GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroB in Dechlorosoma suillum PS

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate Dsui_1095 Dsui_1095 3-dehydroquinate synthase

Query= SwissProt::Q8RU74
         (442 letters)



>FitnessBrowser__PS:Dsui_1095
          Length = 364

 Score =  402 bits (1032), Expect = e-116
 Identities = 208/358 (58%), Positives = 268/358 (74%), Gaps = 8/358 (2%)

Query: 81  VEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPN 140
           ++V LG RSYPI+IG+GLL + DL+  H+  K+ ++V+N TVAPLYL+  ++AL   N  
Sbjct: 6   LQVALGDRSYPIHIGSGLLQRADLILPHLGRKKAVIVSNETVAPLYLEP-LAALLRAN-G 63

Query: 141 VTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRG 200
           V V  V+LPDGE+FK+  TL ++FD  +ESR +R  T +ALGGGVIGD  G+AAA Y RG
Sbjct: 64  VAVSQVVLPDGEEFKDWPTLNRIFDALLESRAERSTTLIALGGGVIGDTTGFAAACYQRG 123

Query: 201 VNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASG 260
           + FIQ+PTT+++QVDSSVGGKT INHPLGKNMIGAFYQP+ VL D DTL+TLP+REL +G
Sbjct: 124 MPFIQVPTTLLSQVDSSVGGKTAINHPLGKNMIGAFYQPKLVLADIDTLDTLPERELKAG 183

Query: 261 LAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRA 320
           LAEVIKYGLIRD +F  W E ++P LLARD      A+ RSC +KA+VV++DE+E+G RA
Sbjct: 184 LAEVIKYGLIRDPQFLGWIESSLPGLLARDKALLAEAVYRSCAHKAEVVARDERETGERA 243

Query: 321 TLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAK 380
            LNLGHTFGHA+ETG+GYG WLHGEAVAAGTVMA ++S RLGWI  + V RV+ + + A 
Sbjct: 244 LLNLGHTFGHAIETGLGYGVWLHGEAVAAGTVMAAELSARLGWIGPAEVARVESVFRLAG 303

Query: 381 LPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETLRA 438
           LP S P+ + VE +  +M  DKKV  GKLRL+L +G +G+ V +      A DE + A
Sbjct: 304 LPVSGPD-LGVERYLELMRHDKKVEAGKLRLVLFRG-IGDAVVS----DAASDEQIAA 355


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: 401
Number of extensions: 9
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: 442
Length of database: 364
Length adjustment: 31
Effective length of query: 411
Effective length of database: 333
Effective search space:   136863
Effective search space used:   136863
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 Dsui_1095 Dsui_1095 (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.2192350.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.6e-118  381.8   0.0   1.8e-118  381.6   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_1095  Dsui_1095 3-dehydroquinate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_1095  Dsui_1095 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  381.6   0.0  1.8e-118  1.8e-118       1     340 [.      15     354 ..      15     358 .. 0.96

  Alignments for each domain:
  == domain 1  score: 381.6 bits;  conditional E-value: 1.8e-118
                         TIGR01357   1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldqll 76 
                                       y++++g+gll+++   l +  ++k+v++++e+v+ l+ e l+++l+++gv+v ++v+pdgee K++ t++++ d+ll
  lcl|FitnessBrowser__PS:Dsui_1095  15 YPIHIGSGLLQRADLILPHlGRKKAVIVSNETVAPLYLEPLAALLRANGVAVSQVVLPDGEEFKDWPTLNRIFDALL 91 
                                       689*******98877777755599***************************************************** PP

                         TIGR01357  77 eeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPkaVlid 153
                                       e+ +er+++l+a+GGGv+gD +GF+Aa y+RG++++qvPTtll++vDssvGGKt+in+plgkN+iGafyqPk+Vl d
  lcl|FitnessBrowser__PS:Dsui_1095  92 ESRAERSTTLIALGGGVIGDTTGFAAACYQRGMPFIQVPTTLLSQVDSSVGGKTAINHPLGKNMIGAFYQPKLVLAD 168
                                       ***************************************************************************** PP

                         TIGR01357 154 lkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDekesglRal 230
                                       +++l tlperel++G+aEviK+gli d +++ ++e+    ll + +++ l+e++ rs+  KaevV++De+e+g Ral
  lcl|FitnessBrowser__PS:Dsui_1095 169 IDTLDTLPERELKAGLAEVIKYGLIRDPQFLGWIESSLPGLLAR-DKALLAEAVYRSCAHKAEVVARDERETGERAL 244
                                       ************************************99988876.55****************************** PP

                         TIGR01357 231 LNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklkkklsveellkal 306
                                       LN+GHt+gHaiE+ l+y+ + HGeaVa G v++a+ls +lg + + ++ r++++++ +glp++ ++ l ve +l+ +
  lcl|FitnessBrowser__PS:Dsui_1095 245 LNLGHTFGHAIETGLGYGvWLHGEAVAAGTVMAAELSARLGWIGPAEVARVESVFRLAGLPVSGPD-LGVERYLELM 320
                                       *****************************************************************7.********** PP

                         TIGR01357 307 lkDKKnegskiklvlleeiGkaalasevteeell 340
                                        +DKK e++k++lvl + iG+a++++  ++e++ 
  lcl|FitnessBrowser__PS:Dsui_1095 321 RHDKKVEAGKLRLVLFRGIGDAVVSDAASDEQIA 354
                                       ************************9877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (364 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.53
//
[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:

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:

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:

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:

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