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_3260 N515DRAFT_3260 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase

Query= BRENDA::P29976
         (525 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3260
          Length = 472

 Score =  411 bits (1057), Expect = e-119
 Identities = 203/443 (45%), Positives = 290/443 (65%), Gaps = 5/443 (1%)

Query: 75  WTPESWKLKKALQLPDYPNANELESVLKTIEAFPPIVFAGEARNLEERLADAAVGKAFLL 134
           WTP SW+L++A Q P Y +  +LE+V + I   PP+V +GE + L+  LADA  G+ FLL
Sbjct: 14  WTPASWRLREAQQQPCYDDRAQLENVARRIGKLPPLVTSGEIQELKRALADAQEGRRFLL 73

Query: 135 QGGDCAESFKEFNATNIRDTFRVLLQMSIVLTFGGQVPVIKVGRMAGQFAKPRSDAFEEK 194
            GGDCAESF + +A  I +  +VL QMS++L  G + PVI+VGR AGQ+AKPRS   E  
Sbjct: 74  HGGDCAESFGDCDADTIVNRLKVLFQMSLILGHGLKQPVIRVGRFAGQYAKPRSSDRETV 133

Query: 195 DGVKLPSYKGDNINGDTFDEKSRIPDPNRMIRAYTQSAATLNLLRAFATGGYAAIQRVTQ 254
            G  LPS++GD +N   FD  +R PDP RM +AY  SA TLN  RA   GG+  ++    
Sbjct: 134 GGETLPSFRGDIVNAAAFDAAARRPDPERMFQAYAFSALTLNFTRALFEGGFGDLRHPEY 193

Query: 255 WNLDFVEQSEQADRYQELANRVDEALGFMSACG--LGTDHPLMTTTDFYTSHECLLLPYE 312
           W LD+++QS +A  Y+     +  +  F+   G  +GT+     +  FYTSHE LLLP+E
Sbjct: 194 WQLDWIDQSPRAIEYRREVEEIANSWRFLHTLGGQVGTER---VSAGFYTSHEALLLPFE 250

Query: 313 QSLTRLDSTSGLYYDCSAHMVWCGERTRQLDGAHVEFLRGIANPLGIKVSNKMDPFELVK 372
           +++TR       +++ S H+ W G RT  +DGAH+E+ RG+ NP+ +KV     P +L++
Sbjct: 251 EAVTRRVPHRRGWFNLSTHLPWIGMRTSDIDGAHIEYFRGLQNPVAMKVGPSTRPADLLR 310

Query: 373 LVEILNPNNKPGRITVIVRMGAENMRVKLPHLIRAVRRSGQIVTWVCDPMHGNTIKAPCG 432
           L+E+LNP+ +PGR+T+I RMG +++   LP L+ AVRR+G+ V WV DPMHGNT   P G
Sbjct: 311 LIEVLNPHEEPGRMTLITRMGCKHIAEALPPLLAAVRRAGRHVLWVVDPMHGNTETTPTG 370

Query: 433 LKTRAFDSILAEVRAFLDVHEQEGSHAGGIHLEMTGQNVTECIGGSRTVTYDDLSSRYHT 492
           +KTR FD+I +E+ A   +H  EG+  GG+HLEMTG++VTEC+GG+R++   DLS  Y T
Sbjct: 371 IKTRHFDNIRSELEAAFQIHGAEGTRLGGVHLEMTGEDVTECLGGARSLQEQDLSRAYKT 430

Query: 493 HCDPRLNASQSLELAFIVAERLR 515
             DPRLN  Q++ELA ++ +  R
Sbjct: 431 TVDPRLNYEQAMELAMLITKVAR 453


Lambda     K      H
   0.318    0.132    0.389 

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: 594
Number of extensions: 23
Number of successful extensions: 2
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: 525
Length of database: 472
Length adjustment: 34
Effective length of query: 491
Effective length of database: 438
Effective search space:   215058
Effective search space used:   215058
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_3260 N515DRAFT_3260 (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.19732.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   5.2e-194  630.7   0.0   5.9e-194  630.5   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3260  N515DRAFT_3260 3-deoxy-D-arabino


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3260  N515DRAFT_3260 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  630.5   0.0  5.9e-194  5.9e-194       1     441 [.      14     454 ..      14     456 .. 0.99

  Alignments for each domain:
  == domain 1  score: 630.5 bits;  conditional E-value: 5.9e-194
                                    TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdca 66 
                                                  w+++swr ++a+q+P y d ++le+v   + +lPPlv++gei++lk+ la++++G++fll gGdca
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3260  14 WTPASWRLREAQQQPCYDDRAQLENVARRIGKLPPLVTSGEIQELKRALADAQEGRRFLLHGGDCA 79 
                                                  89**************************************************************** PP

                                    TIGR01358  67 esfkeveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdv 132
                                                  esf +++ad+i ++l+vl+qm+++l +g + Pv++vgr+aGqyakPrs++ e+ +g tlps+rGd+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3260  80 ESFGDCDADTIVNRLKVLFQMSLILGHGLKQPVIRVGRFAGQYAKPRSSDRETVGGETLPSFRGDI 145
                                                  ****************************************************************** PP

                                    TIGR01358 133 ingaafdeaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryekl 198
                                                  +n+aafd+aar+pdper+ +aya sa tln+ ral +gG+ dl++ ++W+l+++ +sp + +y++ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3260 146 VNAAAFDAAARRPDPERMFQAYAFSALTLNFTRALFEGGFGDLRHPEYWQLDWIDQSPRAIEYRRE 211
                                                  ****************************************************************** PP

                                    TIGR01358 199 aeeidealrfmsavgvaeaealkrvelytsheallldyeealtrvdskegqlfdlsahllWiGert 264
                                                  +eei ++ rf++++g +  ++   + +ytshealll++eea+tr +++++++f+ls+hl WiG+rt
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3260 212 VEEIANSWRFLHTLGGQVGTERVSAGFYTSHEALLLPFEEAVTRRVPHRRGWFNLSTHLPWIGMRT 277
                                                  *****************99999999***************************************** PP

                                    TIGR01358 265 rqldgahveflrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPell 330
                                                    +dgah+e+ rg++nP+++kvgps+++ +ll+lievl+P++ePGr+tli+r+G ++iae lP+ll
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3260 278 SDIDGAHIEYFRGLQNPVAMKVGPSTRPADLLRLIEVLNPHEEPGRMTLITRMGCKHIAEALPPLL 343
                                                  ****************************************************************** PP

                                    TIGR01358 331 eavkaaGravvWvtdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedv 396
                                                   av++aGr+v+Wv dpmhGnt+++++G ktr+fd+i+se+++ f++h aeGt++GGvhle+tGedv
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3260 344 AAVRRAGRHVLWVVDPMHGNTETTPTGIKTRHFDNIRSELEAAFQIHGAEGTRLGGVHLEMTGEDV 409
                                                  ****************************************************************** PP

                                    TIGR01358 397 teclGGareitetdlasryetacdPrlnaeqslelaflvaeklre 441
                                                  teclGGar+++e+dl+++y+t++dPrln+eq++ela+l+++  r+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3260 410 TECLGGARSLQEQDLSRAYKTTVDPRLNYEQAMELAMLITKVARA 454
                                                  ***************************************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (472 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 12.57
//
[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