Alignments for a candidate for hutU in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Cupriavidus basilensis 4G11

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate RR42_RS16915 RR42_RS16915 urocanate hydratase

Query= reanno::Smeli:SM_b21163
         (557 letters)



>FitnessBrowser__Cup4G11:RR42_RS16915
          Length = 560

 Score =  891 bits (2303), Expect = 0.0
 Identities = 425/548 (77%), Positives = 476/548 (86%), Gaps = 4/548 (0%)

Query: 9   REVRSPRGTEISAKSWLTEAPLRMLMNNLDPDVAENPHELVVYGGIGRAARTWADFDRIV 68
           RE+R+PRGTE+  K+WL EA  RML NNLDPDVAE P +LVVYGGIG+AAR W  FD I+
Sbjct: 5   REIRAPRGTELHCKNWLIEAAYRMLQNNLDPDVAERPQDLVVYGGIGKAARNWECFDAIL 64

Query: 69  ASLKDLNEDETLLVQSGKPVGVFRTHKDAPRVLIANSNLVPHWATWDHFNELDKKGLAMY 128
            SL++L E+E+LLVQSGKPVGVFRTH DAPRVLIANSNLVPHWATWD FNELD+ GL MY
Sbjct: 65  DSLRNLGEEESLLVQSGKPVGVFRTHADAPRVLIANSNLVPHWATWDKFNELDRAGLMMY 124

Query: 129 GQMTAGSWIYIGTQGIVQGTYETFVEAGRQHYGGSLKGKWILTGGLGGMGGAQPLAAVMA 188
           GQMTAGSWIYIGTQGIVQGT+ETFVEAGRQHY   L GKWILT GLGGMGGAQ LA V+A
Sbjct: 125 GQMTAGSWIYIGTQGIVQGTFETFVEAGRQHYNNDLTGKWILTAGLGGMGGAQTLAGVLA 184

Query: 189 GACCLAVECNPDSIDFRLRTRYLDEKAETLEEAMEMIERWTKAGEPKSVGLLGNAAEILP 248
           GAC LA+EC    IDFRLRTRY+D+KA +++EA+ MIE  T+  +  SVGLLGNAAEI+P
Sbjct: 185 GACVLAIECQESRIDFRLRTRYVDKKATSIDEALAMIEEATRNKQAISVGLLGNAAEIMP 244

Query: 249 EMVRR----GIRPDMVTDQTSAHDPINGYLPKGWTMAEWKAKRESDPKAVEKAARASMRD 304
           E+V+R    G+RPD+VTDQTSAHD +NGYLP GWT+ +W+A R +DPK+VE AA+ S+  
Sbjct: 245 ELVKRAQAGGMRPDIVTDQTSAHDLVNGYLPAGWTVGQWEAARTADPKSVEAAAKTSIVK 304

Query: 305 HVEAMLAFWDSGVPTLDYGNNIRQVAKDEGLERAFDFPGFVPAYIRPLFCRGIGPFRWAA 364
           HV+AMLAF   GVPTLDYGNNIRQVA DEG+  AFDFPGFVPAYIRPLFCRG GPFRW A
Sbjct: 305 HVQAMLAFQQMGVPTLDYGNNIRQVAFDEGVANAFDFPGFVPAYIRPLFCRGKGPFRWVA 364

Query: 365 LSGDPEDIYRTDRKVKELLPDNKHLHNWLDMARERIAFQGLPARICWVGLGDRHRLGLAF 424
           LSGDPEDIY+TD K+KEL P++ HLH WLDMAR+RIAFQGLPARICWVGL +RHR GLAF
Sbjct: 365 LSGDPEDIYKTDAKMKELFPEDAHLHRWLDMARDRIAFQGLPARICWVGLDERHRAGLAF 424

Query: 425 NEMVRSGELKAPIVIGRDHLDSGSVASPNRETEAMKDGSDAVSDWPLLNALLNTASGATW 484
           NEMV++GELKAPIVIGRDHLD GSVASPNRETEAM+DGSDAVSDWPLLNALLNTA GATW
Sbjct: 425 NEMVKNGELKAPIVIGRDHLDCGSVASPNRETEAMRDGSDAVSDWPLLNALLNTAGGATW 484

Query: 485 VSLHHGGGVGMGFSQHSGMVICCDGTDDAARRIERVLWNDPATGVMRHADAGYDIAVDCA 544
           VSLHHGGGVGMGFSQHSG+VI CDGTD AA+RIERVLWNDPATGVMRHADAGY+ A+DCA
Sbjct: 485 VSLHHGGGVGMGFSQHSGVVIVCDGTDAAAKRIERVLWNDPATGVMRHADAGYESAIDCA 544

