Alignments for a candidate for hutU in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Dyella japonica UNC79MFTsu3.2

Align Urocanate hydratase; Urocanase; Imidazolonepropionate hydrolase; EC 4.2.1.49 (characterized)
to candidate N515DRAFT_0165 N515DRAFT_0165 urocanate hydratase

Query= SwissProt::P25080
         (557 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0165
          Length = 556

 Score =  952 bits (2461), Expect = 0.0
 Identities = 452/543 (83%), Positives = 497/543 (91%)

Query: 12  IRAPRGNKLTAKSWLTEAPLRMLMNNLDPQVAENPKELVVYGGIGRAARNWECYDKIVET 71
           IRAPRG +L+ KSWLTEAP RML NNLDP+VAENP ELVVYGGIGRAARNWEC+D I+  
Sbjct: 13  IRAPRGGELSCKSWLTEAPFRMLQNNLDPEVAENPAELVVYGGIGRAARNWECFDAILRA 72

Query: 72  LTRLEDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWANWEHFNELDAKGLAMYGQ 131
           L  L DDETLL+QSGKPVGVF TH++APRVL+ANSNLVP WANWEHFNELD KGL MYGQ
Sbjct: 73  LRELNDDETLLIQSGKPVGVFPTHADAPRVLLANSNLVPAWANWEHFNELDKKGLMMYGQ 132

Query: 132 MTAGSWIYIGSQGIVQGTYETFVEAGRQHYGGTVKAKWVLTAGLGGMGGAQPLAATLAGA 191
           MTAGSWIYIGSQGIVQGTYETFVE GRQHY G++K KW+LTAGLGGMGGAQPLAA+LAGA
Sbjct: 133 MTAGSWIYIGSQGIVQGTYETFVEMGRQHYAGSLKGKWILTAGLGGMGGAQPLAASLAGA 192

Query: 192 CSLNIECQQSRIDFRLETRYVDEQATDLDDALVRIAKYTAEGKAISIALHGNAAEILPEL 251
           CSLNIECQQSRIDFRL+TRYVDEQATDLDDAL RIA+YTA G+A SIAL GNAA++LPEL
Sbjct: 193 CSLNIECQQSRIDFRLKTRYVDEQATDLDDALARIARYTAAGEAKSIALLGNAADVLPEL 252

Query: 252 VKRGVRPDMVTDQTSAHDPLNGYLPAGWTWEQYRDRAQTEPAAVVKAAKQSMAVHVQAML 311
           V+RGV+PD VTDQTSAHDP+NGYLP GW+ E++ +R +++PA   KAAKQSM  HV+AML
Sbjct: 253 VRRGVKPDAVTDQTSAHDPVNGYLPGGWSVEEWFERRKSDPAGTAKAAKQSMRTHVEAML 312

Query: 312 DFQKQGVPTFDYGNNIRQMAKEEGVANAFDFPGFVPAYIRPLFCRGVGPFRWAALSGEAE 371
            FQ+QG+PTFDYGNNIRQMAK+EG A+AF+FPGFVPAY+RPLFCRGVGPFRW ALSG+ E
Sbjct: 313 AFQRQGIPTFDYGNNIRQMAKDEGCADAFEFPGFVPAYVRPLFCRGVGPFRWVALSGDPE 372

Query: 372 DIYKTDAKVKELIPDDAHLHRWLDMARERISFQGLPARICWVGLGLRAKLGLAFNEMVRS 431
           DIYKTDAKVKELIPDD HLHRWLDMARERISFQGLPARICWVGLGLR KLGLAFNEMVR 
Sbjct: 373 DIYKTDAKVKELIPDDPHLHRWLDMARERISFQGLPARICWVGLGLRHKLGLAFNEMVRK 432

Query: 432 GELSAPVVIGRDHLDSGSVSSPNRETEAMRDGSDAVSDWPLLNALLNTAGGATWVSLHHG 491
           GEL APVVIGRDHLDSGSV+SPNRETEAM+DGSDAVSDWPLLNA+LN AGGATWVSLHHG
Sbjct: 433 GELKAPVVIGRDHLDSGSVASPNRETEAMQDGSDAVSDWPLLNAMLNVAGGATWVSLHHG 492

Query: 492 GGVGMGFSQHSGMVIVCDGTDEAAERIARVLTNDPGTGVMRHADAGYDIAIDCAKEQGLD 551
           GGVGMG+SQHSG+VIVCDG++ A +RIARVL NDPGTGVMRHADAGYDIA+ CAKEQGL 
Sbjct: 493 GGVGMGYSQHSGVVIVCDGSEAADQRIARVLWNDPGTGVMRHADAGYDIAVQCAKEQGLK 552

