Alignments for a candidate for hutU in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Acidovorax sp. GW101-3H11

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate Ac3H11_2557 Urocanate hydratase (EC 4.2.1.49)

Query= reanno::acidovorax_3H11:Ac3H11_2557
         (574 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2557
          Length = 574

 Score = 1167 bits (3019), Expect = 0.0
 Identities = 574/574 (100%), Positives = 574/574 (100%)

Query: 1   MNANDAIIAAASNTDPRHDASRVIRAPRGSQLTCKSWLTEAAYRMIQNNLDAEVAERPQD 60
           MNANDAIIAAASNTDPRHDASRVIRAPRGSQLTCKSWLTEAAYRMIQNNLDAEVAERPQD
Sbjct: 1   MNANDAIIAAASNTDPRHDASRVIRAPRGSQLTCKSWLTEAAYRMIQNNLDAEVAERPQD 60

Query: 61  LVVYGGIGRAARNWECYDQILASLKDLNDDETLLIQSGKPVGVFKTHANAPRVLLANSNL 120
           LVVYGGIGRAARNWECYDQILASLKDLNDDETLLIQSGKPVGVFKTHANAPRVLLANSNL
Sbjct: 61  LVVYGGIGRAARNWECYDQILASLKDLNDDETLLIQSGKPVGVFKTHANAPRVLLANSNL 120

Query: 121 VPKWANWEHFSELDQKGLFMYGQMTAGSWIYIGTQGIVQGTYETFAEAGRKHYGGSLEGK 180
           VPKWANWEHFSELDQKGLFMYGQMTAGSWIYIGTQGIVQGTYETFAEAGRKHYGGSLEGK
Sbjct: 121 VPKWANWEHFSELDQKGLFMYGQMTAGSWIYIGTQGIVQGTYETFAEAGRKHYGGSLEGK 180

Query: 181 WILTAGLGGMGGAQPLAATFAGAVSLNIECQQSSIDFRLRTRYVDKQARDIDHAFELIQQ 240
           WILTAGLGGMGGAQPLAATFAGAVSLNIECQQSSIDFRLRTRYVDKQARDIDHAFELIQQ
Sbjct: 181 WILTAGLGGMGGAQPLAATFAGAVSLNIECQQSSIDFRLRTRYVDKQARDIDHAFELIQQ 240

Query: 241 HTAAKEAVSIALLGNAAEILPELVRRAKAGGLKPDLVTDQTSAHDLVNGYLPAGWTVAQW 300
           HTAAKEAVSIALLGNAAEILPELVRRAKAGGLKPDLVTDQTSAHDLVNGYLPAGWTVAQW
Sbjct: 241 HTAAKEAVSIALLGNAAEILPELVRRAKAGGLKPDLVTDQTSAHDLVNGYLPAGWTVAQW 300

Query: 301 RAAQQDVTQHEVLKKAAAKSCAVHVQAMLDFQHMGIPVVDYGNNIRQVAFDEGVKNAFDF 360
           RAAQQDVTQHEVLKKAAAKSCAVHVQAMLDFQHMGIPVVDYGNNIRQVAFDEGVKNAFDF
Sbjct: 301 RAAQQDVTQHEVLKKAAAKSCAVHVQAMLDFQHMGIPVVDYGNNIRQVAFDEGVKNAFDF 360

Query: 361 PGFVPAYIRPLFCEGKGPFRWVALSGDPEDIRKTDAKIKELFPENKHVHRWLDMAGERIA 420
           PGFVPAYIRPLFCEGKGPFRWVALSGDPEDIRKTDAKIKELFPENKHVHRWLDMAGERIA
Sbjct: 361 PGFVPAYIRPLFCEGKGPFRWVALSGDPEDIRKTDAKIKELFPENKHVHRWLDMAGERIA 420

Query: 421 FQGLPARICWLGLGERHIAGLAFNEMVKNGELKAPIVIGRDHLDTGSVASPNRETEGMKD 480
           FQGLPARICWLGLGERHIAGLAFNEMVKNGELKAPIVIGRDHLDTGSVASPNRETEGMKD
Sbjct: 421 FQGLPARICWLGLGERHIAGLAFNEMVKNGELKAPIVIGRDHLDTGSVASPNRETEGMKD 480

Query: 481 GTDAVSDWPLLNALLNTSGGATWVSLHHGGGVGMGYSQHSGMVIVADGTDAAAQRLANVL 540
           GTDAVSDWPLLNALLNTSGGATWVSLHHGGGVGMGYSQHSGMVIVADGTDAAAQRLANVL
Sbjct: 481 GTDAVSDWPLLNALLNTSGGATWVSLHHGGGVGMGYSQHSGMVIVADGTDAAAQRLANVL 540

Query: 541 VNDCGSGVMRHADAGYELAVETAKKQGLKLPMVK 574
           VNDCGSGVMRHADAGYELAVETAKKQGLKLPMVK
Sbjct: 541 VNDCGSGVMRHADAGYELAVETAKKQGLKLPMVK 574


