Alignments for a candidate for hutU in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Pseudomonas simiae WCS417

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate GFF338 PS417_01720 urocanate hydratase

Query= reanno::WCS417:GFF338
         (556 letters)



>FitnessBrowser__WCS417:GFF338
          Length = 556

 Score = 1135 bits (2935), Expect = 0.0
 Identities = 556/556 (100%), Positives = 556/556 (100%)

Query: 1   MTKPTKYRDVEIRAAHGNKLTAKSWLTEAPLRMLMNNLDPQVAENPKELVVYGGIGRAAR 60
           MTKPTKYRDVEIRAAHGNKLTAKSWLTEAPLRMLMNNLDPQVAENPKELVVYGGIGRAAR
Sbjct: 1   MTKPTKYRDVEIRAAHGNKLTAKSWLTEAPLRMLMNNLDPQVAENPKELVVYGGIGRAAR 60

Query: 61  NWECYDQIVESLTHLNDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWASWEHFNE 120
           NWECYDQIVESLTHLNDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWASWEHFNE
Sbjct: 61  NWECYDQIVESLTHLNDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWASWEHFNE 120

Query: 121 LDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYNSDLTGRWVLTAGLGGMGG 180
           LDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYNSDLTGRWVLTAGLGGMGG
Sbjct: 121 LDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYNSDLTGRWVLTAGLGGMGG 180

Query: 181 AQPLAATLAGACSLNIECQQVSIDFRLNSRYVDEQATDLDDALARIAKYTKEGKAISVAL 240
           AQPLAATLAGACSLNIECQQVSIDFRLNSRYVDEQATDLDDALARIAKYTKEGKAISVAL
Sbjct: 181 AQPLAATLAGACSLNIECQQVSIDFRLNSRYVDEQATDLDDALARIAKYTKEGKAISVAL 240

Query: 241 LGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWDEYRARAKTEPAAVIKAAK 300
           LGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWDEYRARAKTEPAAVIKAAK
Sbjct: 241 LGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWDEYRARAKTEPAAVIKAAK 300

Query: 301 QSMAVHVKAMLEFQKQGIPTFDYGNNIRQMAQEEGVENAFDFPGFVPAYIRPLFCRGIGP 360
           QSMAVHVKAMLEFQKQGIPTFDYGNNIRQMAQEEGVENAFDFPGFVPAYIRPLFCRGIGP
Sbjct: 301 QSMAVHVKAMLEFQKQGIPTFDYGNNIRQMAQEEGVENAFDFPGFVPAYIRPLFCRGIGP 360

Query: 361 FRWAALSGDPQDIYKTDAKVKELIPDDAHLHNWLDMARERISFQGLPARICWVGLGQRAK 420
           FRWAALSGDPQDIYKTDAKVKELIPDDAHLHNWLDMARERISFQGLPARICWVGLGQRAK
Sbjct: 361 FRWAALSGDPQDIYKTDAKVKELIPDDAHLHNWLDMARERISFQGLPARICWVGLGQRAK 420

Query: 421 LGLAFNEMVRSGELSAPVVIGRDHLDSGSVASPNRETEAMQDGSDAVSDWPLLNALLNTA 480
           LGLAFNEMVRSGELSAPVVIGRDHLDSGSVASPNRETEAMQDGSDAVSDWPLLNALLNTA
Sbjct: 421 LGLAFNEMVRSGELSAPVVIGRDHLDSGSVASPNRETEAMQDGSDAVSDWPLLNALLNTA 480

Query: 481 SGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLHNDPATGVMRHADAGYQI 540
           SGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLHNDPATGVMRHADAGYQI
Sbjct: 481 SGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLHNDPATGVMRHADAGYQI 540

