Alignments for a candidate for trpD_2 in Saccharomonospora cyanea NA-134

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Saccharomonospora cyanea NA-134

Align anthranilate phosphoribosyltransferase (EC 2.4.2.18) (characterized)
to candidate WP_005454544.1 SACCYDRAFT_RS06095 anthranilate phosphoribosyltransferase

Query= BRENDA::A5U4M0
         (370 letters)



>NCBI__GCF_000244975.1:WP_005454544.1
          Length = 341

 Score =  364 bits (935), Expect = e-105
 Identities = 192/342 (56%), Positives = 233/342 (68%), Gaps = 5/342 (1%)

Query: 26  SWPQILGRLTDNRDLARGQAAWAMDQIMTGNARPAQIAAFAVAMTMKAPTADEVGELAGV 85
           +WP +L +L +  DL+    AWAMDQ+M+G A PAQIA FAVA+  K  T  E+  +A  
Sbjct: 5   TWPAVLNQLIERVDLSEDATAWAMDQVMSGEATPAQIAGFAVALRAKGETPAEISGMAKA 64

Query: 86  MLSHAHPLPADTVPDDAVDVVGTGGDGVNTVNLSTMAAIVVAAAGVPVVKHGNRAASSLS 145
           ML+H+  +   T     VD+VGTGGD   +VN+STM ++VVAAAG PVVKHGNRAASS S
Sbjct: 65  MLAHSKRIDLGT---RTVDIVGTGGDRKGSVNISTMTSLVVAAAGTPVVKHGNRAASSKS 121

Query: 146 GGADTLEALGVRIDLGPDLVARSLAEVGIGFCFAPRFHPSYRHAAAVRREIGVPTVFNLL 205
           G AD LEALGV I+  PD V R + E+GIGFCFAP FHP+YRH    RRE+GV T FNLL
Sbjct: 122 GAADVLEALGVTIESEPDDVRRCVEELGIGFCFAPVFHPAYRHTGPPRRELGVSTAFNLL 181

Query: 206 GPLTNPARPRAGLIGCAFADLAEVMAGVFAARRSSVLVVHGDDGLDELTTTTTSTIWRVA 265
           GPLTNPA+P +GLIGCA+ D A V+A V+A R  SVL+V GDDG DE+TTTTTST W V+
Sbjct: 182 GPLTNPAQPSSGLIGCAYLDKAPVLAEVYARRGHSVLLVRGDDGFDEITTTTTSTAWVVS 241

Query: 266 AGSVDKLTFDPAGFGFARAQLDQLAGGDAQANAAAVRAVLGGARGPVRDAVVLNAAGAIV 325
            G V   T DP   G   +  D L GGDA ANA  V+ ++GG  GPVRDAV+LNAAGA+ 
Sbjct: 242 NGQVRTTTIDPETLGIPLSTPDALRGGDAAANAEVVKELVGGKTGPVRDAVLLNAAGALA 301

Query: 326 AHAGLSSRAEWLPAWEEGLRRASAAIDTGAAEQLLARWVRFG 367
           A AG S   +       GL  A+ AID+GAA  LL RW+  G
Sbjct: 302 AFAGFSD--DLTADLRAGLELATRAIDSGAAADLLTRWINRG 341


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: 324
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: 370
Length of database: 341
Length adjustment: 29
Effective length of query: 341
Effective length of database: 312
Effective search space:   106392
Effective search space used:   106392
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_005454544.1 SACCYDRAFT_RS06095 (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.8955.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.7e-116  373.6   0.0   5.2e-116  373.5   0.0    1.0  1  lcl|NCBI__GCF_000244975.1:WP_005454544.1  SACCYDRAFT_RS06095 anthranilate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000244975.1:WP_005454544.1  SACCYDRAFT_RS06095 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.5   0.0  5.2e-116  5.2e-116       1     329 [.      10     339 ..      10     340 .. 0.97

  Alignments for each domain:
  == domain 1  score: 373.5 bits;  conditional E-value: 5.2e-116
                                 TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeese 69 
                                               l++l+++ dLse+  +++m+++msgea++aqia + valr+kget+ ei+g+aka+++++k+++    +
  lcl|NCBI__GCF_000244975.1:WP_005454544.1  10 LNQLIERVDLSEDATAWAMDQVMSGEATPAQIAGFAVALRAKGETPAEISGMAKAMLAHSKRIDLG--T 76 
                                               5799***********************************************************985..9 PP

                                 TIGR01245  70 elvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsl 138
                                               + vDivGTGGD   ++NiST+++lv+aaaG++v+KhGnr++ssksG+aDvLealgv++e +p+ v+r++
  lcl|NCBI__GCF_000244975.1:WP_005454544.1  77 RTVDIVGTGGDRKGSVNISTMTSLVVAAAGTPVVKHGNRAASSKSGAADVLEALGVTIESEPDDVRRCV 145
                                               ********************************************************************* PP

                                 TIGR01245 139 eevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlg 207
                                               ee+gigF+fAP +hpa+++  p R+eLgv t fNlLGPL+nPa+++  ++G++  d + vlaev  + g
  lcl|NCBI__GCF_000244975.1:WP_005454544.1 146 EELGIGFCFAPVFHPAYRHTGPPRRELGVSTAFNLLGPLTNPAQPSSGLIGCAYLDKAPVLAEVYARRG 214
                                               ********************************************************************* PP

                                 TIGR01245 208 vkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevle 276
                                                + +l+v+g+dg DEi++t++++ + +++g+++++t++pe++g++  + ++l+gg+a++nae++ke++ 
  lcl|NCBI__GCF_000244975.1:WP_005454544.1 215 HS-VLLVRGDDGFDEITTTTTSTAWVVSNGQVRTTTIDPETLGIPLSTPDALRGGDAAANAEVVKELVG 282
                                               99.**************************************************************9888 PP

                                 TIGR01245 277 gkekkakrdivvlNaaaalyvagka.....kdlkegvelakeaiksgkalekleelva 329
                                               gk  ++ rd+v+lNaa al + +       +dl++g+ela +ai+sg+a+++l+++++
  lcl|NCBI__GCF_000244975.1:WP_005454544.1 283 GKT-GPVRDAVLLNAAGALAAFAGFsddltADLRAGLELATRAIDSGAAADLLTRWIN 339
                                               777.9**************9876655666699**********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (341 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: 6.90
//
[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