Alignments for a candidate for aroB in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Pseudomonas putida KT2440

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate PP_5078 PP_5078 3-dehydroquinate synthase

Query= SwissProt::Q8RU74
         (442 letters)



>FitnessBrowser__Putida:PP_5078
          Length = 365

 Score =  436 bits (1121), Expect = e-127
 Identities = 227/358 (63%), Positives = 269/358 (75%), Gaps = 5/358 (1%)

Query: 81  VEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPN 140
           ++VDLG RSYPIYIG GLLDQP+LL  HI G++V +V+N TVAPLYL++   AL      
Sbjct: 4   LKVDLGERSYPIYIGEGLLDQPELLAPHIAGRQVAIVSNETVAPLYLERLSKALGA---- 59

Query: 141 VTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRG 200
            +V  V+LPDGE  KN ETL  +FD  + +R DRR T VALGGGVIGDM G+AAA Y RG
Sbjct: 60  YSVLPVVLPDGEAHKNWETLQLIFDGLLTARHDRRTTVVALGGGVIGDMAGFAAACYQRG 119

Query: 201 VNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASG 260
           V+FIQ+PTT+++QVDSSVGGKTGINHPLGKNM+GAFYQP+ VLIDT +L TLP REL++G
Sbjct: 120 VDFIQVPTTLLSQVDSSVGGKTGINHPLGKNMVGAFYQPKAVLIDTTSLKTLPARELSAG 179

Query: 261 LAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRA 320
           LAEVIKYGLI D  F  W E NM  L A D  A T AI+RSC  KA VV  DE+ESG+RA
Sbjct: 180 LAEVIKYGLICDKPFLAWLEDNMQALRALDSAALTEAIRRSCAAKAAVVGADERESGLRA 239

Query: 321 TLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAK 380
           TLNLGHTFGHA+ET +GYG WLHGEAVAAGTVMA++MS RLGWID +   R  ++LQ A 
Sbjct: 240 TLNLGHTFGHAIETHMGYGVWLHGEAVAAGTVMALEMSMRLGWIDQAERDRGIRLLQDAG 299

Query: 381 LPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETLRA 438
           LP  PP+ MT   F   MAVDKKV DG+LRL+LL+  +G  V T DY ++ L  TL A
Sbjct: 300 LPVVPPQEMTPAHFMEHMAVDKKVLDGRLRLVLLR-QMGEAVVTDDYSKEILQATLSA 356


Lambda     K      H
   0.318    0.133    0.385 

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: 411
Number of extensions: 9
Number of successful extensions: 2
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: 442
Length of database: 365
Length adjustment: 31
Effective length of query: 411
Effective length of database: 334
Effective search space:   137274
Effective search space used:   137274
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate PP_5078 PP_5078 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

# 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/TIGR01357.hmm
# target sequence database:        /tmp/gapView.13610.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01357  [M=344]
Accession:   TIGR01357
Description: aroB: 3-dehydroquinate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.1e-120  387.4   0.0   3.8e-120  387.1   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_5078  PP_5078 3-dehydroquinate synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_5078  PP_5078 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.1   0.0  3.8e-120  3.8e-120       1     338 [.      13     349 ..      13     354 .. 0.95

  Alignments for each domain:
  == domain 1  score: 387.1 bits;  conditional E-value: 3.8e-120
                           TIGR01357   1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldq 74 
                                         y++++gegll++      +   +++ ++++e+v+ l+ e+l++al +  ++vl +v+pdge +K++et++ + d 
  lcl|FitnessBrowser__Putida:PP_5078  13 YPIYIGEGLLDQPELLAPHiAGRQVAIVSNETVAPLYLERLSKALGA--YSVLPVVLPDGEAHKNWETLQLIFDG 85 
                                         6899******9764444444459**********************76..************************** PP

                           TIGR01357  75 lleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPka 149
                                         ll++ ++r++++va+GGGv+gD+aGF+Aa y+RG++++qvPTtll++vDssvGGKtgin+plgkN++GafyqPka
  lcl|FitnessBrowser__Putida:PP_5078  86 LLTARHDRRTTVVALGGGVIGDMAGFAAACYQRGVDFIQVPTTLLSQVDSSVGGKTGINHPLGKNMVGAFYQPKA 160
                                         *************************************************************************** PP

                           TIGR01357 150 VlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDeke 224
                                         Vlid++ l+tlp rel++G+aEviK+gli d+ ++++le+n ++l+ l + +al+e+i+rs+  Ka vV +De+e
  lcl|FitnessBrowser__Putida:PP_5078 161 VLIDTTSLKTLPARELSAGLAEVIKYGLICDKPFLAWLEDNMQALRAL-DSAALTEAIRRSCAAKAAVVGADERE 234
                                         *******************************************98876.55************************ PP

                           TIGR01357 225 sglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklkkkls 298
                                         sglRa+LN+GHt+gHaiE+ ++y+ + HGeaVa G v+++++s +lg +++ +++r ++ll+ +glp+  +++++
  lcl|FitnessBrowser__Putida:PP_5078 235 SGLRATLNLGHTFGHAIETHMGYGvWLHGEAVAAGTVMALEMSMRLGWIDQAERDRGIRLLQDAGLPVVPPQEMT 309
                                         *************************************************************************** PP

                           TIGR01357 299 veellkallkDKKnegskiklvlleeiGkaalasevteee 338
                                           ++++++  DKK  +++++lvll+++G+a++++++++e 
  lcl|FitnessBrowser__Putida:PP_5078 310 PAHFMEHMAVDKKVLDGRLRLVLLRQMGEAVVTDDYSKEI 349
                                         *******************************998885543 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (365 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: 12.20
//
[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