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.9635.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.23
//
[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:

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:

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:

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:

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