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.5602.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.07
//
[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:

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:

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:

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:

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