Alignments for a candidate for HPD in Nitriliruptor alkaliphilus DSM 45188

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Nitriliruptor alkaliphilus DSM 45188

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_052669195.1 NITAL_RS00610 4-hydroxyphenylpyruvate dioxygenase

Query= BRENDA::Q53586
         (381 letters)



>NCBI__GCF_000969705.1:WP_052669195.1
          Length = 368

 Score =  404 bits (1039), Expect = e-117
 Identities = 212/365 (58%), Positives = 254/365 (69%), Gaps = 9/365 (2%)

Query: 19  PVKGMDAVVFAVGNAKQAAHYYSTAFGMQLVAYSGPENGSRETASYVLTNGSARFVLTSV 78
           P+KG DA+ F VGNAKQAAH+Y TAFG +LV Y+GPE G R+ ASYVL   S RFVLT+ 
Sbjct: 11  PLKGYDAIEFWVGNAKQAAHFYRTAFGFKLVGYAGPETGVRDRASYVLQQRSIRFVLTTG 70

Query: 79  IKPATPWGHFLADHVAEHGDGVVDLAIEVPDARAAHAYAIEHGARSVAEPYELKDEHGTV 138
           +       H +  H A HGDGV D+A  VP A  A   A+E GA    EP  ++DEHG V
Sbjct: 71  LTA----DHEVTRHQAVHGDGVRDVAFRVPAAEEAFRMAVERGATPFTEPEVVEDEHGKV 126

Query: 139 VLAAIATYGKTRHTLVDRTGYDGPYLPGYVA--AAPIVEPPAHRTFQAIDHCVGNVELGR 196
           V AAI  YG T HT V R  Y G YLPGY A  A P+  P       AIDH V NVE G 
Sbjct: 127 VRAAIRAYGDTIHTFVQRDDYSGVYLPGYQAVDADPLARPVG---LSAIDHVVCNVEEGE 183

Query: 197 MNEWVGFYNKVMGFTNMKEFVGDDIATEYSALMSKVVADGTLKVKFPINEPALAKKKSQI 256
           M+ W  FY ++MGF+ ++ F  + I+TEY+ALMSKV+ DG  ++K PINEPA  KKKSQI
Sbjct: 184 MDTWARFYERIMGFSQLRHFDDEAISTEYTALMSKVLWDGHGRIKLPINEPAEGKKKSQI 243

Query: 257 DEYLEFYGGAGVQHIALNTGDIVETVRTMRAAGVQFLDTPDSYYDTLGEWVGDTRVPVDT 316
           DEYL++YG  GVQH+AL+TGDIV TVR +R  GV FL  PD YY    E VG+     D 
Sbjct: 244 DEYLQYYGSPGVQHLALSTGDIVATVRQLRDNGVSFLTVPDEYYLGAKERVGEVDESWDD 303

Query: 317 LRELKILADRDEDGYLLQIFTKPVQDRPTVFFEIIERHGSMGFGKGNFKALFEAIEREQE 376
           L+EL IL DRD++GYLLQIFT+PV+DRPTVF+E+IERHG+MGFG GNFKALFE+IER QE
Sbjct: 304 LQELGILVDRDDEGYLLQIFTEPVEDRPTVFYEVIERHGAMGFGVGNFKALFESIERAQE 363

Query: 377 KRGNL 381
           +RGNL
Sbjct: 364 RRGNL 368


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: 546
Number of extensions: 33
Number of successful extensions: 3
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: 368
Length adjustment: 30
Effective length of query: 351
Effective length of database: 338
Effective search space:   118638
Effective search space used:   118638
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_052669195.1 NITAL_RS00610 (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.21217.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.7e-138  446.8   0.0   4.2e-138  446.6   0.0    1.0  1  lcl|NCBI__GCF_000969705.1:WP_052669195.1  NITAL_RS00610 4-hydroxyphenylpyr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000969705.1:WP_052669195.1  NITAL_RS00610 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.6   0.0  4.2e-138  4.2e-138       2     353 .]      14     368 .]      13     368 .] 0.98

  Alignments for each domain:
  == domain 1  score: 446.6 bits;  conditional E-value: 4.2e-138
                                 TIGR01263   2 gfdfvefavgdakqaakalveklGfeavak...etgsrekastvlrqgeitlvltaelsssseaaafla 67 
                                               g+d +ef+vg+akqaa+ + +++Gf++v++   etg r++as+vl+q +i++vlt+ l+ ++e+++++a
  lcl|NCBI__GCF_000969705.1:WP_052669195.1  14 GYDAIEFWVGNAKQAAHFYRTAFGFKLVGYagpETGVRDRASYVLQQRSIRFVLTTGLTADHEVTRHQA 82 
                                               899****************************************************************** PP

                                 TIGR01263  68 kHGdgvkdvafevedveaafeaavergaeavsapee.ed.ekevklaaikgiGdvvltlveregekgsi 134
                                                HGdgv+dvaf+v  +e+af+ averga+++++pe  ed +++v  aai+++Gd+++t+v+r +++g +
  lcl|NCBI__GCF_000969705.1:WP_052669195.1  83 VHGDGVRDVAFRVPAAEEAFRMAVERGATPFTEPEVvEDeHGKVVRAAIRAYGDTIHTFVQRDDYSGVY 151
                                               **********************************998888***************************** PP

                                 TIGR01263 135 lpgfeevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfd...ikteasaLk 200
                                               lpg+++v  +  l++    vgl aiDHvv nve+ge++++a fye+i+gf+++++fd   i+te++aL+
  lcl|NCBI__GCF_000969705.1:WP_052669195.1 152 LPGYQAVDAD-PLAR---PVGLSAIDHVVCNVEEGEMDTWARFYERIMGFSQLRHFDdeaISTEYTALM 216
                                               *****87775.5555...59************************************************* PP

                                 TIGR01263 201 SkvlasaegkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflkipet 269
                                               Skvl + +g++klp+nepa++kkksQI+eyl++y  +GvQHlAl+t div+tv++lr++gv fl++p++
  lcl|NCBI__GCF_000969705.1:WP_052669195.1 217 SKVLWDGHGRIKLPINEPAEGKKKSQIDEYLQYYGSPGVQHLALSTGDIVATVRQLRDNGVSFLTVPDE 285
                                               ********************************************************************* PP

                                 TIGR01263 270 YYdnlkervkklvkedleelkelkiLvDrdeeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfka 338
                                               YY   kerv++ v+e++++l+el+iLvDrd+eG+LLQiFt+pv dr+t+F+E+I+R+ga+GFG gNfka
  lcl|NCBI__GCF_000969705.1:WP_052669195.1 286 YYLGAKERVGE-VDESWDDLQELGILVDRDDEGYLLQIFTEPVEDRPTVFYEVIERHGAMGFGVGNFKA 353
                                               **********7.********************************************************* PP

                                 TIGR01263 339 LfeaiEreqekrgvl 353
                                               Lfe+iEr qe+rg+l
  lcl|NCBI__GCF_000969705.1:WP_052669195.1 354 LFESIERAQERRGNL 368
                                               *************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (368 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: 11.30
//
[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 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