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 GFF2974 Psest_3030 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::P00888
         (356 letters)



>FitnessBrowser__psRCH2:GFF2974
          Length = 357

 Score =  362 bits (929), Expect = e-105
 Identities = 181/336 (53%), Positives = 235/336 (69%), Gaps = 4/336 (1%)

Query: 15  QVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIHDPETALEYA 74
           Q L +P  L+   PLS    A+I + R +I  ++ GRDPRLLVV GPCS+HDP  ALEYA
Sbjct: 25  QPLPSPAVLRQRLPLSDALAARIDNDRNAIRTVLDGRDPRLLVVVGPCSLHDPVAALEYA 84

Query: 75  RRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQIARKLLLEL 134
            R  ALA EVSD L LVMR Y EKPRTTVGWKGL+ DPH+DGS ++  GL ++R+L+L++
Sbjct: 85  ERLAALAPEVSDQLLLVMRAYVEKPRTTVGWKGLVYDPHLDGSGNMAEGLHLSRRLILDI 144

Query: 135 VNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVGFKNGTDGSL 194
           +  GLP+ATE L P +  Y  DL  W+AIGART+ESQ HRE+ SGL +PVGFKNGTDGSL
Sbjct: 145 LETGLPIATELLQPLAAGYFDDLLGWAAIGARTSESQIHRELVSGLDLPVGFKNGTDGSL 204

Query: 195 ATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGK-APNYSPADVAQCEKE 253
             A +AMR+A  PH+  GI+  G  ALLQT+GNPD H++LRGG  APNY  A VA   + 
Sbjct: 205 GIACDAMRSAEHPHQHFGIDDLGHPALLQTRGNPDTHLVLRGGHGAPNYDAASVAVARRA 264

Query: 254 MEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIESNIHEGNQSS 313
           +E+ G+ P +MVDCSH NS K+  RQP V ESV+AQ   G+ S+ G+M+ES++ +G Q  
Sbjct: 265 LEKQGIAPRIMVDCSHANSGKNPLRQPEVLESVIAQRLAGDASLRGVMLESHLFDGCQPL 324

Query: 314 EQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNG 349
               + ++YGVS+TD C+ W  T+ +LR+    L G
Sbjct: 325 S---AALRYGVSITDGCLGWTATEQMLRDAAHRLRG 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: 419
Number of extensions: 12
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: 357
Length adjustment: 29
Effective length of query: 327
Effective length of database: 328
Effective search space:   107256
Effective search space used:   107256
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 GFF2974 Psest_3030 (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.31703.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     1e-135  437.9   0.0   1.2e-135  437.7   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF2974  Psest_3030 phospho-2-dehydro-3-d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2974  Psest_3030 phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.7   0.0  1.2e-135  1.2e-135       8     338 ..      24     355 ..      17     357 .] 0.98

  Alignments for each domain:
  == domain 1  score: 437.7 bits;  conditional E-value: 1.2e-135
                           TIGR00034   8 idelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklaeklkddl 82 
                                          ++l +P+ l+++ pl+ + a+++ ++r++i  +l+G+d+rllvv+GPcs+hdp aaleya+rl++la +++d+l
  lcl|FitnessBrowser__psRCH2:GFF2974  24 AQPLPSPAVLRQRLPLSDALAARIDNDRNAIRTVLDGRDPRLLVVVGPCSLHDPVAALEYAERLAALAPEVSDQL 98 
                                         57899********************************************************************** PP

                           TIGR00034  83 eivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqyladllswgai 157
                                          +vmr+y+ekPrttvGWkGl+ dP+l++s ++ +Gl+++r+l+ld+ e+glp+atell++ ++ y+ dll w+ai
  lcl|FitnessBrowser__psRCH2:GFF2974  99 LLVMRAYVEKPRTTVGWKGLVYDPHLDGSGNMAEGLHLSRRLILDILETGLPIATELLQPLAAGYFDDLLGWAAI 173
                                         *************************************************************************** PP

                           TIGR00034 158 GarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrGGk 232
                                         Gart+esq+hrel sgl lpvgfkngtdGsl +a da+r+a+++h  +++++ G+ a+++t+Gn+d+h++lrGG+
  lcl|FitnessBrowser__psRCH2:GFF2974 174 GARTSESQIHRELVSGLDLPVGFKNGTDGSLGIACDAMRSAEHPHQHFGIDDLGHPALLQTRGNPDTHLVLRGGH 248
                                         *************************************************************************** PP

                           TIGR00034 233 k.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqs 306
                                           pnyda++va +++ lek g  +++m+d+sh+ns k+  rq+ev esv++q   G+ ++ Gvm+es+l +G q 
  lcl|FitnessBrowser__psRCH2:GFF2974 249 GaPNYDAASVAVARRALEKQGIAPRIMVDCSHANSGKNPLRQPEVLESVIAQRLAGDASLRGVMLESHLFDGCQP 323
                                         99************************************************************************* PP

                           TIGR00034 307 lkeelkyGksvtdacigwedteallrklaeav 338
                                         l+++l yG+s+td c+gw  te++lr+ a+ +
  lcl|FitnessBrowser__psRCH2:GFF2974 324 LSAALRYGVSITDGCLGWTATEQMLRDAAHRL 355
                                         **************************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (357 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: 7.39
//
[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