Alignments for a candidate for HPD in Derxia gummosa DSM 723

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Derxia gummosa DSM 723

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_034411528.1 H566_RS0112640 4-hydroxyphenylpyruvate dioxygenase

Query= reanno::MR1:201123
         (346 letters)



>NCBI__GCF_000482785.1:WP_034411528.1
          Length = 350

 Score =  460 bits (1184), Expect = e-134
 Identities = 228/344 (66%), Positives = 276/344 (80%), Gaps = 2/344 (0%)

Query: 3   SELNPLGLLGIEFTEFASSDTDFMHKVFIDFGFSLLKKAKNKDILYYKQNDINFLLNKQR 62
           ++LNP+GL GIEFTEF  S T+ +  +F  FGFS L++   +DI  Y+QNDI FLLN +R
Sbjct: 9   NDLNPIGLRGIEFTEFTGS-TEQLDALFWAFGFSKLRRHPTRDITVYRQNDIAFLLNAER 67

Query: 63  EGFSAKFAKSHGPAICSMGWRVEDASFAHRVAVERGAKAADDSAKDLPYPAIYGIGDSLI 122
           +GFSA FAK HGP+I SMGWRVE+A+ A   AV RGA+AAD +A DLPYPAIYGIGDSLI
Sbjct: 68  QGFSAGFAKLHGPSIASMGWRVENAAAALAEAVRRGARAADPAACDLPYPAIYGIGDSLI 127

Query: 123 YFIDTFGANNNIYATDFEDLSEPVITQEKGFIEVDHLTNNVYKGTMEHWANFYKNIFGFT 182
           YFI+  GA  +I+ TDF  L +P +  +KGFI +DHLTNNV  G M  WA FYK+IFGFT
Sbjct: 128 YFIERHGAKGSIWETDFVPLDQPQVQADKGFIAIDHLTNNVPAGQMAAWAAFYKDIFGFT 187

Query: 183 EVRYFDISGVQTALVSYALRSPDGSFCIPINEGKGNDKNQIDEYLKEYNGPGVQHLAFRS 242
           EVRYFDI G +T L SYALRSPDGSFCIPIN+ K +D++QI EYL+EYNGPGVQHLAF +
Sbjct: 188 EVRYFDIRGAKTGLTSYALRSPDGSFCIPINQPK-DDRDQIAEYLREYNGPGVQHLAFST 246

Query: 243 RDIVKSLDAMEGSSIQCLDIIPEYYDTIFDKVPQVTENRDRIKHHQILVDGDESGYLLQI 302
           RDI+ SLDA+EGS I+ LDI  +YYD ++ +VPQV E+R+RI+ H +LVDGDE GYLLQI
Sbjct: 247 RDILASLDALEGSPIEMLDIDDDYYDEVYKRVPQVREDRERIRAHSVLVDGDEEGYLLQI 306

Query: 303 FTKNLFGPIFIEIIQRKNNLGFGEGNFTALFQSIERDQMRRGVL 346
           FT+NL GPIFIEIIQR+NNL FGEGNF ALF+SIE+DQ RRGV+
Sbjct: 307 FTRNLIGPIFIEIIQRENNLSFGEGNFGALFRSIEKDQERRGVI 350


Lambda     K      H
   0.321    0.140    0.414 

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: 467
Number of extensions: 14
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: 346
Length of database: 350
Length adjustment: 29
Effective length of query: 317
Effective length of database: 321
Effective search space:   101757
Effective search space used:   101757
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 WP_034411528.1 H566_RS0112640 (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.13734.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-114  369.5   0.0   1.3e-114  369.3   0.0    1.0  1  lcl|NCBI__GCF_000482785.1:WP_034411528.1  H566_RS0112640 4-hydroxyphenylpy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000482785.1:WP_034411528.1  H566_RS0112640 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.3   0.0  1.3e-114  1.3e-114       2     352 ..      18     349 ..      17     350 .] 0.96

  Alignments for each domain:
  == domain 1  score: 369.3 bits;  conditional E-value: 1.3e-114
                                 TIGR01263   2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHG 70 
                                               g++f ef+ + ++  + al++++Gf+++ +   + ++++tv+rq++i ++l+ae +     a f++ HG
  lcl|NCBI__GCF_000482785.1:WP_034411528.1  18 GIEFTEFTGSTEQ--LDALFWAFGFSKLRR---HPTRDITVYRQNDIAFLLNAERQGF--SAGFAKLHG 79 
                                               799****999988..99************8...**********************999..9******** PP

                                 TIGR01263  71 dgvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgfe 139
                                               +++++++++ve+++aa+++av+rga+a++ +      ++ ++ai giGd++++++er+g kgsi ++++
  lcl|NCBI__GCF_000482785.1:WP_034411528.1  80 PSIASMGWRVENAAAALAEAVRRGARAADPAA----CDLPYPAIYGIGDSLIYFIERHGAKGSIWETDF 144
                                               ***************************87775....68*****************************99 PP

                                 TIGR01263 140 evsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasae 208
                                                  ++    + ++d+g++aiDH+++nv++g++ ++a fy++i+gf+e+++fdi++  ++L+S++l+s++
  lcl|NCBI__GCF_000482785.1:WP_034411528.1 145 VPLDQP---QVQADKGFIAIDHLTNNVPAGQMAAWAAFYKDIFGFTEVRYFDIRGAKTGLTSYALRSPD 210
                                               766654...44469******************************************************* PP

                                 TIGR01263 209 gkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflkipetYYdnlker 277
                                               g++++p+n p  k+++ QI eyl+ey+G+GvQHlA++t+di++++++l+ + +e+l+i + YYd++ +r
  lcl|NCBI__GCF_000482785.1:WP_034411528.1 211 GSFCIPINQP--KDDRDQIAEYLREYNGPGVQHLAFSTRDILASLDALEGSPIEMLDIDDDYYDEVYKR 277
                                               *********8..89999**************************************************** PP

                                 TIGR01263 278 vkklvkedleelkelkiLvDrdeeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfeaiEre 346
                                               v++ v+ed e+++++++LvD+deeG+LLQiFt++++  g++F+EiIqR+++  FGegNf aLf +iE++
  lcl|NCBI__GCF_000482785.1:WP_034411528.1 278 VPQ-VREDRERIRAHSVLVDGDEEGYLLQIFTRNLI--GPIFIEIIQRENNLSFGEGNFGALFRSIEKD 343
                                               **7.********************************..******************************* PP

                                 TIGR01263 347 qekrgv 352
                                               qe+rgv
  lcl|NCBI__GCF_000482785.1:WP_034411528.1 344 QERRGV 349
                                               ****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (350 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: 10.89
//
[ok]

This GapMind analysis is from Sep 24 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