Alignments for a candidate for trpD_2 in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Dinoroseobacter shibae DFL-12

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate 3608399 Dshi_1799 anthranilate phosphoribosyltransferase (RefSeq)

Query= SwissProt::P83827
         (329 letters)



>FitnessBrowser__Dino:3608399
          Length = 339

 Score =  243 bits (621), Expect = 4e-69
 Identities = 146/309 (47%), Positives = 185/309 (59%), Gaps = 11/309 (3%)

Query: 14  EEEEAYEVMRALMAGEVSPVRAAGLLVALSLRGERPHEIAAMARAMREAARPLRVHRRPL 73
           E E A+E+   L  GE +P +  GLL+AL  RGE   E AA A  MR     +R     +
Sbjct: 21  EAEAAFEI---LFEGEATPSQMGGLLMALRTRGETVAEYAAAAAVMRAKCNAVRAPEGAM 77

Query: 74  LDIVGTGGDGKGLMNLSTLAALVAAAGGVAVAKHGNRAASSRAGSADLLEALGVDLEAPP 133
            DIVGTGGDGKG +N+ST  A V A  GV VAKHGNR  SS++G+AD L  +G+++   P
Sbjct: 78  -DIVGTGGDGKGTLNISTATAFVVAGAGVPVAKHGNRNLSSKSGAADALAQMGIEVMVGP 136

Query: 134 ERVGEAIEELGFGFLFARVFHPAMRHVAPVRAELGVRTVFNLLGPLTNPAGADAYVLGVF 193
             V  A+ E+G  F+ A + HPA+RHV P RAELG RT+FN+LGPLTNPAG    + G F
Sbjct: 137 AVVERALSEIGIAFMMAPMHHPAIRHVMPTRAELGTRTMFNILGPLTNPAGVKRQLTGAF 196

Query: 194 SPEWLAPMAEALERLGAR-GLVVHG-EGADEL-VLGENRVVEVGKGA---YALTPEEVGL 247
           S + + PMAE L  LG+    +VHG +G DEL + G + V  +  GA   + + PEE GL
Sbjct: 197 SRDLIRPMAETLAALGSDVAWLVHGSDGTDELTITGVSWVAGLSDGAVTEFEVHPEEAGL 256

Query: 248 KRAPLEALKGGGPEENAALARRLLKGEEKGPLADAVALAAGAGFYAAGKTPSLKEGVALA 307
              P EA+ GG PEEN A  R LL GE      DAV L A A    AG+  +L +GV LA
Sbjct: 257 PVHPFEAILGGTPEENGAAFRALLAGEASA-YRDAVLLNAAAALKVAGRVTALPDGVMLA 315

Query: 308 REVLASGEA 316
            E + SG A
Sbjct: 316 AEAIDSGAA 324


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: 329
Number of extensions: 13
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 329
Length of database: 339
Length adjustment: 28
Effective length of query: 301
Effective length of database: 311
Effective search space:    93611
Effective search space used:    93611
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 3608399 Dshi_1799 (anthranilate phosphoribosyltransferase (RefSeq))
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.4913.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.7e-113  365.2   2.6   2.1e-113  364.9   2.6    1.0  1  lcl|FitnessBrowser__Dino:3608399  Dshi_1799 anthranilate phosphori


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608399  Dshi_1799 anthranilate phosphoribosyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  364.9   2.6  2.1e-113  2.1e-113       7     329 ..      14     333 ..      10     334 .. 0.98

  Alignments for each domain:
  == domain 1  score: 364.9 bits;  conditional E-value: 2.1e-113
                         TIGR01245   7 nkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDivGTGGDglk 83 
                                        + L+++eae++++ +++gea+++q++ +l+alr++get+ e a++a ++r+k + v++   e ++DivGTGGDg  
  lcl|FitnessBrowser__Dino:3608399  14 DRPLTRAEAEAAFEILFEGEATPSQMGGLLMALRTRGETVAEYAAAAAVMRAKCNAVRA--PEGAMDIVGTGGDGKG 88 
                                       679******************************************************88..79************** PP

                         TIGR01245  84 tiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPkyhpalkevap 160
                                       t+NiSTa+a+v+a+aGv+vaKhGnr  ssksG+aD L ++g+++ + p+ v+r+l+e gi+F++AP++hpa+++v+p
  lcl|FitnessBrowser__Dino:3608399  89 TLNISTATAFVVAGAGVPVAKHGNRNLSSKSGAADALAQMGIEVMVGPAVVERALSEIGIAFMMAPMHHPAIRHVMP 165
                                       ***************************************************************************** PP

                         TIGR01245 161 vRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEisltgetkvaelkdg 237
                                       +R eLg+rt+fN+LGPL+nPa +k+q+ G +s+dl++ +ae+l +lg++ a +vhg+dg+DE+++tg + va l+dg
  lcl|FitnessBrowser__Dino:3608399 166 TRAELGTRTMFNILGPLTNPAGVKRQLTGAFSRDLIRPMAETLAALGSDVAWLVHGSDGTDELTITGVSWVAGLSDG 242
                                       ***************************************************************************** PP

                         TIGR01245 238 eieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaaalyvagkakdlkegvelakea 314
                                        ++e++++pe+ gl+ ++ e++ gg++een ++++++l g++ +a rd+v+lNaaaal+vag++ +l +gv la ea
  lcl|FitnessBrowser__Dino:3608399 243 AVTEFEVHPEEAGLPVHPFEAILGGTPEENGAAFRALLAGEA-SAYRDAVLLNAAAALKVAGRVTALPDGVMLAAEA 318
                                       ***********************************9999999.899******************************* PP

                         TIGR01245 315 iksgkalekleelva 329
                                       i+sg+al+k++ l++
  lcl|FitnessBrowser__Dino:3608399 319 IDSGAALAKVQGLAQ 333
                                       ********9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (339 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: 00:00:00.00
# Mc/sec: 11.23
//
[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