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.23028.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: 11.27
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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