Alignments for a candidate for aroG in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Pseudomonas fluorescens GW456-L13

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate PfGW456L13_2883 2-keto-3-deoxy-D-arabino-heptulosonate-7- phosphate synthase I alpha (EC 2.5.1.54)

Query= BRENDA::P00888
         (356 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2883
          Length = 358

 Score =  353 bits (905), Expect = e-102
 Identities = 178/320 (55%), Positives = 223/320 (69%), Gaps = 4/320 (1%)

Query: 22  QLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIHDPETALEYARRFKALA 81
           QLK   PL      Q+   R+++  I+ G D RLLV+ GPCSIHDPE+ALEYA     LA
Sbjct: 29  QLKQQLPLGNALTRQVTAHRQAVRAILNGEDSRLLVIVGPCSIHDPESALEYAGNLARLA 88

Query: 82  AEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQIARKLLLELVNMGLPL 141
           AEVSD + LVMR Y EKPRTTVGWKGL  DPH+DGS D+ AGL ++R+L+ E++ +GLP+
Sbjct: 89  AEVSDEMLLVMRAYVEKPRTTVGWKGLAYDPHLDGSDDMAAGLTLSRELMREMLRLGLPV 148

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

Query: 202 RAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGG-KAPNYSPADVAQCEKEMEQAGLR 260
           R+AA PHR  G++  G  A++QT GN D H++LRGG + PNY  A +AQ   ++ +  + 
Sbjct: 209 RSAAHPHRHFGVDSQGHPAIIQTPGNADTHLVLRGGHRGPNYDSASIAQVNSDLTRLRIP 268

Query: 261 PSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIESNIHEGNQSSEQPRSEM 320
             +MVDCSH NS KD  RQPAV   V+ Q   G+RS+IG+MIES++ EG Q      S +
Sbjct: 269 ARIMVDCSHANSGKDPLRQPAVFNDVLEQRLQGDRSLIGMMIESHLFEGCQPLS---SSL 325

Query: 321 KYGVSVTDACISWEMTDALL 340
           KYGVSVTD C+ W  T+ LL
Sbjct: 326 KYGVSVTDGCLGWVGTEQLL 345


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: 406
Number of extensions: 15
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: 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 PfGW456L13_2883 (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.32000.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   4.5e-135  435.8   0.0   5.5e-135  435.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2883  2-keto-3-deoxy-D-arabino-heptulo


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2883  2-keto-3-deoxy-D-arabino-heptulosonate-7- phosphate synthase 
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.5   0.0  5.5e-135  5.5e-135      11     339 ..      24     353 ..      17     356 .. 0.98

  Alignments for each domain:
  == domain 1  score: 435.5 bits;  conditional E-value: 5.5e-135
                                               TIGR00034  11 lltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaal 65 
                                                             l +  +lk++ pl ++ + +v+  r+++  il+G+d+rllv++GPcsihdpe+al
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2883  24 LPSSLQLKQQLPLGNALTRQVTAHRQAVRAILNGEDSRLLVIVGPCSIHDPESAL 78 
                                                             55667899*********************************************** PP

                                               TIGR00034  66 eyakrlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlri 120
                                                             eya  l++la++++d++ +vmr+y+ekPrttvGWkGl  dP+l++s d+ +Gl +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2883  79 EYAGNLARLAAEVSDEMLLVMRAYVEKPRTTVGWKGLAYDPHLDGSDDMAAGLTL 133
                                                             ******************************************************* PP

                                               TIGR00034 121 arkllldlvelglplatelldtispqyladllswgaiGarttesqvhrelasgls 175
                                                             +r+l+ ++  lglp+atell+++++ y+ dllsw aiGarttesq+hre+asgl+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2883 134 SRELMREMLRLGLPVATELLQPMAAGYFDDLLSWVAIGARTTESQIHREMASGLA 188
                                                             ******************************************************* PP

                                               TIGR00034 176 lpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrG 230
                                                             +pvgfkngtdG++ va da+r+aa++h+ ++v+ +G+ ai++t Gn d+h++lrG
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2883 189 MPVGFKNGTDGGVGVASDAMRSAAHPHRHFGVDSQGHPAIIQTPGNADTHLVLRG 243
                                                             ******************************************************* PP

                                               TIGR00034 231 Gkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqi 284
                                                             G++ pnyd++++a+v+++l+++   +++m+d+sh+ns kd  rq++v ++v eq 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2883 244 GHRgPNYDSASIAQVNSDLTRLRIPARIMVDCSHANSGKDPLRQPAVFNDVLEQR 298
                                                             ***9*************************************************** PP

                                               TIGR00034 285 aeGekaiiGvmiesnleeGnqslkeelkyGksvtdacigwedteallrklaeavk 339
                                                              +G++++iG+mies+l eG q l+++lkyG+svtd c+gw  te+ll + a+ ++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2883 299 LQGDRSLIGMMIESHLFEGCQPLSSSLKYGVSVTDGCLGWVGTEQLLLDAADRLR 353
                                                             **********************************************998887766 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.43
//
[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