Alignments for a candidate for hutU in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Stenotrophomonas chelatiphaga DSM 21508

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate WP_057506764.1 ABB28_RS00610 urocanate hydratase

Query= reanno::Korea:Ga0059261_3961
         (556 letters)



>NCBI__GCF_001431535.1:WP_057506764.1
          Length = 555

 Score =  910 bits (2352), Expect = 0.0
 Identities = 443/552 (80%), Positives = 485/552 (87%), Gaps = 3/552 (0%)

Query: 8   RTDNSRHIKAPTGTELSAKSWLTEAPLRMLMNNLDADVAEAPESLVVYGGIGRAARDWQS 67
           R D SR I APTGT L+AKSWLTEAPLRMLMNNL  DVAE P+ LVVYGGIGRAARDW+S
Sbjct: 3   RNDPSRTIIAPTGTTLTAKSWLTEAPLRMLMNNLHPDVAERPQELVVYGGIGRAARDWES 62

Query: 68  YDRIVDALRALDADQTLLVQSGKPVGVFRTHADAPRVLIANSNLVPHWATWEHFNELDRK 127
           +D IVDAL  L+ DQTLLVQSGKPVGVFRTHADAPRVLIANSNLVP WA W+HFNELD+K
Sbjct: 63  FDGIVDALTRLEDDQTLLVQSGKPVGVFRTHADAPRVLIANSNLVPRWANWDHFNELDKK 122

Query: 128 GLAMYGQMTAGSWIYIGTQGIVQGTYETFVEAGRQHYGGDLSGKWVLTAGLGGMGGAQPL 187
           GLAMYGQMTAGSWIYIG QGIVQGT+ETFVE GRQHY G L+GKW+ T GLGGMGGAQPL
Sbjct: 123 GLAMYGQMTAGSWIYIGAQGIVQGTFETFVEMGRQHYDGSLAGKWLFTGGLGGMGGAQPL 182

Query: 188 AATMAGASCLAVECQPSRIEMRLKTRYLDRAANSIDEALEIIR---TSDKPVSVGLLGNA 244
           AA MAGASCLAVEC+ S IEMRL+T YLD   + +DEAL +I    T+ KP+SVGLLGN 
Sbjct: 183 AAVMAGASCLAVECRRSSIEMRLRTGYLDTWTDDLDEALRLIEESCTAKKPLSVGLLGNV 242

Query: 245 AEVLPELVRRGIRPDIVTDQTSAHDPVNGYLPAGWTLDEWFTKRETAPHEVEKAARASMA 304
           A+VL EL+ RGI+PD++TDQTSAHDPVNGYLP GWT++EW  KR +AP  VEKAAR SMA
Sbjct: 243 ADVLDELLVRGIKPDLLTDQTSAHDPVNGYLPQGWTVEEWDDKRVSAPKVVEKAARESMA 302

Query: 305 THVRAMLDFHEMGIPTLDYGNNIRQVAKDEGVENAFAFPGFVPAYIRPLFCRGIGPFRWA 364
            H+RAML FH +G+PT+DYGNN+RQ+A +EGVE+AF FPGFVPAYIRPLFCRGIGPFRWA
Sbjct: 303 NHIRAMLAFHALGVPTVDYGNNLRQMALEEGVEDAFDFPGFVPAYIRPLFCRGIGPFRWA 362

Query: 365 ALSGNPEDIWKTDRKVKELLPGNHHLHNWLDMAKERIAFQGLPARICWVGLGDRHRLALA 424
           ALSG+PEDI KTD KVKEL+P N HLH WLDMA E+I FQGLPARICWVGLGDR RL LA
Sbjct: 363 ALSGDPEDIAKTDAKVKELIPDNPHLHRWLDMAAEKIKFQGLPARICWVGLGDRDRLGLA 422

Query: 425 FNEMVASGELEAPIVIGRDHLDSGSVASPNRETEAMMDGSDAVSDWPLLNALLNTASGAT 484
           FNEMVASGEL+AP+VIGRDHLDSGSVASPNRETEAM DGSDAVSDWPLLNALLNTASGAT
Sbjct: 423 FNEMVASGELKAPVVIGRDHLDSGSVASPNRETEAMADGSDAVSDWPLLNALLNTASGAT 482

Query: 485 WVSLHHGGGVGMGYSQHSGMVIVADGTPEAAKRLERVLWNDPATGVMRHADAGYEIAKNC 544
           WVSLHHGGGVGMG+SQH+GMVIV DGT  AAKR+ RVLWNDPATGVMRHADAGYEIA +C
Sbjct: 483 WVSLHHGGGVGMGFSQHAGMVIVCDGTEAAAKRIARVLWNDPATGVMRHADAGYEIAIDC 542

