Alignments for a candidate for aroG in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Pseudomonas simiae WCS417

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate GFF2099 PS417_10705 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::P00888
         (356 letters)



>FitnessBrowser__WCS417:GFF2099
          Length = 359

 Score =  355 bits (911), Expect = e-102
 Identities = 182/347 (52%), Positives = 236/347 (68%), Gaps = 4/347 (1%)

Query: 5   ALNNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSI 64
           AL + +    Q L +  +LK   PLS     Q+   R ++  I+ G D RLLV+ GPCSI
Sbjct: 12  ALTSANEALTQRLPSSLELKHQLPLSPFLTEQVHAHRHAVRAILNGEDSRLLVIVGPCSI 71

Query: 65  HDPETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGL 124
           HDPE+A+EYAR  K LA EVSD + LV+R Y EKPRTT+GWKGL  DPH+DGS D+ AGL
Sbjct: 72  HDPESAMEYARNLKKLALEVSDQMLLVIRAYVEKPRTTIGWKGLAYDPHLDGSDDMAAGL 131

Query: 125 QIARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPV 184
            ++R+L+ E++ +GLP+ATE L P +  Y  DL SW AIGARTTESQ HREMASGL MPV
Sbjct: 132 TLSRQLMREMLRLGLPVATELLQPMAAGYFDDLLSWVAIGARTTESQIHREMASGLGMPV 191

Query: 185 GFKNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGG-KAPNYS 243
           GFKNGTDG +A A +AMR+A+ PHR  G++  G  A++QT GNPD H++LRGG + PNY 
Sbjct: 192 GFKNGTDGGVAIACDAMRSASHPHRHFGVDSQGHPAIIQTPGNPDTHLVLRGGHRGPNYD 251

Query: 244 PADVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIE 303
              VAQ + ++ ++ +   +MVDCSH NS KD  RQPAV   V+ Q   G+ S+IG+M+E
Sbjct: 252 AQSVAQVKHDLAKSKVAARIMVDCSHANSGKDPLRQPAVFNEVLDQRLQGDTSLIGMMLE 311

Query: 304 SNIHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNGQ 350
           S++ EG Q      + MKYGVSVTD C+ W  T+ LLR   + L  Q
Sbjct: 312 SHLFEGCQPLS---ASMKYGVSVTDGCLGWNGTEQLLRSAAERLREQ 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: 393
Number of extensions: 19
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 GFF2099 PS417_10705 (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.8246.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   6.1e-138  445.2   0.0   7.6e-138  444.9   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF2099  PS417_10705 phospho-2-dehydro-3-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF2099  PS417_10705 phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.9   0.0  7.6e-138  7.6e-138       9     342 .]      22     356 ..      15     356 .. 0.98

  Alignments for each domain:
  == domain 1  score: 444.9 bits;  conditional E-value: 7.6e-138
                           TIGR00034   9 delltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklaeklkddle 83 
                                         ++l +  elk++ pl++  +e+v+  r+++  il+G+d+rllv++GPcsihdpe+a+eya+ lkkla +++d++ 
  lcl|FitnessBrowser__WCS417:GFF2099  22 QRLPSSLELKHQLPLSPFLTEQVHAHRHAVRAILNGEDSRLLVIVGPCSIHDPESAMEYARNLKKLALEVSDQML 96 
                                         56778899******************************************************************* PP

                           TIGR00034  84 ivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqyladllswgaiG 158
                                         +v+r+y+ekPrtt+GWkGl  dP+l++s d+ +Gl ++r+l+ ++  lglp+atell+++++ y+ dllsw aiG
  lcl|FitnessBrowser__WCS417:GFF2099  97 LVIRAYVEKPRTTIGWKGLAYDPHLDGSDDMAAGLTLSRQLMREMLRLGLPVATELLQPMAAGYFDDLLSWVAIG 171
                                         *************************************************************************** PP

                           TIGR00034 159 arttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrGGkk 233
                                         arttesq+hre+asgl +pvgfkngtdG++++a da+r+a+++h+ ++v+ +G+ ai++t Gn+d+h++lrGG++
  lcl|FitnessBrowser__WCS417:GFF2099 172 ARTTESQIHREMASGLGMPVGFKNGTDGGVAIACDAMRSASHPHRHFGVDSQGHPAIIQTPGNPDTHLVLRGGHR 246
                                         *************************************************************************** PP

                           TIGR00034 234 .pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqsl 307
                                          pnyda++va+vk++l k +  +++m+d+sh+ns kd  rq++v ++v +q  +G++++iG+m+es+l eG q l
  lcl|FitnessBrowser__WCS417:GFF2099 247 gPNYDAQSVAQVKHDLAKSKVAARIMVDCSHANSGKDPLRQPAVFNEVLDQRLQGDTSLIGMMLESHLFEGCQPL 321
                                         9************************************************************************** PP

                           TIGR00034 308 keelkyGksvtdacigwedteallrklaeavkerr 342
                                         ++++kyG+svtd c+gw+ te+llr  ae ++e+r
  lcl|FitnessBrowser__WCS417:GFF2099 322 SASMKYGVSVTDGCLGWNGTEQLLRSAAERLREQR 356
                                         ****************************9999875 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: 9.05
//
[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