ************************************************************************* PP

                             TIGR01228 366 rtdkavkelfpedeelhrwidlakekvafqGlparicwlgygereklalainelvrsGelkapvvigrdhlda 438
                                           +td++vkel+p+d +lh+w+d+a+e+++fqGlparicw+g+g+r++l+la+ne+vr+Gelkapvvigrdhld+
  NCBI__GCF_000768355.1:WP_036139592.1 374 KTDAKVKELIPNDPHLHKWLDMAHERISFQGLPARICWVGLGDRHRLGLAFNEMVRNGELKAPVVIGRDHLDS 446
                                           ************************************************************************* PP

                             TIGR01228 439 GsvaspnreteamkdGsdavadwpllnallntaaGaswvslhhGGGvglGfslhaglvivadGtdeaaerlkr 511
                                           Gsv+spnrete+m dGsdav+dwpllna+ln+a+Ga+wvslhhGGGvg+G+s+h+g+viv+dG+++a++rl+r
  NCBI__GCF_000768355.1:WP_036139592.1 447 GSVSSPNRETESMMDGSDAVSDWPLLNAMLNVAGGATWVSLHHGGGVGMGYSQHSGVVIVCDGSEAADQRLAR 519
                                           ************************************************************************* PP

                             TIGR01228 512 vltadpGlGvirhadaGyesaldvakeqgldlpm 545
                                           vl +dpG+Gv+rhadaGye a ++akeqgl+lpm
  NCBI__GCF_000768355.1:WP_036139592.1 520 VLWNDPGTGVMRHADAGYEIAKQCAKEQGLKLPM 553
                                           *********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (554 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 27.71
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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 2024 update 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