Alignments for a candidate for HPD in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Halomonas desiderata SP1

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_086511963.1 BZY95_RS21665 4-hydroxyphenylpyruvate dioxygenase

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



>NCBI__GCF_002151265.1:WP_086511963.1
          Length = 366

 Score =  505 bits (1301), Expect = e-148
 Identities = 251/360 (69%), Positives = 292/360 (81%), Gaps = 4/360 (1%)

Query: 4   VNKIEQHNPIGTDGFEFVEFTAPNAEGIEQLRTLFTQMGFTETAKHRSKEVWLFQQHDIN 63
           V+ I Q NPIGT+GFEFVE++AP+AEGIE+LR LF +MGFTET KHRSK+V+LFQQ ++N
Sbjct: 8   VSPISQDNPIGTNGFEFVEYSAPSAEGIEELRALFNRMGFTETRKHRSKQVFLFQQENVN 67

Query: 64  IVLNGSPTGHVHAFAEKHGPSACAMAFRVKNAAQAAAYVESQGAKLVGSHANFGELNIPC 123
            VLN  P  H   FA+ HGP ACAMA++V +A QA  Y  + GA+ V +    GE+ IP 
Sbjct: 68  FVLNAEPDSHAAEFAKVHGPCACAMAWKVADAKQAFEYALAHGAEAVENPVGPGEVGIPA 127

Query: 124 VEGIGGSLLYLVDRYGD---KSIYDVDFEYIEGRTPNDNAVGLMCIDHLTHNVMRGQMDV 180
           V GIGGSLLY VD   D   ++IYD+DFE I GR+PNDN+VGL  +DHLTHNV RGQMD 
Sbjct: 128 VRGIGGSLLYFVDNKVDSEGRTIYDIDFEPIPGRSPNDNSVGLKVLDHLTHNVDRGQMDK 187

Query: 181 WSGFYERIANFREIRYFDIEGKLTGLFSRAMTAPCGKIRIPINESADDKSQIEEFIREYH 240
           W+ FY  IANFRE RYFDI+GK TGL SRAMTAPCGK+ IPINESADD SQI EF+REY+
Sbjct: 188 WADFYTEIANFRENRYFDIKGKKTGLHSRAMTAPCGKMHIPINESADDSSQIAEFLREYN 247

Query: 241 GEGIQHIALSTDDIYATVRQLRANGVDFMTTPDTYYEKVDTRVAGHGEPTDVLRELNILI 300
           GEGIQH+A++TDDIYATVR LRANGV F+TTPDTYYEKVDTRV  H E  + LREL++LI
Sbjct: 248 GEGIQHLAMATDDIYATVRGLRANGVTFLTTPDTYYEKVDTRVPNHEENVEDLRELSLLI 307

Query: 301 DGAPGDDGILLQIFTNTVIGPIFFEIIQRKGNQGFGEGNFKALFESIEEDQLRRGVIKAD 360
           DG P D+G+LLQ FT TVIGPIFFEIIQRKGN GFGEGNFKALFESIEEDQ+RRGV+KAD
Sbjct: 308 DGGP-DEGVLLQTFTETVIGPIFFEIIQRKGNDGFGEGNFKALFESIEEDQIRRGVLKAD 366


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: 548
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: 366
Length adjustment: 29
Effective length of query: 332
Effective length of database: 337
Effective search space:   111884
Effective search space used:   111884
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_086511963.1 BZY95_RS21665 (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.11657.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-125  404.1   0.0   3.9e-125  403.9   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086511963.1  BZY95_RS21665 4-hydroxyphenylpyr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086511963.1  BZY95_RS21665 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  403.9   0.0  3.9e-125  3.9e-125       2     353 .]      21     363 ..      20     363 .. 0.96

  Alignments for each domain:
  == domain 1  score: 403.9 bits;  conditional E-value: 3.9e-125
                                 TIGR01263   2 gfdfvefavgdak..qaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflak 68 
                                               gf+fve+ ++ a+  + ++al++++Gf++  k   +r+k++ +++q+++++vl+ae+ s+  aa+f++ 
  lcl|NCBI__GCF_002151265.1:WP_086511963.1  21 GFEFVEYSAPSAEgiEELRALFNRMGFTETRK---HRSKQVFLFQQENVNFVLNAEPDSH--AAEFAKV 84 
                                               89********99977899*************9...***********************99..******* PP

                                 TIGR01263  69 HGdgvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlvereg..ekgsil 135
                                               HG++++++a++v+d+++afe a+++gaeav++p+    +ev ++a++giG+++l++v+ +   e  +i+
  lcl|NCBI__GCF_002151265.1:WP_086511963.1  85 HGPCACAMAWKVADAKQAFEYALAHGAEAVENPVG--PGEVGIPAVRGIGGSLLYFVDNKVdsEGRTIY 151
                                               *********************************97..99******************987633566899 PP

                                 TIGR01263 136 pgfeevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvl 204
                                               ++++e     + +   ++vgl+ +DH+++nv+rg+++k+a+fy +i +f+e ++fdik++ ++L+S+++
  lcl|NCBI__GCF_002151265.1:WP_086511963.1 152 DIDFEPIPGRSPN--DNSVGLKVLDHLTHNVDRGQMDKWADFYTEIANFRENRYFDIKGKKTGLHSRAM 218
                                               9999877765444..489*************************************************** PP

                                 TIGR01263 205 asaegkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflkipetYYdn 273
                                               ++++gk+++p+ne  s +++sQI e+l+ey+G+G+QHlA+ t+di++tv+ lra+gv fl++p+tYY++
  lcl|NCBI__GCF_002151265.1:WP_086511963.1 219 TAPCGKMHIPINE--SADDSSQIAEFLREYNGEGIQHLAMATDDIYATVRGLRANGVTFLTTPDTYYEK 285
                                               *************..89**************************************************** PP

                                 TIGR01263 274 lkervkklvkedleelkelkiLvDrd.eeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfe 341
                                               ++ rv++ ++e++e+l+el++L+D+  +eG+LLQ Ft++v+  g++FfEiIqRkg++GFGegNfkaLfe
  lcl|NCBI__GCF_002151265.1:WP_086511963.1 286 VDTRVPN-HEENVEDLRELSLLIDGGpDEGVLLQTFTETVI--GPIFFEIIQRKGNDGFGEGNFKALFE 351
                                               ******7.*****************99**************..************************** PP

                                 TIGR01263 342 aiEreqekrgvl 353
                                               +iE++q++rgvl
  lcl|NCBI__GCF_002151265.1:WP_086511963.1 352 SIEEDQIRRGVL 363
                                               *********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (366 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.44
//
[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