Alignments for a candidate for hutU in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Pseudomonas fluorescens FW300-N2E3

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate AO353_12250 AO353_12250 urocanate hydratase

Query= reanno::pseudo3_N2E3:AO353_12250
         (567 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_12250
          Length = 567

 Score = 1156 bits (2990), Expect = 0.0
 Identities = 567/567 (100%), Positives = 567/567 (100%)

Query: 1   VTDNTQKPTPVTFTKHRDVEIRAPRGNKLTAKSWLTEAPLRMLMNNLDPEVAENPKELVV 60
           VTDNTQKPTPVTFTKHRDVEIRAPRGNKLTAKSWLTEAPLRMLMNNLDPEVAENPKELVV
Sbjct: 1   VTDNTQKPTPVTFTKHRDVEIRAPRGNKLTAKSWLTEAPLRMLMNNLDPEVAENPKELVV 60

Query: 61  YGGIGRAARNWECYDKIVESLTNLNDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPH 120
           YGGIGRAARNWECYDKIVESLTNLNDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPH
Sbjct: 61  YGGIGRAARNWECYDKIVESLTNLNDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPH 120

Query: 121 WASWEHFNELDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYNDNLTGRWVL 180
           WASWEHFNELDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYNDNLTGRWVL
Sbjct: 121 WASWEHFNELDAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYNDNLTGRWVL 180

Query: 181 TAGLGGMGGAQPLAATLAGACSLNIECQQVSIDFRLKSRYVDEQAKDLDDALARIAKYTK 240
           TAGLGGMGGAQPLAATLAGACSLNIECQQVSIDFRLKSRYVDEQAKDLDDALARIAKYTK
Sbjct: 181 TAGLGGMGGAQPLAATLAGACSLNIECQQVSIDFRLKSRYVDEQAKDLDDALARIAKYTK 240

Query: 241 EGKAISIALLGNAAEILPELVRRGVRPDMVTDQTSAHDPLNGYLPAGWTWEEYRARAKTE 300
           EGKAISIALLGNAAEILPELVRRGVRPDMVTDQTSAHDPLNGYLPAGWTWEEYRARAKTE
Sbjct: 241 EGKAISIALLGNAAEILPELVRRGVRPDMVTDQTSAHDPLNGYLPAGWTWEEYRARAKTE 300

Query: 301 PAAVIKAAKQSMAVHVKAMLDFQKQGIPTFDYGNNIRQMAQEEGVENAFDFPGFVPAYIR 360
           PAAVIKAAKQSMAVHVKAMLDFQKQGIPTFDYGNNIRQMAQEEGVENAFDFPGFVPAYIR
Sbjct: 301 PAAVIKAAKQSMAVHVKAMLDFQKQGIPTFDYGNNIRQMAQEEGVENAFDFPGFVPAYIR 360

Query: 361 PLFCRGIGPFRWAALSGNAEDIYKTDAKVKELIPDDAHLHNWLDMARERISFQGLPARIC 420
           PLFCRGIGPFRWAALSGNAEDIYKTDAKVKELIPDDAHLHNWLDMARERISFQGLPARIC
Sbjct: 361 PLFCRGIGPFRWAALSGNAEDIYKTDAKVKELIPDDAHLHNWLDMARERISFQGLPARIC 420

Query: 421 WVGLGLRAKLGLAFNEMVRSGELSAPIVIGRDHLDSGSVASPNRETESMQDGSDAVSDWP 480
           WVGLGLRAKLGLAFNEMVRSGELSAPIVIGRDHLDSGSVASPNRETESMQDGSDAVSDWP
Sbjct: 421 WVGLGLRAKLGLAFNEMVRSGELSAPIVIGRDHLDSGSVASPNRETESMQDGSDAVSDWP 480

Query: 481 LLNALLNTASGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLHNDPATGVM 540
           LLNALLNTASGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLHNDPATGVM
Sbjct: 481 LLNALLNTASGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLHNDPATGVM 540

Query: 541 RHADAGYQIAIDCAKEQGLNLPMITGK 567
           RHADAGYQIAIDCAKEQGLNLPMITGK
Sbjct: 541 RHADAGYQIAIDCAKEQGLNLPMITGK 567


