Alignments for a candidate for aroG in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Dyella japonica UNC79MFTsu3.2

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate N515DRAFT_0700 N515DRAFT_0700 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase

Query= BRENDA::A0A0D5ZBC4
         (539 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0700
          Length = 466

 Score =  402 bits (1034), Expect = e-116
 Identities = 207/447 (46%), Positives = 284/447 (63%), Gaps = 6/447 (1%)

Query: 80  PGKWTVDSWKSKKALQLPEYPDQAELESVLKTLDAFPPIVFAGEARSLEEKLGEAAMGNA 139
           P  WT  SW+ + ALQ P Y +  EL      L   PP+V + E  +L++ L EA  G  
Sbjct: 20  PSAWTPASWQRRTALQQPLYENAGELAQATAHLARLPPLVTSWEVLALKQALAEAQEGQR 79

Query: 140 FLLQGGDCAESFKEFNANNIRDTFRILLQMGAVLMFGGQMPVIKVGRMAGQFAKPRSDPF 199
           FLLQGGDCAESF +  +  I +  ++LLQM  VL+ G +MPV++VGR AGQ+AKPRS   
Sbjct: 80  FLLQGGDCAESFADCTSPVISNRLKVLLQMSLVLVHGMRMPVLRVGRFAGQYAKPRSTDM 139

Query: 200 EEKNGVKLPSYRGDNVNGDSFDEKSRIPDPQRMIRAYCQSAATLNLLRAFATGGYAAMQR 259
           E ++GV LPS+RGD VN   F  ++R  DPQR+I+A+  SA T+N +RA   GG+A +  
Sbjct: 140 ETRDGVTLPSFRGDLVNSPEFTAEARRADPQRLIQAHAHSALTMNFVRALIDGGFADLHH 199

Query: 260 VTQWNLDFTEHSEQGDRYRELASRVDEALGFMAAAGLTVDHPI--MTTTEFWTSHECLLL 317
              W+L + EHS     YR + + + ++L FM     T+  PI   T  +F+TSHE LLL
Sbjct: 200 PEYWDLAWVEHSPLAAEYRRMVAGIGDSLRFME----TLAGPIAGFTRVDFFTSHEALLL 255

Query: 318 PYEQSLTRLDSTSGRYYDCSAHFLWAGERTRQLDGAHVEFLRGVANPLGIKVSDKMDPNE 377
            YE++LTR       +++ S HF W G RT  LDGAHVE+ RG+ NP+ +KV   + P +
Sbjct: 256 HYEEALTRQVPRHPGWFNLSTHFPWIGMRTAALDGAHVEYFRGIRNPIAVKVGPSVTPEQ 315

Query: 378 LVKLIEILNPQNKAGRITVITRMGAENMRVKLPHLIRAVRRAGQIVTWVSDPMHGNTIKA 437
           L+ L+E LNP ++ GR+T+I RMG   +   LP L+ AV+RAG+ V WV+DPMHGNT   
Sbjct: 316 LLPLVEALNPDDEPGRLTLIHRMGNAQIAKALPPLLDAVKRAGRRVLWVADPMHGNTEST 375

Query: 438 PCGLKTRPFDSIRAEVRAFFDVHEQEGSHPGGVHLEMTGQNVTECIGGSRTVTFDDLGSR 497
             G KTR FD+IR E+   FD+H   G+  GGVHLE+TG++VTEC+GG+R ++  DL   
Sbjct: 376 SNGYKTRRFDNIRGELDQAFDIHAAAGTRLGGVHLELTGEDVTECMGGARDLSEADLDRA 435

Query: 498 YHTHCDPRLNASQSLELAFIIAERLRK 524
           Y +  DPRLN  QSLELA +I  + +K
Sbjct: 436 YKSTVDPRLNYEQSLELAMLIVHKSQK 462


Lambda     K      H
   0.318    0.133    0.393 

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: 632
Number of extensions: 22
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: 539
Length of database: 466
Length adjustment: 34
Effective length of query: 505
Effective length of database: 432
Effective search space:   218160
Effective search space used:   218160
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: 52 (24.6 bits)

