Alignments for a candidate for trpD_2 in Trichormus variabilis ATCC 29413

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Trichormus variabilis ATCC 29413

Align Anthranilate phosphoribosyltransferase 2; EC 2.4.2.18 (characterized)
to candidate WP_011321083.1 AVA_RS22385 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8YXQ9
         (362 letters)



>NCBI__GCF_000204075.1:WP_011321083.1
          Length = 362

 Score =  662 bits (1707), Expect = 0.0
 Identities = 345/360 (95%), Positives = 352/360 (97%)

Query: 1   MTSSPTSTQESSTSWYLLLQQLIDGESLSRSQAAELMQGWLSEAVPPELSGAILTALNFK 60
           MT+SP  TQESSTSWYLLLQQLIDGESLSRSQAAELMQGWLSEAVPPELSGAILTALNFK
Sbjct: 1   MTTSPIPTQESSTSWYLLLQQLIDGESLSRSQAAELMQGWLSEAVPPELSGAILTALNFK 60

Query: 61  GVSADELTGMAEVLQSQSKMGTGENYSQLPITNSPFSIIDTCGTGGDGSSTFNISTAVAF 120
           GVSADELTGMAEVLQSQSK+G+GEN SQLPITN  F IIDTCGTGGDGSSTFNISTAVAF
Sbjct: 61  GVSADELTGMAEVLQSQSKLGSGENSSQLPITNYQFPIIDTCGTGGDGSSTFNISTAVAF 120

Query: 121 VAAAYGVPVAKHGNRSASSLTGSADVLEALGVNLGASPEKVQAALQEVGITFLFAPGWHP 180
           VAAAYGVPVAKHGNRSASSLTGSADVLEALGVNLGAS EKVQAALQEVGITFLFAPGWHP
Sbjct: 121 VAAAYGVPVAKHGNRSASSLTGSADVLEALGVNLGASSEKVQAALQEVGITFLFAPGWHP 180

Query: 181 ALKAVATLRRTLRIRTVFNLLGPLVNPLRPTGQVVGLFTPKLLTTVAQALDNLGKQKAIV 240
           ALKAVATLRRTLRIRTVFNLLGPLVNPLRPTGQVVGLFTPKLLTTVAQALDNLGKQKAIV
Sbjct: 181 ALKAVATLRRTLRIRTVFNLLGPLVNPLRPTGQVVGLFTPKLLTTVAQALDNLGKQKAIV 240

Query: 241 LHGRERLDEAGLGDLTDLAVLSDGELQLTTINPQEVGVTPAPIGALRGGDVQENAEILKA 300
           LHGRERLDEAGLGDLTDLAVLSDG+LQLTTINPQEVGVTPAPIGALRGGDVQENAEILKA
Sbjct: 241 LHGRERLDEAGLGDLTDLAVLSDGKLQLTTINPQEVGVTPAPIGALRGGDVQENAEILKA 300

Query: 301 VLQGKGTQAQQDAVALNAALALQVAGAVPLLDHAQGVSVAKEILQTGTAWAKLAQLVYFL 360
           VLQG+GTQAQQDAVALNAALALQVAGAVPLLDHA+GVSVAKEILQTGTAWAKL QLV+FL
Sbjct: 301 VLQGQGTQAQQDAVALNAALALQVAGAVPLLDHAKGVSVAKEILQTGTAWAKLEQLVHFL 360


Lambda     K      H
   0.314    0.130    0.364 

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: 517
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: 362
Length of database: 362
Length adjustment: 29
Effective length of query: 333
Effective length of database: 333
Effective search space:   110889
Effective search space used:   110889
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)

Align candidate WP_011321083.1 AVA_RS22385 (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.15594.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.3e-119  383.3   0.2   6.3e-119  383.1   0.2    1.1  1  lcl|NCBI__GCF_000204075.1:WP_011321083.1  AVA_RS22385 anthranilate phospho


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204075.1:WP_011321083.1  AVA_RS22385 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.1   0.2  6.3e-119  6.3e-119       1     329 [.      19     358 ..      19     359 .. 0.95

  Alignments for each domain:
  == domain 1  score: 383.1 bits;  conditional E-value: 6.3e-119
                                 TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeese 69 
                                               l++l+d+++Ls+ +a++lm+ ++s+ + ++  +Ail+al+ kg +++e++g+a++l++++k  + e+s+
  lcl|NCBI__GCF_000204075.1:WP_011321083.1  19 LQQLIDGESLSRSQAAELMQGWLSEAVPPELSGAILTALNFKGVSADELTGMAEVLQSQSKLGSGENSS 87 
                                               689******************************************************999876665444 PP

                                 TIGR01245  70 .........elvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlel 129
                                                         ++D++GTGGDg++t+NiSTa a+vaaa+Gv+vaKhGnrs+ss  GsaDvLealgvnl +
  lcl|NCBI__GCF_000204075.1:WP_011321083.1  88 qlpitnyqfPIIDTCGTGGDGSSTFNISTAVAFVAAAYGVPVAKHGNRSASSLTGSADVLEALGVNLGA 156
                                               111111122579********************************************************* PP

                                 TIGR01245 130 spekvarsleevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvev 198
                                               s ekv+++l+evgi+FlfAP +hpalk+va +R++L +rtvfNlLGPL+nP+r++ qv+G + ++l+++
  lcl|NCBI__GCF_000204075.1:WP_011321083.1 157 SSEKVQAALQEVGITFLFAPGWHPALKAVATLRRTLRIRTVFNLLGPLVNPLRPTGQVVGLFTPKLLTT 225
                                               ********************************************************************* PP

                                 TIGR01245 199 laevlknlgvkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeen 267
                                               +a++l nlg ++a+v+hg++ lDE  l + t+ a l+dg+ + +t++p++ g+++a++ +l+gg+ +en
  lcl|NCBI__GCF_000204075.1:WP_011321083.1 226 VAQALDNLGKQKAIVLHGRERLDEAGLGDLTDLAVLSDGKLQLTTINPQEVGVTPAPIGALRGGDVQEN 294
                                               ********************************************************************* PP

                                 TIGR01245 268 aellkevlegkekkakrdivvlNaaaalyvagka..kdlkegvelakeaiksgkalekleelva 329
                                               ae+lk+vl+g++++a++d+v+lNaa al+vag++   d+++gv++ake +++g a++kle+lv+
  lcl|NCBI__GCF_000204075.1:WP_011321083.1 295 AEILKAVLQGQGTQAQQDAVALNAALALQVAGAVplLDHAKGVSVAKEILQTGTAWAKLEQLVH 358
                                               *********************************9667999*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (362 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: 7.52
//
[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