Query: 545 ATEMGLDLPGIL 556
           A E GLDLPGIL
Sbjct: 543 AKEKGLDLPGIL 554


Lambda     K      H
   0.318    0.134    0.416 

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: 1208
Number of extensions: 45
Number of successful extensions: 2
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: 556
Length of database: 555
Length adjustment: 36
Effective length of query: 520
Effective length of database: 519
Effective search space:   269880
Effective search space used:   269880
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_057506764.1 ABB28_RS00610 (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.7245.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.1e-291  952.3   0.1   4.7e-291  952.1   0.1    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057506764.1  ABB28_RS00610 urocanate hydratas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057506764.1  ABB28_RS00610 urocanate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  952.1   0.1  4.7e-291  4.7e-291       2     544 ..       9     551 ..       8     552 .. 1.00

  Alignments for each domain:
  == domain 1  score: 952.1 bits;  conditional E-value: 4.7e-291
                                 TIGR01228   2 eiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrledde 70 
                                               +i ap+G++l+ak+w +ea+lr+lmnnl p+vae p+elvvyGG+G+aar+we+fd iv+ l+rledd+
  lcl|NCBI__GCF_001431535.1:WP_057506764.1   9 TIIAPTGTTLTAKSWLTEAPLRMLMNNLHPDVAERPQELVVYGGIGRAARDWESFDGIVDALTRLEDDQ 77 
                                               788****************************************************************** PP

                                 TIGR01228  71 tllvqsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqG 139
                                               tllvqsGkpvgvf+th +aprvliansnlvp+wa+w++f+el++kGl+myGqmtaGswiyiG+qGi+qG
  lcl|NCBI__GCF_001431535.1:WP_057506764.1  78 TLLVQSGKPVGVFRTHADAPRVLIANSNLVPRWANWDHFNELDKKGLAMYGQMTAGSWIYIGAQGIVQG 146
                                               ********************************************************************* PP

                                 TIGR01228 140 tyetlaelarkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektd 208
                                               t+et++e++r+h+ gsl gk+  t GlGgmGGaqpla+ +++a+++ave+ ++ i+ rl+t yld++td
  lcl|NCBI__GCF_001431535.1:WP_057506764.1 147 TFETFVEMGRQHYDGSLAGKWLFTGGLGGMGGAQPLAAVMAGASCLAVECRRSSIEMRLRTGYLDTWTD 215
                                               ********************************************************************* PP

                                 TIGR01228 209 dldealaraeeakaeGkalsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadk 277
                                               dldeal+ +ee+ ++ k+ls+gllGn a+vl+ell rg++pd++tdqtsahd+++Gy+p+g+tve+ d+
  lcl|NCBI__GCF_001431535.1:WP_057506764.1 216 DLDEALRLIEESCTAKKPLSVGLLGNVADVLDELLVRGIKPDLLTDQTSAHDPVNGYLPQGWTVEEWDD 284
                                               ********************************************************************* PP

                                 TIGR01228 278 lrdeepeeyvkaakaslakhvrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfc 346
                                                r   p+ + kaa++s+a+h+ra+la+   G+ t dyGnn+rq+a eeGvedafdfpGfvpayir+lfc
  lcl|NCBI__GCF_001431535.1:WP_057506764.1 285 KRVSAPKVVEKAARESMANHIRAMLAFHALGVPTVDYGNNLRQMALEEGVEDAFDFPGFVPAYIRPLFC 353
                                               ********************************************************************* PP

                                 TIGR01228 347 eGkGpfrwvalsGdpadiyrtdkavkelfpedeelhrwidlakekvafqGlparicwlgygereklala 415
                                               +G Gpfrw+alsGdp+di +td++vkel+p++ +lhrw+d+a+ek++fqGlparicw+g+g+r++l+la
  lcl|NCBI__GCF_001431535.1:WP_057506764.1 354 RGIGPFRWAALSGDPEDIAKTDAKVKELIPDNPHLHRWLDMAAEKIKFQGLPARICWVGLGDRDRLGLA 422
                                               ********************************************************************* PP

                                 TIGR01228 416 inelvrsGelkapvvigrdhldaGsvaspnreteamkdGsdavadwpllnallntaaGaswvslhhGGG 484
                                               +ne+v sGelkapvvigrdhld+Gsvaspnreteam dGsdav+dwpllnallnta+Ga+wvslhhGGG
  lcl|NCBI__GCF_001431535.1:WP_057506764.1 423 FNEMVASGELKAPVVIGRDHLDSGSVASPNRETEAMADGSDAVSDWPLLNALLNTASGATWVSLHHGGG 491
                                               ********************************************************************* PP

                                 TIGR01228 485 vglGfslhaglvivadGtdeaaerlkrvltadpGlGvirhadaGyesaldvakeqgldlp 544
                                               vg+Gfs+hag+viv+dGt++aa+r++rvl +dp +Gv+rhadaGye a+d+ake+gldlp
  lcl|NCBI__GCF_001431535.1:WP_057506764.1 492 VGMGFSQHAGMVIVCDGTEAAAKRIARVLWNDPATGVMRHADAGYEIAIDCAKEKGLDLP 551
                                               **********************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (555 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 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 8.94
//
[ok]

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

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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 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