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.12212.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.77
//
[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:

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:

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:

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:

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