Alignments for a candidate for hutU in Methylobacterium nodulans ORS 2060

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Methylobacterium nodulans ORS 2060

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate WP_015927742.1 MNOD_RS04990 urocanate hydratase

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



>NCBI__GCF_000022085.1:WP_015927742.1
          Length = 554

 Score =  914 bits (2361), Expect = 0.0
 Identities = 434/548 (79%), Positives = 484/548 (88%)

Query: 7   NIREVRSPRGTEISAKSWLTEAPLRMLMNNLDPDVAENPHELVVYGGIGRAARTWADFDR 66
           N R VR+PRG  ++AKSWLTEAPLRMLMNNLDPDVAE P +LVVYGGIGRAAR WA FDR
Sbjct: 6   NARIVRAPRGPALTAKSWLTEAPLRMLMNNLDPDVAERPGDLVVYGGIGRAARDWASFDR 65

Query: 67  IVASLKDLNEDETLLVQSGKPVGVFRTHKDAPRVLIANSNLVPHWATWDHFNELDKKGLA 126
           IVA+LKDL+ED+TLLVQSGKPVG+FRTH DAPRVLIANSNLVPHWATW HF+ELD+KGL 
Sbjct: 66  IVAALKDLDEDQTLLVQSGKPVGIFRTHPDAPRVLIANSNLVPHWATWAHFHELDRKGLM 125

Query: 127 MYGQMTAGSWIYIGTQGIVQGTYETFVEAGRQHYGGSLKGKWILTGGLGGMGGAQPLAAV 186
           MYGQMTAGSWIYIG+QGIVQGTYETFVE GRQHYGG L G+WILT GLGGMGGAQPLAA 
Sbjct: 126 MYGQMTAGSWIYIGSQGIVQGTYETFVEMGRQHYGGDLAGRWILTAGLGGMGGAQPLAAT 185

Query: 187 MAGACCLAVECNPDSIDFRLRTRYLDEKAETLEEAMEMIERWTKAGEPKSVGLLGNAAEI 246
           MAGA CLAVEC   SI+FRLRT Y+D +A  L+EA+ +I+   +A  P+SV L+GNAAE+
Sbjct: 186 MAGASCLAVECRASSIEFRLRTGYVDVQARDLDEALALIDESCRARVPRSVALIGNAAEV 245

Query: 247 LPEMVRRGIRPDMVTDQTSAHDPINGYLPKGWTMAEWKAKRESDPKAVEKAARASMRDHV 306
             E+ RRG+RPD VTDQTSAHDP+NGYLP+GW++AEW+A+RESDP  V  AA+ SM + V
Sbjct: 246 FAEIQRRGVRPDCVTDQTSAHDPVNGYLPRGWSIAEWEARRESDPDGVAAAAKRSMAEQV 305

Query: 307 EAMLAFWDSGVPTLDYGNNIRQVAKDEGLERAFDFPGFVPAYIRPLFCRGIGPFRWAALS 366
             MLAF  +GVPT+DYGNNIRQ+A +EG+  AF FPGFVPAYIRPLFCRG+GPFRW ALS
Sbjct: 306 RVMLAFHRAGVPTVDYGNNIRQMALEEGVADAFAFPGFVPAYIRPLFCRGVGPFRWCALS 365

Query: 367 GDPEDIYRTDRKVKELLPDNKHLHNWLDMARERIAFQGLPARICWVGLGDRHRLGLAFNE 426
           GDPEDIYRTD KVK+LLPDN HLH WLDMAR++I FQGLPARICWVGLGDRHRLGLAFN 
Sbjct: 366 GDPEDIYRTDAKVKQLLPDNAHLHRWLDMARDKIRFQGLPARICWVGLGDRHRLGLAFNA 425

Query: 427 MVRSGELKAPIVIGRDHLDSGSVASPNRETEAMKDGSDAVSDWPLLNALLNTASGATWVS 486
           MVRSGELKAPIVIGRDHLDSGSVASPNRETEAM+DGSDAVSDWPLLNALLNTASGATWVS
Sbjct: 426 MVRSGELKAPIVIGRDHLDSGSVASPNRETEAMRDGSDAVSDWPLLNALLNTASGATWVS 485

Query: 487 LHHGGGVGMGFSQHSGMVICCDGTDDAARRIERVLWNDPATGVMRHADAGYDIAVDCARE 546
           LHHGGGVGMGFSQH+GMVI CDG++ A RR+ERVLWNDPATGVMRHADAGY  A+ CARE
Sbjct: 486 LHHGGGVGMGFSQHAGMVIVCDGSEAADRRLERVLWNDPATGVMRHADAGYPEAIACARE 545

