Alignments for a candidate for dapA in Phaeobacter inhibens BS107

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.5929.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.61
//
[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