Aligments for a candidate for hutU in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Aligments for a candidate for hutU in Shewanella sp. ANA-3

Align Urocanate hydratase; Urocanase; Imidazolonepropionate hydrolase; EC 4.2.1.49 (characterized)
to candidate 7022849 Shewana3_0100 urocanate hydratase (RefSeq)

Query= SwissProt::P25080
         (557 letters)



>FitnessBrowser__ANA3:7022849
          Length = 556

 Score =  870 bits (2249), Expect = 0.0
 Identities = 417/544 (76%), Positives = 467/544 (85%)

Query: 12  IRAPRGNKLTAKSWLTEAPLRMLMNNLDPQVAENPKELVVYGGIGRAARNWECYDKIVET 71
           I AP G++L+ KSWLTEAP+RMLMNNL P VAE P++LVVYGGIGRAAR+W+CYDKI+E 
Sbjct: 11  IIAPHGSQLSCKSWLTEAPMRMLMNNLHPDVAERPEDLVVYGGIGRAARDWDCYDKIIEV 70

Query: 72  LTRLEDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWANWEHFNELDAKGLAMYGQ 131
           L RLEDDETL+VQSGKPVGVF+TH++APRVLIANSNLVPHWANWEHFNELD +GLAMYGQ
Sbjct: 71  LKRLEDDETLMVQSGKPVGVFRTHADAPRVLIANSNLVPHWANWEHFNELDKQGLAMYGQ 130

Query: 132 MTAGSWIYIGSQGIVQGTYETFVEAGRQHYGGTVKAKWVLTAGLGGMGGAQPLAATLAGA 191
           MTAGSWIYIG+QGIVQGTYETFV   +QH+GG    KW+LT GLGGMGGAQ LA T+AG 
Sbjct: 131 MTAGSWIYIGTQGIVQGTYETFVAVAKQHFGGVAAGKWILTGGLGGMGGAQTLAGTMAGF 190

Query: 192 CSLNIECQQSRIDFRLETRYVDEQATDLDDALVRIAKYTAEGKAISIALHGNAAEILPEL 251
             L  E  ++RIDFRL TRYVD++AT LD+AL  I    A GK +S+ L  NAA++  EL
Sbjct: 191 SVLACEVDETRIDFRLRTRYVDKKATSLDEALAMINDANASGKPVSVGLLANAADVFAEL 250

Query: 252 VKRGVRPDMVTDQTSAHDPLNGYLPAGWTWEQYRDRAQTEPAAVVKAAKQSMAVHVQAML 311
           VKRG+ PD+VTDQTSAHDPLNGYLP GWT  Q  D  +T+ AAVVKAAK SMAV VQAML
Sbjct: 251 VKRGITPDVVTDQTSAHDPLNGYLPQGWTMAQAADMRKTDEAAVVKAAKASMAVQVQAML 310

Query: 312 DFQKQGVPTFDYGNNIRQMAKEEGVANAFDFPGFVPAYIRPLFCRGVGPFRWAALSGEAE 371
           + Q  G  T DYGNNIRQMA E GV NAFDFPGFVPAYIRPLFC G+GPFRW ALSG+ E
Sbjct: 311 ELQAAGAATLDYGNNIRQMAFETGVKNAFDFPGFVPAYIRPLFCEGIGPFRWVALSGDPE 370

Query: 372 DIYKTDAKVKELIPDDAHLHRWLDMARERISFQGLPARICWVGLGLRAKLGLAFNEMVRS 431
           DIYKTDAKVKELIPD+ HLH WLDMARERI+FQGLPARICWVGL  RA+L  AFNEMV++
Sbjct: 371 DIYKTDAKVKELIPDNPHLHNWLDMARERIAFQGLPARICWVGLKDRARLAQAFNEMVKN 430

Query: 432 GELSAPVVIGRDHLDSGSVSSPNRETEAMRDGSDAVSDWPLLNALLNTAGGATWVSLHHG 491
           GELSAP+VIGRDHLDSGSV+SPNRETE+M DGSDAVSDWPLLNALLNTA GATWVSLHHG
Sbjct: 431 GELSAPIVIGRDHLDSGSVASPNRETESMMDGSDAVSDWPLLNALLNTASGATWVSLHHG 490

Query: 492 GGVGMGFSQHSGMVIVCDGTDEAAERIARVLTNDPGTGVMRHADAGYDIAIDCAKEQGLD 551
           GGVGMGFSQHSG+VIVCDGT+ AA+R+ RVL NDP TGVMRHADAGY+IA +CAKEQGLD
Sbjct: 491 GGVGMGFSQHSGVVIVCDGTEAAAKRVGRVLWNDPATGVMRHADAGYEIAKNCAKEQGLD 550

