Alignments for a candidate for hutU in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Sphingomonas koreensis DSMZ 15582

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate Ga0059261_3961 Ga0059261_3961 urocanate hydratase (EC 4.2.1.49)

Query= reanno::Korea:Ga0059261_3961
         (556 letters)



>FitnessBrowser__Korea:Ga0059261_3961
          Length = 556

 Score = 1136 bits (2939), Expect = 0.0
 Identities = 556/556 (100%), Positives = 556/556 (100%)

Query: 1   MTSAMTNRTDNSRHIKAPTGTELSAKSWLTEAPLRMLMNNLDADVAEAPESLVVYGGIGR 60
           MTSAMTNRTDNSRHIKAPTGTELSAKSWLTEAPLRMLMNNLDADVAEAPESLVVYGGIGR
Sbjct: 1   MTSAMTNRTDNSRHIKAPTGTELSAKSWLTEAPLRMLMNNLDADVAEAPESLVVYGGIGR 60

Query: 61  AARDWQSYDRIVDALRALDADQTLLVQSGKPVGVFRTHADAPRVLIANSNLVPHWATWEH 120
           AARDWQSYDRIVDALRALDADQTLLVQSGKPVGVFRTHADAPRVLIANSNLVPHWATWEH
Sbjct: 61  AARDWQSYDRIVDALRALDADQTLLVQSGKPVGVFRTHADAPRVLIANSNLVPHWATWEH 120

Query: 121 FNELDRKGLAMYGQMTAGSWIYIGTQGIVQGTYETFVEAGRQHYGGDLSGKWVLTAGLGG 180
           FNELDRKGLAMYGQMTAGSWIYIGTQGIVQGTYETFVEAGRQHYGGDLSGKWVLTAGLGG
Sbjct: 121 FNELDRKGLAMYGQMTAGSWIYIGTQGIVQGTYETFVEAGRQHYGGDLSGKWVLTAGLGG 180

Query: 181 MGGAQPLAATMAGASCLAVECQPSRIEMRLKTRYLDRAANSIDEALEIIRTSDKPVSVGL 240
           MGGAQPLAATMAGASCLAVECQPSRIEMRLKTRYLDRAANSIDEALEIIRTSDKPVSVGL
Sbjct: 181 MGGAQPLAATMAGASCLAVECQPSRIEMRLKTRYLDRAANSIDEALEIIRTSDKPVSVGL 240

Query: 241 LGNAAEVLPELVRRGIRPDIVTDQTSAHDPVNGYLPAGWTLDEWFTKRETAPHEVEKAAR 300
           LGNAAEVLPELVRRGIRPDIVTDQTSAHDPVNGYLPAGWTLDEWFTKRETAPHEVEKAAR
Sbjct: 241 LGNAAEVLPELVRRGIRPDIVTDQTSAHDPVNGYLPAGWTLDEWFTKRETAPHEVEKAAR 300

Query: 301 ASMATHVRAMLDFHEMGIPTLDYGNNIRQVAKDEGVENAFAFPGFVPAYIRPLFCRGIGP 360
           ASMATHVRAMLDFHEMGIPTLDYGNNIRQVAKDEGVENAFAFPGFVPAYIRPLFCRGIGP
Sbjct: 301 ASMATHVRAMLDFHEMGIPTLDYGNNIRQVAKDEGVENAFAFPGFVPAYIRPLFCRGIGP 360

Query: 361 FRWAALSGNPEDIWKTDRKVKELLPGNHHLHNWLDMAKERIAFQGLPARICWVGLGDRHR 420
           FRWAALSGNPEDIWKTDRKVKELLPGNHHLHNWLDMAKERIAFQGLPARICWVGLGDRHR
Sbjct: 361 FRWAALSGNPEDIWKTDRKVKELLPGNHHLHNWLDMAKERIAFQGLPARICWVGLGDRHR 420

Query: 421 LALAFNEMVASGELEAPIVIGRDHLDSGSVASPNRETEAMMDGSDAVSDWPLLNALLNTA 480
           LALAFNEMVASGELEAPIVIGRDHLDSGSVASPNRETEAMMDGSDAVSDWPLLNALLNTA
Sbjct: 421 LALAFNEMVASGELEAPIVIGRDHLDSGSVASPNRETEAMMDGSDAVSDWPLLNALLNTA 480

Query: 481 SGATWVSLHHGGGVGMGYSQHSGMVIVADGTPEAAKRLERVLWNDPATGVMRHADAGYEI 540
           SGATWVSLHHGGGVGMGYSQHSGMVIVADGTPEAAKRLERVLWNDPATGVMRHADAGYEI
Sbjct: 481 SGATWVSLHHGGGVGMGYSQHSGMVIVADGTPEAAKRLERVLWNDPATGVMRHADAGYEI 540

