Alignments for a candidate for hutU in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Sinorhizobium meliloti 1021

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate SM_b21163 SM_b21163 urocanate hydratase

Query= reanno::Smeli:SM_b21163
         (557 letters)



>FitnessBrowser__Smeli:SM_b21163
          Length = 557

 Score = 1153 bits (2983), Expect = 0.0
 Identities = 557/557 (100%), Positives = 557/557 (100%)

Query: 1   MNNPRHNIREVRSPRGTEISAKSWLTEAPLRMLMNNLDPDVAENPHELVVYGGIGRAART 60
           MNNPRHNIREVRSPRGTEISAKSWLTEAPLRMLMNNLDPDVAENPHELVVYGGIGRAART
Sbjct: 1   MNNPRHNIREVRSPRGTEISAKSWLTEAPLRMLMNNLDPDVAENPHELVVYGGIGRAART 60

Query: 61  WADFDRIVASLKDLNEDETLLVQSGKPVGVFRTHKDAPRVLIANSNLVPHWATWDHFNEL 120
           WADFDRIVASLKDLNEDETLLVQSGKPVGVFRTHKDAPRVLIANSNLVPHWATWDHFNEL
Sbjct: 61  WADFDRIVASLKDLNEDETLLVQSGKPVGVFRTHKDAPRVLIANSNLVPHWATWDHFNEL 120

Query: 121 DKKGLAMYGQMTAGSWIYIGTQGIVQGTYETFVEAGRQHYGGSLKGKWILTGGLGGMGGA 180
           DKKGLAMYGQMTAGSWIYIGTQGIVQGTYETFVEAGRQHYGGSLKGKWILTGGLGGMGGA
Sbjct: 121 DKKGLAMYGQMTAGSWIYIGTQGIVQGTYETFVEAGRQHYGGSLKGKWILTGGLGGMGGA 180

Query: 181 QPLAAVMAGACCLAVECNPDSIDFRLRTRYLDEKAETLEEAMEMIERWTKAGEPKSVGLL 240
           QPLAAVMAGACCLAVECNPDSIDFRLRTRYLDEKAETLEEAMEMIERWTKAGEPKSVGLL
Sbjct: 181 QPLAAVMAGACCLAVECNPDSIDFRLRTRYLDEKAETLEEAMEMIERWTKAGEPKSVGLL 240

Query: 241 GNAAEILPEMVRRGIRPDMVTDQTSAHDPINGYLPKGWTMAEWKAKRESDPKAVEKAARA 300
           GNAAEILPEMVRRGIRPDMVTDQTSAHDPINGYLPKGWTMAEWKAKRESDPKAVEKAARA
Sbjct: 241 GNAAEILPEMVRRGIRPDMVTDQTSAHDPINGYLPKGWTMAEWKAKRESDPKAVEKAARA 300

Query: 301 SMRDHVEAMLAFWDSGVPTLDYGNNIRQVAKDEGLERAFDFPGFVPAYIRPLFCRGIGPF 360
           SMRDHVEAMLAFWDSGVPTLDYGNNIRQVAKDEGLERAFDFPGFVPAYIRPLFCRGIGPF
Sbjct: 301 SMRDHVEAMLAFWDSGVPTLDYGNNIRQVAKDEGLERAFDFPGFVPAYIRPLFCRGIGPF 360

Query: 361 RWAALSGDPEDIYRTDRKVKELLPDNKHLHNWLDMARERIAFQGLPARICWVGLGDRHRL 420
           RWAALSGDPEDIYRTDRKVKELLPDNKHLHNWLDMARERIAFQGLPARICWVGLGDRHRL
Sbjct: 361 RWAALSGDPEDIYRTDRKVKELLPDNKHLHNWLDMARERIAFQGLPARICWVGLGDRHRL 420

Query: 421 GLAFNEMVRSGELKAPIVIGRDHLDSGSVASPNRETEAMKDGSDAVSDWPLLNALLNTAS 480
           GLAFNEMVRSGELKAPIVIGRDHLDSGSVASPNRETEAMKDGSDAVSDWPLLNALLNTAS
Sbjct: 421 GLAFNEMVRSGELKAPIVIGRDHLDSGSVASPNRETEAMKDGSDAVSDWPLLNALLNTAS 480

Query: 481 GATWVSLHHGGGVGMGFSQHSGMVICCDGTDDAARRIERVLWNDPATGVMRHADAGYDIA 540
           GATWVSLHHGGGVGMGFSQHSGMVICCDGTDDAARRIERVLWNDPATGVMRHADAGYDIA
Sbjct: 481 GATWVSLHHGGGVGMGFSQHSGMVICCDGTDDAARRIERVLWNDPATGVMRHADAGYDIA 540

