Alignments for a candidate for hutU in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Phaeobacter inhibens BS107

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate GFF3577 PGA1_c36320 urocanate hydratase HutU

Query= reanno::Phaeo:GFF3577
         (559 letters)



>FitnessBrowser__Phaeo:GFF3577
          Length = 559

 Score = 1157 bits (2993), Expect = 0.0
 Identities = 559/559 (100%), Positives = 559/559 (100%)

Query: 1   MSDPRKNTRDIFPPTGPEITAKSWMTEAPMRMMMNNLHPDVAENPHELVVYGGIGRAART 60
           MSDPRKNTRDIFPPTGPEITAKSWMTEAPMRMMMNNLHPDVAENPHELVVYGGIGRAART
Sbjct: 1   MSDPRKNTRDIFPPTGPEITAKSWMTEAPMRMMMNNLHPDVAENPHELVVYGGIGRAART 60

Query: 61  WQDFDLIVETLKNLEEDQTLMVQSGKPVGVFQTHKDAPRVLIANSNLVPHWANWDHFNEL 120
           WQDFDLIVETLKNLEEDQTLMVQSGKPVGVFQTHKDAPRVLIANSNLVPHWANWDHFNEL
Sbjct: 61  WQDFDLIVETLKNLEEDQTLMVQSGKPVGVFQTHKDAPRVLIANSNLVPHWANWDHFNEL 120

Query: 121 DKKGLMMYGQMTAGSWIYIGTQGIVQGTYETFAEAGRQHFGGSLKGKWILTGGLGGMGGA 180
           DKKGLMMYGQMTAGSWIYIGTQGIVQGTYETFAEAGRQHFGGSLKGKWILTGGLGGMGGA
Sbjct: 121 DKKGLMMYGQMTAGSWIYIGTQGIVQGTYETFAEAGRQHFGGSLKGKWILTGGLGGMGGA 180

Query: 181 QPLAAVFAGASCLAVECNPDSIDFRLRTKYLDEKAETLDEALQMIERWTAAGEAKSVGLL 240
           QPLAAVFAGASCLAVECNPDSIDFRLRTKYLDEKAETLDEALQMIERWTAAGEAKSVGLL
Sbjct: 181 QPLAAVFAGASCLAVECNPDSIDFRLRTKYLDEKAETLDEALQMIERWTAAGEAKSVGLL 240

Query: 241 GNAAEIFPELVKRAETGGIRPDIVTDQTSAHDPVNGYLPLGWTMGEWKERRESDKKAVEK 300
           GNAAEIFPELVKRAETGGIRPDIVTDQTSAHDPVNGYLPLGWTMGEWKERRESDKKAVEK
Sbjct: 241 GNAAEIFPELVKRAETGGIRPDIVTDQTSAHDPVNGYLPLGWTMGEWKERRESDKKAVEK 300

Query: 301 AARASMKVQVKAMCDFHAMGVPTVDYGNNIRQMALEEGLENAFDFPGFVPAYIRPLFCRG 360
           AARASMKVQVKAMCDFHAMGVPTVDYGNNIRQMALEEGLENAFDFPGFVPAYIRPLFCRG
Sbjct: 301 AARASMKVQVKAMCDFHAMGVPTVDYGNNIRQMALEEGLENAFDFPGFVPAYIRPLFCRG 360

Query: 361 IGPFRWAALSGDPEDIRKTDAKMKELFPENAGLHRWLDMAQERIAFQGLPARICWIGLGD 420
           IGPFRWAALSGDPEDIRKTDAKMKELFPENAGLHRWLDMAQERIAFQGLPARICWIGLGD
Sbjct: 361 IGPFRWAALSGDPEDIRKTDAKMKELFPENAGLHRWLDMAQERIAFQGLPARICWIGLGD 420

Query: 421 RHKAGLAFNEMVRTGELSAPVVIGRDHLDSGSVASPNRETESMLDGSDAVSDWPLLNALL 480
           RHKAGLAFNEMVRTGELSAPVVIGRDHLDSGSVASPNRETESMLDGSDAVSDWPLLNALL
Sbjct: 421 RHKAGLAFNEMVRTGELSAPVVIGRDHLDSGSVASPNRETESMLDGSDAVSDWPLLNALL 480

Query: 481 NTASGATWVSLHHGGGVGMGFSQHSGVVICCDGSEDADRRVGRVLWNDPATGVMRHADAG 540
           NTASGATWVSLHHGGGVGMGFSQHSGVVICCDGSEDADRRVGRVLWNDPATGVMRHADAG
Sbjct: 481 NTASGATWVSLHHGGGVGMGFSQHSGVVICCDGSEDADRRVGRVLWNDPATGVMRHADAG 540

