Alignments for a candidate for trpD_2 in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Azospirillum brasilense Sp245

Align anthranilate phosphoribosyltransferase (EC 2.4.2.18) (characterized)
to candidate AZOBR_RS07455 AZOBR_RS07455 anthranilate phosphoribosyltransferase

Query= BRENDA::A5U4M0
         (370 letters)



>FitnessBrowser__azobra:AZOBR_RS07455
          Length = 357

 Score =  250 bits (639), Expect = 4e-71
 Identities = 149/350 (42%), Positives = 203/350 (58%), Gaps = 11/350 (3%)

Query: 16  SPKAEAASVPSWPQILGRLTDNRDLARGQAAWAMDQIMTGNARPAQIAAFAVAMTMKAPT 75
           +P A    +     IL ++     L   +AA A D IM+GNA P+Q+  F +A+ ++  T
Sbjct: 3   TPSAPHGDLTDMKAILAKVAAGNALNEPEAALAFDIIMSGNATPSQMGGFLMALRVRGET 62

Query: 76  ADEVGELAGVMLSHAHPLPADTVPDDAVDVVGTGGDGVNTVNLSTMAAIVVAAAGVPVVK 135
            DE+   A VM + A P+ A   PD  +D  GTGGDG  T N+ST AA+V+AA GVPV K
Sbjct: 63  VDEITGAARVMRAKAIPVEA---PDGTIDTCGTGGDGSGTYNISTAAAVVIAACGVPVAK 119

Query: 136 HGNRAASSLSGGADTLEALGVRIDLGPDLVARSLAEVGIGFCFAPRFHPSYRHAAAVRRE 195
           HGNRA SS SG AD L ALGV +D    LV ++L +  IGF  APR H + R+    R E
Sbjct: 120 HGNRAMSSKSGAADVLGALGVNLDCDMGLVRKALWDARIGFLMAPRHHLAMRNVGPTRVE 179

Query: 196 IGVPTVFNLLGPLTNPARPRAGLIGCAFADLAEVMAGVFAARRS-SVLVVHGDDGLDELT 254
           +G  T+FNLLGPL+NPA  +  L+G       E +A V     S +  +VHG DGLDE+T
Sbjct: 180 LGTRTIFNLLGPLSNPASAKRQLLGVYAKQWVEPLAHVLKRLGSEAAWIVHGSDGLDEIT 239

Query: 255 TTTTSTIWRVAAGSVDKLTFDPAGFGFARAQLDQLAGGDAQANAAAVRAVLGGARGPVRD 314
           TT  +T+ ++  G V     +P   G  RA+ + L GGDA  NA A+RA+  G +G  RD
Sbjct: 240 TTGPTTVAQLKDGEVTVFEIEPEQAGIFRARPELLKGGDAHVNAEAIRALFDGVQGAYRD 299

Query: 315 AVVLNAAGAIVAHAGLSSRAEWLPAWEEGLRRASAAIDTGAAEQLLARWV 364
            V+LNAA A+     ++ +A  L   +EG+ +A  AID+GAA  +L   V
Sbjct: 300 IVLLNAAAAL----HVAGKAGDL---KEGVEQARHAIDSGAARAVLQHLV 342


Lambda     K      H
   0.318    0.132    0.391 

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: 306
Number of extensions: 12
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: 370
Length of database: 357
Length adjustment: 29
Effective length of query: 341
Effective length of database: 328
Effective search space:   111848
Effective search space used:   111848
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 AZOBR_RS07455 AZOBR_RS07455 (anthranilate phosphoribosyltransferase)
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.12713.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-123  398.5   0.2   1.4e-123  398.3   0.2    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS07455  AZOBR_RS07455 anthranilate phosp


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS07455  AZOBR_RS07455 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.3   0.2  1.4e-123  1.4e-123       2     329 ..      19     343 ..      18     344 .. 0.98

  Alignments for each domain:
  == domain 1  score: 398.3 bits;  conditional E-value: 1.4e-123
                                 TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeesee 70 
                                                k++ ++ L+e ea+ +++ imsg+a+++q++ +l+alrv+get++ei+g+a+++r+ka  ve+   + 
  lcl|FitnessBrowser__azobra:AZOBR_RS07455  19 AKVAAGNALNEPEAALAFDIIMSGNATPSQMGGFLMALRVRGETVDEITGAARVMRAKAIPVEA--PDG 85 
                                               688999********************************************************88..69* PP

                                 TIGR01245  71 lvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsle 139
                                                +D++GTGGDg+ t+NiSTa+a+v+aa+Gv+vaKhGnr++ssksG+aDvL algvnl+ ++  v+++l 
  lcl|FitnessBrowser__azobra:AZOBR_RS07455  86 TIDTCGTGGDGSGTYNISTAAAVVIAACGVPVAKHGNRAMSSKSGAADVLGALGVNLDCDMGLVRKALW 154
                                               ********************************************************************* PP

                                 TIGR01245 140 evgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgv 208
                                               +  igFl+AP++h a+++v p+R eLg+rt+fNlLGPL+nPa+ak+q+lGvy k+ ve la+vlk+lg+
  lcl|FitnessBrowser__azobra:AZOBR_RS07455 155 DARIGFLMAPRHHLAMRNVGPTRVELGTRTIFNLLGPLSNPASAKRQLLGVYAKQWVEPLAHVLKRLGS 223
                                               ********************************************************************* PP

                                 TIGR01245 209 kralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevleg 277
                                               + a +vhg+dglDEi++tg+t+va+lkdge++ ++++pe+ g+ ra+ e lkgg+a+ nae++++++ g
  lcl|FitnessBrowser__azobra:AZOBR_RS07455 224 EAAWIVHGSDGLDEITTTGPTTVAQLKDGEVTVFEIEPEQAGIFRARPELLKGGDAHVNAEAIRALFDG 292
                                               ****************************************************************88888 PP

                                 TIGR01245 278 kekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329
                                                + +a rdiv+lNaaaal vagka dlkegve+a++ai+sg+a ++l++lv+
  lcl|FitnessBrowser__azobra:AZOBR_RS07455 293 VQ-GAYRDIVLLNAAAALHVAGKAGDLKEGVEQARHAIDSGAARAVLQHLVS 343
                                               77.9********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (357 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: 00:00:00.01
# Mc/sec: 7.84
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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