Alignments for a candidate for hutU in Desulfacinum infernum DSM 9756

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Desulfacinum infernum DSM 9756

Align Urocanate hydratase; Urocanase; Imidazolonepropionate hydrolase; EC 4.2.1.49 (characterized)
to candidate WP_073039909.1 BUB04_RS12250 urocanate hydratase

Query= SwissProt::Q5L084
         (551 letters)



>NCBI__GCF_900129305.1:WP_073039909.1
          Length = 570

 Score =  796 bits (2057), Expect = 0.0
 Identities = 372/546 (68%), Positives = 446/546 (81%)

Query: 5   RTVSPPAGTERRAKGWIQEAALRMLNNNLHPDVAERPDELIVYGGIGKAARNWECYEAIV 64
           R V  P GTE   KGW QEAALRML NNL P+  E+PDELIVYGG GKAARNWEC++AIV
Sbjct: 21  RPVKAPRGTELHCKGWHQEAALRMLCNNLDPETGEKPDELIVYGGTGKAARNWECFDAIV 80

Query: 65  DTLLRLENDETLLIQSGKPVAVFRTHPDAPRVLIANSNLVPAWATWDHFHELDKKGLIMY 124
            +LL LENDETLL+QSGKPV + +T+P +PRVLIAN+NLVPAWATWD+FHEL+ KGLIM+
Sbjct: 81  RSLLELENDETLLVQSGKPVGIVKTYPTSPRVLIANANLVPAWATWDYFHELEAKGLIMF 140

Query: 125 GQMTAGSWIYIGSQGIVQGTYETFAEVARQHFGGTLAGTITLTAGLGGMGGAQPLAVTMN 184
           GQMTAGSWIYIG+QGI+QGTYETFA +A +HFGG+LAG IT+T GLGGMGGAQPLAVTMN
Sbjct: 141 GQMTAGSWIYIGTQGILQGTYETFAALAEKHFGGSLAGKITVTGGLGGMGGAQPLAVTMN 200

Query: 185 GGVCLAIEVDPARIQRRIDTNYLDTMTDSLDAALEMAKQAKEEKKALSIGLVGNAAEVLP 244
            GV + +EVD  RIQRR+DT YLD M D L+ A+ MA++A E KK LSIGL+GN AE+LP
Sbjct: 201 EGVAICVEVDRHRIQRRLDTRYLDVMVDDLERAVAMAREAAESKKPLSIGLLGNCAEILP 260

Query: 245 RLVEMGFVPDVLTDQTSAHDPLNGYIPAGLTLDEAAELRARDPKQYIARAKQSIAAHVRA 304
           ++V+M F+PDV+TDQTSAHD LNGY+PAG+  +EA  LR  DPK+YI  + +S+A H RA
Sbjct: 261 KMVDMNFIPDVVTDQTSAHDELNGYVPAGIPYEEALALRKSDPKRYIQMSMESMAVHCRA 320

Query: 305 MLAMQKQGAVTFDYGNNIRQVAKDEGVDDAFSFPGFVPAYIRPLFCEGKGPFRWVALSGD 364
           +L MQ +GAV FDYGNN+R  A  +GV +AF FPGFVPAYIRPLFCEG+GPFRW ALSGD
Sbjct: 321 ILDMQARGAVAFDYGNNLRGQALKQGVQNAFDFPGFVPAYIRPLFCEGEGPFRWAALSGD 380

Query: 365 PEDIYKTDEVILREFSDNERLCHWIRMAQKRIKFQGLPARICWLGYGERAKFGKIINDMV 424
           P+DI  TD  ++  F +  R+  W++MA++R+   GLPARICWLGYGER K GKI ND+V
Sbjct: 381 PQDIIVTDHALMEAFPEKTRMVRWLQMAEERVAHMGLPARICWLGYGERDKAGKIFNDLV 440

Query: 425 AKGELKAPIVIGRDHLDSGSVASPNRETEGMKDGSDAIADWPILNALLNAVGGASWVSVH 484
            KG +KAPIVIGRDHLD GSVASPNRETE MKDGSDA+ADWP+LNA++N   GASWVS H
Sbjct: 441 RKGAVKAPIVIGRDHLDCGSVASPNRETEAMKDGSDAVADWPLLNAMVNTTSGASWVSFH 500

Query: 485 HGGGVGMGYSIHAGMVIVADGTKEAEKRLERVLTTDPGLGVVRHADAGYELAIRTAKEKG 544
           HGGGVG+GY++HAG V VADGT E E R+  VL  DP  GV+RHADAGYE AI+ A+E+G
Sbjct: 501 HGGGVGIGYALHAGQVTVADGTDEGEVRVTTVLRNDPATGVIRHADAGYEKAIQVARERG 560

