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_1068 N515DRAFT_1068 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase

Query= BRENDA::C3TIE2
         (350 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1068
          Length = 365

 Score =  424 bits (1090), Expect = e-123
 Identities = 214/344 (62%), Positives = 254/344 (73%)

Query: 6   DDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHD 65
           DDLRI+ I  L  P  ++    A E A +TVAHAR A+H IL G DDRL+VVIGPCSIHD
Sbjct: 7   DDLRIRAITPLSTPAEVMRDCHAGELALDTVAHARAAVHDILAGQDDRLVVVIGPCSIHD 66

Query: 66  PVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRI 125
             AA EYA RLL  R    D LEIVMRVYFEKPRTTVGWKGLINDP +D SF+I+ GLR+
Sbjct: 67  TAAAMEYARRLLGQRRRFADTLEIVMRVYFEKPRTTVGWKGLINDPDLDGSFRIDKGLRL 126

Query: 126 ARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGF 185
           AR LL DIN  G+PA  EFLDMITPQY+ADL++WGAIGARTTESQVHRELASGLSCPVGF
Sbjct: 127 ARTLLRDINQLGVPAGCEFLDMITPQYIADLVAWGAIGARTTESQVHRELASGLSCPVGF 186

Query: 186 KNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKH 245
           KNGTDG +K+A+DA+ AA  PH F++VTK G +AI +T GN DCH+ILRGGK+PNY A  
Sbjct: 187 KNGTDGNVKIAVDAVQAASQPHHFMAVTKDGRTAIASTMGNEDCHVILRGGKQPNYDAAS 246

Query: 246 VAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHL 305
           V    E + + GL  ++M+D SHANSSKQ + Q  V  D+  Q+  GE+ IIGVMVESHL
Sbjct: 247 VDAACEAIARGGLSPRLMVDASHANSSKQPENQPLVIDDIALQLEDGERRIIGVMVESHL 306

Query: 306 VEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349
           + G Q L   + L YG+SITD CI W  +  +L +L  AV+ RR
Sbjct: 307 LGGRQELVPEQSLRYGQSITDGCIDWNASVGVLERLDEAVRRRR 350


Lambda     K      H
   0.317    0.134    0.397 

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: 422
Number of extensions: 8
Number of successful extensions: 1
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: 350
Length of database: 365
Length adjustment: 29
Effective length of query: 321
Effective length of database: 336
Effective search space:   107856
Effective search space used:   107856
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: 49 (23.5 bits)

Align candidate N515DRAFT_1068 N515DRAFT_1068 (3-deoxy-D-arabinoheptulosonate-7-phosphate synthase)
to HMM TIGR00034 (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/TIGR00034.hmm
# target sequence database:        /tmp/gapView.5848.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00034  [M=342]
Accession:   TIGR00034
Description: aroFGH: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   6.8e-162  524.0   0.0   7.7e-162  523.8   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_1068  N515DRAFT_1068 3-deoxy-D-arabino


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_1068  N515DRAFT_1068 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  523.8   0.0  7.7e-162  7.7e-162       1     342 []       7     350 ..       7     350 .. 0.99

  Alignments for each domain:
  == domain 1  score: 523.8 bits;  conditional E-value: 7.7e-162
                                    TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaale 66 
                                                  ddlri +i +l tP+e+++   + e a ++va++r +++dilaG+ddrl+vviGPcsihd  aa+e
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1068   7 DDLRIRAITPLSTPAEVMRDCHAGELALDTVAHARAAVHDILAGQDDRLVVVIGPCSIHDTAAAME 72 
                                                  799*************************************************************** PP

                                    TIGR00034  67 yakrlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelg 132
                                                  ya+rl   + ++ d leivmrvyfekPrttvGWkGlindPdl++sf+++kGlr+ar ll d+++lg
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1068  73 YARRLLGQRRRFADTLEIVMRVYFEKPRTTVGWKGLINDPDLDGSFRIDKGLRLARTLLRDINQLG 138
                                                  ****************************************************************** PP

                                    TIGR00034 133 lplatelldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaa 198
                                                  +p+++e+ld+i+pqy+adl++wgaiGarttesqvhrelasgls+pvgfkngtdG++k+a+da++aa
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1068 139 VPAGCEFLDMITPQYIADLVAWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNVKIAVDAVQAA 204
                                                  ****************************************************************** PP

                                    TIGR00034 199 aaehlflsvtkaGqvaivetkGnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshg 264
                                                  +++h+f++vtk+G++ai +t Gned+h+ilrGGk+pnyda++v++++e + + gl+++lm+d+sh+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1068 205 SQPHHFMAVTKDGRTAIASTMGNEDCHVILRGGKQPNYDAASVDAACEAIARGGLSPRLMVDASHA 270
                                                  ****************************************************************** PP

                                    TIGR00034 265 nsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedte 328
                                                  ns+k+ ++q+ v ++++ q+++Ge+ iiGvm+es+l +G+q+l  +++l yG+s+td ci+w+ + 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1068 271 NSSKQPENQPLVIDDIALQLEDGERRIIGVMVESHLLGGRQELvpEQSLRYGQSITDGCIDWNASV 336
                                                  ******************************************98999******************* PP

                                    TIGR00034 329 allrklaeavkerr 342
                                                   +l++l eav++rr
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1068 337 GVLERLDEAVRRRR 350
                                                  ***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (365 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: 10.79
//
[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