Alignments for a candidate for hutU in Belnapia rosea CPCC 100156

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Belnapia rosea CPCC 100156

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate WP_090661094.1 BLR02_RS05135 urocanate hydratase

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



>NCBI__GCF_900101615.1:WP_090661094.1
          Length = 558

 Score =  876 bits (2263), Expect = 0.0
 Identities = 429/556 (77%), Positives = 472/556 (84%), Gaps = 4/556 (0%)

Query: 1   MTSAMTNRTDNSRHIKAPTGTELSAKSWLTEAPLRMLMNNLDADVAEAPESLVVYGGIGR 60
           MT     R  N+  I+AP G E +A  W TEAPLRMLMNNLDA+VAE P  LVVYGGIGR
Sbjct: 1   MTDPAAARFRNAPAIRAPRGLERTALHWTTEAPLRMLMNNLDAEVAERPGELVVYGGIGR 60

Query: 61  AARDWQSYDRIVDALRALDADQTLLVQSGKPVGVFRTHADAPRVLIANSNLVPHWATWEH 120
           AARDW SY+RIV+ LR L  DQTLLVQSGKPVGVF THADAPRVLIANSNLVP WATWEH
Sbjct: 61  AARDWASYERIVETLRRLREDQTLLVQSGKPVGVFETHADAPRVLIANSNLVPRWATWEH 120

Query: 121 FNELDRKGLAMYGQMTAGSWIYIGTQGIVQGTYETFVEAGRQHYGGDLSGKWVLTAGLGG 180
           F+ELDR+GL MYGQMTAGSWIYIG+QGIVQGTYETF EAGRQH+GGDL G+W+LT GLGG
Sbjct: 121 FSELDRRGLMMYGQMTAGSWIYIGSQGIVQGTYETFAEAGRQHFGGDLGGRWILTGGLGG 180

Query: 181 MGGAQPLAATMAGASCLAVECQPSRIEMRLKTRYLDRAANSIDEALEIIRTS---DKPVS 237
           MGGAQPLA   AGAS LAVECQPS IE RL+T+YLD  A+ +D AL +IR +    + +S
Sbjct: 181 MGGAQPLAGVFAGASVLAVECQPSSIEKRLETKYLDHRADDLDTALGMIRAACAERRAIS 240

Query: 238 VGLLGNAAEVLPELVRRGIRPDIVTDQTSAHDPVNGYLPAGWTLDEWFTKRETAPHEVEK 297
           VGLLGNAAEV PELVRRG+ PDIVTDQTSAHDP NGYLPAGWTL EW  KRET P  V  
Sbjct: 241 VGLLGNAAEVFPELVRRGVVPDIVTDQTSAHDPANGYLPAGWTLAEWTAKRETDPAAVAA 300

Query: 298 AARASMATHVRAMLDFHEMGIPTLDYGNNIRQVAKDEGVENAFAFPGFVPAYIRPLFCRG 357
           AAR SM  HV+AMLDF  +G   LDYGNNIRQ+AK+EG+ +AF FPGFVPAYIRPLFCRG
Sbjct: 301 AARRSMVAHVQAMLDFQALGAKVLDYGNNIRQMAKEEGLADAFGFPGFVPAYIRPLFCRG 360

Query: 358 IGPFRWAALSGNPEDIWKTDRKVKELLPGNHHLHNWLDMAKERIAFQGLPARICWVGLGD 417
           IGPFRWAALSG+PEDI++TD KV+EL+P + HLH WLDMA+ RI+FQGLPARICWVGLG 
Sbjct: 361 IGPFRWAALSGDPEDIYRTDAKVRELIPEDAHLHRWLDMARARISFQGLPARICWVGLGQ 420

Query: 418 RHRLALAFNEMVASGELEAPIVIGRDHLDSGSVASPNRETEAMMDGSDAVSDWPLLNALL 477
           R RL LAFNEMVA GE+  PIVIGRDHLDSGSVASPNRETEAM DGSDAVSDWPLLNALL
Sbjct: 421 RDRLGLAFNEMVARGEI-GPIVIGRDHLDSGSVASPNRETEAMRDGSDAVSDWPLLNALL 479

Query: 478 NTASGATWVSLHHGGGVGMGYSQHSGMVIVADGTPEAAKRLERVLWNDPATGVMRHADAG 537
           NTASGATWVSLHHGGGVGMG+SQH+GMVIV DGT +AA+RL+RVLWNDPATGVMRHADAG
Sbjct: 480 NTASGATWVSLHHGGGVGMGFSQHAGMVIVCDGTADAARRLKRVLWNDPATGVMRHADAG 539