Query: 541 AKNCATEMGLDLPGIL 556
           AKNCATEMGLDLPGIL
Sbjct: 541 AKNCATEMGLDLPGIL 556


Lambda     K      H
   0.318    0.134    0.416 

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: 1314
Number of extensions: 45
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: 556
Length of database: 556
Length adjustment: 36
Effective length of query: 520
Effective length of database: 520
Effective search space:   270400
Effective search space used:   270400
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 Ga0059261_3961 Ga0059261_3961 (urocanate hydratase (EC 4.2.1.49))
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.16349.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-290  949.5   0.2   3.2e-290  949.3   0.2    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_3961  Ga0059261_3961 urocanate hydrata


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3961  Ga0059261_3961 urocanate hydratase (EC 4.2.1.49)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  949.3   0.2  3.2e-290  3.2e-290       1     544 [.      13     553 ..      13     554 .. 0.99

  Alignments for each domain:
  == domain 1  score: 949.3 bits;  conditional E-value: 3.2e-290
                                 TIGR01228   1 keiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrledd 69 
                                               ++i+ap+G+el+ak+w +ea+lr+lmnnld +vae pe+lvvyGG+G+aar+w+++d+iv+ l+ l+ d
  lcl|FitnessBrowser__Korea:Ga0059261_3961  13 RHIKAPTGTELSAKSWLTEAPLRMLMNNLDADVAEAPESLVVYGGIGRAARDWQSYDRIVDALRALDAD 81 
                                               579****************************************************************** PP

                                 TIGR01228  70 etllvqsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilq 138
                                               +tllvqsGkpvgvf+th +aprvliansnlvp+wa+we+f+el++kGl+myGqmtaGswiyiGtqGi+q
  lcl|FitnessBrowser__Korea:Ga0059261_3961  82 QTLLVQSGKPVGVFRTHADAPRVLIANSNLVPHWATWEHFNELDRKGLAMYGQMTAGSWIYIGTQGIVQ 150
                                               ********************************************************************* PP

                                 TIGR01228 139 GtyetlaelarkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldekt 207
                                               Gtyet++e++r+h+gg+l+gk+vltaGlGgmGGaqpla+t+++a+++ave++++ri+ rl+t+yld+ +
  lcl|FitnessBrowser__Korea:Ga0059261_3961 151 GTYETFVEAGRQHYGGDLSGKWVLTAGLGGMGGAQPLAATMAGASCLAVECQPSRIEMRLKTRYLDRAA 219
                                               ********************************************************************* PP

                                 TIGR01228 208 ddldealaraeeakaeGkalsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedad 276
                                               +++deal+ +       k++s+gllGnaaevl+el++rg++pd+vtdqtsahd+++Gy+p+g+t+++  
  lcl|FitnessBrowser__Korea:Ga0059261_3961 220 NSIDEALEIIRT---SDKPVSVGLLGNAAEVLPELVRRGIRPDIVTDQTSAHDPVNGYLPAGWTLDEWF 285
                                               *******99865...579*************************************************** PP

                                 TIGR01228 277 klrdeepeeyvkaakaslakhvrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlf 345
                                                 r++ p+e+ kaa+as+a+hvra+l++ + G  t+dyGnnirqvak+eGve+af fpGfvpayir+lf
  lcl|FitnessBrowser__Korea:Ga0059261_3961 286 TKRETAPHEVEKAARASMATHVRAMLDFHEMGIPTLDYGNNIRQVAKDEGVENAFAFPGFVPAYIRPLF 354
                                               ********************************************************************* PP

                                 TIGR01228 346 ceGkGpfrwvalsGdpadiyrtdkavkelfpedeelhrwidlakekvafqGlparicwlgygereklal 414
                                               c+G Gpfrw+alsG+p+di++td++vkel+p +++lh+w+d+ake++afqGlparicw+g+g+r++lal
  lcl|FitnessBrowser__Korea:Ga0059261_3961 355 CRGIGPFRWAALSGNPEDIWKTDRKVKELLPGNHHLHNWLDMAKERIAFQGLPARICWVGLGDRHRLAL 423
                                               ********************************************************************* PP

                                 TIGR01228 415 ainelvrsGelkapvvigrdhldaGsvaspnreteamkdGsdavadwpllnallntaaGaswvslhhGG 483
                                               a+ne+v sGel+ap+vigrdhld+Gsvaspnreteam dGsdav+dwpllnallnta+Ga+wvslhhGG
  lcl|FitnessBrowser__Korea:Ga0059261_3961 424 AFNEMVASGELEAPIVIGRDHLDSGSVASPNRETEAMMDGSDAVSDWPLLNALLNTASGATWVSLHHGG 492
                                               ********************************************************************* PP

                                 TIGR01228 484 GvglGfslhaglvivadGtdeaaerlkrvltadpGlGvirhadaGyesaldvakeqgldlp 544
                                               Gvg+G+s+h+g+vivadGt eaa+rl+rvl +dp +Gv+rhadaGye a ++a e gldlp
  lcl|FitnessBrowser__Korea:Ga0059261_3961 493 GVGMGYSQHSGMVIVADGTPEAAKRLERVLWNDPATGVMRHADAGYEIAKNCATEMGLDLP 553
                                               **********************************************************998 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: 00:00:00.02
# Mc/sec: 11.46
//
[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
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