Alignments for a candidate for trpD_2 in Chlorobaculum parvum NCIB 8327

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Chlorobaculum parvum NCIB 8327

Align Anthranilate phosphoribosyltransferase 2; EC 2.4.2.18 (characterized)
to candidate WP_012501830.1 CPAR_RS02930 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8YXQ9
         (362 letters)



>NCBI__GCF_000020505.1:WP_012501830.1
          Length = 351

 Score =  241 bits (614), Expect = 3e-68
 Identities = 139/344 (40%), Positives = 200/344 (58%), Gaps = 17/344 (4%)

Query: 18  LLQQLIDGESLSRSQAAELMQGWLSEAVPPELSGAILTALNFKGVSADELTGMAEVLQSQ 77
           L+Q+L+ G  LS  +    +   +        +GAIL  L  KGV+  E  G  E L ++
Sbjct: 6   LIQKLLAGADLSAQEMEACIDSIMENRFTDAGTGAILALLQKKGVTPTEAIGAYENLMTR 65

Query: 78  SKMGTGENYSQLPITNSPFSIIDTCGTGGDGSSTFNISTAVAFVAAAYGVPVAKHGNRSA 137
                       PIT  P   +DTCGTGGD   TFNISTA AF+AA  GVP+AKHGNRS 
Sbjct: 66  VT----------PIT-LPAHAVDTCGTGGDHRGTFNISTAAAFIAAGAGVPIAKHGNRSI 114

Query: 138 SSLTGSADVLEALGVNLGASPEKVQAALQEVGITFLFAPGWHPALKAVATLRRTLRIRTV 197
           +S  GSADVLEALG  +       +   +E G  FLFAP +HP++KAVA++RR L IRT+
Sbjct: 115 TSKCGSADVLEALGYRVDLPASATEEQFRETGFAFLFAPLYHPSMKAVASIRRELGIRTL 174

Query: 198 FNLLGPLVNPLRPTGQVVGLFTPKLLTTVAQALDNLGKQKAIVLHGR----ERLDEAGLG 253
           FNLLGPL+NP +   Q +G+F P ++   A  L + G Q A+++HG+    + LDEA + 
Sbjct: 175 FNLLGPLINPAKVKRQFIGVFDPSVMELYADVLIHAGCQHAMIVHGKTEHGDGLDEASVS 234

Query: 254 DLTDLAVLSDGELQLTTINPQEVGVTPAPIGALRGGDVQENAEILKAVLQGKGTQAQQDA 313
             T +  L +G L   T+NP++ G+    I  L GGD + NA+I++ +L G  TQAQ DA
Sbjct: 235 GPTTIIELFEGRLCHHTVNPEDFGLNRWSIDELAGGDAETNAQIIRQILDGSATQAQIDA 294

Query: 314 VALNAALALQVAGAVPLLDHAQGVSVAKEILQTGTAWAKLAQLV 357
               +A+   V+G    +D  +G+S++KE L++  A   + +++
Sbjct: 295 ALFASAITCYVSGMGSCID--EGMSMSKESLESLAAMENMNRII 336


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: 260
Number of extensions: 12
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: 362
Length of database: 351
Length adjustment: 29
Effective length of query: 333
Effective length of database: 322
Effective search space:   107226
Effective search space used:   107226
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_012501830.1 CPAR_RS02930 (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.28493.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-114  367.9   0.1     3e-114  367.7   0.1    1.0  1  lcl|NCBI__GCF_000020505.1:WP_012501830.1  CPAR_RS02930 anthranilate phosph


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020505.1:WP_012501830.1  CPAR_RS02930 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  367.7   0.1    3e-114    3e-114       1     329 [.       7     337 ..       7     338 .. 0.98

  Alignments for each domain:
  == domain 1  score: 367.7 bits;  conditional E-value: 3e-114
                                 TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeese 69 
                                               ++kll + dLs++e+e+ ++ im+++++da  +Ail++l+ kg t+ e  g+++ l+ + + ++    +
  lcl|NCBI__GCF_000020505.1:WP_012501830.1   7 IQKLLAGADLSAQEMEACIDSIMENRFTDAGTGAILALLQKKGVTPTEAIGAYENLMTRVTPITL--PA 73 
                                               6899**********************************************************988..69 PP

                                 TIGR01245  70 elvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsl 138
                                               ++vD++GTGGD+  t+NiSTa+a++aa+aGv++aKhGnrs++sk+GsaDvLealg++++l + + ++++
  lcl|NCBI__GCF_000020505.1:WP_012501830.1  74 HAVDTCGTGGDHRGTFNISTAAAFIAAGAGVPIAKHGNRSITSKCGSADVLEALGYRVDLPASATEEQF 142
                                               ********************************************************************* PP

                                 TIGR01245 139 eevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlg 207
                                               +e+g++FlfAP yhp++k+va++R+eLg+rt+fNlLGPL+nPa++k+q +Gv++++++e++a vl + g
  lcl|NCBI__GCF_000020505.1:WP_012501830.1 143 RETGFAFLFAPLYHPSMKAVASIRRELGIRTLFNLLGPLINPAKVKRQFIGVFDPSVMELYADVLIHAG 211
                                               ********************************************************************* PP

                                 TIGR01245 208 vkralvvhg....edglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellk 272
                                                ++a++vhg     dglDE s+ g+t+++el +g+  + t++pedfgl+r +++el+gg+ae na++++
  lcl|NCBI__GCF_000020505.1:WP_012501830.1 212 CQHAMIVHGktehGDGLDEASVSGPTTIIELFEGRLCHHTVNPEDFGLNRWSIDELAGGDAETNAQIIR 280
                                               *********777669****************************************************** PP

                                 TIGR01245 273 evlegkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329
                                               ++l g +++a+ d+ ++  a+  yv+g+ + + eg+++ ke+++s +a+e ++++++
  lcl|NCBI__GCF_000020505.1:WP_012501830.1 281 QILDGSATQAQIDAALFASAITCYVSGMGSCIDEGMSMSKESLESLAAMENMNRIIE 337
                                               ***************************************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (351 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: 12.33
//
[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