Alignments for a candidate for hutU in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Burkholderia phytofirmans PsJN

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate BPHYT_RS07565 BPHYT_RS07565 urocanate hydratase

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



>FitnessBrowser__BFirm:BPHYT_RS07565
          Length = 562

 Score =  848 bits (2191), Expect = 0.0
 Identities = 402/558 (72%), Positives = 467/558 (83%), Gaps = 6/558 (1%)

Query: 1   MNNPRH------NIREVRSPRGTEISAKSWLTEAPLRMLMNNLDPDVAENPHELVVYGGI 54
           MNNP+H        R +R+PRG E + K+W+ EA  RM+ NNLDP+VAE+PH LVVYGGI
Sbjct: 1   MNNPKHIDPRLDPTRTIRAPRGAEKTCKTWIAEAAYRMIQNNLDPEVAEHPHALVVYGGI 60

Query: 55  GRAARTWADFDRIVASLKDLNEDETLLVQSGKPVGVFRTHKDAPRVLIANSNLVPHWATW 114
           GRAAR W  FD+I+ SLKDL E+ETLL+QSGKPVGVFRTH DAPRVL+ANSNLVPHWATW
Sbjct: 61  GRAARNWDCFDQILKSLKDLEENETLLIQSGKPVGVFRTHADAPRVLLANSNLVPHWATW 120

Query: 115 DHFNELDKKGLAMYGQMTAGSWIYIGTQGIVQGTYETFVEAGRQHYGGSLKGKWILTGGL 174
           +HF+ELD+KGL MYGQMTAGSWIYIG+QGIVQGTYETF     QH+ G   G+WILTGGL
Sbjct: 121 EHFHELDRKGLMMYGQMTAGSWIYIGSQGIVQGTYETFFSVANQHFNGDPSGRWILTGGL 180

Query: 175 GGMGGAQPLAAVMAGACCLAVECNPDSIDFRLRTRYLDEKAETLEEAMEMIERWTKAGEP 234
           GGMGGAQPLAA MAG   +AVEC+   IDFRL+TRY+D+KA TL+EA+ M+E   KAG+P
Sbjct: 181 GGMGGAQPLAATMAGFSMIAVECDETRIDFRLKTRYVDKKAATLDEALAMLEEAKKAGKP 240

Query: 235 KSVGLLGNAAEILPEMVRRGIRPDMVTDQTSAHDPINGYLPKGWTMAEWKAKRESDPKAV 294
            S+GLLGNAA++  E V RGI PD VTDQTSAHDPI+GYLP+GW + +W+ ++++ P ++
Sbjct: 241 VSIGLLGNAADVFAECVTRGITPDCVTDQTSAHDPIHGYLPQGWNVEDWRERQKTVPDSI 300

Query: 295 EKAARASMRDHVEAMLAFWDSGVPTLDYGNNIRQVAKDEGLERAFDFPGFVPAYIRPLFC 354
              A+ SM   V+AML   + G  TLDYGNNIRQ+A + G+E AFDFPGFVPAYIRPLFC
Sbjct: 301 VLPAKQSMAKQVQAMLTLQERGAATLDYGNNIRQMALEMGVENAFDFPGFVPAYIRPLFC 360

Query: 355 RGIGPFRWAALSGDPEDIYRTDRKVKELLPDNKHLHNWLDMARERIAFQGLPARICWVGL 414
            G GPFRW ALSGDPEDIY+TD KVKEL+PD+ HLHNWLDMARERIAFQGLPARICWVG+
Sbjct: 361 EGKGPFRWVALSGDPEDIYKTDAKVKELIPDDPHLHNWLDMARERIAFQGLPARICWVGV 420

Query: 415 GDRHRLGLAFNEMVRSGELKAPIVIGRDHLDSGSVASPNRETEAMKDGSDAVSDWPLLNA 474
            DR+RLG AFNEMV++GELKAPIVIGRDHLD+GSVASPNRETE+MKDGSDAVSDWPLLNA
Sbjct: 421 KDRYRLGQAFNEMVKNGELKAPIVIGRDHLDTGSVASPNRETESMKDGSDAVSDWPLLNA 480

Query: 475 LLNTASGATWVSLHHGGGVGMGFSQHSGMVICCDGTDDAARRIERVLWNDPATGVMRHAD 534
           LLNTA GA+WVSLHHGGGVGMGFSQHSG+VI  DGTD A  R+ RVL+NDPATGVMRHAD
Sbjct: 481 LLNTAGGASWVSLHHGGGVGMGFSQHSGVVIVADGTDAAKERLGRVLFNDPATGVMRHAD 540

