Alignments for a candidate for trpD_2 in Nitratifractor salsuginis DSM 16511

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Nitratifractor salsuginis DSM 16511

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_013554809.1 NITSA_RS09475 anthranilate phosphoribosyltransferase

Query= SwissProt::P83827
         (329 letters)



>NCBI__GCF_000186245.1:WP_013554809.1
          Length = 326

 Score =  238 bits (608), Expect = 1e-67
 Identities = 141/309 (45%), Positives = 190/309 (61%), Gaps = 9/309 (2%)

Query: 25  LMAGEVSPVRAAGLLVALSLRGERPHEIAAMARAMREAARPLRVH---RRPLLDIVGTGG 81
           L A E+S   A   LVAL  +GE P EIAA A  MR  +  L V    R+ L+D+VGTGG
Sbjct: 12  LFANEMSEEEARDFLVALYEKGESPEEIAAAAEVMRAHSVKLPVPEDLRQKLIDVVGTGG 71

Query: 82  DGKGLMNLSTLAALVAAAGGVAVAKHGNRAASSRAGSADLLEALGVDLEAPPERVGEAIE 141
           D  G  N+ST  AL+ AA G  VAKHGNR+ +S++GSAD+L+ALG+ L+  PE+    +E
Sbjct: 72  DKSGSFNISTTVALLLAASGSYVAKHGNRSITSKSGSADVLDALGMRLDLSPEQQVMMLE 131

Query: 142 ELGFGFLFARVFHPAMRHVAPVRAELGVRTVFNLLGPLTNPAGADAYVLGVFSPEWLAPM 201
           E GF F+FA   HPAM+H+ P+R  L  RT+FN+LGPLTNPAGA  Y+LGVFSP+++ P+
Sbjct: 132 ETGFTFIFAIHHHPAMKHIMPIRRSLDHRTIFNILGPLTNPAGARKYLLGVFSPDYVCPI 191

Query: 202 AEALERLGA-RGLVVHGE-GADELVLG---ENRVVEVGK-GAYALTPEEVGLKRAPLEAL 255
           A+AL  L   R  V+  E G DE+ +        VE  K     + PE  G +RAP EA+
Sbjct: 192 AKALLDLDVERAYVLSSEDGMDEISISAPTRFAYVEAEKVSEGVIEPEAHGFRRAPKEAI 251

Query: 256 KGGGPEENAALARRLLKGEEKGPLADAVALAAGAGFYAAGKTPSLKEGVALAREVLASGE 315
            GG  EENA + RR+L GEE+GP  + V L       A G+   ++E + +  E + SG+
Sbjct: 252 LGGEAEENATILRRILSGEEQGPKREIVLLNGAYALSADGRVRDIQEAIEILSETIDSGK 311

Query: 316 AYLLLERYV 324
           A   LE+ +
Sbjct: 312 AAEHLEKTI 320


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: 302
Number of extensions: 14
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: 326
Length adjustment: 28
Effective length of query: 301
Effective length of database: 298
Effective search space:    89698
Effective search space used:    89698
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: 48 (23.1 bits)

Align candidate WP_013554809.1 NITSA_RS09475 (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.31143.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-112  362.6   0.0   1.2e-112  362.5   0.0    1.0  1  lcl|NCBI__GCF_000186245.1:WP_013554809.1  NITSA_RS09475 anthranilate phosp


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000186245.1:WP_013554809.1  NITSA_RS09475 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.5   0.0  1.2e-112  1.2e-112      15     329 ..       5     321 ..       1     322 [. 0.97

  Alignments for each domain:
  == domain 1  score: 362.5 bits;  conditional E-value: 1.2e-112
                                 TIGR01245  15 aeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkveke..eseelvDivGTGGDg 81 
                                               +++ ++ ++++e+s+++   +lval  kge++eeia++a+++r++++k+++    +++l+D+vGTGGD+
  lcl|NCBI__GCF_000186245.1:WP_013554809.1   5 VKKEFERLFANEMSEEEARDFLVALYEKGESPEEIAAAAEVMRAHSVKLPVPedLRQKLIDVVGTGGDK 73 
                                               5677899999************************************99765423789************ PP

                                 TIGR01245  82 lktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPk 150
                                               + ++NiST+ al++aa G  vaKhGnrs++sksGsaDvL+alg++l+lspe+   +lee+g++F+fA +
  lcl|NCBI__GCF_000186245.1:WP_013554809.1  74 SGSFNISTTVALLLAASGSYVAKHGNRSITSKSGSADVLDALGMRLDLSPEQQVMMLEETGFTFIFAIH 142
                                               ********************************************************************* PP

                                 TIGR01245 151 yhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedg 219
                                               +hpa+k+++p+R++L  rt+fN+LGPL+nPa a+  +lGv+s+d+v  +a++l  l v+ra v+++edg
  lcl|NCBI__GCF_000186245.1:WP_013554809.1 143 HHPAMKHIMPIRRSLDHRTIFNILGPLTNPAGARKYLLGVFSPDYVCPIAKALLDLDVERAYVLSSEDG 211
                                               ********************************************************************* PP

                                 TIGR01245 220 lDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivv 288
                                               +DEis+ ++t+ a +++++++e  ++pe  g+ ra++e++ gg+aeena++l+++l+g+e+++kr+iv+
  lcl|NCBI__GCF_000186245.1:WP_013554809.1 212 MDEISISAPTRFAYVEAEKVSEGVIEPEAHGFRRAPKEAILGGEAEENATILRRILSGEEQGPKREIVL 280
                                               ********************************************************************* PP

                                 TIGR01245 289 lNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329
                                               lN a al + g+++d++e++e  +e+i+sgka+e+le+ ++
  lcl|NCBI__GCF_000186245.1:WP_013554809.1 281 LNGAYALSADGRVRDIQEAIEILSETIDSGKAAEHLEKTIR 321
                                               *************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (326 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: 11.45
//
[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