Query: 545 REKGLRLP 552
            EKGL LP
Sbjct: 545 HEKGLNLP 552


Lambda     K      H
   0.319    0.137    0.431 

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: 1133
Number of extensions: 41
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: 557
Length of database: 560
Length adjustment: 36
Effective length of query: 521
Effective length of database: 524
Effective search space:   273004
Effective search space used:   273004
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate RR42_RS16915 RR42_RS16915 (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.6734.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-296  970.4   0.9   1.5e-296  970.2   0.9    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS16915  RR42_RS16915 urocanate hydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS16915  RR42_RS16915 urocanate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  970.2   0.9  1.5e-296  1.5e-296       1     545 []       5     553 ..       5     553 .. 0.99

  Alignments for each domain:
  == domain 1  score: 970.2 bits;  conditional E-value: 1.5e-296
                                 TIGR01228   1 keiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrledd 69 
                                               +eiraprG+el++k w  eaa r+l+nnldp+vae p++lvvyGG+Gkaarnwe+fd+i+++l++l ++
  lcl|FitnessBrowser__Cup4G11:RR42_RS16915   5 REIRAPRGTELHCKNWLIEAAYRMLQNNLDPDVAERPQDLVVYGGIGKAARNWECFDAILDSLRNLGEE 73 
                                               68******************************************************************* PP

                                 TIGR01228  70 etllvqsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilq 138
                                               e+llvqsGkpvgvf+th +aprvliansnlvp+wa+w+kf+el+++Gl+myGqmtaGswiyiGtqGi+q
  lcl|FitnessBrowser__Cup4G11:RR42_RS16915  74 ESLLVQSGKPVGVFRTHADAPRVLIANSNLVPHWATWDKFNELDRAGLMMYGQMTAGSWIYIGTQGIVQ 142
                                               ********************************************************************* PP

                                 TIGR01228 139 GtyetlaelarkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldekt 207
                                               Gt+et++e++r+h+ ++l gk++ltaGlGgmGGaq la  l++a+++a+e++e+rid+rl+t+y+d+k+
  lcl|FitnessBrowser__Cup4G11:RR42_RS16915 143 GTFETFVEAGRQHYNNDLTGKWILTAGLGGMGGAQTLAGVLAGACVLAIECQESRIDFRLRTRYVDKKA 211
                                               ********************************************************************* PP

                                 TIGR01228 208 ddldealaraeeakaeGkalsigllGnaaevleeller....gvvpdvvtdqtsahdellGyipegytv 272
                                               +++deala++eea+ + +a+s+gllGnaae+++el++r    g++pd+vtdqtsahd ++Gy+p+g+tv
  lcl|FitnessBrowser__Cup4G11:RR42_RS16915 212 TSIDEALAMIEEATRNKQAISVGLLGNAAEIMPELVKRaqagGMRPDIVTDQTSAHDLVNGYLPAGWTV 280
                                               *************************************96555699************************ PP

                                 TIGR01228 273 edadklrdeepeeyvkaakaslakhvrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayi 341
                                                + +  r  +p+ +  aak s++khv+a+la+q+ G+ t+dyGnnirqva++eGv++afdfpGfvpayi
  lcl|FitnessBrowser__Cup4G11:RR42_RS16915 281 GQWEAARTADPKSVEAAAKTSIVKHVQAMLAFQQMGVPTLDYGNNIRQVAFDEGVANAFDFPGFVPAYI 349
                                               ********************************************************************* PP

                                 TIGR01228 342 rdlfceGkGpfrwvalsGdpadiyrtdkavkelfpedeelhrwidlakekvafqGlparicwlgygere 410
                                               r+lfc+GkGpfrwvalsGdp+diy+td+++kelfped++lhrw+d+a++++afqGlparicw+g+ er+
  lcl|FitnessBrowser__Cup4G11:RR42_RS16915 350 RPLFCRGKGPFRWVALSGDPEDIYKTDAKMKELFPEDAHLHRWLDMARDRIAFQGLPARICWVGLDERH 418
                                               ********************************************************************* PP

                                 TIGR01228 411 klalainelvrsGelkapvvigrdhldaGsvaspnreteamkdGsdavadwpllnallntaaGaswvsl 479
                                               +++la+ne+v++Gelkap+vigrdhld+Gsvaspnreteam+dGsdav+dwpllnallnta+Ga+wvsl
  lcl|FitnessBrowser__Cup4G11:RR42_RS16915 419 RAGLAFNEMVKNGELKAPIVIGRDHLDCGSVASPNRETEAMRDGSDAVSDWPLLNALLNTAGGATWVSL 487
                                               ********************************************************************* PP

                                 TIGR01228 480 hhGGGvglGfslhaglvivadGtdeaaerlkrvltadpGlGvirhadaGyesaldvakeqgldlpm 545
                                               hhGGGvg+Gfs+h+g+viv+dGtd+aa+r++rvl +dp +Gv+rhadaGyesa+d+a+e+gl+lpm
  lcl|FitnessBrowser__Cup4G11:RR42_RS16915 488 HHGGGVGMGFSQHSGVVIVCDGTDAAAKRIERVLWNDPATGVMRHADAGYESAIDCAHEKGLNLPM 553
                                               *****************************************************************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: 7.77
//
[ok]

This GapMind analysis is from Sep 17 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