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_RS14645 RR42_RS14645 urocanate hydratase

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



>FitnessBrowser__Cup4G11:RR42_RS14645
          Length = 561

 Score = 1055 bits (2729), Expect = 0.0
 Identities = 507/554 (91%), Positives = 530/554 (95%)

Query: 9   EKYRDVEIRAPRGNTLTAKSWLTEAPLRMLMNNLDPEVAENPKELVVYGGIGRAARNWEC 68
           +++RDVEIRAPRGN L AKSW TEAPLRMLMNNLDPEVAENPKELVVYGGIGRAARNW C
Sbjct: 5   DRFRDVEIRAPRGNQLNAKSWQTEAPLRMLMNNLDPEVAENPKELVVYGGIGRAARNWAC 64

Query: 69  YDKIVESLTNLNDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWASWEHFNELDAK 128
           YDKIVE+L  LNDDETLLVQSGKPVGVFKTH NAPRVLIANSNLVPHWA+WEHFNELDAK
Sbjct: 65  YDKIVETLKTLNDDETLLVQSGKPVGVFKTHGNAPRVLIANSNLVPHWATWEHFNELDAK 124

Query: 129 GLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYDSNLKGRWVLTAGLGGMGGAQPL 188
           GLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHY+ NLKGRWVLTAGLGGMGGAQPL
Sbjct: 125 GLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYNGNLKGRWVLTAGLGGMGGAQPL 184

Query: 189 AATLAGACSLNIECQQVSIDFRLKTRYVDEQATDLDDALARIEKYTAEGKAISIALCGNA 248
           AATLAGACSLNIECQQ SIDFRL+TRYVDEQATDLDDALARI +YTAEG+A+SIALC NA
Sbjct: 185 AATLAGACSLNIECQQASIDFRLRTRYVDEQATDLDDALARIARYTAEGRAVSIALCANA 244

Query: 249 AEILPEMVRRGVRPDMVTDQTSAHDPLNGYLPAGWTWDEYRARAKTEPAAVVKAAKQSMA 308
           AE+LPE+VRRGVRPDMVTDQTSAHDPLNGYLP GWTW +YR RA+TEPA VVKAAKQSMA
Sbjct: 245 AEVLPELVRRGVRPDMVTDQTSAHDPLNGYLPVGWTWGQYRDRAQTEPARVVKAAKQSMA 304

Query: 309 IHVKAMLAFQKMGVPTFDYGNNIRQMAQEEGVENAFDFPGFVPAYIRPLFCRGIGPFRWA 368
           +HV+AML FQK+GVPTFDYGNNIRQMA+EEGV NAFDFPGFVPAYIRPLFCRG+GPFRWA
Sbjct: 305 LHVQAMLDFQKLGVPTFDYGNNIRQMAKEEGVANAFDFPGFVPAYIRPLFCRGVGPFRWA 364

Query: 369 ALSGDPQDIYKTDAKVKELIPDDAHLHNWLDMARERISFQGLPARICWVGLGQRAKLGLA 428
           ALSGDPQDIYKTDAKVKELIPDDAHLH WLDMARERISFQGLPARICWVGLG RAKLGLA
Sbjct: 365 ALSGDPQDIYKTDAKVKELIPDDAHLHRWLDMARERISFQGLPARICWVGLGLRAKLGLA 424

Query: 429 FNEMVRSGELSAPIVIGRDHLDSGSVASPNRETESMQDGSDAVSDWPLLNALLNTASGAT 488
           FNEMVRSGELSAP+VIGRDHLDSGSVASPNRETESMQDGSDAVSDWPLLNALLNTASGAT
Sbjct: 425 FNEMVRSGELSAPVVIGRDHLDSGSVASPNRETESMQDGSDAVSDWPLLNALLNTASGAT 484

Query: 489 WVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLHNDPGTGVMRHADAGYQIAIDC 548
           WVSLHHGGGVGMGFSQHSG+VIVCDGTDEAA RIARVLHNDP TGVMRHADAGY IAIDC
Sbjct: 485 WVSLHHGGGVGMGFSQHSGVVIVCDGTDEAAARIARVLHNDPATGVMRHADAGYDIAIDC 544

