Alignments for a candidate for HPD in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Echinicola vietnamensis KMM 6221, DSM 17526

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate Echvi_2983 Echvi_2983 4-hydroxyphenylpyruvate dioxygenase

Query= BRENDA::Q6KZ98
         (368 letters)



>FitnessBrowser__Cola:Echvi_2983
          Length = 363

 Score =  402 bits (1034), Expect = e-117
 Identities = 204/351 (58%), Positives = 253/351 (72%), Gaps = 3/351 (0%)

Query: 21  HVEFYVSSAKTWSYFMNRGLGFKTVAYAGPETGIRDKISYVMSQGTARISFTSSMNDDSY 80
           HVEFYV +AK  + +     GF+ VAYAGPETGIRD+ SYV+ QG  R+  T+++  D  
Sbjct: 13  HVEFYVGNAKQSAMYYQAAFGFELVAYAGPETGIRDRASYVLKQGKIRLVLTTALYQDHP 72

Query: 81  ISNHVKKHGDGVKDIALEVDDLDEAKSLIEKYGTKVSKINEI-KDGNGKIRTAEIKTYGE 139
           I+ HV KHGDGVK +AL VDD D+A       G    +   I +D NG ++ A I TYGE
Sbjct: 73  IAKHVSKHGDGVKVLALGVDDADKAWQETTSRGAVSHESPRITQDSNGSVKVASICTYGE 132

Query: 140 TVHTLIETGDYNGVFMPGYE-ESEINSKNTGIKKIDHIVGNVYEGEMDSWVNFYIEKLGF 198
           T+HT +E  +Y+G F+PGY  E  IN+ + G+K IDH VGNV  GEM+ WV+FY + +GF
Sbjct: 133 TIHTFVERKNYSGPFLPGYRVEKGINTTSVGLKHIDHCVGNVGWGEMNEWVSFYKKVMGF 192

Query: 199 EHLITFDDKDIRTDYSALRSKVVKY-NDDIVFPINEPAKGLRKSQIEEYLDYYRSEGVQH 257
             L+TFDDKDI T+YSAL SKVV   N  I FPINEPAKG +KSQIEEYLD+Y   GVQH
Sbjct: 193 NLLVTFDDKDISTEYSALMSKVVSNGNGYIKFPINEPAKGKKKSQIEEYLDFYNGPGVQH 252

Query: 258 IALLTDDIIKTVSMMEENGIEFLKTPGSYYESLSSRIGSIDEDLNEIEKHNILVDRDENG 317
           IA+ TDDII TVS + + G+ FL  P +YY++L  R+G IDE +  +++ NILVDRDE G
Sbjct: 253 IAIATDDIISTVSELRKRGVSFLMVPDNYYDNLKDRVGKIDEAIEALKQLNILVDRDEEG 312

Query: 318 YLLQIFTKPVTDRPTFFFEVIQRKGARSFGNGNFKALFEAIEREQAKRGNL 368
           YLLQIFT+PV DRPT F+E+IQRKGA+SFG GNFKALFEAIEREQ  RGNL
Sbjct: 313 YLLQIFTRPVQDRPTLFYEIIQRKGAQSFGKGNFKALFEAIEREQNLRGNL 363


Lambda     K      H
   0.316    0.136    0.384 

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: 500
Number of extensions: 31
Number of successful extensions: 5
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: 368
Length of database: 363
Length adjustment: 30
Effective length of query: 338
Effective length of database: 333
Effective search space:   112554
Effective search space used:   112554
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 (21.5 bits)
S2: 49 (23.5 bits)

Align candidate Echvi_2983 Echvi_2983 (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.9143.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   2.2e-143  463.9   0.1   2.5e-143  463.8   0.1    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2983  Echvi_2983 4-hydroxyphenylpyruva


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2983  Echvi_2983 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  463.8   0.1  2.5e-143  2.5e-143       2     353 .]      10     363 .]       9     363 .] 0.97

  Alignments for each domain:
  == domain 1  score: 463.8 bits;  conditional E-value: 2.5e-143
                            TIGR01263   2 gfdfvefavgdakqaakalveklGfeavak...etgsrekastvlrqgeitlvltaelsssseaaaflakHGdg 72 
                                          g d+vef+vg+akq+a +++ ++Gfe+va+   etg r++as+vl+qg+i+lvlt++l +++++a++++kHGdg
  lcl|FitnessBrowser__Cola:Echvi_2983  10 GTDHVEFYVGNAKQSAMYYQAAFGFELVAYagpETGIRDRASYVLKQGKIRLVLTTALYQDHPIAKHVSKHGDG 83 
                                          689*********************************************************************** PP

                            TIGR01263  73 vkdvafevedveaafeaavergaeavsapee.ed.ekevklaaikgiGdvvltlveregekgsilpgfeevsek 144
                                          vk +a+ v+d+++a+++  +rga + ++p+  +d +++vk+a i ++G++++t+ver++++g +lpg++  ++ 
  lcl|FitnessBrowser__Cola:Echvi_2983  84 VKVLALGVDDADKAWQETTSRGAVSHESPRItQDsNGSVKVASICTYGETIHTFVERKNYSGPFLPGYRV-EKG 156
                                          ***************************99987778********************************994.443 PP

                            TIGR01263 145 aalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfd...ikteasaLkSkvlasaegkvklpl 215
                                               ++++vgl+ iDH+vgnv +ge++++++fy+k++gf+ + +fd   i+te+saL+Skv+ + +g +k+p+
  lcl|FitnessBrowser__Cola:Echvi_2983 157 ----INTTSVGLKHIDHCVGNVGWGEMNEWVSFYKKVMGFNLLVTFDdkdISTEYSALMSKVVSNGNGYIKFPI 226
                                          ....34578**********************************9999999************************ PP

                            TIGR01263 216 nepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflkipetYYdnlkervkklvkedleel 289
                                          nepa++kkksQIeeyl++y+G+GvQH+A+ t+di++tv+elr+rgv fl +p++YYdnlk+rv+k ++e +e l
  lcl|FitnessBrowser__Cola:Echvi_2983 227 NEPAKGKKKSQIEEYLDFYNGPGVQHIAIATDDIISTVSELRKRGVSFLMVPDNYYDNLKDRVGK-IDEAIEAL 299
                                          ****************************************************************6.******** PP

                            TIGR01263 290 kelkiLvDrdeeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfeaiEreqekrgvl 353
                                          k+l+iLvDrdeeG+LLQiFt+pv+dr+tlF+EiIqRkga+ FG+gNfkaLfeaiEreq+ rg+l
  lcl|FitnessBrowser__Cola:Echvi_2983 300 KQLNILVDRDEEGYLLQIFTRPVQDRPTLFYEIIQRKGAQSFGKGNFKALFEAIEREQNLRGNL 363
                                          *************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (363 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: 8.38
//
[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