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: 1379
Number of extensions: 53
Number of successful extensions: 3
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: 574
Length of database: 574
Length adjustment: 36
Effective length of query: 538
Effective length of database: 538
Effective search space:   289444
Effective search space used:   289444
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 Ac3H11_2557 (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.23205.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   2.1e-289  946.6   1.6   2.4e-289  946.4   1.6    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2557  Urocanate hydratase (EC 4.2.1.49


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2557  Urocanate hydratase (EC 4.2.1.49)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  946.4   1.6  2.4e-289  2.4e-289       2     545 .]      23     572 ..      22     572 .. 0.98

  Alignments for each domain:
  == domain 1  score: 946.4 bits;  conditional E-value: 2.4e-289
                                        TIGR01228   2 eiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveel 63 
                                                       iraprG++l++k+w +eaa r+++nnld evae p++lvvyGG+G+aarnwe++d+i+++l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2557  23 VIRAPRGSQLTCKSWLTEAAYRMIQNNLDAEVAERPQDLVVYGGIGRAARNWECYDQILASL 84 
                                                      69************************************************************ PP

                                        TIGR01228  64 krleddetllvqsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmta 125
                                                      k l+ddetll+qsGkpvgvfkth +aprvl+ansnlvpkwa+we+f+el++kGl myGqmta
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2557  85 KDLNDDETLLIQSGKPVGVFKTHANAPRVLLANSNLVPKWANWEHFSELDQKGLFMYGQMTA 146
                                                      ************************************************************** PP

                                        TIGR01228 126 GswiyiGtqGilqGtyetlaelarkhfggslkgklvltaGlGgmGGaqplavtlneavsiav 187
                                                      GswiyiGtqGi+qGtyet+ae++rkh+ggsl+gk++ltaGlGgmGGaqpla+t+++avs+++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2557 147 GSWIYIGTQGIVQGTYETFAEAGRKHYGGSLEGKWILTAGLGGMGGAQPLAATFAGAVSLNI 208
                                                      ************************************************************** PP

                                        TIGR01228 188 evdeeridkrletkyldektddldealaraeeakaeGkalsigllGnaaevleeller.... 245
                                                      e++++ id+rl+t+y+d+++ d+d+a++ +++ +a+ +a+si+llGnaae+l+el++r    
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2557 209 ECQQSSIDFRLRTRYVDKQARDIDHAFELIQQHTAAKEAVSIALLGNAAEILPELVRRakag 270
                                                      ********************************************************995555 PP

                                        TIGR01228 246 gvvpdvvtdqtsahdellGyipegytvedadklrde..epeeyvkaakaslakhvrallalq 305
                                                      g++pd+vtdqtsahd ++Gy+p+g+tv++ +  +++  ++e  +kaa +s a+hv+a+l++q
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2557 271 GLKPDLVTDQTSAHDLVNGYLPAGWTVAQWRAAQQDvtQHEVLKKAAAKSCAVHVQAMLDFQ 332
                                                      69**************************98887776325677788999************** PP

                                        TIGR01228 306 kkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfceGkGpfrwvalsGdpadiyrt 367
                                                      + G  + dyGnnirqva++eGv++afdfpGfvpayir+lfceGkGpfrwvalsGdp+di +t
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2557 333 HMGIPVVDYGNNIRQVAFDEGVKNAFDFPGFVPAYIRPLFCEGKGPFRWVALSGDPEDIRKT 394
                                                      ************************************************************** PP

                                        TIGR01228 368 dkavkelfpedeelhrwidlakekvafqGlparicwlgygereklalainelvrsGelkapv 429
                                                      d+++kelfpe++++hrw+d+a e++afqGlparicwlg+ger+ ++la+ne+v++Gelkap+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2557 395 DAKIKELFPENKHVHRWLDMAGERIAFQGLPARICWLGLGERHIAGLAFNEMVKNGELKAPI 456
                                                      ************************************************************** PP

                                        TIGR01228 430 vigrdhldaGsvaspnreteamkdGsdavadwpllnallntaaGaswvslhhGGGvglGfsl 491
                                                      vigrdhld+Gsvaspnrete mkdG+dav+dwpllnallnt +Ga+wvslhhGGGvg+G+s+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2557 457 VIGRDHLDTGSVASPNRETEGMKDGTDAVSDWPLLNALLNTSGGATWVSLHHGGGVGMGYSQ 518
                                                      ************************************************************** PP

                                        TIGR01228 492 haglvivadGtdeaaerlkrvltadpGlGvirhadaGyesaldvakeqgldlpm 545
                                                      h+g+vivadGtd+aa+rl+ vl +d G Gv+rhadaGye a+++ak+qgl+lpm
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2557 519 HSGMVIVADGTDAAAQRLANVLVNDCGSGVMRHADAGYELAVETAKKQGLKLPM 572
                                                      *****************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (574 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: 00:00:00.02
# Mc/sec: 13.11
//
[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