Alignments for a candidate for hutU in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Shewanella loihica PV-4

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate 5211345 Shew_3757 urocanate hydratase (RefSeq)

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



>FitnessBrowser__PV4:5211345
          Length = 556

 Score =  877 bits (2267), Expect = 0.0
 Identities = 423/544 (77%), Positives = 468/544 (86%)

Query: 16  IRAPRGNTLTAKSWLTEAPLRMLMNNLDPEVAENPKELVVYGGIGRAARNWECYDKIVES 75
           I AP G TL+ KSWLTEAP+RMLMNNL P+VAE P++LVVYGGIGRAAR+W+CYDKIVE 
Sbjct: 11  IIAPHGTTLSCKSWLTEAPMRMLMNNLHPDVAERPEDLVVYGGIGRAARDWQCYDKIVEV 70

Query: 76  LTNLNDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWASWEHFNELDAKGLAMYGQ 135
           L  L +DETLLVQSGKPVGVFKTHSNAPRV+IANSNLVPHWA+WEHFNELD KGLAMYGQ
Sbjct: 71  LQRLEEDETLLVQSGKPVGVFKTHSNAPRVIIANSNLVPHWANWEHFNELDKKGLAMYGQ 130

Query: 136 MTAGSWIYIGSQGIVQGTYETFVEAGRQHYDSNLKGRWVLTAGLGGMGGAQPLAATLAGA 195
           MTAGSWIYIGSQGIVQGTYETFV   +QH+  +  G+W+LT GLGGMGGAQPLA T+AG 
Sbjct: 131 MTAGSWIYIGSQGIVQGTYETFVAMAKQHFGGDASGKWILTGGLGGMGGAQPLAGTMAGY 190

Query: 196 CSLNIECQQVSIDFRLKTRYVDEQATDLDDALARIEKYTAEGKAISIALCGNAAEILPEM 255
             L  E  +  IDFRL+TRYVD++AT LD+ALA I++    GK +S+ L  NAA+I  E+
Sbjct: 191 SVLACEVDETRIDFRLRTRYVDKKATSLDEALAMIDEANKSGKPVSVGLLANAADIFAEL 250

Query: 256 VRRGVRPDMVTDQTSAHDPLNGYLPAGWTWDEYRARAKTEPAAVVKAAKQSMAIHVKAML 315
           V RG+ PD+VTDQTSAHDPLNGYLP GWT +      K + AAVVKAAKQSMA+ VKAML
Sbjct: 251 VERGITPDVVTDQTSAHDPLNGYLPQGWTLEYAAEMRKQDEAAVVKAAKQSMAVQVKAML 310

Query: 316 AFQKMGVPTFDYGNNIRQMAQEEGVENAFDFPGFVPAYIRPLFCRGIGPFRWAALSGDPQ 375
           A Q  G  T DYGNNIRQMA EEGVENAFDFPGFVPAY+RPLFC GIGPFRWAALSGDP+
Sbjct: 311 ALQAAGAATTDYGNNIRQMAFEEGVENAFDFPGFVPAYVRPLFCEGIGPFRWAALSGDPE 370

Query: 376 DIYKTDAKVKELIPDDAHLHNWLDMARERISFQGLPARICWVGLGQRAKLGLAFNEMVRS 435
           DIYKTDAKVKELIPD+ HLHNWLDMARERI+FQGLPARICWVGL  RA+L  AFNEMV++
Sbjct: 371 DIYKTDAKVKELIPDNPHLHNWLDMARERIAFQGLPARICWVGLKDRARLAKAFNEMVKN 430

Query: 436 GELSAPIVIGRDHLDSGSVASPNRETESMQDGSDAVSDWPLLNALLNTASGATWVSLHHG 495
           GELSAPIVIGRDHLDSGSVASPNRETESM DGSDAVSDWPL+NALLNTASGATWVSLHHG
Sbjct: 431 GELSAPIVIGRDHLDSGSVASPNRETESMLDGSDAVSDWPLMNALLNTASGATWVSLHHG 490

Query: 496 GGVGMGFSQHSGMVIVCDGTDEAAERIARVLHNDPGTGVMRHADAGYQIAIDCAKEQGLN 555
           GGVGMGFSQHSG+VIV DGTDEA  R+ RVL NDP TGVMRHADAGY+IA  CAKEQGL+
Sbjct: 491 GGVGMGFSQHSGVVIVADGTDEAEARLGRVLWNDPATGVMRHADAGYEIAKQCAKEQGLD 550

