Alignments for a candidate for aroG in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Pseudomonas fluorescens FW300-N2E2

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate Pf6N2E2_2025 2-keto-3-deoxy-D-arabino-heptulosonate-7- phosphate synthase I alpha (EC 2.5.1.54)

Query= BRENDA::P00888
         (356 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2025
          Length = 356

 Score =  355 bits (911), Expect = e-102
 Identities = 179/327 (54%), Positives = 226/327 (69%), Gaps = 4/327 (1%)

Query: 22  QLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIHDPETALEYARRFKALA 81
           QLK   PLS     Q++  R++I  I+ G D RLLV+ GPCSIHDP++ALEYA     +A
Sbjct: 29  QLKHQLPLSTALSHQVSVHRQAIRAILNGEDARLLVIVGPCSIHDPKSALEYATNLARVA 88

Query: 82  AEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQIARKLLLELVNMGLPL 141
            EVSDS+ LVMR Y EKPRTTVGWKGL  DP +DGS D+ AGL ++R+L+ E++ +GLP+
Sbjct: 89  HEVSDSMLLVMRAYVEKPRTTVGWKGLAYDPGLDGSDDMAAGLTLSRELMREMLQLGLPV 148

Query: 142 ATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVGFKNGTDGSLATAINAM 201
           ATE L P +  Y  DL SW AIGARTTESQ HREMASGL MPVGFKNGTDG +  A +AM
Sbjct: 149 ATELLQPMAASYFDDLLSWVAIGARTTESQIHREMASGLGMPVGFKNGTDGGVGIACDAM 208

Query: 202 RAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGG-KAPNYSPADVAQCEKEMEQAGLR 260
           R+AA PHR  G++  G  A++QT GNPD H++LRGG + PNY    V Q   ++ +  + 
Sbjct: 209 RSAAHPHRHFGVDSQGHPAIIQTPGNPDTHLVLRGGHRGPNYDQQSVTQIHHDLTRLKIP 268

Query: 261 PSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIESNIHEGNQSSEQPRSEM 320
             +MVDCSH NS KD  RQP V   V+ Q   GNR++IG+M+ES++ EG Q        M
Sbjct: 269 ARIMVDCSHANSGKDPLRQPQVFNDVLEQRLQGNRALIGMMLESHLFEGCQPL---GPSM 325

Query: 321 KYGVSVTDACISWEMTDALLREIHQDL 347
           +YGVSVTD C+ WE T+ LLRE H+ L
Sbjct: 326 RYGVSVTDGCLGWESTERLLREAHRKL 352


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: 424
Number of extensions: 17
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: 356
Length adjustment: 29
Effective length of query: 327
Effective length of database: 327
Effective search space:   106929
Effective search space used:   106929
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 Pf6N2E2_2025 (2-keto-3-deoxy-D-arabino-heptulosonate-7- phosphate synthase I alpha (EC 2.5.1.54))
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.12694.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.9e-136  440.3   0.0   2.5e-136  439.9   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2025  2-keto-3-deoxy-D-arabino-heptulo


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2025  2-keto-3-deoxy-D-arabino-heptulosonate-7- phosphate synthase I alpha (
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.9   0.0  2.5e-136  2.5e-136      11     338 ..      24     352 ..      16     354 .. 0.98

  Alignments for each domain:
  == domain 1  score: 439.9 bits;  conditional E-value: 2.5e-136
                                      TIGR00034  11 lltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkkl 74 
                                                    l +  +lk++ pl+++  ++v   r++i  il+G+d rllv++GPcsihdp++aleya+ l+++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2025  24 LPSSLQLKHQLPLSTALSHQVSVHRQAIRAILNGEDARLLVIVGPCSIHDPKSALEYATNLARV 87 
                                                    55667899******************************************************** PP

                                      TIGR00034  75 aeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplate 138
                                                    a++++d++ +vmr+y+ekPrttvGWkGl  dP l++s d+ +Gl ++r+l+ ++ +lglp+ate
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2025  88 AHEVSDSMLLVMRAYVEKPRTTVGWKGLAYDPGLDGSDDMAAGLTLSRELMREMLQLGLPVATE 151
                                                    **************************************************************** PP

                                      TIGR00034 139 lldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaeh 202
                                                    ll+++++ y+ dllsw aiGarttesq+hre+asgl +pvgfkngtdG++ +a da+r+aa++h
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2025 152 LLQPMAASYFDDLLSWVAIGARTTESQIHREMASGLGMPVGFKNGTDGGVGIACDAMRSAAHPH 215
                                                    **************************************************************** PP

                                      TIGR00034 203 lflsvtkaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgn 265
                                                    + ++v+ +G+ ai++t Gn+d+h++lrGG++ pnyd+++v +++++l++++  +++m+d+sh+n
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2025 216 RHFGVDSQGHPAIIQTPGNPDTHLVLRGGHRgPNYDQQSVTQIHHDLTRLKIPARIMVDCSHAN 279
                                                    *******************************9******************************** PP

                                      TIGR00034 266 snkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqslkeelkyGksvtdacigwedtea 329
                                                    s kd  rq++v ++v eq  +G++a+iG+m+es+l eG q l+ ++ yG+svtd c+gwe+te+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2025 280 SGKDPLRQPQVFNDVLEQRLQGNRALIGMMLESHLFEGCQPLGPSMRYGVSVTDGCLGWESTER 343
                                                    **************************************************************** PP

                                      TIGR00034 330 llrklaeav 338
                                                    llr+ ++++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2025 344 LLREAHRKL 352
                                                    ***988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (356 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 11.84
//
[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