GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_2 in Thioalkalivibrio paradoxus ARh 1

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_006746919.1 THITH_RS15385 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8PD71
         (345 letters)



>NCBI__GCF_000227685.2:WP_006746919.1
          Length = 343

 Score =  299 bits (765), Expect = 8e-86
 Identities = 164/339 (48%), Positives = 216/339 (63%), Gaps = 3/339 (0%)

Query: 3   ITPQQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAAT 62
           +T Q+A+   IE + +    M  +MR +M G+ + A + A+L  LR+K ET  EI  AA 
Sbjct: 1   MTIQEAIAALIERKNLDAGAMTSVMRTVMTGQATPAQIGALLVALRMKGETPDEIVAAAR 60

Query: 63  VMREFSRRVEV-TDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSK 121
           VMRE + RV V TD   +VD  GTGGD S TFN+ST +  VAAA GA+VAKHGNRSVSS+
Sbjct: 61  VMRELATRVPVPTDG--LVDTCGTGGDASGTFNVSTASALVAAAAGARVAKHGNRSVSSR 118

Query: 122 SGSADALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNI 181
           SGSAD LEALG  + + P+ VA  + + G+GF++AP HH AM+     RRE+GVRT+FN+
Sbjct: 119 SGSADVLEALGVRLGIAPDGVATCIERIGVGFLFAPAHHGAMRHAIGPRRELGVRTMFNV 178

Query: 182 LGPLTNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGE 241
           LGPLTNPAG+PN ++GVF    +   A  LQ LG+   LVV   DG+DE+S+ A T V E
Sbjct: 179 LGPLTNPAGAPNQVLGVFSEQWLRPLAEALQMLGSRHVLVVHAEDGLDEISIAAPTRVAE 238

Query: 242 LRDGQVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGAA 301
           LRD  + EY + P D G+  +   +++V     S AM+  VL   PG A DIV +NAGAA
Sbjct: 239 LRDATIREYTLAPGDLGLQSAPLDSIRVDGVEASAAMIRSVLAGDPGAARDIVLMNAGAA 298

Query: 302 LYVAGVADSIADGIVRARQVLADGSARACLDAYVAFTQQ 340
           LYV G A+S   G+ RA Q +  G+A   L   V  TQ+
Sbjct: 299 LYVGGYAESHLQGVARAAQAIDSGAAADRLRQLVELTQE 337


Lambda     K      H
   0.320    0.134    0.377 

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: 347
Number of extensions: 18
Number of successful extensions: 2
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: 345
Length of database: 343
Length adjustment: 29
Effective length of query: 316
Effective length of database: 314
Effective search space:    99224
Effective search space used:    99224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_006746919.1 THITH_RS15385 (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.2367268.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.2e-131  423.5   0.5   3.7e-131  423.3   0.5    1.0  1  NCBI__GCF_000227685.2:WP_006746919.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000227685.2:WP_006746919.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.3   0.5  3.7e-131  3.7e-131       2     329 ..       8     333 ..       7     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 423.3 bits;  conditional E-value: 3.7e-131
                             TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDi 74 
                                             l+++k+L+++ ++++m+++m+g+a++aqi+A+lvalr+kget++ei+++a+++re a++v++ +++ lvD+
  NCBI__GCF_000227685.2:WP_006746919.1   8 AALIERKNLDAGAMTSVMRTVMTGQATPAQIGALLVALRMKGETPDEIVAAARVMRELATRVPV-PTDGLVDT 79 
                                           5799************************************************************.7******* PP

                             TIGR01245  75 vGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlf 147
                                           +GTGGD++ t+N+STasalvaaaaG++vaKhGnrsvss+sGsaDvLealgv+l + p+ va ++e+ g+gFlf
  NCBI__GCF_000227685.2:WP_006746919.1  80 CGTGGDASGTFNVSTASALVAAAAGARVAKHGNRSVSSRSGSADVLEALGVRLGIAPDGVATCIERIGVGFLF 152
                                           ************************************************************************* PP

                             TIGR01245 148 APkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedgl 220
                                           AP++h a++++++ R+eLgvrt+fN+LGPL+nPa a++qvlGv+s++ ++ lae+l+ lg++++lvvh+edgl
  NCBI__GCF_000227685.2:WP_006746919.1 153 APAHHGAMRHAIGPRRELGVRTMFNVLGPLTNPAGAPNQVLGVFSEQWLRPLAEALQMLGSRHVLVVHAEDGL 225
                                           ************************************************************************* PP

                             TIGR01245 221 DEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaa 293
                                           DEis+ ++t+vael+d +i+eytl p d+gl+ a+l++++++  e++a+++++vl g   +a+rdiv++Na+a
  NCBI__GCF_000227685.2:WP_006746919.1 226 DEISIAAPTRVAELRDATIREYTLAPGDLGLQSAPLDSIRVDGVEASAAMIRSVLAGDP-GAARDIVLMNAGA 297
                                           *********************************************************99.999********** PP

                             TIGR01245 294 alyvagkakdlkegvelakeaiksgkalekleelva 329
                                           alyv g+a+++ +gv +a +ai+sg+a++ l++lv+
  NCBI__GCF_000227685.2:WP_006746919.1 298 ALYVGGYAESHLQGVARAAQAIDSGAAADRLRQLVE 333
                                           ********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (343 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 16.83
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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