GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Phaeobacter inhibens BS107

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate GFF2847 PGA1_c28930 dihydrodipicolinate synthase DapA

Query= BRENDA::Q8UGL3
         (294 letters)



>FitnessBrowser__Phaeo:GFF2847
          Length = 290

 Score =  380 bits (975), Expect = e-110
 Identities = 195/293 (66%), Positives = 228/293 (77%), Gaps = 3/293 (1%)

Query: 1   MFKGSIPALITPFTDNGSVDEKAFAAHVEWQIAEGSNGLVPVGTTGESPTLSHDEHKRVV 60
           MFKGS+PAL+TPF+ NG +D       VEW I +GS  LVPVGTTGESPTL+H+EH+ V+
Sbjct: 1   MFKGSMPALVTPFS-NGELDLDTLKRLVEWHIDQGSTALVPVGTTGESPTLTHEEHETVI 59

Query: 61  ELCIEVAAKRVPVIAGAGSNNTDEAIELALHAQEAGADALLVVTPYYNKPTQKGLFAHFS 120
              +++AA RVPVIAGAGSNNT E       A E GADA LVVTPYYNKPTQ+GL AHF+
Sbjct: 60  AEVVKIAAGRVPVIAGAGSNNTVEGKRFVQFAAEVGADAALVVTPYYNKPTQRGLIAHFT 119

Query: 121 AVAEAVKLPIVIYNIPPRSVVDMSPETMGALVKAHKNIIGVKDATGKLDRVSEQRISCGK 180
            +     +PIVIYNIP RSV+DM+P TMG L K  + IIGVKDATG + RVS+QR SCG 
Sbjct: 120 ELHNCADIPIVIYNIPGRSVIDMTPATMGELAKLER-IIGVKDATGDIARVSQQRASCGA 178

Query: 181 DFVQLSGEDGTALGFNAHGGVGCISVTANVAPRLCSEFQAAMLAGDYAKALEYQDRLMPL 240
           DF+QLSGED TALGFNAHGGVGCISVTANVAP+LC+EFQAA LAGDYA ALEYQD+LMPL
Sbjct: 179 DFIQLSGEDATALGFNAHGGVGCISVTANVAPKLCAEFQAATLAGDYALALEYQDKLMPL 238

Query: 241 HRAIFMEPGVCGTKYALSKTRGGNRRVRSPLMSTLEPATEAAIDAALKHAGLM 293
           H AIF+EPG+ G KY LSK    +  VR PL + LE +T+AAIDAA+ HAGL+
Sbjct: 239 HEAIFIEPGLAGAKYGLSKLGLCSEEVRLPL-TGLEDSTKAAIDAAMAHAGLL 290


Lambda     K      H
   0.317    0.133    0.384 

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: 352
Number of extensions: 11
Number of successful extensions: 4
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: 294
Length of database: 290
Length adjustment: 26
Effective length of query: 268
Effective length of database: 264
Effective search space:    70752
Effective search space used:    70752
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: 48 (23.1 bits)

Align candidate GFF2847 PGA1_c28930 (dihydrodipicolinate synthase DapA)
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))

# 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/TIGR00674.hmm
# target sequence database:        /tmp/gapView.18193.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00674  [M=286]
Accession:   TIGR00674
Description: dapA: 4-hydroxy-tetrahydrodipicolinate 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-97  310.9   0.0    3.4e-97  310.7   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2847  PGA1_c28930 dihydrodipicolinate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2847  PGA1_c28930 dihydrodipicolinate synthase DapA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.7   0.0   3.4e-97   3.4e-97       2     284 ..       5     285 ..       4     287 .. 0.98

  Alignments for each domain:
  == domain 1  score: 310.7 bits;  conditional E-value: 3.4e-97
                          TIGR00674   2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGtgsn 77 
                                        +++Al+TPf + + +d+++l++l+e +i++g+ a+v+vGtTGEs+tL++eE+++vi  +v+++++rvpviaG+gsn
  lcl|FitnessBrowser__Phaeo:GFF2847   5 SMPALVTPFSNGE-LDLDTLKRLVEWHIDQGSTALVPVGTTGESPTLTHEEHETVIAEVVKIAAGRVPVIAGAGSN 79 
                                        789******9888.************************************************************** PP

                          TIGR00674  78 ateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkrLaeeve 153
                                        +t e  +++++a+++g+d++lvvtPyYnkPtq+Gl++hf ++++++++Pi++Yn+P+R++++++p t+ +La+ ++
  lcl|FitnessBrowser__Phaeo:GFF2847  80 NTVEGKRFVQFAAEVGADAALVVTPYYNKPTQRGLIAHFTELHNCADIPIVIYNIPGRSVIDMTPATMGELAKLER 155
                                        **************************************************************************** PP

                          TIGR00674 154 ivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaalegdteearei 229
                                        i+++K+a+gd++rvs+ +a  ++df  lsG+Da++l + a G+ G iSV++nvapk+++e+ +a+l+gd++ a+e 
  lcl|FitnessBrowser__Phaeo:GFF2847 156 IIGVKDATGDIARVSQQRASCGADFIQLSGEDATALGFNAHGGVGCISVTANVAPKLCAEFQAATLAGDYALALEY 231
                                        **************************************************************************** PP

                          TIGR00674 230 hqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlk 284
                                        + kl++l++a+fie+   + K+ l  lgl+ + e+RlPLt l++++k  ++++++
  lcl|FitnessBrowser__Phaeo:GFF2847 232 QDKLMPLHEAIFIEPGLAGAKYGLSKLGLCSE-EVRLPLTGLEDSTKAAIDAAMA 285
                                        ********************************.*************999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (290 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: 00:00:00.00
# Mc/sec: 9.08
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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