Query: 552 LPMI 555
           LPM+
Sbjct: 551 LPML 554


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: 1077
Number of extensions: 53
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 7022849 Shewana3_0100 (urocanate hydratase (RefSeq))
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.19985.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.7e-296  969.4   2.5   3.2e-296  969.1   2.5    1.0  1  lcl|FitnessBrowser__ANA3:7022849  Shewana3_0100 urocanate hydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7022849  Shewana3_0100 urocanate hydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  969.1   2.5  3.2e-296  3.2e-296       2     545 .]      10     553 ..       9     553 .. 1.00

  Alignments for each domain:
  == domain 1  score: 969.1 bits;  conditional E-value: 3.2e-296
                         TIGR01228   2 eiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddetllvqsGk 78 
                                        i ap+G++l++k+w +ea++r+lmnnl p+vae pe+lvvyGG+G+aar+w+++dki+e lkrleddetl+vqsGk
  lcl|FitnessBrowser__ANA3:7022849  10 RIIAPHGSQLSCKSWLTEAPMRMLMNNLHPDVAERPEDLVVYGGIGRAARDWDCYDKIIEVLKRLEDDETLMVQSGK 86 
                                       5789************************************************************************* PP

                         TIGR01228  79 pvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGtyetlaelarkhfggs 155
                                       pvgvf+th +aprvliansnlvp+wa+we+f+el+++Gl+myGqmtaGswiyiGtqGi+qGtyet++++a++hfgg 
  lcl|FitnessBrowser__ANA3:7022849  87 PVGVFRTHADAPRVLIANSNLVPHWANWEHFNELDKQGLAMYGQMTAGSWIYIGTQGIVQGTYETFVAVAKQHFGGV 163
                                       ***************************************************************************** PP

                         TIGR01228 156 lkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddldealaraeeakaeGkalsigll 232
                                         gk++lt GlGgmGGaq la t+++ +++a evde+rid+rl+t+y+d+k+++ldeala++++a+a Gk++s+gll
  lcl|FitnessBrowser__ANA3:7022849 164 AAGKWILTGGLGGMGGAQTLAGTMAGFSVLACEVDETRIDFRLRTRYVDKKATSLDEALAMINDANASGKPVSVGLL 240
                                       ***************************************************************************** PP

                         TIGR01228 233 GnaaevleellergvvpdvvtdqtsahdellGyipegytvedadklrdeepeeyvkaakaslakhvrallalqkkGa 309
                                        naa+v+ el++rg++pdvvtdqtsahd+l+Gy+p+g+t+++a+++r+++++++vkaakas+a++v+a+l+lq +Ga
  lcl|FitnessBrowser__ANA3:7022849 241 ANAADVFAELVKRGITPDVVTDQTSAHDPLNGYLPQGWTMAQAADMRKTDEAAVVKAAKASMAVQVQAMLELQAAGA 317
                                       ***************************************************************************** PP

                         TIGR01228 310 vtfdyGnnirqvakeeGvedafdfpGfvpayirdlfceGkGpfrwvalsGdpadiyrtdkavkelfpedeelhrwid 386
                                        t+dyGnnirq+a+e+Gv++afdfpGfvpayir+lfceG GpfrwvalsGdp+diy+td++vkel+p++ +lh+w+d
  lcl|FitnessBrowser__ANA3:7022849 318 ATLDYGNNIRQMAFETGVKNAFDFPGFVPAYIRPLFCEGIGPFRWVALSGDPEDIYKTDAKVKELIPDNPHLHNWLD 394
                                       ***************************************************************************** PP

                         TIGR01228 387 lakekvafqGlparicwlgygereklalainelvrsGelkapvvigrdhldaGsvaspnreteamkdGsdavadwpl 463
                                       +a+e++afqGlparicw+g+++r++la a+ne+v++Gel+ap+vigrdhld+Gsvaspnrete+m dGsdav+dwpl
  lcl|FitnessBrowser__ANA3:7022849 395 MARERIAFQGLPARICWVGLKDRARLAQAFNEMVKNGELSAPIVIGRDHLDSGSVASPNRETESMMDGSDAVSDWPL 471
                                       ***************************************************************************** PP

                         TIGR01228 464 lnallntaaGaswvslhhGGGvglGfslhaglvivadGtdeaaerlkrvltadpGlGvirhadaGyesaldvakeqg 540
                                       lnallnta+Ga+wvslhhGGGvg+Gfs+h+g+viv+dGt++aa+r+ rvl +dp +Gv+rhadaGye a ++akeqg
  lcl|FitnessBrowser__ANA3:7022849 472 LNALLNTASGATWVSLHHGGGVGMGFSQHSGVVIVCDGTEAAAKRVGRVLWNDPATGVMRHADAGYEIAKNCAKEQG 548
                                       ***************************************************************************** PP

                         TIGR01228 541 ldlpm 545
                                       ldlpm
  lcl|FitnessBrowser__ANA3:7022849 549 LDLPM 553
                                       ****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: 10.74
//
[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, or view the source code.

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