Query: 541 YDIAKDCAQEHGLNLPGIL 559
           YDIAKDCAQEHGLNLPGIL
Sbjct: 541 YDIAKDCAQEHGLNLPGIL 559


Lambda     K      H
   0.319    0.136    0.426 

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: 1284
Number of extensions: 31
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: 559
Length of database: 559
Length adjustment: 36
Effective length of query: 523
Effective length of database: 523
Effective search space:   273529
Effective search space used:   273529
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate GFF3577 PGA1_c36320 (urocanate hydratase HutU)
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.16899.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   2.2e-285  933.4   0.1   2.5e-285  933.1   0.1    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3577  PGA1_c36320 urocanate hydratase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3577  PGA1_c36320 urocanate hydratase HutU
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  933.1   0.1  2.5e-285  2.5e-285       3     544 ..      11     556 ..       9     557 .. 0.99

  Alignments for each domain:
  == domain 1  score: 933.1 bits;  conditional E-value: 2.5e-285
                          TIGR01228   3 iraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddetllvqsGk 78 
                                        i  p+G e++ak+w++ea++r++mnnl p+vae+p+elvvyGG+G+aar w+ fd ive+lk+le+d+tl+vqsGk
  lcl|FitnessBrowser__Phaeo:GFF3577  11 IFPPTGPEITAKSWMTEAPMRMMMNNLHPDVAENPHELVVYGGIGRAARTWQDFDLIVETLKNLEEDQTLMVQSGK 86 
                                        6679************************************************************************ PP

                          TIGR01228  79 pvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGtyetlaelarkhfgg 154
                                        pvgvf+th++aprvliansnlvp+wa+w++f+el++kGl+myGqmtaGswiyiGtqGi+qGtyet+ae++r+hfgg
  lcl|FitnessBrowser__Phaeo:GFF3577  87 PVGVFQTHKDAPRVLIANSNLVPHWANWDHFNELDKKGLMMYGQMTAGSWIYIGTQGIVQGTYETFAEAGRQHFGG 162
                                        **************************************************************************** PP

                          TIGR01228 155 slkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddldealaraeeakaeGkalsig 230
                                        slkgk++lt GlGgmGGaqpla+ +++a+++ave++++ id+rl+tkyldek++ ldeal+++e+ +a+G+a+s+g
  lcl|FitnessBrowser__Phaeo:GFF3577 163 SLKGKWILTGGLGGMGGAQPLAAVFAGASCLAVECNPDSIDFRLRTKYLDEKAETLDEALQMIERWTAAGEAKSVG 238
                                        **************************************************************************** PP

                          TIGR01228 231 llGnaaevleeller....gvvpdvvtdqtsahdellGyipegytvedadklrdeepeeyvkaakaslakhvrall 302
                                        llGnaae+++el++r    g++pd+vtdqtsahd+++Gy+p g+t+ + +++r+ +++++ kaa+as++++v+a+ 
  lcl|FitnessBrowser__Phaeo:GFF3577 239 LLGNAAEIFPELVKRaetgGIRPDIVTDQTSAHDPVNGYLPLGWTMGEWKERRESDKKAVEKAARASMKVQVKAMC 314
                                        *************99666569******************************************************* PP

                          TIGR01228 303 alqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfceGkGpfrwvalsGdpadiyrtdkavkelfped 378
                                        ++   G+ t dyGnnirq+a eeG+e+afdfpGfvpayir+lfc+G Gpfrw+alsGdp+di +td+++kelfpe+
  lcl|FitnessBrowser__Phaeo:GFF3577 315 DFHAMGVPTVDYGNNIRQMALEEGLENAFDFPGFVPAYIRPLFCRGIGPFRWAALSGDPEDIRKTDAKMKELFPEN 390
                                        **************************************************************************** PP

                          TIGR01228 379 eelhrwidlakekvafqGlparicwlgygereklalainelvrsGelkapvvigrdhldaGsvaspnreteamkdG 454
                                        + lhrw+d+a+e++afqGlparicw+g+g+r+k++la+ne+vr+Gel+apvvigrdhld+Gsvaspnrete+m dG
  lcl|FitnessBrowser__Phaeo:GFF3577 391 AGLHRWLDMAQERIAFQGLPARICWIGLGDRHKAGLAFNEMVRTGELSAPVVIGRDHLDSGSVASPNRETESMLDG 466
                                        **************************************************************************** PP

                          TIGR01228 455 sdavadwpllnallntaaGaswvslhhGGGvglGfslhaglvivadGtdeaaerlkrvltadpGlGvirhadaGye 530
                                        sdav+dwpllnallnta+Ga+wvslhhGGGvg+Gfs+h+g+vi +dG+++a++r+ rvl +dp +Gv+rhadaGy+
  lcl|FitnessBrowser__Phaeo:GFF3577 467 SDAVSDWPLLNALLNTASGATWVSLHHGGGVGMGFSQHSGVVICCDGSEDADRRVGRVLWNDPATGVMRHADAGYD 542
                                        **************************************************************************** PP

                          TIGR01228 531 saldvakeqgldlp 544
                                         a d+a+e+gl+lp
  lcl|FitnessBrowser__Phaeo:GFF3577 543 IAKDCAQEHGLNLP 556
                                        ***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (559 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: 11.54
//
[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