Alignments for a candidate for aroG in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Pseudomonas simiae WCS417

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate GFF1656 PS417_08430 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::P00888
         (356 letters)



>FitnessBrowser__WCS417:GFF1656
          Length = 358

 Score =  417 bits (1071), 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 DI+ G D RL VV GPCSIH
Sbjct: 6   INDLNVESNETLITPDQLKREIPLSDAALQTVTKGREVIRDILDGTDHRLFVVIGPCSIH 65

Query: 66  DPETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQ 125
           D + A EYA R K LAAEVSD+LYLVMRVYFEKPRTTVGWKGLINDP++D SF ++ GL 
Sbjct: 66  DLKAAHEYAERLKVLAAEVSDTLYLVMRVYFEKPRTTVGWKGLINDPYLDDSFKIQDGLH 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+  +  ++++YGVS+TDACI W  T+  LR +H  L   L  R
Sbjct: 306 HLNWGCQAIPKDLADLQYGVSITDACIDWSATENTLRSMHAKLKDVLPKR 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: 417
Number of extensions: 11
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 GFF1656 PS417_08430 (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.5276.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.7e-154  498.5   0.0   4.3e-154  498.3   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF1656  PS417_08430 phospho-2-dehydro-3-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF1656  PS417_08430 phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  498.3   0.0  4.3e-154  4.3e-154       2     339 ..       8     349 ..       7     352 .. 0.98

  Alignments for each domain:
  == domain 1  score: 498.3 bits;  conditional E-value: 4.3e-154
                           TIGR00034   2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklae 76 
                                         dl++++ + l+tP++lk+++pl+ +a ++v+k r+ i dil+G d+rl+vviGPcsihd++aa eya+rlk la+
  lcl|FitnessBrowser__WCS417:GFF1656   8 DLNVESNETLITPDQLKREIPLSDAALQTVTKGREVIRDILDGTDHRLFVVIGPCSIHDLKAAHEYAERLKVLAA 82 
                                         78899999******************************************************************* PP

                           TIGR00034  77 klkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqyladl 151
                                         +++d l++vmrvyfekPrttvGWkGlindP+l++sf++++Gl+i r+llldl+e+glp+ate+ld+ispqyl dl
  lcl|FitnessBrowser__WCS417:GFF1656  83 EVSDTLYLVMRVYFEKPRTTVGWKGLINDPYLDDSFKIQDGLHIGRQLLLDLAEMGLPTATEALDPISPQYLQDL 157
                                         *************************************************************************** PP

                           TIGR00034 152 lswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghi 226
                                         +sw+aiGarttesq+hre+asgls +vgfkngtdG+l vai+a+++ +++h+fl+++++G v+iv+tkGn +gh+
  lcl|FitnessBrowser__WCS417:GFF1656 158 ISWSAIGARTTESQTHREMASGLSSAVGFKNGTDGGLTVAINALQSVSSPHRFLGINQEGGVSIVTTKGNAYGHV 232
                                         *************************************************************************** PP

                           TIGR00034 227 ilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnl 300
                                         +lrGG+  pnyd+ +va +++ l+ka+ k+++m+d+sh+nsnkd   q+ v+e+v++qi eG+++iiG+m+es+l
  lcl|FitnessBrowser__WCS417:GFF1656 233 VLRGGNGkPNYDSVSVALCEQALNKAKIKPNIMVDCSHANSNKDPALQPLVMENVANQILEGNQSIIGLMVESHL 307
                                         *****988******************************************************************* PP

                           TIGR00034 301 eeGnqsl...keelkyGksvtdacigwedteallrklaeavk 339
                                         + G q +    ++l+yG+s+tdaci+w  te+ lr +++++k
  lcl|FitnessBrowser__WCS417:GFF1656 308 NWGCQAIpkdLADLQYGVSITDACIDWSATENTLRSMHAKLK 349
                                         *******53234689**********************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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.14
//
[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