Query: 556 LPMI 559
           LPM+
Sbjct: 551 LPML 554


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: 1107
Number of extensions: 51
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: 556
Length adjustment: 36
Effective length of query: 526
Effective length of database: 520
Effective search space:   273520
Effective search space used:   273520
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 5211345 Shew_3757 (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.27002.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   5.2e-297  971.7   1.2     6e-297  971.5   1.2    1.0  1  lcl|FitnessBrowser__PV4:5211345  Shew_3757 urocanate hydratase (R


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5211345  Shew_3757 urocanate hydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  971.5   1.2    6e-297    6e-297       2     545 .]      10     553 ..       9     553 .. 1.00

  Alignments for each domain:
  == domain 1  score: 971.5 bits;  conditional E-value: 6e-297
                        TIGR01228   2 eiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddetllvqsGkp 79 
                                       i ap+G++l++k+w +ea++r+lmnnl p+vae pe+lvvyGG+G+aar+w+++dkive l+rle+detllvqsGkp
  lcl|FitnessBrowser__PV4:5211345  10 RIIAPHGTTLSCKSWLTEAPMRMLMNNLHPDVAERPEDLVVYGGIGRAARDWQCYDKIVEVLQRLEEDETLLVQSGKP 87 
                                      578*************************************************************************** PP

                        TIGR01228  80 vgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGtyetlaelarkhfggslk 157
                                      vgvfkth++aprv+iansnlvp+wa+we+f+el++kGl+myGqmtaGswiyiG+qGi+qGtyet++++a++hfgg+ +
  lcl|FitnessBrowser__PV4:5211345  88 VGVFKTHSNAPRVIIANSNLVPHWANWEHFNELDKKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVAMAKQHFGGDAS 165
                                      ****************************************************************************** PP

                        TIGR01228 158 gklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddldealaraeeakaeGkalsigllGna 235
                                      gk++lt GlGgmGGaqpla t+++ +++a evde+rid+rl+t+y+d+k+++ldeala+++ea++ Gk++s+gll na
  lcl|FitnessBrowser__PV4:5211345 166 GKWILTGGLGGMGGAQPLAGTMAGYSVLACEVDETRIDFRLRTRYVDKKATSLDEALAMIDEANKSGKPVSVGLLANA 243
                                      ****************************************************************************** PP

                        TIGR01228 236 aevleellergvvpdvvtdqtsahdellGyipegytvedadklrdeepeeyvkaakaslakhvrallalqkkGavtfd 313
                                      a+++ el+erg++pdvvtdqtsahd+l+Gy+p+g+t+e a+++r+++++++vkaak+s+a++v+a+lalq +Ga t d
  lcl|FitnessBrowser__PV4:5211345 244 ADIFAELVERGITPDVVTDQTSAHDPLNGYLPQGWTLEYAAEMRKQDEAAVVKAAKQSMAVQVKAMLALQAAGAATTD 321
                                      ****************************************************************************** PP

                        TIGR01228 314 yGnnirqvakeeGvedafdfpGfvpayirdlfceGkGpfrwvalsGdpadiyrtdkavkelfpedeelhrwidlakek 391
                                      yGnnirq+a+eeGve+afdfpGfvpay+r+lfceG Gpfrw+alsGdp+diy+td++vkel+p++ +lh+w+d+a+e+
  lcl|FitnessBrowser__PV4:5211345 322 YGNNIRQMAFEEGVENAFDFPGFVPAYVRPLFCEGIGPFRWAALSGDPEDIYKTDAKVKELIPDNPHLHNWLDMARER 399
                                      ****************************************************************************** PP

                        TIGR01228 392 vafqGlparicwlgygereklalainelvrsGelkapvvigrdhldaGsvaspnreteamkdGsdavadwpllnalln 469
                                      +afqGlparicw+g+++r++la+a+ne+v++Gel+ap+vigrdhld+Gsvaspnrete+m dGsdav+dwpl+nalln
  lcl|FitnessBrowser__PV4:5211345 400 IAFQGLPARICWVGLKDRARLAKAFNEMVKNGELSAPIVIGRDHLDSGSVASPNRETESMLDGSDAVSDWPLMNALLN 477
                                      ****************************************************************************** PP

                        TIGR01228 470 taaGaswvslhhGGGvglGfslhaglvivadGtdeaaerlkrvltadpGlGvirhadaGyesaldvakeqgldlpm 545
                                      ta+Ga+wvslhhGGGvg+Gfs+h+g+vivadGtdea+ rl rvl +dp +Gv+rhadaGye a ++akeqgldlpm
  lcl|FitnessBrowser__PV4:5211345 478 TASGATWVSLHHGGGVGMGFSQHSGVVIVADGTDEAEARLGRVLWNDPATGVMRHADAGYEIAKQCAKEQGLDLPM 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: 00:00:00.03
# Mc/sec: 8.74
//
[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