Lambda     K      H
   0.318    0.134    0.410 

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: 1303
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: 567
Length of database: 567
Length adjustment: 36
Effective length of query: 531
Effective length of database: 531
Effective search space:   281961
Effective search space used:   281961
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 AO353_12250 AO353_12250 (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.14275.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 1019.1   0.3          0 1018.9   0.3    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12250  AO353_12250 urocanate hydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_12250  AO353_12250 urocanate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1018.9   0.3         0         0       2     545 .]      20     563 ..      19     563 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1018.9 bits;  conditional E-value: 0
                                     TIGR01228   2 eiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrl 66 
                                                   eiraprG++l+ak+w +ea+lr+lmnnldpevae+p+elvvyGG+G+aarnwe++dkive+l++l
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12250  20 EIRAPRGNKLTAKSWLTEAPLRMLMNNLDPEVAENPKELVVYGGIGRAARNWECYDKIVESLTNL 84 
                                                   79*************************************************************** PP

                                     TIGR01228  67 eddetllvqsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyi 131
                                                   +ddetllvqsGkpvgvfkth++aprvliansnlvp+wa+we+f+el+akGl+myGqmtaGswiyi
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12250  85 NDDETLLVQSGKPVGVFKTHSNAPRVLIANSNLVPHWASWEHFNELDAKGLAMYGQMTAGSWIYI 149
                                                   ***************************************************************** PP

                                     TIGR01228 132 GtqGilqGtyetlaelarkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridk 196
                                                   G+qGi+qGtyet++e++r+h+ ++l g++vltaGlGgmGGaqpla+tl++a+s+++e+++  id+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12250 150 GSQGIVQGTYETFVEAGRQHYNDNLTGRWVLTAGLGGMGGAQPLAATLAGACSLNIECQQVSIDF 214
                                                   ***************************************************************** PP

                                     TIGR01228 197 rletkyldektddldealaraeeakaeGkalsigllGnaaevleellergvvpdvvtdqtsahde 261
                                                   rl+++y+de+++dld+alar++++++eGka+si+llGnaae+l+el++rgv+pd+vtdqtsahd+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12250 215 RLKSRYVDEQAKDLDDALARIAKYTKEGKAISIALLGNAAEILPELVRRGVRPDMVTDQTSAHDP 279
                                                   ***************************************************************** PP

                                     TIGR01228 262 llGyipegytvedadklrdeepeeyvkaakaslakhvrallalqkkGavtfdyGnnirqvakeeG 326
                                                   l+Gy+p+g+t+e+++ ++++ep++++kaak+s+a+hv+a+l++qk+G  tfdyGnnirq+a+eeG
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12250 280 LNGYLPAGWTWEEYRARAKTEPAAVIKAAKQSMAVHVKAMLDFQKQGIPTFDYGNNIRQMAQEEG 344
                                                   ***************************************************************** PP

                                     TIGR01228 327 vedafdfpGfvpayirdlfceGkGpfrwvalsGdpadiyrtdkavkelfpedeelhrwidlakek 391
                                                   ve+afdfpGfvpayir+lfc+G Gpfrw+alsG+++diy+td++vkel+p+d++lh+w+d+a+e+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12250 345 VENAFDFPGFVPAYIRPLFCRGIGPFRWAALSGNAEDIYKTDAKVKELIPDDAHLHNWLDMARER 409
                                                   ***************************************************************** PP

                                     TIGR01228 392 vafqGlparicwlgygereklalainelvrsGelkapvvigrdhldaGsvaspnreteamkdGsd 456
                                                   ++fqGlparicw+g+g r+kl+la+ne+vrsGel+ap+vigrdhld+Gsvaspnrete+m+dGsd
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12250 410 ISFQGLPARICWVGLGLRAKLGLAFNEMVRSGELSAPIVIGRDHLDSGSVASPNRETESMQDGSD 474
                                                   ***************************************************************** PP

                                     TIGR01228 457 avadwpllnallntaaGaswvslhhGGGvglGfslhaglvivadGtdeaaerlkrvltadpGlGv 521
                                                   av+dwpllnallnta+Ga+wvslhhGGGvg+Gfs+h+g+viv+dGtdeaaer++rvl +dp +Gv
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12250 475 AVSDWPLLNALLNTASGATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAERIARVLHNDPATGV 539
                                                   ***************************************************************** PP

                                     TIGR01228 522 irhadaGyesaldvakeqgldlpm 545
                                                   +rhadaGy+ a+d+akeqgl+lpm
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_12250 540 MRHADAGYQIAIDCAKEQGLNLPM 563
                                                   ***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (567 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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Candidates (tab-delimited)
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