Query: 535 AGYDIAVDCAREKGLRLP 552
           AGY++A + ARE GL LP
Sbjct: 541 AGYELAQETAREAGLNLP 558


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: 1130
Number of extensions: 52
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: 562
Length adjustment: 36
Effective length of query: 521
Effective length of database: 526
Effective search space:   274046
Effective search space used:   274046
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 BPHYT_RS07565 BPHYT_RS07565 (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.24069.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.1e-294  964.0   0.2   1.3e-294  963.8   0.2    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS07565  BPHYT_RS07565 urocanate hydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS07565  BPHYT_RS07565 urocanate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  963.8   0.2  1.3e-294  1.3e-294       1     545 []      15     559 ..      15     559 .. 1.00

  Alignments for each domain:
  == domain 1  score: 963.8 bits;  conditional E-value: 1.3e-294
                                TIGR01228   1 keiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrledde 70 
                                              ++iraprG e+++k+w+ eaa r+++nnldpevae+p+ lvvyGG+G+aarnw++fd+i+++lk le++e
  lcl|FitnessBrowser__BFirm:BPHYT_RS07565  15 RTIRAPRGAEKTCKTWIAEAAYRMIQNNLDPEVAEHPHALVVYGGIGRAARNWDCFDQILKSLKDLEENE 84 
                                              689******************************************************************* PP

                                TIGR01228  71 tllvqsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGt 140
                                              tll+qsGkpvgvf+th +aprvl+ansnlvp+wa+we+f+el++kGl+myGqmtaGswiyiG+qGi+qGt
  lcl|FitnessBrowser__BFirm:BPHYT_RS07565  85 TLLIQSGKPVGVFRTHADAPRVLLANSNLVPHWATWEHFHELDRKGLMMYGQMTAGSWIYIGSQGIVQGT 154
                                              ********************************************************************** PP

                                TIGR01228 141 yetlaelarkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddl 210
                                              yet+ ++a++hf g+ +g+++lt GlGgmGGaqpla+t+++ ++iave+de+rid+rl+t+y+d+k++ l
  lcl|FitnessBrowser__BFirm:BPHYT_RS07565 155 YETFFSVANQHFNGDPSGRWILTGGLGGMGGAQPLAATMAGFSMIAVECDETRIDFRLKTRYVDKKAATL 224
                                              ********************************************************************** PP

                                TIGR01228 211 dealaraeeakaeGkalsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadklrd 280
                                              deala+ eeak++Gk++sigllGnaa+v+ e ++rg++pd vtdqtsahd++ Gy+p+g+ ved +++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS07565 225 DEALAMLEEAKKAGKPVSIGLLGNAADVFAECVTRGITPDCVTDQTSAHDPIHGYLPQGWNVEDWRERQK 294
                                              ********************************************************************** PP

                                TIGR01228 281 eepeeyvkaakaslakhvrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfceGkG 350
                                              + p+ +v  ak+s+ak+v+a+l+lq++Ga t+dyGnnirq+a e Gve+afdfpGfvpayir+lfceGkG
  lcl|FitnessBrowser__BFirm:BPHYT_RS07565 295 TVPDSIVLPAKQSMAKQVQAMLTLQERGAATLDYGNNIRQMALEMGVENAFDFPGFVPAYIRPLFCEGKG 364
                                              ********************************************************************** PP

                                TIGR01228 351 pfrwvalsGdpadiyrtdkavkelfpedeelhrwidlakekvafqGlparicwlgygereklalainelv 420
                                              pfrwvalsGdp+diy+td++vkel+p+d +lh+w+d+a+e++afqGlparicw+g ++r +l+ a+ne+v
  lcl|FitnessBrowser__BFirm:BPHYT_RS07565 365 PFRWVALSGDPEDIYKTDAKVKELIPDDPHLHNWLDMARERIAFQGLPARICWVGVKDRYRLGQAFNEMV 434
                                              ********************************************************************** PP

                                TIGR01228 421 rsGelkapvvigrdhldaGsvaspnreteamkdGsdavadwpllnallntaaGaswvslhhGGGvglGfs 490
                                              ++Gelkap+vigrdhld+Gsvaspnrete+mkdGsdav+dwpllnallnta+GaswvslhhGGGvg+Gfs
  lcl|FitnessBrowser__BFirm:BPHYT_RS07565 435 KNGELKAPIVIGRDHLDTGSVASPNRETESMKDGSDAVSDWPLLNALLNTAGGASWVSLHHGGGVGMGFS 504
                                              ********************************************************************** PP

                                TIGR01228 491 lhaglvivadGtdeaaerlkrvltadpGlGvirhadaGyesaldvakeqgldlpm 545
                                              +h+g+vivadGtd+a+erl rvl +dp +Gv+rhadaGye a ++a+e gl+lpm
  lcl|FitnessBrowser__BFirm:BPHYT_RS07565 505 QHSGVVIVADGTDAAKERLGRVLFNDPATGVMRHADAGYELAQETAREAGLNLPM 559
                                              ******************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (562 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 7.17
//
[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