Alignments for a candidate for aroB in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Pseudomonas simiae WCS417

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate GFF390 PS417_01985 3-dehydroquinate synthase

Query= SwissProt::Q8RU74
         (442 letters)



>FitnessBrowser__WCS417:GFF390
          Length = 366

 Score =  431 bits (1107), Expect = e-125
 Identities = 224/358 (62%), Positives = 270/358 (75%), Gaps = 5/358 (1%)

Query: 81  VEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPN 140
           ++VDLG RSYPI+IG GLLDQP+LL  HI G++V +++N TVAPLYL++   +L      
Sbjct: 4   LKVDLGERSYPIHIGEGLLDQPELLAPHIAGRQVAIISNETVAPLYLERLSRSLAA---- 59

Query: 141 VTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRG 200
            +V SVILPDGE  KN ETL  +FD  + +R DRR T +ALGGGVIGDM G+AAA Y RG
Sbjct: 60  YSVISVILPDGEAHKNWETLQLIFDGLLTARHDRRTTVIALGGGVIGDMAGFAAACYQRG 119

Query: 201 VNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASG 260
           V+FIQ+PTT+++QVDSSVGGKTGINHPLGKNM+GAFYQPQ VLIDT TLNTLP REL++G
Sbjct: 120 VDFIQVPTTLLSQVDSSVGGKTGINHPLGKNMVGAFYQPQAVLIDTTTLNTLPPRELSAG 179

Query: 261 LAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRA 320
           LAEVIKYGLI D  F  W E+++  L   D  A T AI RSC  KA VV+ DE+ESGVRA
Sbjct: 180 LAEVIKYGLICDEPFLTWLEEHVDALRNLDQAALTEAISRSCAAKALVVNADERESGVRA 239

Query: 321 TLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAK 380
           TLNLGHTFGHA+ET +GYG WLHGEAVAAGTVMA++MS+RLGWI      R  ++ Q+A 
Sbjct: 240 TLNLGHTFGHAIETHMGYGVWLHGEAVAAGTVMALEMSQRLGWISAQERDRGIRLFQRAG 299

Query: 381 LPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETLRA 438
           LP  PPE MT   F   MA+DKKV DG+LRL+LL+  +G  V T DY ++ L  TL A
Sbjct: 300 LPVIPPEEMTEADFLEHMAIDKKVIDGRLRLVLLR-HMGEAVVTDDYPKEILQATLGA 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: 409
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: 366
Length adjustment: 31
Effective length of query: 411
Effective length of database: 335
Effective search space:   137685
Effective search space used:   137685
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 GFF390 PS417_01985 (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.1454349.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                      -----------
   4.9e-121  390.1   0.0   5.8e-121  389.8   0.0    1.0  1  FitnessBrowser__WCS417:GFF390  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__WCS417:GFF390  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  389.8   0.0  5.8e-121  5.8e-121       1     338 [.      13     349 ..      13     354 .. 0.96

  Alignments for each domain:
  == domain 1  score: 389.8 bits;  conditional E-value: 5.8e-121
                      TIGR01357   1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldqlleek 79 
                                    y++++gegll++      +   +++ +i++e+v+ l+ e+l++ l++  ++v+ +++pdge +K++et++ + d ll++ 
  FitnessBrowser__WCS417:GFF390  13 YPIHIGEGLLDQPELLAPHiAGRQVAIISNETVAPLYLERLSRSLAA--YSVISVILPDGEAHKNWETLQLIFDGLLTAR 90 
                                    689********774444444459**********************76..******************************* PP

                      TIGR01357  80 lerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPkaVlidlkvlet 159
                                    ++r+++++a+GGGv+gD+aGF+Aa y+RG++++qvPTtll++vDssvGGKtgin+plgkN++GafyqP+aVlid+++l+t
  FitnessBrowser__WCS417:GFF390  91 HDRRTTVIALGGGVIGDMAGFAAACYQRGVDFIQVPTTLLSQVDSSVGGKTGINHPLGKNMVGAFYQPQAVLIDTTTLNT 170
                                    ******************************************************************************** PP

                      TIGR01357 160 lperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDekesglRalLNfGHtlgH 239
                                    lp rel++G+aEviK+gli d+ ++++le++ ++l++l +++al+e+i+rs+  Ka vV++De+esg+Ra+LN+GHt+gH
  FitnessBrowser__WCS417:GFF390 171 LPPRELSAGLAEVIKYGLICDEPFLTWLEEHVDALRNL-DQAALTEAISRSCAAKALVVNADERESGVRATLNLGHTFGH 249
                                    *********************************99986.55*************************************** PP

                      TIGR01357 240 aiEallkyk.lsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklkkklsveellkallkDKKnegskik 318
                                    aiE+ ++y+ + HGeaVa G v+++++s++lg ++a++++r ++l++++glp+  +++++   +l+++  DKK  +++++
  FitnessBrowser__WCS417:GFF390 250 AIETHMGYGvWLHGEAVAAGTVMALEMSQRLGWISAQERDRGIRLFQRAGLPVIPPEEMTEADFLEHMAIDKKVIDGRLR 329
                                    ******************************************************************************** PP

                      TIGR01357 319 lvlleeiGkaalasevteee 338
                                    lvll+++G+a++++++++e 
  FitnessBrowser__WCS417:GFF390 330 LVLLRHMGEAVVTDDYPKEI 349
                                    ***********998887664 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (366 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 14.71
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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