Alignments for a candidate for HPD in Amycolatopsis halophila YIM 93223

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Amycolatopsis halophila YIM 93223

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_034269963.1 AMYHA_RS09050 4-hydroxyphenylpyruvate dioxygenase

Query= BRENDA::Q53586
         (381 letters)



>NCBI__GCF_000504245.1:WP_034269963.1
          Length = 400

 Score =  500 bits (1287), Expect = e-146
 Identities = 251/371 (67%), Positives = 297/371 (80%), Gaps = 9/371 (2%)

Query: 16  DPFPVKGMDAVVFAVGNAKQAAHYYSTAFGMQLVAYSGPENGSRETASYVLTNGSARFVL 75
           DPFPVK MDAVVF  GNA Q A +Y  AFGM+LVAY+GPE+G+ +  +YVLT+GSARFV+
Sbjct: 34  DPFPVKAMDAVVFVSGNATQTALFYQFAFGMKLVAYTGPEHGTADHKAYVLTSGSARFVI 93

Query: 76  TSVIKPATPWGHFLADHVAEHGDGVVDLAIEVPDARAAHAYAIEHGARSVAEPYELKDEH 135
              +KP +P    L DH  +HGDGVVDLA+EV D     A+A   GA  + EP+++ DEH
Sbjct: 94  KGGVKPDSP----LLDHHRKHGDGVVDLALEVADVDKCIAHARSCGATVLDEPHDVSDEH 149

Query: 136 GTVVLAAIATYGKTRHTLVDRTGYDGPYLPGYVAAAPIVEPPA---HRTFQAIDHCVGNV 192
           GTV +AAIATYG+TRHTL+DR+ Y GPYLPGYVA    ++ PA    R FQAIDHCVGNV
Sbjct: 150 GTVRMAAIATYGETRHTLIDRSRYTGPYLPGYVARESGLQRPAGAPKRLFQAIDHCVGNV 209

Query: 193 ELGRMNEWVGFYNKVMGFTNMKEFVGDDIATEYSALMSKVVADGTLKVKFPINEPALAKK 252
           ELG+M+ WV FYN+VMGF NM EFVGDDIATEYSALMSKVV++G  +VKFP+NEPA+AKK
Sbjct: 210 ELGKMDYWVDFYNRVMGFVNMAEFVGDDIATEYSALMSKVVSNGNHRVKFPLNEPAIAKK 269

Query: 253 KSQIDEYLEFYGGAGVQHIALNTGDIVETVRTMRAAGVQFLDTPDSYYD--TLGEWVGDT 310
           +SQIDEYLEFYGG G QHIAL T DI+ T+  MRAAGV+FL  PDSYYD   L E +G+ 
Sbjct: 270 RSQIDEYLEFYGGPGCQHIALATNDIITTITQMRAAGVEFLAVPDSYYDDPALRERIGEV 329

Query: 311 RVPVDTLRELKILADRDEDGYLLQIFTKPVQDRPTVFFEIIERHGSMGFGKGNFKALFEA 370
           RVP++TL+E  IL DRDEDGYLLQ+FTKP+ DRPTVFFE+IERHGS+GFG GNFKALFEA
Sbjct: 330 RVPIETLKEHGILVDRDEDGYLLQMFTKPIGDRPTVFFELIERHGSLGFGIGNFKALFEA 389

Query: 371 IEREQEKRGNL 381
           IEREQE+RGNL
Sbjct: 390 IEREQERRGNL 400


Lambda     K      H
   0.318    0.136    0.403 

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: 639
Number of extensions: 31
Number of successful extensions: 4
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: 381
Length of database: 400
Length adjustment: 31
Effective length of query: 350
Effective length of database: 369
Effective search space:   129150
Effective search space used:   129150
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_034269963.1 AMYHA_RS09050 (4-hydroxyphenylpyruvate dioxygenase)
to HMM TIGR01263 (hppD: 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27))

# 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/TIGR01263.hmm
# target sequence database:        /tmp/gapView.3321307.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01263  [M=353]
Accession:   TIGR01263
Description: 4HPPD: 4-hydroxyphenylpyruvate dioxygenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.1e-129  416.7   0.0   6.1e-129  416.4   0.0    1.1  1  NCBI__GCF_000504245.1:WP_034269963.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000504245.1:WP_034269963.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.4   0.0  6.1e-129  6.1e-129       2     353 .]      40     400 .]      39     400 .] 0.98

  Alignments for each domain:
  == domain 1  score: 416.4 bits;  conditional E-value: 6.1e-129
                             TIGR01263   2 gfdfvefavgdakqaakalveklGfeavak...etgsrekastvlrqgeitlvltaelsssseaaaflakHGd 71 
                                           ++d v f++g+a+q+a  ++ ++G+++va+   e+g+++++++vl++g++++v++   +++s++ ++ +kHGd
  NCBI__GCF_000504245.1:WP_034269963.1  40 AMDAVVFVSGNATQTALFYQFAFGMKLVAYtgpEHGTADHKAYVLTSGSARFVIKGGVKPDSPLLDHHRKHGD 112
                                           6899********************************************************************* PP

                             TIGR01263  72 gvkdvafevedveaafeaavergaeavsapee.ed.ekevklaaikgiGdvvltlveregekgsilpgfeevs 142
                                           gv d+a+ev+dv+++ ++a + ga+++++p++ +d +++v++aai ++G++++tl++r++++g +lpg+++ +
  NCBI__GCF_000504245.1:WP_034269963.1 113 GVVDLALEVADVDKCIAHARSCGATVLDEPHDvSDeHGTVRMAAIATYGETRHTLIDRSRYTGPYLPGYVARE 185
                                           *******************************99888************************************* PP

                             TIGR01263 143 ekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfd...ikteasaLkSkvlasaegkvk 212
                                           +  +     ++  ++aiDH+vgnve g+++++++fy++++gf ++++f    i te+saL+Skv+ + +++vk
  NCBI__GCF_000504245.1:WP_034269963.1 186 SGLQRPAGAPKRLFQAIDHCVGNVELGKMDYWVDFYNRVMGFVNMAEFVgddIATEYSALMSKVVSNGNHRVK 258
                                           *99999999***************************************8899********************* PP

                             TIGR01263 213 lplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflkipetYYdn..lkervkklvk 283
                                           +plnepa  kk+sQI+eyle+y G+G QH+Al t+di++t++++ra gvefl +p++YYd+  l+er+++ v+
  NCBI__GCF_000504245.1:WP_034269963.1 259 FPLNEPAIAKKRSQIDEYLEFYGGPGCQHIALATNDIITTITQMRAAGVEFLAVPDSYYDDpaLRERIGE-VR 330
                                           ************************************************************65599****7.** PP

                             TIGR01263 284 edleelkelkiLvDrdeeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfeaiEreqekrgvl 353
                                            ++e+lke++iLvDrde+G+LLQ+Ftkp+ dr+t+FfE+I+R+g+ GFG gNfkaLfeaiEreqe+rg+l
  NCBI__GCF_000504245.1:WP_034269963.1 331 VPIETLKEHGILVDRDEDGYLLQMFTKPIGDRPTVFFELIERHGSLGFGIGNFKALFEAIEREQERRGNL 400
                                           ********************************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (400 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: 00:00:00.00
# Mc/sec: 16.45
//
[ok]

This GapMind analysis is from Sep 24 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 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