Alignments for a candidate for HPD in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Pedobacter sp. GW460-11-11-14-LB5

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate CA265_RS03130 CA265_RS03130 4-hydroxyphenylpyruvate dioxygenase

Query= BRENDA::Q53586
         (381 letters)



>FitnessBrowser__Pedo557:CA265_RS03130
          Length = 376

 Score =  371 bits (953), Expect = e-107
 Identities = 195/371 (52%), Positives = 250/371 (67%), Gaps = 6/371 (1%)

Query: 12  ARQADPFPVKGMDAVVFAVGNAKQAAHYYSTAFGMQLVAYSGPENGSRETASYVLTNGSA 71
           ++  D  P+ G D + F VGNAKQAAHYY TAFG Q +AY+GPE G R+ +SYVL  G  
Sbjct: 11  SKAPDFLPINGTDYIEFYVGNAKQAAHYYKTAFGFQSLAYAGPETGVRDRSSYVLQQGKI 70

Query: 72  RFVLTSVIKPATPWGHFLADHVAEHGDGVVDLAIEVPDARAAHAYAIEHGARSVAEPYEL 131
           R +LT+ +K   P    +A+HV +HGDGV  LA+ V DA +A     + GA+    P  L
Sbjct: 71  RLILTTALKSDHP----IAEHVKKHGDGVKVLALWVDDAYSAFEETTKRGAKPYLAPQTL 126

Query: 132 KDEHGTVVLAAIATYGKTRHTLVDRTGYDGPYLPGYVAAAPIVEPPAHRTFQAIDHCVGN 191
            DE+G + ++ I TYG+T H  ++R  Y+G ++PGY       +P A      IDHCVGN
Sbjct: 127 TDENGELKMSGIYTYGETVHMFIERKNYNGTFMPGYRVWESDYQP-ADAGLLYIDHCVGN 185

Query: 192 VELGRMNEWVGFYNKVMGFTNMKEFVGDDIATEYSALMSKVVADGTLKVKFPINEPALAK 251
           V   RMNE V +Y  VMGF N+  F    I TEYSALMSKV+++G    KFPINEPA  K
Sbjct: 186 VGWNRMNEAVQWYEDVMGFVNILSFDDKQINTEYSALMSKVMSNGNGYSKFPINEPAEGK 245

Query: 252 KKSQIDEYLEFYGGAGVQHIALNTGDIVETVRTMRAAGVQFLDT-PDSYYDTLGEWVGDT 310
           KKSQI+EYLE+Y G GVQHIA+ T DIV+TV+ ++A GV+FL   P++YYD + + VG  
Sbjct: 246 KKSQIEEYLEYYEGEGVQHIAVATKDIVKTVKELKARGVEFLSAPPEAYYDMMPQRVGKI 305

Query: 311 RVPVDTLRELKILADRDEDGYLLQIFTKPVQDRPTVFFEIIERHGSMGFGKGNFKALFEA 370
              +  L  L IL D DE+GYLLQIFTKPV+DRPT+FFE+I+R G+  FG GNFKALFE+
Sbjct: 306 DEEIALLESLGILVDCDEEGYLLQIFTKPVEDRPTLFFEVIQRKGAQSFGAGNFKALFES 365

Query: 371 IEREQEKRGNL 381
           +EREQE RGNL
Sbjct: 366 LEREQELRGNL 376


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: 488
Number of extensions: 26
Number of successful extensions: 4
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: 376
Length adjustment: 30
Effective length of query: 351
Effective length of database: 346
Effective search space:   121446
Effective search space used:   121446
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 CA265_RS03130 CA265_RS03130 (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.9713.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   3.6e-140  453.4   0.0     4e-140  453.2   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS03130  CA265_RS03130 4-hydroxyphenylpyr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS03130  CA265_RS03130 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  453.2   0.0    4e-140    4e-140       2     353 .]      21     376 .]      20     376 .] 0.98

  Alignments for each domain:
  == domain 1  score: 453.2 bits;  conditional E-value: 4e-140
                                  TIGR01263   2 gfdfvefavgdakqaakalveklGfeavak...etgsrekastvlrqgeitlvltaelsssseaaafl 66 
                                                g d++ef+vg+akqaa+++ +++Gf+ +a+   etg r++ s+vl+qg+i+l+lt++l+s++++a+++
  lcl|FitnessBrowser__Pedo557:CA265_RS03130  21 GTDYIEFYVGNAKQAAHYYKTAFGFQSLAYagpETGVRDRSSYVLQQGKIRLILTTALKSDHPIAEHV 88 
                                                689***************************************************************** PP

                                  TIGR01263  67 akHGdgvkdvafevedveaafeaavergaeavsapee.ed.ekevklaaikgiGdvvltlveregekg 132
                                                +kHGdgvk +a+ v+d+ +afe+  +rga+++ ap++ +d ++e+k+  i ++G++v+ ++er++++g
  lcl|FitnessBrowser__Pedo557:CA265_RS03130  89 KKHGDGVKVLALWVDDAYSAFEETTKRGAKPYLAPQTlTDeNGELKMSGIYTYGETVHMFIERKNYNG 156
                                                *************************************9888*************************** PP

                                  TIGR01263 133 silpgfeevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfd...ikteas 197
                                                +++pg++ ++++     +++d+gl +iDH+vgnv ++++++++++ye+++gf +i sfd   i+te+s
  lcl|FitnessBrowser__Pedo557:CA265_RS03130 157 TFMPGYRVWESD----YQPADAGLLYIDHCVGNVGWNRMNEAVQWYEDVMGFVNILSFDdkqINTEYS 220
                                                *******99996....45689*********************************************** PP

                                  TIGR01263 198 aLkSkvlasaegkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflk 265
                                                aL+Skv+ + +g  k+p+nepa++kkksQIeeyle+yeG+GvQH+A+ t+divktv+el+argvefl+
  lcl|FitnessBrowser__Pedo557:CA265_RS03130 221 ALMSKVMSNGNGYSKFPINEPAEGKKKSQIEEYLEYYEGEGVQHIAVATKDIVKTVKELKARGVEFLS 288
                                                ******************************************************************** PP

                                  TIGR01263 266 .ipetYYdnlkervkklvkedleelkelkiLvDrdeeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFG 332
                                                 +pe+YYd++ +rv+k ++e++  l++l+iLvD deeG+LLQiFtkpv dr+tlFfE+IqRkga+ FG
  lcl|FitnessBrowser__Pedo557:CA265_RS03130 289 aPPEAYYDMMPQRVGK-IDEEIALLESLGILVDCDEEGYLLQIFTKPVEDRPTLFFEVIQRKGAQSFG 355
                                                99*************6.*************************************************** PP

                                  TIGR01263 333 egNfkaLfeaiEreqekrgvl 353
                                                +gNfkaLfe++Ereqe rg+l
  lcl|FitnessBrowser__Pedo557:CA265_RS03130 356 AGNFKALFESLEREQELRGNL 376
                                                ******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (376 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: 10.12
//
[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, or view the source code.

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