Alignments for a candidate for HPD in Rhizobium leguminosarum 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Rhizobium leguminosarum 3841

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_011651485.1 RL_RS09700 4-hydroxyphenylpyruvate dioxygenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2935
         (358 letters)



>NCBI__GCF_000009265.1:WP_011651485.1
          Length = 369

 Score =  371 bits (953), Expect = e-107
 Identities = 184/354 (51%), Positives = 243/354 (68%), Gaps = 5/354 (1%)

Query: 6   ENPMGLMGFEFIELASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILNNEPHS 65
           +NP G  GFEF+E A P P TL  +F  MG+  VA H++KD+ ++RQG IN +LN EP S
Sbjct: 16  DNPAGTDGFEFVEFAHPEPETLRELFTRMGYVAVARHKTKDITVWRQGDINYVLNAEPGS 75

Query: 66  VASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGIGGAPL 125
            A+ F A HGP    MA+RV D+Q A+K A+  GA P   E     L++PAI GIGG+ L
Sbjct: 76  HAARFVASHGPCAPSMAWRVVDAQHAFKHAVSKGAVPY--EGDDKALDVPAIVGIGGSLL 133

Query: 126 YLIDRFGEGSSIYDIDFVFIEGVDRHPVGAGLKIIDHLTHNVYRGRMAYWANFYEKLFNF 185
           Y ++ +G   S YD +F ++   D HP G G   +DHLTHNV+RG M  W +FY  LFNF
Sbjct: 134 YFVETYGARGSAYDAEFDWLGESDPHPQGIGFYYLDHLTHNVFRGNMDKWWDFYRNLFNF 193

Query: 186 REIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQHVAFL 245
           ++I +FDI G  TGL S+A+T+P G IRIPLN ES     QIEE+L ++ GEGIQH+A  
Sbjct: 194 KQIHFFDIDGRITGLVSRAITSPCGKIRIPLN-ESKDDTSQIEEYLKKYKGEGIQHIAVG 252

Query: 246 SDDLIKTWDHLKSIGMRFMTAPPETYYEMLEGRLPNHGEPVDQLQARGILLDGSS--ESG 303
           ++D+    D L   G+RFM  PPETYY+M   R+  H EPV++++  GIL+DG      G
Sbjct: 253 TEDIYDATDRLADNGLRFMPGPPETYYDMSYERVNGHSEPVERMKKHGILIDGEGVVNGG 312

Query: 304 DKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLST 357
             ++LLQIFS+T++GP+FFEFIQRKGD+GFGEGNF+ALFESIE DQ++RGV+ T
Sbjct: 313 MTKILLQIFSKTVIGPIFFEFIQRKGDEGFGEGNFRALFESIEADQIKRGVIGT 366


Lambda     K      H
   0.321    0.141    0.419 

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: 480
Number of extensions: 24
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: 358
Length of database: 369
Length adjustment: 29
Effective length of query: 329
Effective length of database: 340
Effective search space:   111860
Effective search space used:   111860
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_011651485.1 RL_RS09700 (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.8029.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-127  411.2   0.0   2.7e-127  411.0   0.0    1.0  1  lcl|NCBI__GCF_000009265.1:WP_011651485.1  RL_RS09700 4-hydroxyphenylpyruva


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009265.1:WP_011651485.1  RL_RS09700 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.0   0.0  2.7e-127  2.7e-127       2     352 ..      23     363 ..      22     364 .. 0.97

  Alignments for each domain:
  == domain 1  score: 411.0 bits;  conditional E-value: 2.7e-127
                                 TIGR01263   2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHG 70 
                                               gf+fvefa+++++ ++++l++++G+ ava+   +++k++tv+rqg+i++vl+ae+ s+  aa+f+a+HG
  lcl|NCBI__GCF_000009265.1:WP_011651485.1  23 GFEFVEFAHPEPE-TLRELFTRMGYVAVAR---HKTKDITVWRQGDINYVLNAEPGSH--AARFVASHG 85 
                                               8***********9.***************8...*************************..********* PP

                                 TIGR01263  71 dgvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgfe 139
                                               +++ ++a++v d+++af++av++ga +++      +k+++++ai giG+++l++ve++g +gs +++++
  lcl|NCBI__GCF_000009265.1:WP_011651485.1  86 PCAPSMAWRVVDAQHAFKHAVSKGAVPYEGD----DKALDVPAIVGIGGSLLYFVETYGARGSAYDAEF 150
                                               ***************************8776....479******************************* PP

                                 TIGR01263 140 evsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasae 208
                                               ++  +   + +++++g++++DH+++nv rg+++k+++fy+++++fk+i+ fdi++++++L+S++++s++
  lcl|NCBI__GCF_000009265.1:WP_011651485.1 151 DWLGE--SDPHPQGIGFYYLDHLTHNVFRGNMDKWWDFYRNLFNFKQIHFFDIDGRITGLVSRAITSPC 217
                                               ****7..566679******************************************************** PP

                                 TIGR01263 209 gkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflk.ipetYYdnlke 276
                                               gk+++plne  sk+++sQIeeyl++y+G+G+QH+A+ tedi++++++l ++g++f++ +petYYd+  e
  lcl|NCBI__GCF_000009265.1:WP_011651485.1 218 GKIRIPLNE--SKDDTSQIEEYLKKYKGEGIQHIAVGTEDIYDATDRLADNGLRFMPgPPETYYDMSYE 284
                                               *********..9********************************************************* PP

                                 TIGR01263 277 rvkklvkedleelkelkiLvDrd...eeG...lLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaL 339
                                               rv+  ++e++e++k+++iL+D++   + G   +LLQiF+k+v+  g++FfE+IqRkg++GFGegNf+aL
  lcl|NCBI__GCF_000009265.1:WP_011651485.1 285 RVNG-HSEPVERMKKHGILIDGEgvvNGGmtkILLQIFSKTVI--GPIFFEFIQRKGDEGFGEGNFRAL 350
                                               ***7.******************9966669999**********..************************ PP

                                 TIGR01263 340 feaiEreqekrgv 352
                                               fe+iE +q+krgv
  lcl|NCBI__GCF_000009265.1:WP_011651485.1 351 FESIEADQIKRGV 363
                                               ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (369 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 11.07
//
[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