Query: 547 KGLRLPGI 554
           +GL LP +
Sbjct: 546 QGLVLPSL 553


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: 1169
Number of extensions: 48
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: 554
Length adjustment: 36
Effective length of query: 521
Effective length of database: 518
Effective search space:   269878
Effective search space used:   269878
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 WP_015927742.1 MNOD_RS04990 (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.967657.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.8e-289  944.9   0.1   7.9e-289  944.7   0.1    1.0  1  NCBI__GCF_000022085.1:WP_015927742.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000022085.1:WP_015927742.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  944.7   0.1  7.9e-289  7.9e-289       2     544 ..       9     551 ..       8     552 .. 1.00

  Alignments for each domain:
  == domain 1  score: 944.7 bits;  conditional E-value: 7.9e-289
                             TIGR01228   2 eiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddetllv 74 
                                            +raprG  l+ak+w +ea+lr+lmnnldp+vae p +lvvyGG+G+aar+w +fd+iv+ lk l++d+tllv
  NCBI__GCF_000022085.1:WP_015927742.1   9 IVRAPRGPALTAKSWLTEAPLRMLMNNLDPDVAERPGDLVVYGGIGRAARDWASFDRIVAALKDLDEDQTLLV 81 
                                           589********************************************************************** PP

                             TIGR01228  75 qsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGtyetlael 147
                                           qsGkpvg+f+th +aprvliansnlvp+wa+w +f+el++kGl+myGqmtaGswiyiG+qGi+qGtyet++e+
  NCBI__GCF_000022085.1:WP_015927742.1  82 QSGKPVGIFRTHPDAPRVLIANSNLVPHWATWAHFHELDRKGLMMYGQMTAGSWIYIGSQGIVQGTYETFVEM 154
                                           ************************************************************************* PP

                             TIGR01228 148 arkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddldealaraeea 220
                                           +r+h+gg+l g+++ltaGlGgmGGaqpla+t+++a+++ave+  + i++rl+t y+d ++ dldeala ++e+
  NCBI__GCF_000022085.1:WP_015927742.1 155 GRQHYGGDLAGRWILTAGLGGMGGAQPLAATMAGASCLAVECRASSIEFRLRTGYVDVQARDLDEALALIDES 227
                                           ************************************************************************* PP

                             TIGR01228 221 kaeGkalsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadklrdeepeeyvkaakas 293
                                             +  ++s++l Gnaaev+ e+ +rgv+pd vtdqtsahd+++Gy+p g+++++ + +r+ +p+ +  aak s
  NCBI__GCF_000022085.1:WP_015927742.1 228 CRARVPRSVALIGNAAEVFAEIQRRGVRPDCVTDQTSAHDPVNGYLPRGWSIAEWEARRESDPDGVAAAAKRS 300
                                           ************************************************************************* PP

                             TIGR01228 294 lakhvrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfceGkGpfrwvalsGdpadiyr 366
                                           +a++vr +la+ ++G+ t dyGnnirq+a eeGv+daf fpGfvpayir+lfc+G Gpfrw alsGdp+diyr
  NCBI__GCF_000022085.1:WP_015927742.1 301 MAEQVRVMLAFHRAGVPTVDYGNNIRQMALEEGVADAFAFPGFVPAYIRPLFCRGVGPFRWCALSGDPEDIYR 373
                                           ************************************************************************* PP

                             TIGR01228 367 tdkavkelfpedeelhrwidlakekvafqGlparicwlgygereklalainelvrsGelkapvvigrdhldaG 439
                                           td++vk+l+p++++lhrw+d+a++k++fqGlparicw+g+g+r++l+la+n +vrsGelkap+vigrdhld+G
  NCBI__GCF_000022085.1:WP_015927742.1 374 TDAKVKQLLPDNAHLHRWLDMARDKIRFQGLPARICWVGLGDRHRLGLAFNAMVRSGELKAPIVIGRDHLDSG 446
                                           ************************************************************************* PP

                             TIGR01228 440 svaspnreteamkdGsdavadwpllnallntaaGaswvslhhGGGvglGfslhaglvivadGtdeaaerlkrv 512
                                           svaspnreteam+dGsdav+dwpllnallnta+Ga+wvslhhGGGvg+Gfs+hag+viv+dG+++a++rl+rv
  NCBI__GCF_000022085.1:WP_015927742.1 447 SVASPNRETEAMRDGSDAVSDWPLLNALLNTASGATWVSLHHGGGVGMGFSQHAGMVIVCDGSEAADRRLERV 519
                                           ************************************************************************* PP

                             TIGR01228 513 ltadpGlGvirhadaGyesaldvakeqgldlp 544
                                           l +dp +Gv+rhadaGy +a+ +a+eqgl lp
  NCBI__GCF_000022085.1:WP_015927742.1 520 LWNDPATGVMRHADAGYPEAIACAREQGLVLP 551
                                           *****************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (554 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 27.48
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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