Alignments for a candidate for trpD_2 in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Mycolicibacterium vanbaalenii PYR-1

Align anthranilate phosphoribosyltransferase (EC 2.4.2.18) (characterized)
to candidate WP_083767274.1 MVAN_RS31235 anthranilate phosphoribosyltransferase

Query= BRENDA::A5U4M0
         (370 letters)



>NCBI__GCF_000015305.1:WP_083767274.1
          Length = 342

 Score =  541 bits (1395), Expect = e-159
 Identities = 274/341 (80%), Positives = 300/341 (87%)

Query: 30  ILGRLTDNRDLARGQAAWAMDQIMTGNARPAQIAAFAVAMTMKAPTADEVGELAGVMLSH 89
           ILGRLT  + LA GQ AWAMDQIMTG A PAQIAAFAV+M MK PT+ EV ELA +ML H
Sbjct: 2   ILGRLTTGQGLAPGQTAWAMDQIMTGTATPAQIAAFAVSMKMKRPTSAEVTELADIMLKH 61

Query: 90  AHPLPADTVPDDAVDVVGTGGDGVNTVNLSTMAAIVVAAAGVPVVKHGNRAASSLSGGAD 149
           A  +P D +    VD+VGTGGDG NTVNLSTMAAIVVAAAGVPVVKHGNRAASSLSGGAD
Sbjct: 62  ARRVPTDVIGTATVDIVGTGGDGANTVNLSTMAAIVVAAAGVPVVKHGNRAASSLSGGAD 121

Query: 150 TLEALGVRIDLGPDLVARSLAEVGIGFCFAPRFHPSYRHAAAVRREIGVPTVFNLLGPLT 209
           TLEALG+RIDLGPD VAR +AEVGIGF FAP+FHPSYRHA AVRREIGVPTVFNLLGPLT
Sbjct: 122 TLEALGLRIDLGPDEVARCVAEVGIGFAFAPQFHPSYRHAGAVRREIGVPTVFNLLGPLT 181

Query: 210 NPARPRAGLIGCAFADLAEVMAGVFAARRSSVLVVHGDDGLDELTTTTTSTIWRVAAGSV 269
           NPA PRAGLIGCA+ADLAEVMAGVFA R SSVLVVHGDDGLDELTTTTTSTIWRV AG+V
Sbjct: 182 NPASPRAGLIGCAWADLAEVMAGVFATRGSSVLVVHGDDGLDELTTTTTSTIWRVQAGTV 241

Query: 270 DKLTFDPAGFGFARAQLDQLAGGDAQANAAAVRAVLGGARGPVRDAVVLNAAGAIVAHAG 329
           ++LTFDPA FGFARA + +L GGDA++NAA+ RAVLGGA+GPVRDAVVLNAAGA+VAHAG
Sbjct: 242 ERLTFDPAAFGFARAHVSELTGGDAESNAASARAVLGGAKGPVRDAVVLNAAGALVAHAG 301

Query: 330 LSSRAEWLPAWEEGLRRASAAIDTGAAEQLLARWVRFGRQI 370
           LSS A+W+PAWE GL RA  AID+GAAEQLLARWVRF +Q+
Sbjct: 302 LSSDAKWVPAWESGLARAKDAIDSGAAEQLLARWVRFTQQL 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: 439
Number of extensions: 15
Number of successful extensions: 1
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: 342
Length adjustment: 29
Effective length of query: 341
Effective length of database: 313
Effective search space:   106733
Effective search space used:   106733
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 WP_083767274.1 MVAN_RS31235 (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.13372.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.6e-119  382.5   0.1   1.1e-118  382.3   0.1    1.0  1  lcl|NCBI__GCF_000015305.1:WP_083767274.1  MVAN_RS31235 anthranilate phosph


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_083767274.1  MVAN_RS31235 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.3   0.1  1.1e-118  1.1e-118       2     329 ..       4     337 ..       3     338 .. 0.97

  Alignments for each domain:
  == domain 1  score: 382.3 bits;  conditional E-value: 1.1e-118
                                 TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkveke.ese 69 
                                                +l++++ L+ ++ +++m++im+g a++aqiaA+ v +++k  t  e+++la +++++a++v+++   +
  lcl|NCBI__GCF_000015305.1:WP_083767274.1   4 GRLTTGQGLAPGQTAWAMDQIMTGTATPAQIAAFAVSMKMKRPTSAEVTELADIMLKHARRVPTDvIGT 72 
                                               5789999*********************************************************97789 PP

                                 TIGR01245  70 elvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsl 138
                                                 vDivGTGGDg++t+N+ST++a+v+aaaGv+v+KhGnr++ss sG+aD+Lealg++++l p++var++
  lcl|NCBI__GCF_000015305.1:WP_083767274.1  73 ATVDIVGTGGDGANTVNLSTMAAIVVAAAGVPVVKHGNRAASSLSGGADTLEALGLRIDLGPDEVARCV 141
                                               99******************************************************************* PP

                                 TIGR01245 139 eevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlg 207
                                               +evgigF fAP++hp+++++ +vR+e+gv+tvfNlLGPL+nPa++++ ++G++ +dl+ev+a v+ + g
  lcl|NCBI__GCF_000015305.1:WP_083767274.1 142 AEVGIGFAFAPQFHPSYRHAGAVRREIGVPTVFNLLGPLTNPASPRAGLIGCAWADLAEVMAGVFATRG 210
                                               ********************************************************************* PP

                                 TIGR01245 208 vkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevle 276
                                               ++ +lvvhg+dglDE+++t++++++++++g++e+ t++p+ fg++ra+++el gg+ae na+  ++vl 
  lcl|NCBI__GCF_000015305.1:WP_083767274.1 211 SS-VLVVHGDDGLDELTTTTTSTIWRVQAGTVERLTFDPAAFGFARAHVSELTGGDAESNAASARAVLG 278
                                               99.*************************************************************97665 PP

                                 TIGR01245 277 gkekkakrdivvlNaaaalyvagka.......kdlkegvelakeaiksgkalekleelva 329
                                               g +k++ rd+vvlNaa al++++          +++ g+ +ak+ai+sg+a ++l+++v+
  lcl|NCBI__GCF_000015305.1:WP_083767274.1 279 G-AKGPVRDAVVLNAAGALVAHAGLssdakwvPAWESGLARAKDAIDSGAAEQLLARWVR 337
                                               5.56*****************9988788888899***********************997 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 11.86
//
[ok]

This GapMind analysis is from Apr 10 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