Alignments for a candidate for HPD in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Caulobacter crescentus NA1000

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate CCNA_02616 CCNA_02616 4-hydroxyphenylpyruvate dioxygenase

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



>FitnessBrowser__Caulo:CCNA_02616
          Length = 357

 Score =  384 bits (985), Expect = e-111
 Identities = 202/357 (56%), Positives = 251/357 (70%), Gaps = 7/357 (1%)

Query: 7   IEQHNPIGTDGFEFVEFTAPNAEGIEQLRTLFTQMGFTETAKHRSKEVWLFQQHDINIVL 66
           +   NP+G DGFEFVEFT+P+      ++ L  Q+GF   +KH +K    ++Q  +N+++
Sbjct: 4   VTDQNPLGLDGFEFVEFTSPDPAA---MKALIEQLGFVAASKHPTKAATRYKQGRVNLIV 60

Query: 67  NGSPTGHVHAFAEKHGPSACAMAFRVKNAAQAAAYVESQGAKLVGSHANFGELNIPCVEG 126
           N   TG V  F   HGPSA  MAFRV+NA QA A    +GAK   +  +    +   +EG
Sbjct: 61  NEETTGQVADFRADHGPSANGMAFRVENAEQAYADAVKRGAKPADASRSLLGADAKVLEG 120

Query: 127 IGGSLLYLVDRYGDK-SIYDVDFEYIEGRTPND--NAVGLMCIDHLTHNVMRGQMDVWSG 183
           IGGSLLYLVDRYGD  +IYD  +E + G    +  N VGL  +DHLTHNV RGQM  WS 
Sbjct: 121 IGGSLLYLVDRYGDAGTIYDA-WEQVPGAALAEAKNNVGLDLLDHLTHNVKRGQMRTWST 179

Query: 184 FYERIANFREIRYFDIEGKLTGLFSRAMTAPCGKIRIPINESADDKSQIEEFIREYHGEG 243
           FY +I  F E +YFDI+G+ TGLFS+AM AP   IRIP+NES DDKSQIEEFIR+Y+GEG
Sbjct: 180 FYNQIFGFEEQKYFDIKGQATGLFSQAMIAPDKAIRIPLNESQDDKSQIEEFIRQYNGEG 239

Query: 244 IQHIALSTDDIYATVRQLRANGVDFMTTPDTYYEKVDTRVAGHGEPTDVLRELNILIDGA 303
           IQH+A++TD+IY TV +LRA GV    T +TYYE VD RV GHGE  + LR+  ILIDGA
Sbjct: 240 IQHLAMTTDNIYDTVEKLRARGVKLQDTIETYYELVDKRVPGHGEDLERLRKNRILIDGA 299

Query: 304 PGDDGILLQIFTNTVIGPIFFEIIQRKGNQGFGEGNFKALFESIEEDQLRRGVIKAD 360
            G++G+LLQIFT  + GPIFFEIIQRKGN+GFG GNF+ALFESIE DQ+RRGVI  D
Sbjct: 300 VGEEGLLLQIFTENLFGPIFFEIIQRKGNEGFGNGNFQALFESIELDQIRRGVITVD 356


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: 446
Number of extensions: 17
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: 361
Length of database: 357
Length adjustment: 29
Effective length of query: 332
Effective length of database: 328
Effective search space:   108896
Effective search space used:   108896
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 CCNA_02616 CCNA_02616 (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.16034.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     6e-132  426.3   0.1   6.8e-132  426.2   0.1    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02616  CCNA_02616 4-hydroxyphenylpyruva


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02616  CCNA_02616 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.2   0.1  6.8e-132  6.8e-132       2     352 ..      14     352 ..      13     353 .. 0.98

  Alignments for each domain:
  == domain 1  score: 426.2 bits;  conditional E-value: 6.8e-132
                             TIGR01263   2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHGdgvk 74 
                                           gf+fvef+++d+  a+kal+e+lGf a++k   + +ka+t ++qg+++l++++e++ +  +a+f a+HG++++
  lcl|FitnessBrowser__Caulo:CCNA_02616  14 GFEFVEFTSPDPA-AMKALIEQLGFVAASK---HPTKAATRYKQGRVNLIVNEETTGQ--VADFRADHGPSAN 80 
                                           8************.*************999...*************************..************* PP

                             TIGR01263  75 dvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgfeevsekaal 147
                                           ++af+ve++e+a+++av+rga++++a+++     +++++++giG+++l+lv+r+g++g+i+++ e+v   aal
  lcl|FitnessBrowser__Caulo:CCNA_02616  81 GMAFRVENAEQAYADAVKRGAKPADASRS--LLGADAKVLEGIGGSLLYLVDRYGDAGTIYDAWEQVPG-AAL 150
                                           *************************9996..78999***************************887777.689 PP

                             TIGR01263 148 kekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasaegkvklplnepas 220
                                           +e++++vgl+ +DH+++nv+rg+++++++fy++i+gf+e+k+fdik++a++L S+++ ++++++++plne  s
  lcl|FitnessBrowser__Caulo:CCNA_02616 151 AEAKNNVGLDLLDHLTHNVKRGQMRTWSTFYNQIFGFEEQKYFDIKGQATGLFSQAMIAPDKAIRIPLNE--S 221
                                           9999******************************************************************..9 PP

                             TIGR01263 221 kkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflkipetYYdnlkervkklvkedleelkelk 293
                                           +++ksQIee++++y+G+G+QHlA++t++i++tve+lrargv++ ++ etYY+ +++rv+  + edle+l++++
  lcl|FitnessBrowser__Caulo:CCNA_02616 222 QDDKSQIEEFIRQYNGEGIQHLAMTTDNIYDTVEKLRARGVKLQDTIETYYELVDKRVPG-HGEDLERLRKNR 293
                                           ***********************************************************7.************ PP

                             TIGR01263 294 iLvDrd..eeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfeaiEreqekrgv 352
                                           iL+D++  eeGlLLQiFt++++  g++FfEiIqRkg++GFG+gNf+aLfe+iE +q++rgv
  lcl|FitnessBrowser__Caulo:CCNA_02616 294 ILIDGAvgEEGLLLQIFTENLF--GPIFFEIIQRKGNEGFGNGNFQALFESIELDQIRRGV 352
                                           **********************..***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (357 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: 8.01
//
[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