Alignments for a candidate for hutU in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Azospirillum brasilense Sp245

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate AZOBR_RS21740 AZOBR_RS21740 urocanate hydratase

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



>FitnessBrowser__azobra:AZOBR_RS21740
          Length = 562

 Score =  910 bits (2351), Expect = 0.0
 Identities = 451/556 (81%), Positives = 476/556 (85%), Gaps = 5/556 (0%)

Query: 4   PRHNIREVRSPRGTEISAKSWLTEAPLRMLMNNLDPDVAENPHELVVYGGIGRAARTWAD 63
           P  N R +R+P GT++SAKSWLTEAPLRMLMNNLDPDVAENP ELVVYGGIGRAAR W  
Sbjct: 6   PPANRRVIRAPHGTDLSAKSWLTEAPLRMLMNNLDPDVAENPDELVVYGGIGRAARNWDC 65

Query: 64  FDRIVASLKDLNEDETLLVQSGKPVGVFRTHKDAPRVLIANSNLVPHWATWDHFNELDKK 123
           FD IVASLK LNEDETLLVQSGKPVGVFRTH DAPRVLIANSNLVPHWATWDHF ELD K
Sbjct: 66  FDAIVASLKTLNEDETLLVQSGKPVGVFRTHADAPRVLIANSNLVPHWATWDHFRELDAK 125

Query: 124 GLAMYGQMTAGSWIYIGTQGIVQGTYETFVEAGRQHYGGSLKGKWILTGGLGGMGGAQPL 183
           GL MYGQMTAGSWIYIG+QGIVQGTYETFVE GR+HYGG LKG+WILTGGLGGMGGAQPL
Sbjct: 126 GLMMYGQMTAGSWIYIGSQGIVQGTYETFVEVGRRHYGGDLKGRWILTGGLGGMGGAQPL 185

Query: 184 AAVMAGACCLAVECNPDSIDFRLRTRYLDEKAETLEEAMEMIERWTKAGEPKSVGLLGNA 243
           AA MAGA  LAVEC+  SI+ RL T+YLD  A +L+EAM ++     AG   SVGLLGNA
Sbjct: 186 AATMAGASMLAVECSARSIERRLETKYLDRSATSLDEAMAILWEAQAAGTAVSVGLLGNA 245

Query: 244 AEILPEMVRRG-----IRPDMVTDQTSAHDPINGYLPKGWTMAEWKAKRESDPKAVEKAA 298
           AE+ PE+VRR       RPD VTDQTSAHDP+NGYLP GWTM E + KR SDP AV  AA
Sbjct: 246 AEVFPELVRRAKTDPRFRPDAVTDQTSAHDPLNGYLPAGWTMEEAETKRRSDPAAVVAAA 305

Query: 299 RASMRDHVEAMLAFWDSGVPTLDYGNNIRQVAKDEGLERAFDFPGFVPAYIRPLFCRGIG 358
           +ASM  HV AML F   GVPTLDYGNNIRQVAKDEG+  AF FPGFVPAYIRPLFCRGIG
Sbjct: 306 KASMATHVRAMLDFHAMGVPTLDYGNNIRQVAKDEGVADAFAFPGFVPAYIRPLFCRGIG 365

Query: 359 PFRWAALSGDPEDIYRTDRKVKELLPDNKHLHNWLDMARERIAFQGLPARICWVGLGDRH 418
           PFRWAALSGDPEDIYRTD KVKEL+PDN HLHNWLDMARERI FQGLPARICWVGLGDR 
Sbjct: 366 PFRWAALSGDPEDIYRTDAKVKELIPDNPHLHNWLDMARERIRFQGLPARICWVGLGDRA 425

Query: 419 RLGLAFNEMVRSGELKAPIVIGRDHLDSGSVASPNRETEAMKDGSDAVSDWPLLNALLNT 478
           RLGLAFNEMV  GELKAPIVIGRDHLDSGSVASPNRETE M DGSDAVSDWPLLNALLN 
Sbjct: 426 RLGLAFNEMVAKGELKAPIVIGRDHLDSGSVASPNRETEGMIDGSDAVSDWPLLNALLNC 485

Query: 479 ASGATWVSLHHGGGVGMGFSQHSGMVICCDGTDDAARRIERVLWNDPATGVMRHADAGYD 538
           ASGATWVSLHHGGGVGMGFSQHSGMVI  DGTD AA+R+ERVL NDP TGVMRHADAGYD
Sbjct: 486 ASGATWVSLHHGGGVGMGFSQHSGMVIVADGTDAAAKRLERVLTNDPGTGVMRHADAGYD 545

