Alignments for a candidate for HPD in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Sphingomonas koreensis DSMZ 15582

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate Ga0059261_2984 Ga0059261_2984 4-hydroxyphenylpyruvate dioxygenase

Query= reanno::psRCH2:GFF3449
         (361 letters)



>FitnessBrowser__Korea:Ga0059261_2984
          Length = 345

 Score =  351 bits (901), Expect = e-101
 Identities = 192/352 (54%), Positives = 240/352 (68%), Gaps = 15/352 (4%)

Query: 11  NPIGTDGFEFVEFTAPNAEGIEQLRTLFTQMGFTETAKHRSKEVWLFQQHDINIVLNGSP 70
           NP+G +GFEFVEFT+P+      +   F Q+GF  + +H +K +  ++Q  IN++LN   
Sbjct: 6   NPLGLNGFEFVEFTSPDPAA---MAAQFEQLGFVASHRHPTKNITRYKQGRINLMLNRDD 62

Query: 71  TGHVHAFAEKHGPSACAMAFRVKNAAQAAAYVESQGAKLVGSHANFGELNIPCVEGIGGS 130
            G V  F  +HGPSA AMAFRV +  +A  +  + GA+         E +   + GIGGS
Sbjct: 63  AGRVAKFRGEHGPSASAMAFRVADPVKAMEWALAHGAERT-------EEDDTVILGIGGS 115

Query: 131 LLYLVDRYGDKSIYDVDFEYIEGRTPND--NAVGLMCIDHLTHNVMRGQMDVWSGFYERI 188
            LY +    D  +Y+ ++  I G    +  N VGL  +DHLTHNV RGQM VWS FY+ +
Sbjct: 116 YLYFIQDGHD--LYE-NWAEIPGWQEAEAANNVGLDLLDHLTHNVRRGQMRVWSQFYKTL 172

Query: 189 ANFREIRYFDIEGKLTGLFSRAMTAPCGKIRIPINESADDKSQIEEFIREYHGEGIQHIA 248
             F E +YFDI+G+ TGLFS+AM AP   IRIP+NES DDKSQIEEFIREY GEGIQH+A
Sbjct: 173 FGFEEQKYFDIKGQATGLFSQAMIAPDKAIRIPLNESQDDKSQIEEFIREYKGEGIQHLA 232

Query: 249 LSTDDIYATVRQLRANGVDFMTTPDTYYEKVDTRVAGHGEPTDVLRELNILIDGAPGDDG 308
           L+TDDIY TV +LRA GV    T +TYYE VD RV GHGE  + LR+  ILIDG  G++G
Sbjct: 233 LTTDDIYDTVERLRARGVRLQDTIETYYELVDKRVPGHGEDLERLRKNRILIDGNVGEEG 292

Query: 309 ILLQIFTNTVIGPIFFEIIQRKGNQGFGEGNFKALFESIEEDQLRRGVIKAD 360
           ILLQIFT  + GPIFFEIIQRKGN+GFG GNF+ALFESIE DQ+RRGVIK D
Sbjct: 293 ILLQIFTENMFGPIFFEIIQRKGNEGFGNGNFQALFESIELDQIRRGVIKVD 344


Lambda     K      H
   0.320    0.139    0.412 

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: 444
Number of extensions: 18
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 361
Length of database: 345
Length adjustment: 29
Effective length of query: 332
Effective length of database: 316
Effective search space:   104912
Effective search space used:   104912
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: 49 (23.5 bits)

Align candidate Ga0059261_2984 Ga0059261_2984 (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.29866.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.6e-117  376.5   0.1   9.8e-117  376.3   0.1    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_2984  Ga0059261_2984 4-hydroxyphenylpy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_2984  Ga0059261_2984 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  376.3   0.1  9.8e-117  9.8e-117       2     352 ..      12     340 ..      11     341 .. 0.95

  Alignments for each domain:
  == domain 1  score: 376.3 bits;  conditional E-value: 9.8e-117
                                 TIGR01263   2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHG 70 
                                               gf+fvef+++d+  a++a +e+lGf a  +   + +k++t ++qg+i+l+l+   + +  +a+f  +HG
  lcl|FitnessBrowser__Korea:Ga0059261_2984  12 GFEFVEFTSPDPA-AMAAQFEQLGFVASHR---HPTKNITRYKQGRINLMLNRDDAGR--VAKFRGEHG 74 
                                               89***********.9999*******88776...**********************999..********* PP

                                 TIGR01263  71 dgvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgfe 139
                                               ++++++af+v+d  +a e a+++gae  ++ +          +i giG++ l++++ +   +++++   
  lcl|FitnessBrowser__Korea:Ga0059261_2984  75 PSASAMAFRVADPVKAMEWALAHGAERTEEDD---------TVILGIGGSYLYFIQDG---HDLYENWA 131
                                               **************************965554.........689***********985...45688877 PP

                                 TIGR01263 140 evsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasae 208
                                               e+   +  +e+ ++vgl+ +DH+++nv+rg+++ +++fy+ ++gf+e+k+fdik++a++L S+++ +++
  lcl|FitnessBrowser__Korea:Ga0059261_2984 132 EIPGWQ-EAEAANNVGLDLLDHLTHNVRRGQMRVWSQFYKTLFGFEEQKYFDIKGQATGLFSQAMIAPD 199
                                               777754.5555799******************************************************* PP

                                 TIGR01263 209 gkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflkipetYYdnlker 277
                                               +++++plne  s+++ksQIee+++ey+G+G+QHlAl+t+di++tve+lrargv++ ++ etYY+ +++r
  lcl|FitnessBrowser__Korea:Ga0059261_2984 200 KAIRIPLNE--SQDDKSQIEEFIREYKGEGIQHLALTTDDIYDTVERLRARGVRLQDTIETYYELVDKR 266
                                               *********..9********************************************************* PP

                                 TIGR01263 278 vkklvkedleelkelkiLvDrd..eeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfeaiE 344
                                               v+  + edle+l++++iL+D++  eeG+LLQiFt++++  g++FfEiIqRkg++GFG+gNf+aLfe+iE
  lcl|FitnessBrowser__Korea:Ga0059261_2984 267 VPG-HGEDLERLRKNRILIDGNvgEEGILLQIFTENMF--GPIFFEIIQRKGNEGFGNGNFQALFESIE 332
                                               **7.**********************************..***************************** PP

                                 TIGR01263 345 reqekrgv 352
                                                +q++rgv
  lcl|FitnessBrowser__Korea:Ga0059261_2984 333 LDQIRRGV 340
                                               ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (345 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.97
//
[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