Align candidate N515DRAFT_0700 N515DRAFT_0700 (3-deoxy-D-arabinoheptulosonate-7-phosphate synthase)
to HMM TIGR01358 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

# 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.aa/TIGR01358.hmm
# target sequence database:        /tmp/gapView.2787.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01358  [M=443]
Accession:   TIGR01358
Description: DAHP_synth_II: 3-deoxy-7-phosphoheptulonate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.5e-208  678.7   0.0   1.9e-208  678.3   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0700  N515DRAFT_0700 3-deoxy-D-arabino


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0700  N515DRAFT_0700 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  678.3   0.0  1.9e-208  1.9e-208       1     441 [.      23     462 ..      23     463 .. 0.99

  Alignments for each domain:
  == domain 1  score: 678.3 bits;  conditional E-value: 1.9e-208
                                    TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdca 66 
                                                  w+++sw+ ++a+q+P y +a++l + +++l++lPPlv+++e+l+lk+ lae+++G++fllqgGdca
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0700  23 WTPASWQRRTALQQPLYENAGELAQATAHLARLPPLVTSWEVLALKQALAEAQEGQRFLLQGGDCA 88 
                                                  89**************************************************************** PP

                                    TIGR01358  67 esfkeveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdv 132
                                                  esf +++++ i+++l+vllqm++vl++g ++Pv++vgr+aGqyakPrs+++e++dgvtlps+rGd 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0700  89 ESFADCTSPVISNRLKVLLQMSLVLVHGMRMPVLRVGRFAGQYAKPRSTDMETRDGVTLPSFRGDL 154
                                                  ****************************************************************** PP

                                    TIGR01358 133 ingaafdeaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryekl 198
                                                  +n+++f+++ar+ dp+rl++a+a+sa t+n++ral++gG+adl++ ++W+l +v++sp +a+y+++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0700 155 VNSPEFTAEARRADPQRLIQAHAHSALTMNFVRALIDGGFADLHHPEYWDLAWVEHSPLAAEYRRM 220
                                                  ****************************************************************** PP

                                    TIGR01358 199 aeeidealrfmsavgvaeaealkrvelytsheallldyeealtrvdskegqlfdlsahllWiGert 264
                                                  +  i+++lrfm++++   a  ++rv+++tshealll+yeealtr+++++ ++f+ls+h+ WiG+rt
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0700 221 VAGIGDSLRFMETLAGPIAG-FTRVDFFTSHEALLLHYEEALTRQVPRHPGWFNLSTHFPWIGMRT 285
                                                  **************998877.********************************************* PP

                                    TIGR01358 265 rqldgahveflrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPell 330
                                                    ldgahve+ rg++nPi++kvgps+++++ll l+e l+P++ePGrltli+r+G+++ia+ lP+ll
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0700 286 AALDGAHVEYFRGIRNPIAVKVGPSVTPEQLLPLVEALNPDDEPGRLTLIHRMGNAQIAKALPPLL 351
                                                  ****************************************************************** PP

                                    TIGR01358 331 eavkaaGravvWvtdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedv 396
                                                  +avk+aGr+v+Wv+dpmhGnt+++++Gyktrrfd+i+ e+ + f++h+a+Gt++GGvhleltGedv
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0700 352 DAVKRAGRRVLWVADPMHGNTESTSNGYKTRRFDNIRGELDQAFDIHAAAGTRLGGVHLELTGEDV 417
                                                  ****************************************************************** PP

                                    TIGR01358 397 teclGGareitetdlasryetacdPrlnaeqslelaflvaeklre 441
                                                  tec+GGar+++e dl+++y++++dPrln+eqslela+l+++k ++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0700 418 TECMGGARDLSEADLDRAYKSTVDPRLNYEQSLELAMLIVHKSQK 462
                                                  ****************************************99775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (466 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.18
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis