Alignments for a candidate for aroG in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Dechlorosoma suillum PS

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate Dsui_2381 Dsui_2381 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::P00888
         (356 letters)



>FitnessBrowser__PS:Dsui_2381
          Length = 358

 Score =  383 bits (984), Expect = e-111
 Identities = 194/352 (55%), Positives = 248/352 (70%), Gaps = 1/352 (0%)

Query: 6   LNNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIH 65
           ++N++I     + TP  + A+ PLS +    +   R+ + +I+  +D RL VV GPCSIH
Sbjct: 6   IDNINIAAFDPMPTPAAMLASQPLSEKAATVVRQGRQDLKNILDRKDHRLFVVVGPCSIH 65

Query: 66  DPETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQ 125
           DP   L+YARR KALA EVSD+L LVMRVYFEKPRTTVGWKG INDP MD SF V+ G+ 
Sbjct: 66  DPVAGLDYARRLKALADEVSDTLLLVMRVYFEKPRTTVGWKGYINDPFMDDSFRVDVGMA 125

Query: 126 IARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVG 185
            AR+ LL++  +GLP  TEALDPNSPQY GDL SW+AIGARTTESQTHREM+SGLS PVG
Sbjct: 126 KAREFLLQVNEIGLPAGTEALDPNSPQYYGDLISWTAIGARTTESQTHREMSSGLSTPVG 185

Query: 186 FKNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGKA-PNYSP 244
           FKNGTDG+   AINA+ +A++PH F+G+N  GQVA+++T GN  GH++LRGG   PNY  
Sbjct: 186 FKNGTDGNTEIAINAILSASKPHSFLGLNDQGQVAIVRTTGNAYGHIVLRGGGGRPNYDT 245

Query: 245 ADVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIES 304
             V+  E+ M +A L P+++VDCSH NS K    QP V   VV QI+ GN+S++G+MIES
Sbjct: 246 VSVSVAEQAMVKAKLIPNVVVDCSHANSLKKPELQPLVMSDVVNQIRLGNKSMVGVMIES 305

Query: 305 NIHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNGQLTARVA 356
           NI  GNQS     S++KYG SVTD C+ W  T+ ++R+    L   L  R A
Sbjct: 306 NIEAGNQSIPADLSQLKYGCSVTDGCVDWATTEKMIRDAATLLRDVLPERQA 357


Lambda     K      H
   0.316    0.131    0.378 

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: 414
Number of extensions: 19
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: 356
Length of database: 358
Length adjustment: 29
Effective length of query: 327
Effective length of database: 329
Effective search space:   107583
Effective search space used:   107583
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate Dsui_2381 Dsui_2381 (phospho-2-dehydro-3-deoxyheptonate aldolase)
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.31320.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     2e-146  473.1   0.0   2.3e-146  472.9   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_2381  Dsui_2381 phospho-2-dehydro-3-de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_2381  Dsui_2381 phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.9   0.0  2.3e-146  2.3e-146       1     338 [.       7     348 ..       7     352 .. 0.98

  Alignments for each domain:
  == domain 1  score: 472.9 bits;  conditional E-value: 2.3e-146
                         TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklaek 77 
                                       d+++i+++d++ tP+++ a  pl+ekaa+ v++ r+++++il+ kd+rl+vv+GPcsihdp a l+ya+rlk+la++
  lcl|FitnessBrowser__PS:Dsui_2381   7 DNINIAAFDPMPTPAAMLASQPLSEKAATVVRQGRQDLKNILDRKDHRLFVVVGPCSIHDPVAGLDYARRLKALADE 83 
                                       68999************************************************************************ PP

                         TIGR00034  78 lkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqyladllsw 154
                                       ++d l +vmrvyfekPrttvGWkG indP +++sf+v+ G++ ar++ll+++e+glp++te+ld++spqy++dl+sw
  lcl|FitnessBrowser__PS:Dsui_2381  84 VSDTLLLVMRVYFEKPRTTVGWKGYINDPFMDDSFRVDVGMAKAREFLLQVNEIGLPAGTEALDPNSPQYYGDLISW 160
                                       ***************************************************************************** PP

                         TIGR00034 155 gaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrGG 231
                                       +aiGarttesq+hre++sgls pvgfkngtdG++++ai+ai +a+++h fl+ +++Gqvaiv+t+Gn +ghi+lrGG
  lcl|FitnessBrowser__PS:Dsui_2381 161 TAIGARTTESQTHREMSSGLSTPVGFKNGTDGNTEIAINAILSASKPHSFLGLNDQGQVAIVRTTGNAYGHIVLRGG 237
                                       ***************************************************************************99 PP

                         TIGR00034 232 kk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqsl 307
                                          pnyd+ +v  +++ + ka+l +++++d+sh+ns k+ + q+ v+++vv+qi+ G+k+++Gvmiesn+e Gnqs+
  lcl|FitnessBrowser__PS:Dsui_2381 238 GGrPNYDTVSVSVAEQAMVKAKLIPNVVVDCSHANSLKKPELQPLVMSDVVNQIRLGNKSMVGVMIESNIEAGNQSI 314
                                       877************************************************************************** PP

                         TIGR00034 308 ...keelkyGksvtdacigwedteallrklaeav 338
                                           ++lkyG+svtd c++w +te+++r+ a+ +
  lcl|FitnessBrowser__PS:Dsui_2381 315 padLSQLKYGCSVTDGCVDWATTEKMIRDAATLL 348
                                       6544689********************9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (358 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: 00:00:00.01
# Mc/sec: 10.52
//
[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