Alignments for a candidate for trpD_2 in Phaeobacter inhibens BS107

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.18989.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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.30
//
[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