Alignments for a candidate for aroG in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Pseudomonas putida KT2440

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate PP_3080 PP_3080 tyr-sensitive phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::P00888
         (356 letters)



>FitnessBrowser__Putida:PP_3080
          Length = 353

 Score =  360 bits (924), Expect = e-104
 Identities = 177/332 (53%), Positives = 232/332 (69%), Gaps = 3/332 (0%)

Query: 17  LMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIHDPETALEYARR 76
           L +P  LK   PL  +   Q+   R++I +I+ GRDPRLLV+ GPCSIHDP +ALEYA R
Sbjct: 24  LPSPHLLKQQMPLPSELAQQVQAHRQAIRNILEGRDPRLLVIVGPCSIHDPRSALEYADR 83

Query: 77  FKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQIARKLLLELVN 136
             AL  EV+D L LVMR Y EKPRTTVGWKGL  DPH+DGS D+ +G+ ++R L+L ++ 
Sbjct: 84  LAALGREVNDKLLLVMRAYVEKPRTTVGWKGLAYDPHLDGSDDMHSGIALSRGLMLSMIE 143

Query: 137 MGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVGFKNGTDGSLAT 196
            GLP+ATE L P +  Y  DL +W+AIGARTTESQ HREM SGL +PVGFKNGTDG +A 
Sbjct: 144 RGLPIATELLQPMAAGYFDDLLAWAAIGARTTESQIHREMVSGLELPVGFKNGTDGGIAI 203

Query: 197 AINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGG-KAPNYSPADVAQCEKEME 255
           A +AMR+AA PHR  G++  G  A+++T GNPD H++LRGG K PN+    +A   + + 
Sbjct: 204 ASDAMRSAAHPHRHFGMDAQGHPAIIETLGNPDTHLVLRGGHKGPNHDANSIAMARQALA 263

Query: 256 QAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIESNIHEGNQSSEQ 315
           +AGL+  +MVDCSH NS KD  RQPAV   V+ Q   G+RS++G+MIE ++ +G Q+   
Sbjct: 264 KAGLQARIMVDCSHANSGKDPARQPAVFNDVLEQRLAGDRSLVGVMIEGHLFDGCQA--L 321

Query: 316 PRSEMKYGVSVTDACISWEMTDALLREIHQDL 347
            +  +KYGVS+TD C+ W  T+ LLRE  Q L
Sbjct: 322 GKGTLKYGVSITDGCLGWASTETLLREAAQKL 353


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: 408
Number of extensions: 14
Number of successful extensions: 3
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: 353
Length adjustment: 29
Effective length of query: 327
Effective length of database: 324
Effective search space:   105948
Effective search space used:   105948
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 PP_3080 PP_3080 (tyr-sensitive 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.13739.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.4e-137  441.6   0.0   8.4e-137  441.5   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_3080  PP_3080 tyr-sensitive phospho-2-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_3080  PP_3080 tyr-sensitive phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.5   0.0  8.4e-137  8.4e-137       8     337 ..      21     352 ..      14     353 .] 0.98

  Alignments for each domain:
  == domain 1  score: 441.5 bits;  conditional E-value: 8.4e-137
                           TIGR00034   8 idelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklaeklkddl 82 
                                           +l +P+ lk+++pl ++ a++v+  r++i +il+G+d+rllv++GPcsihdp++aleya+rl++l  +++d+l
  lcl|FitnessBrowser__Putida:PP_3080  21 SRRLPSPHLLKQQMPLPSELAQQVQAHRQAIRNILEGRDPRLLVIVGPCSIHDPRSALEYADRLAALGREVNDKL 95 
                                         56799********************************************************************** PP

                           TIGR00034  83 eivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqyladllswgai 157
                                          +vmr+y+ekPrttvGWkGl  dP+l++s d+++G++++r l+l + e glp+atell+++++ y+ dll+w+ai
  lcl|FitnessBrowser__Putida:PP_3080  96 LLVMRAYVEKPRTTVGWKGLAYDPHLDGSDDMHSGIALSRGLMLSMIERGLPIATELLQPMAAGYFDDLLAWAAI 170
                                         *************************************************************************** PP

                           TIGR00034 158 GarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrGGk 232
                                         Garttesq+hre+ sgl lpvgfkngtdG++++a da+r+aa++h+ ++++ +G+ ai+et Gn+d+h++lrGG+
  lcl|FitnessBrowser__Putida:PP_3080 171 GARTTESQIHREMVSGLELPVGFKNGTDGGIAIASDAMRSAAHPHRHFGMDAQGHPAIIETLGNPDTHLVLRGGH 245
                                         *************************************************************************** PP

                           TIGR00034 233 k.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqs 306
                                         k pn+da+++a +++ l kagl++++m+d+sh+ns kd  rq++v ++v eq   G+++++Gvmie +l +G q 
  lcl|FitnessBrowser__Putida:PP_3080 246 KgPNHDANSIAMARQALAKAGLQARIMVDCSHANSGKDPARQPAVFNDVLEQRLAGDRSLVGVMIEGHLFDGCQA 320
                                         *************************************************************************** PP

                           TIGR00034 307 l.keelkyGksvtdacigwedteallrklaea 337
                                         l k +lkyG+s+td c+gw +te+llr+ a++
  lcl|FitnessBrowser__Putida:PP_3080 321 LgKGTLKYGVSITDGCLGWASTETLLREAAQK 352
                                         *7778**********************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (353 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: 9.42
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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