Alignments for a candidate for trpD_2 in Pyrolobus fumarii 1A

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Pyrolobus fumarii 1A

Align anthranilate phosphoribosyltransferase (EC 2.4.2.18) (characterized)
to candidate WP_014027355.1 PYRFU_RS08955 anthranilate phosphoribosyltransferase

Query= BRENDA::Q9YGB4
         (325 letters)



>NCBI__GCF_000223395.1:WP_014027355.1
          Length = 345

 Score =  256 bits (655), Expect = 4e-73
 Identities = 157/329 (47%), Positives = 211/329 (64%), Gaps = 12/329 (3%)

Query: 3   LLAKIVDGKNLSFEEAYEL-FNELKGS-DGVLIGAYLAALQTKGYTGEELAGLARAMRDS 60
           LL KI+ G  L+ +EA E+    LKG  D V I A L AL+ +G T E +AG A A+R++
Sbjct: 7   LLEKILSGPGLTHQEAREIALMMLKGGIDDVGIAAILVALRARGETPEVVAGFAAALRET 66

Query: 61  AVKLDLG---KVADTAGTGGDGSSTINVSTASALILSAF-TRVAKHGNVSITSKSGSANV 116
            VK+ +    +  DTAGTGGD S TIN STA+AL  SA    V KHGN S++SKSGSA+ 
Sbjct: 67  CVKVQVPPGVEPIDTAGTGGDRSHTINASTAAALAASALGAYVLKHGNRSVSSKSGSADF 126

Query: 117 LEALGLNIRVSPERAREMVESTNFTFIFAPAYHPALRPIMPVRKALGIKTVFNVIGPLAN 176
           LE LG  I   P+ AR M+E   F F++AP YHPA++ +MPVR+ LGI+TVFN++GPL+N
Sbjct: 127 LERLGYKIDHGPDEARCMLEKARFAFLYAPRYHPAMKRVMPVRRKLGIRTVFNLVGPLSN 186

Query: 177 PADPAYQVVGVNSPELLEPVAEALEFLGVERALVVHGS-GMDEVSPHRETLV--LEVGNG 233
           P     QV+GV SP+LLE +++A   LG ER LVVHG  G+DEVS    T V  +E G+ 
Sbjct: 187 PGLVKRQVLGVASPQLLETMSKAGAILGYERLLVVHGEPGIDEVSVTGATTVVLVEKGSV 246

Query: 234 VERYTLSPEDFGIE--PVKPLPCSSPEESAARIKAVLGGSGRREDRDFILVNASAALYAS 291
           ++    +PE+ G +  P+  L   +P ES  R++ V  G G   D DFI VN   ALYA+
Sbjct: 247 LDTVRYTPEELGAKRHPLHLLRVETPGESVERVRRVFQGEGAPHDTDFIAVNTGFALYAA 306

Query: 292 GVAEDFREGLEMAREALGQGML-EKLEEI 319
           GV  + REG+E+ ++AL +G L E LE +
Sbjct: 307 GVVSEPREGVELFKQALAEGRLAEHLENV 335


Lambda     K      H
   0.314    0.133    0.365 

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: 280
Number of extensions: 9
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: 325
Length of database: 345
Length adjustment: 28
Effective length of query: 297
Effective length of database: 317
Effective search space:    94149
Effective search space used:    94149
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: 42 (22.0 bits)
S2: 49 (23.5 bits)

Align candidate WP_014027355.1 PYRFU_RS08955 (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.27512.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.6e-115  370.7   0.0     4e-115  370.6   0.0    1.0  1  lcl|NCBI__GCF_000223395.1:WP_014027355.1  PYRFU_RS08955 anthranilate phosp


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000223395.1:WP_014027355.1  PYRFU_RS08955 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.6   0.0    4e-115    4e-115       1     328 [.       8     336 ..       8     338 .. 0.98

  Alignments for each domain:
  == domain 1  score: 370.6 bits;  conditional E-value: 4e-115
                                 TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeese 69 
                                               lek+l++  L+++ea+++  ++++g ++d+ iaAilvalr++get+e +ag+a alre+ +kv++ +  
  lcl|NCBI__GCF_000223395.1:WP_014027355.1   8 LEKILSGPGLTHQEAREIALMMLKGGIDDVGIAAILVALRARGETPEVVAGFAAALRETCVKVQVPPGV 76 
                                               68999999************************************************************* PP

                                 TIGR01245  70 elvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsl 138
                                               e +D++GTGGD ++tiN STa+al a+a+G+ v KhGnrsvssksGsaD+Le lg+++++ p++++ +l
  lcl|NCBI__GCF_000223395.1:WP_014027355.1  77 EPIDTAGTGGDRSHTINASTAAALAASALGAYVLKHGNRSVSSKSGSADFLERLGYKIDHGPDEARCML 145
                                               ********************************************************************* PP

                                 TIGR01245 139 eevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlg 207
                                               e+  ++Fl+AP+yhpa+k+v+pvR++Lg+rtvfNl+GPL+nP  +k+qvlGv+s++l+e+++++   lg
  lcl|NCBI__GCF_000223395.1:WP_014027355.1 146 EKARFAFLYAPRYHPAMKRVMPVRRKLGIRTVFNLVGPLSNPGLVKRQVLGVASPQLLETMSKAGAILG 214
                                               ********************************************************************* PP

                                 TIGR01245 208 vkralvvhgedglDEisltgetkvaelkdgeie.eytlspedfglkraeleelkggsaeenaellkevl 275
                                               ++r lvvhge g+DE+s+tg t+v+ +++g++  + + +pe++g kr++l+ l+++++ e++e++++v+
  lcl|NCBI__GCF_000223395.1:WP_014027355.1 215 YERLLVVHGEPGIDEVSVTGATTVVLVEKGSVLdTVRYTPEELGAKRHPLHLLRVETPGESVERVRRVF 283
                                               ******************************99615789******************************* PP

                                 TIGR01245 276 egkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelv 328
                                               +g++  +++d++++N+++aly+ag++++ +egvel k+a+ +g+ +e+le++ 
  lcl|NCBI__GCF_000223395.1:WP_014027355.1 284 QGEGAPHDTDFIAVNTGFALYAAGVVSEPREGVELFKQALAEGRLAEHLENVL 336
                                               **************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (345 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: 9.78
//
[ok]

This GapMind analysis is from Apr 10 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