Query: 545 IDMPML 550
           + +PM+
Sbjct: 561 VKLPMI 566


Lambda     K      H
   0.319    0.136    0.411 

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: 854
Number of extensions: 25
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: 551
Length of database: 570
Length adjustment: 36
Effective length of query: 515
Effective length of database: 534
Effective search space:   275010
Effective search space used:   275010
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 WP_073039909.1 BUB04_RS12250 (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.24955.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-287  939.9   0.2   2.6e-287  939.7   0.2    1.0  1  lcl|NCBI__GCF_900129305.1:WP_073039909.1  BUB04_RS12250 urocanate hydratas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900129305.1:WP_073039909.1  BUB04_RS12250 urocanate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  939.7   0.2  2.6e-287  2.6e-287       3     545 .]      23     565 ..      21     565 .. 1.00

  Alignments for each domain:
  == domain 1  score: 939.7 bits;  conditional E-value: 2.6e-287
                                 TIGR01228   3 iraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddet 71 
                                               ++aprG+el++kgw+qeaalr+l nnldpe  e+p+el+vyGG+Gkaarnwe+fd+iv++l  le+det
  lcl|NCBI__GCF_900129305.1:WP_073039909.1  23 VKAPRGTELHCKGWHQEAALRMLCNNLDPETGEKPDELIVYGGTGKAARNWECFDAIVRSLLELENDET 91 
                                               89******************************************************************* PP

                                 TIGR01228  72 llvqsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGt 140
                                               llvqsGkpvg++kt  ++prvlian+nlvp wa+w+ f+eleakGlim+GqmtaGswiyiGtqGilqGt
  lcl|NCBI__GCF_900129305.1:WP_073039909.1  92 LLVQSGKPVGIVKTYPTSPRVLIANANLVPAWATWDYFHELEAKGLIMFGQMTAGSWIYIGTQGILQGT 160
                                               ********************************************************************* PP

                                 TIGR01228 141 yetlaelarkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektdd 209
                                               yet+a+la khfggsl gk+++t GlGgmGGaqplavt+ne+v+i vevd++ri++rl+t+yld + dd
  lcl|NCBI__GCF_900129305.1:WP_073039909.1 161 YETFAALAEKHFGGSLAGKITVTGGLGGMGGAQPLAVTMNEGVAICVEVDRHRIQRRLDTRYLDVMVDD 229
                                               ********************************************************************* PP

                                 TIGR01228 210 ldealaraeeakaeGkalsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadkl 278
                                               l+ a+a+a ea++  k+lsigllGn ae+l++++++++ pdvvtdqtsahdel+Gy+p+g   e+a  l
  lcl|NCBI__GCF_900129305.1:WP_073039909.1 230 LERAVAMAREAAESKKPLSIGLLGNCAEILPKMVDMNFIPDVVTDQTSAHDELNGYVPAGIPYEEALAL 298
                                               ********************************************************************* PP

                                 TIGR01228 279 rdeepeeyvkaakaslakhvrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfce 347
                                               r+ +p+ y++++++s+a+h ra+l++q +Gav+fdyGnn+r +a ++Gv++afdfpGfvpayir+lfce
  lcl|NCBI__GCF_900129305.1:WP_073039909.1 299 RKSDPKRYIQMSMESMAVHCRAILDMQARGAVAFDYGNNLRGQALKQGVQNAFDFPGFVPAYIRPLFCE 367
                                               ********************************************************************* PP

                                 TIGR01228 348 GkGpfrwvalsGdpadiyrtdkavkelfpedeelhrwidlakekvafqGlparicwlgygereklalai 416
                                               G+Gpfrw+alsGdp+di  td+a++e fpe+ +++rw+++a+e+va  Glparicwlgyger+k+++++
  lcl|NCBI__GCF_900129305.1:WP_073039909.1 368 GEGPFRWAALSGDPQDIIVTDHALMEAFPEKTRMVRWLQMAEERVAHMGLPARICWLGYGERDKAGKIF 436
                                               ********************************************************************* PP

                                 TIGR01228 417 nelvrsGelkapvvigrdhldaGsvaspnreteamkdGsdavadwpllnallntaaGaswvslhhGGGv 485
                                               n+lvr+G +kap+vigrdhld+GsvaspnreteamkdGsdavadwpllna++nt++Gaswvs+hhGGGv
  lcl|NCBI__GCF_900129305.1:WP_073039909.1 437 NDLVRKGAVKAPIVIGRDHLDCGSVASPNRETEAMKDGSDAVADWPLLNAMVNTTSGASWVSFHHGGGV 505
                                               ********************************************************************* PP

                                 TIGR01228 486 glGfslhaglvivadGtdeaaerlkrvltadpGlGvirhadaGyesaldvakeqgldlpm 545
                                               g+G++lhag v vadGtde + r++ vl +dp +GvirhadaGye+a++va+e+g++lpm
  lcl|NCBI__GCF_900129305.1:WP_073039909.1 506 GIGYALHAGQVTVADGTDEGEVRVTTVLRNDPATGVIRHADAGYEKAIQVARERGVKLPM 565
                                               ***********************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (570 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: 00:00:00.02
# Mc/sec: 11.47
//
[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 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