Query: 538 YEIAKNCATEMGLDLP 553
           Y+IA +CA E GLDLP
Sbjct: 540 YDIAIDCAREHGLDLP 555


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: 1175
Number of extensions: 49
Number of successful extensions: 3
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: 558
Length adjustment: 36
Effective length of query: 520
Effective length of database: 522
Effective search space:   271440
Effective search space used:   271440
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_090661094.1 BLR02_RS05135 (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.747015.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.3e-288  942.7   0.3   3.8e-288  942.5   0.3    1.0  1  NCBI__GCF_900101615.1:WP_090661094.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900101615.1:WP_090661094.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  942.5   0.3  3.8e-288  3.8e-288       2     545 .]      14     556 ..      13     556 .. 1.00

  Alignments for each domain:
  == domain 1  score: 942.5 bits;  conditional E-value: 3.8e-288
                             TIGR01228   2 eiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddetllv 74 
                                           +iraprG e +a  w++ea+lr+lmnnld evae p elvvyGG+G+aar+w ++++ive+l+rl++d+tllv
  NCBI__GCF_900101615.1:WP_090661094.1  14 AIRAPRGLERTALHWTTEAPLRMLMNNLDAEVAERPGELVVYGGIGRAARDWASYERIVETLRRLREDQTLLV 86 
                                           69*********************************************************************** PP

                             TIGR01228  75 qsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGtyetlael 147
                                           qsGkpvgvf+th +aprvliansnlvp+wa+we+f+el+++Gl+myGqmtaGswiyiG+qGi+qGtyet+ae+
  NCBI__GCF_900101615.1:WP_090661094.1  87 QSGKPVGVFETHADAPRVLIANSNLVPRWATWEHFSELDRRGLMMYGQMTAGSWIYIGSQGIVQGTYETFAEA 159
                                           ************************************************************************* PP

                             TIGR01228 148 arkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddldealaraeea 220
                                           +r+hfgg+l g+++lt GlGgmGGaqpla  +++a+++ave++++ i+krletkyld+++ddld al ++ +a
  NCBI__GCF_900101615.1:WP_090661094.1 160 GRQHFGGDLGGRWILTGGLGGMGGAQPLAGVFAGASVLAVECQPSSIEKRLETKYLDHRADDLDTALGMIRAA 232
                                           ************************************************************************* PP

                             TIGR01228 221 kaeGkalsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadklrdeepeeyvkaakas 293
                                            ae +a+s+gllGnaaev++el++rgvvpd+vtdqtsahd+ +Gy+p+g+t+++ +  r+++p+++  aa+ s
  NCBI__GCF_900101615.1:WP_090661094.1 233 CAERRAISVGLLGNAAEVFPELVRRGVVPDIVTDQTSAHDPANGYLPAGWTLAEWTAKRETDPAAVAAAARRS 305
                                           ************************************************************************* PP

                             TIGR01228 294 lakhvrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfceGkGpfrwvalsGdpadiyr 366
                                           +++hv+a+l++q  Ga+++dyGnnirq+akeeG++daf fpGfvpayir+lfc+G Gpfrw+alsGdp+diyr
  NCBI__GCF_900101615.1:WP_090661094.1 306 MVAHVQAMLDFQALGAKVLDYGNNIRQMAKEEGLADAFGFPGFVPAYIRPLFCRGIGPFRWAALSGDPEDIYR 378
                                           ************************************************************************* PP

                             TIGR01228 367 tdkavkelfpedeelhrwidlakekvafqGlparicwlgygereklalainelvrsGelkapvvigrdhldaG 439
                                           td++v el+ped++lhrw+d+a+ +++fqGlparicw+g+g+r++l+la+ne+v  Ge+  p+vigrdhld+G
  NCBI__GCF_900101615.1:WP_090661094.1 379 TDAKVRELIPEDAHLHRWLDMARARISFQGLPARICWVGLGQRDRLGLAFNEMVARGEI-GPIVIGRDHLDSG 450
                                           **********************************************************9.6************ PP

                             TIGR01228 440 svaspnreteamkdGsdavadwpllnallntaaGaswvslhhGGGvglGfslhaglvivadGtdeaaerlkrv 512
                                           svaspnreteam+dGsdav+dwpllnallnta+Ga+wvslhhGGGvg+Gfs+hag+viv+dGt +aa+rlkrv
  NCBI__GCF_900101615.1:WP_090661094.1 451 SVASPNRETEAMRDGSDAVSDWPLLNALLNTASGATWVSLHHGGGVGMGFSQHAGMVIVCDGTADAARRLKRV 523
                                           ************************************************************************* PP

                             TIGR01228 513 ltadpGlGvirhadaGyesaldvakeqgldlpm 545
                                           l +dp +Gv+rhadaGy+ a+d+a+e+gldlpm
  NCBI__GCF_900101615.1:WP_090661094.1 524 LWNDPATGVMRHADAGYDIAIDCAREHGLDLPM 556
                                           ********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (558 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 29.48
//
[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 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