Alignments for a candidate for hutU in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Halomonas desiderata SP1

Align Urocanate hydratase; Urocanase; Imidazolonepropionate hydrolase; EC 4.2.1.49 (characterized)
to candidate WP_086509679.1 BZY95_RS09385 urocanate hydratase

Query= SwissProt::P25080
         (557 letters)



>NCBI__GCF_002151265.1:WP_086509679.1
          Length = 562

 Score =  947 bits (2447), Expect = 0.0
 Identities = 451/545 (82%), Positives = 498/545 (91%)

Query: 11  EIRAPRGNKLTAKSWLTEAPLRMLMNNLDPQVAENPKELVVYGGIGRAARNWECYDKIVE 70
           +I +P G++L+ KSWLTEAP+RMLMNNL P VAE P++LVVYGGIGRAAR+W+CYD IV 
Sbjct: 17  QIASPTGSELSCKSWLTEAPMRMLMNNLHPDVAERPEDLVVYGGIGRAARDWQCYDTIVA 76

Query: 71  TLTRLEDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWANWEHFNELDAKGLAMYG 130
           TL RLED++TLL+QSGKPVGVF+TH +APRVL+ANSNLVP WANWEHFNELD KGL MYG
Sbjct: 77  TLKRLEDNQTLLIQSGKPVGVFETHKDAPRVLLANSNLVPAWANWEHFNELDRKGLMMYG 136

Query: 131 QMTAGSWIYIGSQGIVQGTYETFVEAGRQHYGGTVKAKWVLTAGLGGMGGAQPLAATLAG 190
           QMTAGSWIYIGSQGIVQGTYETFVEAGRQHY G +  +W+LTAGLGGMGGAQPLAA+LAG
Sbjct: 137 QMTAGSWIYIGSQGIVQGTYETFVEAGRQHYAGDLTGRWILTAGLGGMGGAQPLAASLAG 196

Query: 191 ACSLNIECQQSRIDFRLETRYVDEQATDLDDALVRIAKYTAEGKAISIALHGNAAEILPE 250
           A SLNIECQQSRIDFRL TRY+DEQA DLDDAL R+ +YTAEGKA+SI L  NAA++LPE
Sbjct: 197 ASSLNIECQQSRIDFRLRTRYLDEQADDLDDALARLERYTAEGKAVSIGLCANAADVLPE 256

Query: 251 LVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWEQYRDRAQTEPAAVVKAAKQSMAVHVQAM 310
           LVKRGVRPDMVTDQTSAHDPL+GYLP+GW+W++Y  R + EP AVVKAAKQSMAVHVQAM
Sbjct: 257 LVKRGVRPDMVTDQTSAHDPLHGYLPSGWSWDEYVARGKREPEAVVKAAKQSMAVHVQAM 316

Query: 311 LDFQKQGVPTFDYGNNIRQMAKEEGVANAFDFPGFVPAYIRPLFCRGVGPFRWAALSGEA 370
           LDFQ+ GVPTFDYGNNIRQMAKEEGVANAFDFPGFVPAYIRPLFC+G+GPFRWAALSG+ 
Sbjct: 317 LDFQQMGVPTFDYGNNIRQMAKEEGVANAFDFPGFVPAYIRPLFCQGIGPFRWAALSGDP 376

Query: 371 EDIYKTDAKVKELIPDDAHLHRWLDMARERISFQGLPARICWVGLGLRAKLGLAFNEMVR 430
           EDIYKTD KVKELIPDD HLHRWLDMARERISFQGLPARICWVGL  RA+LG AFNEMV+
Sbjct: 377 EDIYKTDQKVKELIPDDPHLHRWLDMARERISFQGLPARICWVGLKDRARLGQAFNEMVK 436

Query: 431 SGELSAPVVIGRDHLDSGSVSSPNRETEAMRDGSDAVSDWPLLNALLNTAGGATWVSLHH 490
           +GEL APVVIGRDHLDSGSV+SPNRETEAM DGSDAVSDWPLLNALLNTAGGATWVSLHH
Sbjct: 437 NGELKAPVVIGRDHLDSGSVASPNRETEAMMDGSDAVSDWPLLNALLNTAGGATWVSLHH 496

Query: 491 GGGVGMGFSQHSGMVIVCDGTDEAAERIARVLTNDPGTGVMRHADAGYDIAIDCAKEQGL 550
           GGGVGMGFSQH+G+VIV DGTD+A  R+ RVL NDPGTGVMRHADAGY+IA  CA+E GL
Sbjct: 497 GGGVGMGFSQHAGVVIVADGTDDAHARLGRVLRNDPGTGVMRHADAGYEIAKQCARENGL 556