Query: 539 IAVDCAREKGLRLPGI 554
           IA DCA+E+GL LP I
Sbjct: 546 IAKDCAKEQGLTLPMI 561


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: 1172
Number of extensions: 56
Number of successful extensions: 2
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 AZOBR_RS21740 AZOBR_RS21740 (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.23776.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     9e-297  970.9   0.3     1e-296  970.7   0.3    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS21740  AZOBR_RS21740 urocanate hydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS21740  AZOBR_RS21740 urocanate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  970.7   0.3    1e-296    1e-296       2     545 .]      12     560 ..      11     560 .. 0.99

  Alignments for each domain:
  == domain 1  score: 970.7 bits;  conditional E-value: 1e-296
                                 TIGR01228   2 eiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrledde 70 
                                                irap+G++l+ak+w +ea+lr+lmnnldp+vae+p+elvvyGG+G+aarnw++fd+iv++lk+l++de
  lcl|FitnessBrowser__azobra:AZOBR_RS21740  12 VIRAPHGTDLSAKSWLTEAPLRMLMNNLDPDVAENPDELVVYGGIGRAARNWDCFDAIVASLKTLNEDE 80 
                                               69******************************************************************* PP

                                 TIGR01228  71 tllvqsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqG 139
                                               tllvqsGkpvgvf+th +aprvliansnlvp+wa+w++f+el+akGl+myGqmtaGswiyiG+qGi+qG
  lcl|FitnessBrowser__azobra:AZOBR_RS21740  81 TLLVQSGKPVGVFRTHADAPRVLIANSNLVPHWATWDHFRELDAKGLMMYGQMTAGSWIYIGSQGIVQG 149
                                               ********************************************************************* PP

                                 TIGR01228 140 tyetlaelarkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektd 208
                                               tyet++e++r+h+gg+lkg+++lt GlGgmGGaqpla+t+++a+++ave+  + i++rletkyld+ ++
  lcl|FitnessBrowser__azobra:AZOBR_RS21740 150 TYETFVEVGRRHYGGDLKGRWILTGGLGGMGGAQPLAATMAGASMLAVECSARSIERRLETKYLDRSAT 218
                                               ********************************************************************* PP

                                 TIGR01228 209 dldealaraeeakaeGkalsigllGnaaevleellerg.....vvpdvvtdqtsahdellGyipegytv 272
                                               +ldea+a   ea+a+G+a+s+gllGnaaev++el++r      ++pd vtdqtsahd+l+Gy+p+g+t+
  lcl|FitnessBrowser__azobra:AZOBR_RS21740 219 SLDEAMAILWEAQAAGTAVSVGLLGNAAEVFPELVRRAktdprFRPDAVTDQTSAHDPLNGYLPAGWTM 287
                                               ***********************************9953444489************************ PP

                                 TIGR01228 273 edadklrdeepeeyvkaakaslakhvrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayi 341
                                               e+a+  r  +p+++v aakas+a+hvra+l++   G+ t+dyGnnirqvak+eGv+daf fpGfvpayi
  lcl|FitnessBrowser__azobra:AZOBR_RS21740 288 EEAETKRRSDPAAVVAAAKASMATHVRAMLDFHAMGVPTLDYGNNIRQVAKDEGVADAFAFPGFVPAYI 356
                                               ********************************************************************* PP

                                 TIGR01228 342 rdlfceGkGpfrwvalsGdpadiyrtdkavkelfpedeelhrwidlakekvafqGlparicwlgygere 410
                                               r+lfc+G Gpfrw+alsGdp+diyrtd++vkel+p++ +lh+w+d+a+e+++fqGlparicw+g+g+r+
  lcl|FitnessBrowser__azobra:AZOBR_RS21740 357 RPLFCRGIGPFRWAALSGDPEDIYRTDAKVKELIPDNPHLHNWLDMARERIRFQGLPARICWVGLGDRA 425
                                               ********************************************************************* PP

                                 TIGR01228 411 klalainelvrsGelkapvvigrdhldaGsvaspnreteamkdGsdavadwpllnallntaaGaswvsl 479
                                               +l+la+ne+v +Gelkap+vigrdhld+Gsvaspnrete m dGsdav+dwpllnalln a+Ga+wvsl
  lcl|FitnessBrowser__azobra:AZOBR_RS21740 426 RLGLAFNEMVAKGELKAPIVIGRDHLDSGSVASPNRETEGMIDGSDAVSDWPLLNALLNCASGATWVSL 494
                                               ********************************************************************* PP

                                 TIGR01228 480 hhGGGvglGfslhaglvivadGtdeaaerlkrvltadpGlGvirhadaGyesaldvakeqgldlpm 545
                                               hhGGGvg+Gfs+h+g+vivadGtd+aa+rl+rvlt+dpG+Gv+rhadaGy+ a d+akeqgl+lpm
  lcl|FitnessBrowser__azobra:AZOBR_RS21740 495 HHGGGVGMGFSQHSGMVIVADGTDAAAKRLERVLTNDPGTGVMRHADAGYDIAKDCAKEQGLTLPM 560
                                               *****************************************************************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: 12.04
//
[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