Alignments for a candidate for aroG in Pseudomonas fluorescens FW300-N2E3

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Pseudomonas fluorescens FW300-N2E3

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate AO353_21815 AO353_21815 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::P00888
         (356 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21815
          Length = 359

 Score =  366 bits (940), Expect = e-106
 Identities = 183/336 (54%), Positives = 234/336 (69%), Gaps = 4/336 (1%)

Query: 15  QVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIHDPETALEYA 74
           Q L +  QLK   PLSL    Q+A  R+++  I+ G D RLLVV GPCSIHDP++ALEYA
Sbjct: 22  QRLPSSLQLKHQLPLSLTLTQQVAAHREAVRAILDGEDSRLLVVVGPCSIHDPQSALEYA 81

Query: 75  RRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQIARKLLLEL 134
            +   LA +VSD + +VMR Y EKPRTTVGWKGL  DPH+DGS D+  GL ++R+L+ E+
Sbjct: 82  GKLARLATDVSDEMLVVMRAYIEKPRTTVGWKGLAYDPHLDGSDDMVGGLTLSRELMREM 141

Query: 135 VNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVGFKNGTDGSL 194
           + +GLP+ATE L P +  Y  DL SW AIGARTTESQ HREMASGL MPVGFKNGTDG +
Sbjct: 142 LRLGLPIATELLQPMAASYFDDLLSWVAIGARTTESQIHREMASGLGMPVGFKNGTDGGV 201

Query: 195 ATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGG-KAPNYSPADVAQCEKE 253
             A +AMR+AA PHR  G++  G  A++QTQGNPD H++LRGG + PNY    VAQ + +
Sbjct: 202 GVATDAMRSAAHPHRHFGVDSQGHPAIIQTQGNPDTHLVLRGGHRGPNYDVQSVAQIQND 261

Query: 254 MEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIESNIHEGNQSS 313
           +++  +   +MVDCSH NS KD  RQPAV   V+ Q   GNRS+IG+M+ES++ EG Q  
Sbjct: 262 LQKLKIASRIMVDCSHANSGKDPLRQPAVFNEVLEQRLSGNRSLIGMMLESHLFEGCQPL 321

Query: 314 EQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNG 349
               + ++YGVSVTD C+ WE T+ LLR     L G
Sbjct: 322 S---TSLRYGVSVTDGCLGWEATEQLLRNASLKLRG 354


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: 421
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: 359
Length adjustment: 29
Effective length of query: 327
Effective length of database: 330
Effective search space:   107910
Effective search space used:   107910
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 AO353_21815 AO353_21815 (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.25259.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   2.6e-137  443.1   0.0   3.4e-137  442.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21815  AO353_21815 phospho-2-dehydro-3-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_21815  AO353_21815 phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.8   0.0  3.4e-137  3.4e-137       9     335 ..      22     349 ..      16     355 .. 0.98

  Alignments for each domain:
  == domain 1  score: 442.8 bits;  conditional E-value: 3.4e-137
                                     TIGR00034   9 delltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkk 73 
                                                   ++l +  +lk++ pl+ + +++va  r+++  il+G+d+rllvv+GPcsihdp++aleya +l++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21815  22 QRLPSSLQLKHQLPLSLTLTQQVAAHREAVRAILDGEDSRLLVVVGPCSIHDPQSALEYAGKLAR 86 
                                                   56778899********************************************************* PP

                                     TIGR00034  74 laeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplate 138
                                                   la +++d++ +vmr+y+ekPrttvGWkGl  dP+l++s d+  Gl ++r+l+ ++  lglp+ate
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21815  87 LATDVSDEMLVVMRAYIEKPRTTVGWKGLAYDPHLDGSDDMVGGLTLSRELMREMLRLGLPIATE 151
                                                   ***************************************************************** PP

                                     TIGR00034 139 lldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehl 203
                                                   ll+++++ y+ dllsw aiGarttesq+hre+asgl +pvgfkngtdG++ va da+r+aa++h+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21815 152 LLQPMAASYFDDLLSWVAIGARTTESQIHREMASGLGMPVGFKNGTDGGVGVATDAMRSAAHPHR 216
                                                   ***************************************************************** PP

                                     TIGR00034 204 flsvtkaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsn 267
                                                    ++v+ +G+ ai++t+Gn+d+h++lrGG++ pnyd ++va+++++l+k++  +++m+d+sh+ns 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21815 217 HFGVDSQGHPAIIQTQGNPDTHLVLRGGHRgPNYDVQSVAQIQNDLQKLKIASRIMVDCSHANSG 281
                                                   ******************************9********************************** PP

                                     TIGR00034 268 kdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqslkeelkyGksvtdacigwedteallr 332
                                                   kd  rq++v ++v eq  +G++++iG+m+es+l eG q l+ +l yG+svtd c+gwe te+llr
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21815 282 KDPLRQPAVFNEVLEQRLSGNRSLIGMMLESHLFEGCQPLSTSLRYGVSVTDGCLGWEATEQLLR 346
                                                   ****************************************************************9 PP

                                     TIGR00034 333 kla 335
                                                   + +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21815 347 NAS 349
                                                   865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (359 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: 8.64
//
[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