Query: 552 LPM 554
           LPM
Sbjct: 553 LPM 555


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: 1156
Number of extensions: 42
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: 556
Length adjustment: 36
Effective length of query: 521
Effective length of database: 520
Effective search space:   270920
Effective search space used:   270920
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 N515DRAFT_0165 N515DRAFT_0165 (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.22675.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   8.6e-304  994.1   0.0   9.8e-304  993.9   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0165  N515DRAFT_0165 urocanate hydrata


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0165  N515DRAFT_0165 urocanate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  993.9   0.0  9.8e-304  9.8e-304       1     545 []      11     555 ..      11     555 .. 1.00

  Alignments for each domain:
  == domain 1  score: 993.9 bits;  conditional E-value: 9.8e-304
                                    TIGR01228   1 keiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrl 66 
                                                  ++iraprG el++k+w +ea+ r+l+nnldpevae+p+elvvyGG+G+aarnwe+fd+i++ l+ l
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0165  11 RTIRAPRGGELSCKSWLTEAPFRMLQNNLDPEVAENPAELVVYGGIGRAARNWECFDAILRALREL 76 
                                                  689*************************************************************** PP

                                    TIGR01228  67 eddetllvqsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiG 132
                                                  +ddetll+qsGkpvgvf th +aprvl+ansnlvp wa+we+f+el++kGl+myGqmtaGswiyiG
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0165  77 NDDETLLIQSGKPVGVFPTHADAPRVLLANSNLVPAWANWEHFNELDKKGLMMYGQMTAGSWIYIG 142
                                                  ****************************************************************** PP

                                    TIGR01228 133 tqGilqGtyetlaelarkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrl 198
                                                  +qGi+qGtyet++e++r+h++gslkgk++ltaGlGgmGGaqpla+ l++a+s+++e++++rid+rl
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0165 143 SQGIVQGTYETFVEMGRQHYAGSLKGKWILTAGLGGMGGAQPLAASLAGACSLNIECQQSRIDFRL 208
                                                  ****************************************************************** PP

                                    TIGR01228 199 etkyldektddldealaraeeakaeGkalsigllGnaaevleellergvvpdvvtdqtsahdellG 264
                                                  +t+y+de+++dld+alar+++++a+G+a+si+llGnaa+vl+el++rgv+pd vtdqtsahd+++G
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0165 209 KTRYVDEQATDLDDALARIARYTAAGEAKSIALLGNAADVLPELVRRGVKPDAVTDQTSAHDPVNG 274
                                                  ****************************************************************** PP

                                    TIGR01228 265 yipegytvedadklrdeepeeyvkaakaslakhvrallalqkkGavtfdyGnnirqvakeeGveda 330
                                                  y+p g++ve+  ++r+ +p+   kaak+s+ +hv+a+la+q++G  tfdyGnnirq+ak+eG +da
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0165 275 YLPGGWSVEEWFERRKSDPAGTAKAAKQSMRTHVEAMLAFQRQGIPTFDYGNNIRQMAKDEGCADA 340
                                                  ****************************************************************** PP

                                    TIGR01228 331 fdfpGfvpayirdlfceGkGpfrwvalsGdpadiyrtdkavkelfpedeelhrwidlakekvafqG 396
                                                  f+fpGfvpay+r+lfc+G GpfrwvalsGdp+diy+td++vkel+p+d +lhrw+d+a+e+++fqG
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0165 341 FEFPGFVPAYVRPLFCRGVGPFRWVALSGDPEDIYKTDAKVKELIPDDPHLHRWLDMARERISFQG 406
                                                  ****************************************************************** PP

                                    TIGR01228 397 lparicwlgygereklalainelvrsGelkapvvigrdhldaGsvaspnreteamkdGsdavadwp 462
                                                  lparicw+g+g r+kl+la+ne+vr+Gelkapvvigrdhld+Gsvaspnreteam+dGsdav+dwp
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0165 407 LPARICWVGLGLRHKLGLAFNEMVRKGELKAPVVIGRDHLDSGSVASPNRETEAMQDGSDAVSDWP 472
                                                  ****************************************************************** PP

                                    TIGR01228 463 llnallntaaGaswvslhhGGGvglGfslhaglvivadGtdeaaerlkrvltadpGlGvirhadaG 528
                                                  llna+ln+a+Ga+wvslhhGGGvg+G+s+h+g+viv+dG+++a++r++rvl +dpG+Gv+rhadaG
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0165 473 LLNAMLNVAGGATWVSLHHGGGVGMGYSQHSGVVIVCDGSEAADQRIARVLWNDPGTGVMRHADAG 538
                                                  ****************************************************************** PP

                                    TIGR01228 529 yesaldvakeqgldlpm 545
                                                  y+ a+++akeqgl+lpm
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0165 539 YDIAVQCAKEQGLKLPM 555
                                                  ****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (556 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 0.01s 00:00:00.02 Elapsed: 00:00:00.05
# Mc/sec: 5.26
//
[ok]

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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