Alignments for a candidate for aroG in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Pseudomonas stutzeri RCH2

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate GFF2286 Psest_2331 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::P00888
         (356 letters)



>FitnessBrowser__psRCH2:GFF2286
          Length = 358

 Score =  421 bits (1081), Expect = e-122
 Identities = 205/350 (58%), Positives = 261/350 (74%), Gaps = 1/350 (0%)

Query: 6   LNNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIH 65
           ++++++     L+TPEQLK   PL+      ++  R+ + DI+ G+D RL VV GPCSIH
Sbjct: 6   IDDLNVASNVTLITPEQLKREIPLTASALHTVSHGRQVVRDILDGKDHRLFVVIGPCSIH 65

Query: 66  DPETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQ 125
           D + A EYA R K LA +VSDSL+L+MRVYFEKPRTTVGWKGLINDP+MD SF ++ GL 
Sbjct: 66  DLKAAHEYAERLKVLAEKVSDSLFLIMRVYFEKPRTTVGWKGLINDPYMDDSFKIQDGLH 125

Query: 126 IARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVG 185
           I RKLLL+L  MGLP ATEALDP SPQYL DL SWSAIGARTTESQTHREMASGLS  VG
Sbjct: 126 IGRKLLLDLAEMGLPTATEALDPISPQYLQDLISWSAIGARTTESQTHREMASGLSSAVG 185

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

Query: 245 ADVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIES 304
             VA CE+E+ +AG+RP++M+DCSH NSNKD   QP V ++V  QI +GN SI+GLM+ES
Sbjct: 246 VSVALCEQELTKAGIRPNIMIDCSHANSNKDPALQPLVMDNVANQILEGNDSIVGLMVES 305

Query: 305 NIHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNGQLTAR 354
           ++  GNQ+  +   ++KYGVS+TDACI W+ T+  +  +H  L   L  R
Sbjct: 306 HLGWGNQAIPKDLCDLKYGVSITDACIDWDTTEKAVMSMHDKLKDVLPKR 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: 440
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 GFF2286 Psest_2331 (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.822.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.7e-155  501.5   0.0   5.5e-155  501.3   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF2286  Psest_2331 phospho-2-dehydro-3-d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2286  Psest_2331 phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  501.3   0.0  5.5e-155  5.5e-155       1     339 [.       7     349 ..       7     352 .. 0.97

  Alignments for each domain:
  == domain 1  score: 501.3 bits;  conditional E-value: 5.5e-155
                           TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkkla 75 
                                         ddl++++   l+tPe+lk+++plt++a ++v + r+ + dil+Gkd+rl+vviGPcsihd++aa eya+rlk la
  lcl|FitnessBrowser__psRCH2:GFF2286   7 DDLNVASNVTLITPEQLKREIPLTASALHTVSHGRQVVRDILDGKDHRLFVVIGPCSIHDLKAAHEYAERLKVLA 81 
                                         6788888889***************************************************************** PP

                           TIGR00034  76 eklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqylad 150
                                         ek++d+l ++mrvyfekPrttvGWkGlindP++++sf++++Gl+i rkllldl+e+glp+ate+ld+ispqyl d
  lcl|FitnessBrowser__psRCH2:GFF2286  82 EKVSDSLFLIMRVYFEKPRTTVGWKGLINDPYMDDSFKIQDGLHIGRKLLLDLAEMGLPTATEALDPISPQYLQD 156
                                         *************************************************************************** PP

                           TIGR00034 151 llswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedgh 225
                                         l+sw+aiGarttesq+hre+asgls +vgfkngtdGsl vai+a+++ +++h+fl+++++G v+iv+tkGn++gh
  lcl|FitnessBrowser__psRCH2:GFF2286 157 LISWSAIGARTTESQTHREMASGLSSAVGFKNGTDGSLTVAINALQSVSSPHRFLGINQSGGVSIVTTKGNNYGH 231
                                         *************************************************************************** PP

                           TIGR00034 226 iilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesn 299
                                         ++lrGG+  pnyd+ +va +++el+kag ++++mid+sh+nsnkd   q+ v+++v++qi eG+++i+G+m+es+
  lcl|FitnessBrowser__psRCH2:GFF2286 232 VVLRGGNGkPNYDSVSVALCEQELTKAGIRPNIMIDCSHANSNKDPALQPLVMDNVANQILEGNDSIVGLMVESH 306
                                         ******988****************************************************************** PP

                           TIGR00034 300 leeGnqslke...elkyGksvtdacigwedteallrklaeavk 339
                                         l  Gnq + +   +lkyG+s+tdaci+w++te+ +  +++++k
  lcl|FitnessBrowser__psRCH2:GFF2286 307 LGWGNQAIPKdlcDLKYGVSITDACIDWDTTEKAVMSMHDKLK 349
                                         ********55233689********************9999886 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: 9.75
//
[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