Query: 541 AIDCAKEQGLNLPMIK 556
           AIDCAKEQGLNLPMIK
Sbjct: 541 AIDCAKEQGLNLPMIK 556


Lambda     K      H
   0.318    0.134    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: 1266
Number of extensions: 55
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 GFF338 PS417_01720 (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.753.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
          0 1017.4   0.6          0 1017.2   0.6    1.0  1  lcl|FitnessBrowser__WCS417:GFF338  PS417_01720 urocanate hydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF338  PS417_01720 urocanate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1017.2   0.6         0         0       2     545 .]      11     554 ..      10     554 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1017.2 bits;  conditional E-value: 0
                          TIGR01228   2 eiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddetllvqsG 77 
                                        eira++G++l+ak+w +ea+lr+lmnnldp+vae+p+elvvyGG+G+aarnwe++d+ive+l++l+ddetllvqsG
  lcl|FitnessBrowser__WCS417:GFF338  11 EIRAAHGNKLTAKSWLTEAPLRMLMNNLDPQVAENPKELVVYGGIGRAARNWECYDQIVESLTHLNDDETLLVQSG 86 
                                        79************************************************************************** PP

                          TIGR01228  78 kpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGtyetlaelarkhfg 153
                                        kpvgvfkth++aprvliansnlvp+wa+we+f+el+akGl+myGqmtaGswiyiG+qGi+qGtyet++e++r+h+ 
  lcl|FitnessBrowser__WCS417:GFF338  87 KPVGVFKTHSNAPRVLIANSNLVPHWASWEHFNELDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYN 162
                                        **************************************************************************** PP

                          TIGR01228 154 gslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddldealaraeeakaeGkalsi 229
                                         +l g++vltaGlGgmGGaqpla+tl++a+s+++e+++  id+rl+++y+de+++dld+alar++++++eGka+s+
  lcl|FitnessBrowser__WCS417:GFF338 163 SDLTGRWVLTAGLGGMGGAQPLAATLAGACSLNIECQQVSIDFRLNSRYVDEQATDLDDALARIAKYTKEGKAISV 238
                                        **************************************************************************** PP

                          TIGR01228 230 gllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadklrdeepeeyvkaakaslakhvrallalq 305
                                        +llGnaae+l+el++rgv+pd+vtdqtsahd+l+Gy+p+g+t+++++ ++++ep++++kaak+s+a+hv+a+l++q
  lcl|FitnessBrowser__WCS417:GFF338 239 ALLGNAAEILPELVKRGVRPDMVTDQTSAHDPLNGYLPAGWTWDEYRARAKTEPAAVIKAAKQSMAVHVKAMLEFQ 314
                                        **************************************************************************** PP

                          TIGR01228 306 kkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfceGkGpfrwvalsGdpadiyrtdkavkelfpedeel 381
                                        k+G  tfdyGnnirq+a+eeGve+afdfpGfvpayir+lfc+G Gpfrw+alsGdp+diy+td++vkel+p+d++l
  lcl|FitnessBrowser__WCS417:GFF338 315 KQGIPTFDYGNNIRQMAQEEGVENAFDFPGFVPAYIRPLFCRGIGPFRWAALSGDPQDIYKTDAKVKELIPDDAHL 390
                                        **************************************************************************** PP

                          TIGR01228 382 hrwidlakekvafqGlparicwlgygereklalainelvrsGelkapvvigrdhldaGsvaspnreteamkdGsda 457
                                        h+w+d+a+e+++fqGlparicw+g+g+r+kl+la+ne+vrsGel+apvvigrdhld+Gsvaspnreteam+dGsda
  lcl|FitnessBrowser__WCS417:GFF338 391 HNWLDMARERISFQGLPARICWVGLGQRAKLGLAFNEMVRSGELSAPVVIGRDHLDSGSVASPNRETEAMQDGSDA 466
                                        **************************************************************************** PP

                          TIGR01228 458 vadwpllnallntaaGaswvslhhGGGvglGfslhaglvivadGtdeaaerlkrvltadpGlGvirhadaGyesal 533
                                        v+dwpllnallnta+Ga+wvslhhGGGvg+Gfs+h+g+viv+dGtdeaaer++rvl +dp +Gv+rhadaGy+ a+
  lcl|FitnessBrowser__WCS417:GFF338 467 VSDWPLLNALLNTASGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLHNDPATGVMRHADAGYQIAI 542
                                        **************************************************************************** PP

                          TIGR01228 534 dvakeqgldlpm 545
                                        d+akeqgl+lpm
  lcl|FitnessBrowser__WCS417:GFF338 543 DCAKEQGLNLPM 554
                                        ***********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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.81
//
[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