Query: 551 DLPMI 555
           DLPM+
Sbjct: 557 DLPML 561


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: 1152
Number of extensions: 52
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: 562
Length adjustment: 36
Effective length of query: 521
Effective length of database: 526
Effective search space:   274046
Effective search space used:   274046
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_086509679.1 BZY95_RS09385 (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.9012.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-301  986.9   0.2   1.5e-301  986.7   0.2    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086509679.1  BZY95_RS09385 urocanate hydratas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086509679.1  BZY95_RS09385 urocanate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  986.7   0.2  1.5e-301  1.5e-301       2     545 .]      17     560 ..      16     560 .. 1.00

  Alignments for each domain:
  == domain 1  score: 986.7 bits;  conditional E-value: 1.5e-301
                                 TIGR01228   2 eiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrledde 70 
                                               +i +p+G+el++k+w +ea++r+lmnnl p+vae pe+lvvyGG+G+aar+w+++d+iv++lkrled++
  lcl|NCBI__GCF_002151265.1:WP_086509679.1  17 QIASPTGSELSCKSWLTEAPMRMLMNNLHPDVAERPEDLVVYGGIGRAARDWQCYDTIVATLKRLEDNQ 85 
                                               6889***************************************************************** PP

                                 TIGR01228  71 tllvqsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqG 139
                                               tll+qsGkpvgvf+th++aprvl+ansnlvp wa+we+f+el++kGl+myGqmtaGswiyiG+qGi+qG
  lcl|NCBI__GCF_002151265.1:WP_086509679.1  86 TLLIQSGKPVGVFETHKDAPRVLLANSNLVPAWANWEHFNELDRKGLMMYGQMTAGSWIYIGSQGIVQG 154
                                               ********************************************************************* PP

                                 TIGR01228 140 tyetlaelarkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektd 208
                                               tyet++e++r+h++g+l g+++ltaGlGgmGGaqpla+ l++a+s+++e++++rid+rl+t+ylde++d
  lcl|NCBI__GCF_002151265.1:WP_086509679.1 155 TYETFVEAGRQHYAGDLTGRWILTAGLGGMGGAQPLAASLAGASSLNIECQQSRIDFRLRTRYLDEQAD 223
                                               ********************************************************************* PP

                                 TIGR01228 209 dldealaraeeakaeGkalsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadk 277
                                               dld+alar e+++aeGka+sigl  naa+vl+el++rgv+pd+vtdqtsahd+l Gy+p+g++++++  
  lcl|NCBI__GCF_002151265.1:WP_086509679.1 224 DLDDALARLERYTAEGKAVSIGLCANAADVLPELVKRGVRPDMVTDQTSAHDPLHGYLPSGWSWDEYVA 292
                                               ********************************************************************* PP

                                 TIGR01228 278 lrdeepeeyvkaakaslakhvrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfc 346
                                               + + epe++vkaak+s+a+hv+a+l++q+ G+ tfdyGnnirq+akeeGv++afdfpGfvpayir+lfc
  lcl|NCBI__GCF_002151265.1:WP_086509679.1 293 RGKREPEAVVKAAKQSMAVHVQAMLDFQQMGVPTFDYGNNIRQMAKEEGVANAFDFPGFVPAYIRPLFC 361
                                               ********************************************************************* PP

                                 TIGR01228 347 eGkGpfrwvalsGdpadiyrtdkavkelfpedeelhrwidlakekvafqGlparicwlgygereklala 415
                                               +G Gpfrw+alsGdp+diy+td++vkel+p+d +lhrw+d+a+e+++fqGlparicw+g+++r++l+ a
  lcl|NCBI__GCF_002151265.1:WP_086509679.1 362 QGIGPFRWAALSGDPEDIYKTDQKVKELIPDDPHLHRWLDMARERISFQGLPARICWVGLKDRARLGQA 430
                                               ********************************************************************* PP

                                 TIGR01228 416 inelvrsGelkapvvigrdhldaGsvaspnreteamkdGsdavadwpllnallntaaGaswvslhhGGG 484
                                               +ne+v++Gelkapvvigrdhld+Gsvaspnreteam dGsdav+dwpllnallnta+Ga+wvslhhGGG
  lcl|NCBI__GCF_002151265.1:WP_086509679.1 431 FNEMVKNGELKAPVVIGRDHLDSGSVASPNRETEAMMDGSDAVSDWPLLNALLNTAGGATWVSLHHGGG 499
                                               ********************************************************************* PP

                                 TIGR01228 485 vglGfslhaglvivadGtdeaaerlkrvltadpGlGvirhadaGyesaldvakeqgldlpm 545
                                               vg+Gfs+hag+vivadGtd+a+ rl rvl +dpG+Gv+rhadaGye a ++a+e+gldlpm
  lcl|NCBI__GCF_002151265.1:WP_086509679.1 500 VGMGFSQHAGVVIVADGTDDAHARLGRVLRNDPGTGVMRHADAGYEIAKQCARENGLDLPM 560
                                               ************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (562 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: 00:00:00.02
# Mc/sec: 10.33
//
[ok]

This GapMind analysis is from Sep 24 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