Alignments for a candidate for hutU in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Klebsiella michiganensis M5al

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate BWI76_RS08735 BWI76_RS08735 urocanate hydratase

Query= reanno::Koxy:BWI76_RS08735
         (562 letters)



>FitnessBrowser__Koxy:BWI76_RS08735
          Length = 562

 Score = 1154 bits (2984), Expect = 0.0
 Identities = 562/562 (100%), Positives = 562/562 (100%)

Query: 1   MSQSKYRQQDVRAPRGTTLNAKSWLTEAPLRMLMNNLDPDVAENPHELVVYGGIGRAARN 60
           MSQSKYRQQDVRAPRGTTLNAKSWLTEAPLRMLMNNLDPDVAENPHELVVYGGIGRAARN
Sbjct: 1   MSQSKYRQQDVRAPRGTTLNAKSWLTEAPLRMLMNNLDPDVAENPHELVVYGGIGRAARN 60

Query: 61  WECYDAIVKALKNLESDETLLVQSGKPVGVFKTHENSPRVLIANSNLVPHWATWEHFNEL 120
           WECYDAIVKALKNLESDETLLVQSGKPVGVFKTHENSPRVLIANSNLVPHWATWEHFNEL
Sbjct: 61  WECYDAIVKALKNLESDETLLVQSGKPVGVFKTHENSPRVLIANSNLVPHWATWEHFNEL 120

Query: 121 DAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYQGSLKGRWVLTAGLGGMGGA 180
           DAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYQGSLKGRWVLTAGLGGMGGA
Sbjct: 121 DAKGLAMYGQMTAGSWIYIGSQGIVQGTYETFVEAGRQHYQGSLKGRWVLTAGLGGMGGA 180

Query: 181 QPLAATLAGACSLNIECQQSRIDFRLRTRYVDEQATSLDDALARIKKYTAEGRAISIALC 240
           QPLAATLAGACSLNIECQQSRIDFRLRTRYVDEQATSLDDALARIKKYTAEGRAISIALC
Sbjct: 181 QPLAATLAGACSLNIECQQSRIDFRLRTRYVDEQATSLDDALARIKKYTAEGRAISIALC 240

Query: 241 GNAADIVPEMVKRGVRPDMVTDQTSAHDPLHGYLPKGWNWEEYQAKAESDPRGTILAAKR 300
           GNAADIVPEMVKRGVRPDMVTDQTSAHDPLHGYLPKGWNWEEYQAKAESDPRGTILAAKR
Sbjct: 241 GNAADIVPEMVKRGVRPDMVTDQTSAHDPLHGYLPKGWNWEEYQAKAESDPRGTILAAKR 300

Query: 301 SMADHVQAMLAFHDMGVPTFDYGNNIRQMAQEMGVDNAFAFPGFVPAYIRPLFCRGIGPF 360
           SMADHVQAMLAFHDMGVPTFDYGNNIRQMAQEMGVDNAFAFPGFVPAYIRPLFCRGIGPF
Sbjct: 301 SMADHVQAMLAFHDMGVPTFDYGNNIRQMAQEMGVDNAFAFPGFVPAYIRPLFCRGIGPF 360

Query: 361 RWVALSGDPQDIYKTDAKVKEIVKDDKHLHHWLDMARERISFQGLPARICWVGLEWRQKL 420
           RWVALSGDPQDIYKTDAKVKEIVKDDKHLHHWLDMARERISFQGLPARICWVGLEWRQKL
Sbjct: 361 RWVALSGDPQDIYKTDAKVKEIVKDDKHLHHWLDMARERISFQGLPARICWVGLEWRQKL 420

Query: 421 GLAFNEMVRSGELSAPIVIGRDHLDSGSVASPNRETEAMRDGSDAVSDWPLLNALLNTAS 480
           GLAFNEMVRSGELSAPIVIGRDHLDSGSVASPNRETEAMRDGSDAVSDWPLLNALLNTAS
Sbjct: 421 GLAFNEMVRSGELSAPIVIGRDHLDSGSVASPNRETEAMRDGSDAVSDWPLLNALLNTAS 480

Query: 481 GATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAARIARVLHNDPATGVMRHADAGYDIA 540
           GATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAARIARVLHNDPATGVMRHADAGYDIA
Sbjct: 481 GATWVSLHHGGGVGMGFSQHSGMVIVCDGTDEAAARIARVLHNDPATGVMRHADAGYDIA 540

