GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_2 in Phaeobacter inhibens BS107

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate GFF1666 PGA1_c16890 anthranilate phosphoribosyltransferase TrpD

Query= SwissProt::P83827
         (329 letters)



>FitnessBrowser__Phaeo:GFF1666
          Length = 342

 Score =  229 bits (583), Expect = 1e-64
 Identities = 137/311 (44%), Positives = 176/311 (56%), Gaps = 9/311 (2%)

Query: 13  LEEEEAYEVMRALMAGEVSPVRAAGLLVALSLRGERPHEIAAMARAMREAARPLRVHRRP 72
           L  EEA      L  G  +P +  GLL+AL  RGE   E AA A  MR    P+ V    
Sbjct: 17  LSREEAEAAFTQLFEGNATPSQMGGLLMALRTRGETVDEYAAAAAVMRAKCNPV-VAPAG 75

Query: 73  LLDIVGTGGDGKGLMNLSTLAALVAAAGGVAVAKHGNRAASSRAGSADLLEALGVDLEAP 132
            +DIVGTGGDGKG +N+ST  A V A  G  VAKHGNR  SS++G+AD L  +G+++   
Sbjct: 76  AMDIVGTGGDGKGTLNISTATAFVVAGAGTVVAKHGNRNLSSKSGAADALGQMGINVMVG 135

Query: 133 PERVGEAIEELGFGFLFARVFHPAMRHVAPVRAELGVRTVFNLLGPLTNPAGADAYVLGV 192
           P+   +A+ E G  F+ A + HPA+ HV P R ELG RT+FN+LGPLTNPAG    + G 
Sbjct: 136 PKVAEQALREAGICFMMAPMHHPAIAHVMPTRQELGTRTIFNILGPLTNPAGVKRQLTGA 195

Query: 193 FSPEWLAPMAEALERLGA-RGLVVHG-EGADEL-VLGENRVVEVGKGA----YALTPEEV 245
           FS + + PMAE L +LG+ +  +VHG +G DEL + G + V  +  G       + PE+ 
Sbjct: 196 FSRDLIRPMAETLGQLGSEQAWLVHGSDGTDELTITGVSWVAALNPGGSVTEMEIHPEDA 255

Query: 246 GLKRAPLEALKGGGPEENAALARRLLKGEEKGPLADAVALAAGAGFYAAGKTPSLKEGVA 305
           GL   P EA+ GG PEENA     LL GE      DAV L + A    AG    LK G  
Sbjct: 256 GLSVHPFEAIVGGTPEENAKAFAALLSGEASA-YRDAVLLNSAAALVVAGAASDLKTGAE 314

Query: 306 LAREVLASGEA 316
           +AR  + SG A
Sbjct: 315 MARASIDSGAA 325


Lambda     K      H
   0.317    0.136    0.380 

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: 297
Number of extensions: 10
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: 329
Length of database: 342
Length adjustment: 28
Effective length of query: 301
Effective length of database: 314
Effective search space:    94514
Effective search space used:    94514
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: 49 (23.5 bits)

Align candidate GFF1666 PGA1_c16890 (anthranilate phosphoribosyltransferase TrpD)
to HMM TIGR01245 (trpD: anthranilate phosphoribosyltransferase (EC 2.4.2.18))

# 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/TIGR01245.hmm
# target sequence database:        /tmp/gapView.637.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01245  [M=330]
Accession:   TIGR01245
Description: trpD: anthranilate phosphoribosyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     3e-114  367.7   3.7   3.4e-114  367.5   3.7    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1666  PGA1_c16890 anthranilate phospho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1666  PGA1_c16890 anthranilate phosphoribosyltransferase TrpD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  367.5   3.7  3.4e-114  3.4e-114       6     329 ..      13     334 ..       8     335 .. 0.98

  Alignments for each domain:
  == domain 1  score: 367.5 bits;  conditional E-value: 3.4e-114
                          TIGR01245   6 dnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDivGTGGDg 81 
                                         ++ Ls+eeae++++++++g+a+++q++ +l+alr++get++e a++a ++r+k + v +   + ++DivGTGGDg
  lcl|FitnessBrowser__Phaeo:GFF1666  13 AERALSREEAEAAFTQLFEGNATPSQMGGLLMALRTRGETVDEYAAAAAVMRAKCNPVVA--PAGAMDIVGTGGDG 86 
                                        5789****************************************************9977..79************ PP

                          TIGR01245  82 lktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPkyhpalke 157
                                          t+NiSTa+a+v+a+aG+ vaKhGnr  ssksG+aD L ++g+n+ + p+ ++++l+e gi+F++AP++hpa+++
  lcl|FitnessBrowser__Phaeo:GFF1666  87 KGTLNISTATAFVVAGAGTVVAKHGNRNLSSKSGAADALGQMGINVMVGPKVAEQALREAGICFMMAPMHHPAIAH 162
                                        **************************************************************************** PP

                          TIGR01245 158 vapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEisltgetkvae 233
                                        v+p+R+eLg+rt+fN+LGPL+nPa +k+q+ G +s+dl++ +ae+l +lg+++a +vhg+dg+DE+++tg + va 
  lcl|FitnessBrowser__Phaeo:GFF1666 163 VMPTRQELGTRTIFNILGPLTNPAGVKRQLTGAFSRDLIRPMAETLGQLGSEQAWLVHGSDGTDELTITGVSWVAA 238
                                        **************************************************************************** PP

                          TIGR01245 234 lkd.geieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaaalyvagkakdlkegv 308
                                        l+  g+++e++++ped gl  ++ e++ gg++eena+++ ++l+g++ +a rd+v+lN aaal+vag+a+dlk g+
  lcl|FitnessBrowser__Phaeo:GFF1666 239 LNPgGSVTEMEIHPEDAGLSVHPFEAIVGGTPEENAKAFAALLSGEA-SAYRDAVLLNSAAALVVAGAASDLKTGA 313
                                        *96268**********************************9999999.899************************* PP

                          TIGR01245 309 elakeaiksgkalekleelva 329
                                        e+a+++i+sg+a ek+e+l++
  lcl|FitnessBrowser__Phaeo:GFF1666 314 EMARASIDSGAAREKIEALAR 334
                                        ****************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (342 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.50
//
[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