Query: 541 VDCAREKGLRLPGILGE 557
           VDCAREKGLRLPGILGE
Sbjct: 541 VDCAREKGLRLPGILGE 557


Lambda     K      H
   0.319    0.137    0.431 

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: 1357
Number of extensions: 44
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: 557
Length of database: 557
Length adjustment: 36
Effective length of query: 521
Effective length of database: 521
Effective search space:   271441
Effective search space used:   271441
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 SM_b21163 SM_b21163 (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.31336.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   1.7e-299  979.9   0.0     2e-299  979.7   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SM_b21163  SM_b21163 urocanate hydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b21163  SM_b21163 urocanate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  979.7   0.0    2e-299    2e-299       1     544 [.       9     552 ..       9     553 .. 1.00

  Alignments for each domain:
  == domain 1  score: 979.7 bits;  conditional E-value: 2e-299
                            TIGR01228   1 keiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddetllv 74 
                                          +e+r+prG+e++ak+w +ea+lr+lmnnldp+vae+p+elvvyGG+G+aar w  fd+iv++lk l++detllv
  lcl|FitnessBrowser__Smeli:SM_b21163   9 REVRSPRGTEISAKSWLTEAPLRMLMNNLDPDVAENPHELVVYGGIGRAARTWADFDRIVASLKDLNEDETLLV 82 
                                          689*********************************************************************** PP

                            TIGR01228  75 qsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGtyetlaela 148
                                          qsGkpvgvf+th++aprvliansnlvp+wa+w++f+el++kGl+myGqmtaGswiyiGtqGi+qGtyet++e++
  lcl|FitnessBrowser__Smeli:SM_b21163  83 QSGKPVGVFRTHKDAPRVLIANSNLVPHWATWDHFNELDKKGLAMYGQMTAGSWIYIGTQGIVQGTYETFVEAG 156
                                          ************************************************************************** PP

                            TIGR01228 149 rkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddldealaraeeaka 222
                                          r+h+ggslkgk++lt GlGgmGGaqpla+ +++a+++ave++++ id+rl+t+yldek++ l+ea++++e+ ++
  lcl|FitnessBrowser__Smeli:SM_b21163 157 RQHYGGSLKGKWILTGGLGGMGGAQPLAAVMAGACCLAVECNPDSIDFRLRTRYLDEKAETLEEAMEMIERWTK 230
                                          ************************************************************************** PP

                            TIGR01228 223 eGkalsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadklrdeepeeyvkaakaslak 296
                                          +G+++s+gllGnaae+l+e+++rg++pd+vtdqtsahd+++Gy+p+g+t+++ +  r+ +p+++ kaa+as+  
  lcl|FitnessBrowser__Smeli:SM_b21163 231 AGEPKSVGLLGNAAEILPEMVRRGIRPDMVTDQTSAHDPINGYLPKGWTMAEWKAKRESDPKAVEKAARASMRD 304
                                          ************************************************************************** PP

                            TIGR01228 297 hvrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfceGkGpfrwvalsGdpadiyrtdka 370
                                          hv+a+la+ + G+ t+dyGnnirqvak+eG+e afdfpGfvpayir+lfc+G Gpfrw+alsGdp+diyrtd++
  lcl|FitnessBrowser__Smeli:SM_b21163 305 HVEAMLAFWDSGVPTLDYGNNIRQVAKDEGLERAFDFPGFVPAYIRPLFCRGIGPFRWAALSGDPEDIYRTDRK 378
                                          ************************************************************************** PP

                            TIGR01228 371 vkelfpedeelhrwidlakekvafqGlparicwlgygereklalainelvrsGelkapvvigrdhldaGsvasp 444
                                          vkel+p++++lh+w+d+a+e++afqGlparicw+g+g+r++l+la+ne+vrsGelkap+vigrdhld+Gsvasp
  lcl|FitnessBrowser__Smeli:SM_b21163 379 VKELLPDNKHLHNWLDMARERIAFQGLPARICWVGLGDRHRLGLAFNEMVRSGELKAPIVIGRDHLDSGSVASP 452
                                          ************************************************************************** PP

                            TIGR01228 445 nreteamkdGsdavadwpllnallntaaGaswvslhhGGGvglGfslhaglvivadGtdeaaerlkrvltadpG 518
                                          nreteamkdGsdav+dwpllnallnta+Ga+wvslhhGGGvg+Gfs+h+g+vi +dGtd+aa+r++rvl +dp 
  lcl|FitnessBrowser__Smeli:SM_b21163 453 NRETEAMKDGSDAVSDWPLLNALLNTASGATWVSLHHGGGVGMGFSQHSGMVICCDGTDDAARRIERVLWNDPA 526
                                          ************************************************************************** PP

                            TIGR01228 519 lGvirhadaGyesaldvakeqgldlp 544
                                          +Gv+rhadaGy+ a+d+a+e+gl+lp
  lcl|FitnessBrowser__Smeli:SM_b21163 527 TGVMRHADAGYDIAVDCAREKGLRLP 552
                                          ************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (557 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: 00:00:00.03
# Mc/sec: 9.44
//
[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)
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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