Query: 541 IECATEQGLNLPMVAATQGHAK 562
           IECATEQGLNLPMVAATQGHAK
Sbjct: 541 IECATEQGLNLPMVAATQGHAK 562


Lambda     K      H
   0.319    0.134    0.416 

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: 1294
Number of extensions: 39
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: 562
Length of database: 562
Length adjustment: 36
Effective length of query: 526
Effective length of database: 526
Effective search space:   276676
Effective search space used:   276676
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 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate BWI76_RS08735 BWI76_RS08735 (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.27258.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   5.6e-305  998.0   0.5   6.4e-305  997.8   0.5    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS08735  BWI76_RS08735 urocanate hydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS08735  BWI76_RS08735 urocanate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  997.8   0.5  6.4e-305  6.4e-305       2     545 .]      10     553 ..       9     553 .. 1.00

  Alignments for each domain:
  == domain 1  score: 997.8 bits;  conditional E-value: 6.4e-305
                               TIGR01228   2 eiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddetl 72 
                                             ++raprG++l+ak+w +ea+lr+lmnnldp+vae+p+elvvyGG+G+aarnwe++d+iv+ lk+le detl
  lcl|FitnessBrowser__Koxy:BWI76_RS08735  10 DVRAPRGTTLNAKSWLTEAPLRMLMNNLDPDVAENPHELVVYGGIGRAARNWECYDAIVKALKNLESDETL 80 
                                             79********************************************************************* PP

                               TIGR01228  73 lvqsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGtyet 143
                                             lvqsGkpvgvfkthe++prvliansnlvp+wa+we+f+el+akGl+myGqmtaGswiyiG+qGi+qGtyet
  lcl|FitnessBrowser__Koxy:BWI76_RS08735  81 LVQSGKPVGVFKTHENSPRVLIANSNLVPHWATWEHFNELDAKGLAMYGQMTAGSWIYIGSQGIVQGTYET 151
                                             *********************************************************************** PP

                               TIGR01228 144 laelarkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddldeal 214
                                             ++e++r+h+ gslkg++vltaGlGgmGGaqpla+tl++a+s+++e++++rid+rl+t+y+de++++ld+al
  lcl|FitnessBrowser__Koxy:BWI76_RS08735 152 FVEAGRQHYQGSLKGRWVLTAGLGGMGGAQPLAATLAGACSLNIECQQSRIDFRLRTRYVDEQATSLDDAL 222
                                             *********************************************************************** PP

                               TIGR01228 215 araeeakaeGkalsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadklrdeepee 285
                                             ar+++++aeG+a+si+l Gnaa++++e+++rgv+pd+vtdqtsahd+l Gy+p+g+ +e+++  ++ +p  
  lcl|FitnessBrowser__Koxy:BWI76_RS08735 223 ARIKKYTAEGRAISIALCGNAADIVPEMVKRGVRPDMVTDQTSAHDPLHGYLPKGWNWEEYQAKAESDPRG 293
                                             *********************************************************************** PP

                               TIGR01228 286 yvkaakaslakhvrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfceGkGpfrwva 356
                                              + aak s+a hv+a+la+ + G+ tfdyGnnirq+a+e Gv++af fpGfvpayir+lfc+G Gpfrwva
  lcl|FitnessBrowser__Koxy:BWI76_RS08735 294 TILAAKRSMADHVQAMLAFHDMGVPTFDYGNNIRQMAQEMGVDNAFAFPGFVPAYIRPLFCRGIGPFRWVA 364
                                             *********************************************************************** PP

                               TIGR01228 357 lsGdpadiyrtdkavkelfpedeelhrwidlakekvafqGlparicwlgygereklalainelvrsGelka 427
                                             lsGdp+diy+td++vke++++d++lh+w+d+a+e+++fqGlparicw+g+  r+kl+la+ne+vrsGel+a
  lcl|FitnessBrowser__Koxy:BWI76_RS08735 365 LSGDPQDIYKTDAKVKEIVKDDKHLHHWLDMARERISFQGLPARICWVGLEWRQKLGLAFNEMVRSGELSA 435
                                             *********************************************************************** PP

                               TIGR01228 428 pvvigrdhldaGsvaspnreteamkdGsdavadwpllnallntaaGaswvslhhGGGvglGfslhaglviv 498
                                             p+vigrdhld+Gsvaspnreteam+dGsdav+dwpllnallnta+Ga+wvslhhGGGvg+Gfs+h+g+viv
  lcl|FitnessBrowser__Koxy:BWI76_RS08735 436 PIVIGRDHLDSGSVASPNRETEAMRDGSDAVSDWPLLNALLNTASGATWVSLHHGGGVGMGFSQHSGMVIV 506
                                             *********************************************************************** PP

                               TIGR01228 499 adGtdeaaerlkrvltadpGlGvirhadaGyesaldvakeqgldlpm 545
                                             +dGtdeaa r++rvl +dp +Gv+rhadaGy+ a+++a eqgl+lpm
  lcl|FitnessBrowser__Koxy:BWI76_RS08735 507 CDGTDEAAARIARVLHNDPATGVMRHADAGYDIAIECATEQGLNLPM 553
                                             **********************************************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 0.02s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.35
//
[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