Query: 549 AKEQGLNLPMITGK 562
           A+EQGLNLPM+  K
Sbjct: 545 AREQGLNLPMLNSK 558


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: 1220
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: 561
Length adjustment: 36
Effective length of query: 526
Effective length of database: 525
Effective search space:   276150
Effective search space used:   276150
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 RR42_RS14645 RR42_RS14645 (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.32100.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
          0 1015.7   0.4          0 1015.5   0.4    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS14645  RR42_RS14645 urocanate hydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS14645  RR42_RS14645 urocanate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1015.5   0.4         0         0       2     545 .]      11     554 ..      10     554 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1015.5 bits;  conditional E-value: 0
                                 TIGR01228   2 eiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrledde 70 
                                               eiraprG++l+ak+w++ea+lr+lmnnldpevae+p+elvvyGG+G+aarnw ++dkive+lk+l+dde
  lcl|FitnessBrowser__Cup4G11:RR42_RS14645  11 EIRAPRGNQLNAKSWQTEAPLRMLMNNLDPEVAENPKELVVYGGIGRAARNWACYDKIVETLKTLNDDE 79 
                                               79******************************************************************* PP

                                 TIGR01228  71 tllvqsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqG 139
                                               tllvqsGkpvgvfkth +aprvliansnlvp+wa+we+f+el+akGl+myGqmtaGswiyiG+qGi+qG
  lcl|FitnessBrowser__Cup4G11:RR42_RS14645  80 TLLVQSGKPVGVFKTHGNAPRVLIANSNLVPHWATWEHFNELDAKGLAMYGQMTAGSWIYIGSQGIVQG 148
                                               ********************************************************************* PP

                                 TIGR01228 140 tyetlaelarkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektd 208
                                               tyet++e++r+h+ g+lkg++vltaGlGgmGGaqpla+tl++a+s+++e++++ id+rl+t+y+de+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS14645 149 TYETFVEAGRQHYNGNLKGRWVLTAGLGGMGGAQPLAATLAGACSLNIECQQASIDFRLRTRYVDEQAT 217
                                               ********************************************************************* PP

                                 TIGR01228 209 dldealaraeeakaeGkalsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadk 277
                                               dld+alar+++++aeG+a+si+l  naaevl+el++rgv+pd+vtdqtsahd+l+Gy+p g+t+ ++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS14645 218 DLDDALARIARYTAEGRAVSIALCANAAEVLPELVRRGVRPDMVTDQTSAHDPLNGYLPVGWTWGQYRD 286
                                               ********************************************************************* PP

                                 TIGR01228 278 lrdeepeeyvkaakaslakhvrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfc 346
                                               ++++ep+ +vkaak+s+a hv+a+l++qk G+ tfdyGnnirq+akeeGv++afdfpGfvpayir+lfc
  lcl|FitnessBrowser__Cup4G11:RR42_RS14645 287 RAQTEPARVVKAAKQSMALHVQAMLDFQKLGVPTFDYGNNIRQMAKEEGVANAFDFPGFVPAYIRPLFC 355
                                               ********************************************************************* PP

                                 TIGR01228 347 eGkGpfrwvalsGdpadiyrtdkavkelfpedeelhrwidlakekvafqGlparicwlgygereklala 415
                                               +G Gpfrw+alsGdp+diy+td++vkel+p+d++lhrw+d+a+e+++fqGlparicw+g+g r+kl+la
  lcl|FitnessBrowser__Cup4G11:RR42_RS14645 356 RGVGPFRWAALSGDPQDIYKTDAKVKELIPDDAHLHRWLDMARERISFQGLPARICWVGLGLRAKLGLA 424
                                               ********************************************************************* PP

                                 TIGR01228 416 inelvrsGelkapvvigrdhldaGsvaspnreteamkdGsdavadwpllnallntaaGaswvslhhGGG 484
                                               +ne+vrsGel+apvvigrdhld+Gsvaspnrete+m+dGsdav+dwpllnallnta+Ga+wvslhhGGG
  lcl|FitnessBrowser__Cup4G11:RR42_RS14645 425 FNEMVRSGELSAPVVIGRDHLDSGSVASPNRETESMQDGSDAVSDWPLLNALLNTASGATWVSLHHGGG 493
                                               ********************************************************************* PP

                                 TIGR01228 485 vglGfslhaglvivadGtdeaaerlkrvltadpGlGvirhadaGyesaldvakeqgldlpm 545
                                               vg+Gfs+h+g+viv+dGtdeaa r++rvl +dp +Gv+rhadaGy+ a+d+a+eqgl+lpm
  lcl|FitnessBrowser__Cup4G11:RR42_RS14645 494 VGMGFSQHSGVVIVCDGTDEAAARIARVLHNDPATGVMRHADAGYDIAIDCAREQGLNLPM 554
                                               ************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (561 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: 8.79
//
[ok]

This GapMind analysis is from Sep 17 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