GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Pseudomonas fluorescens FW300-N2E3

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate AO353_19030 AO353_19030 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::P00888
         (356 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_19030
          Length = 358

 Score =  416 bits (1068), Expect = e-121
 Identities = 207/350 (59%), Positives = 259/350 (74%), Gaps = 1/350 (0%)

Query: 6   LNNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIH 65
           +N++++   + L+TP+QLK   PLS      +   R+ I +I+ G D RL VV GPCSIH
Sbjct: 6   INDLNVASNETLITPDQLKRDIPLSDAALRTVTKGREVIRNILDGTDHRLFVVIGPCSIH 65

Query: 66  DPETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQ 125
           D + A EYA R K LAAEVSD+LYLVMRVYFEKPRTTVGWKGLINDP++D SF ++ GL 
Sbjct: 66  DIKAAHEYAERLKVLAAEVSDTLYLVMRVYFEKPRTTVGWKGLINDPYLDDSFKIQDGLH 125

Query: 126 IARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVG 185
           I R+LLL+L  MGLP ATEALDP SPQYL DL SWSAIGARTTESQTHREMASGLS  VG
Sbjct: 126 IGRQLLLDLAEMGLPTATEALDPISPQYLQDLISWSAIGARTTESQTHREMASGLSSAVG 185

Query: 186 FKNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGKA-PNYSP 244
           FKNGTDG L  AINA+++ + PHRF+GINQ G V+++ T+GN  GHV+LRGG   PNY  
Sbjct: 186 FKNGTDGGLTVAINALQSVSSPHRFLGINQEGGVSIVTTKGNAYGHVVLRGGNGKPNYDS 245

Query: 245 ADVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIES 304
             VA CE+ + +A ++P++MVDCSH NSNKD   QP V E+V  QI +GN+SIIGLM+ES
Sbjct: 246 VSVALCEQALNKAKIKPNIMVDCSHANSNKDPALQPLVMENVANQILEGNQSIIGLMVES 305

Query: 305 NIHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNGQLTAR 354
           +++ G Q+  +  +E++YGVS+TDACI W  T+  LR +H  L   L  R
Sbjct: 306 HLNWGCQAIPKDLAELQYGVSITDACIDWTATENTLRSMHAKLKDVLPKR 355


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: 407
Number of extensions: 10
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 AO353_19030 AO353_19030 (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.2998.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   2.2e-153  496.0   0.0   2.5e-153  495.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_19030  AO353_19030 phospho-2-dehydro-3-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_19030  AO353_19030 phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  495.8   0.0  2.5e-153  2.5e-153       2     339 ..       8     349 ..       7     352 .. 0.98

  Alignments for each domain:
  == domain 1  score: 495.8 bits;  conditional E-value: 2.5e-153
                                     TIGR00034   2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaale 66 
                                                   dl++++ + l+tP++lk+ +pl+ +a  +v+k r+ i +il+G d+rl+vviGPcsihd +aa e
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_19030   8 DLNVASNETLITPDQLKRDIPLSDAALRTVTKGREVIRNILDGTDHRLFVVIGPCSIHDIKAAHE 72 
                                                   7889999********************************************************** PP

                                     TIGR00034  67 yakrlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvel 131
                                                   ya+rlk la++++d l++vmrvyfekPrttvGWkGlindP+l++sf++++Gl+i r+llldl+e+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_19030  73 YAERLKVLAAEVSDTLYLVMRVYFEKPRTTVGWKGLINDPYLDDSFKIQDGLHIGRQLLLDLAEM 137
                                                   ***************************************************************** PP

                                     TIGR00034 132 glplatelldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidair 196
                                                   glp+ate+ld+ispqyl dl+sw+aiGarttesq+hre+asgls +vgfkngtdG+l vai+a++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_19030 138 GLPTATEALDPISPQYLQDLISWSAIGARTTESQTHREMASGLSSAVGFKNGTDGGLTVAINALQ 202
                                                   ***************************************************************** PP

                                     TIGR00034 197 aaaaehlflsvtkaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmid 260
                                                   + +++h+fl+++++G v+iv+tkGn +gh++lrGG+  pnyd+ +va +++ l+ka+ k+++m+d
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_19030 203 SVSSPHRFLGINQEGGVSIVTTKGNAYGHVVLRGGNGkPNYDSVSVALCEQALNKAKIKPNIMVD 267
                                                   ***********************************988*************************** PP

                                     TIGR00034 261 fshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqsl...keelkyGksvtdaci 322
                                                   +sh+nsnkd   q+ v+e+v++qi eG+++iiG+m+es+l+ G q +    +el+yG+s+tdaci
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_19030 268 CSHANSNKDPALQPLVMENVANQILEGNQSIIGLMVESHLNWGCQAIpkdLAELQYGVSITDACI 332
                                                   ***********************************************63335789********** PP

                                     TIGR00034 323 gwedteallrklaeavk 339
                                                   +w  te+ lr +++++k
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_19030 333 DWTATENTLRSMHAKLK 349
                                                   ************99876 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.53
//
[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