GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_2 in Marivita geojedonensis DPG-138

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_085637395.1 MGEO_RS11335 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8PD71
         (345 letters)



>NCBI__GCF_002115805.1:WP_085637395.1
          Length = 338

 Score =  258 bits (660), Expect = 1e-73
 Identities = 145/309 (46%), Positives = 188/309 (60%), Gaps = 2/309 (0%)

Query: 33  GEVSDAMVSAILTGLRVKKETIGEIAGAATVMREFSRRVEVTDRRHMVDIVGTGGDGSHT 92
           GE + A +  +L  LR + E + E A AA VMR     V+  +    +DIVGTGGDG  T
Sbjct: 32  GEATPAQMGGLLMALRARGEAVSEYAAAAAVMRAKCTAVKAPEGA--MDIVGTGGDGMGT 89

Query: 93  FNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSADALEALGAVIELQPEQVAASLAQTGIG 152
            NIST   FV A  G  VAKHGNR++SSKSGSADAL  +G  + + PE V  ++A+ GIG
Sbjct: 90  LNISTATAFVVAGAGVPVAKHGNRNLSSKSGSADALTEMGINVMVSPEVVERAIAEVGIG 149

Query: 153 FMYAPVHHPAMKVVAPVRREMGVRTIFNILGPLTNPAGSPNILMGVFHPDLVGIQARVLQ 212
           FM AP+HHPAMK V PVR+E+G +TIFNILGPLTNPAG    L G F  DL+   A  L+
Sbjct: 150 FMMAPMHHPAMKHVMPVRQELGSKTIFNILGPLTNPAGVKRQLTGAFAIDLIFPMAETLK 209

Query: 213 ELGAERALVVWGRDGMDELSLGAGTLVGELRDGQVHEYEVHPEDFGIAMSASRNLKVADA 272
           ELG+E+A +V G DG DE+S+ A T V  L DG++   EVHPED G+ +   R++     
Sbjct: 210 ELGSEKAWLVHGGDGTDEISISAPTQVAVLEDGKIRGREVHPEDAGLPVHPFRDILGGTP 269

Query: 273 AESRAMLLQVLDNVPGPALDIVALNAGAALYVAGVADSIADGIVRARQVLADGSARACLD 332
           AE+      +LD       D V LNA AAL VA  A  +  G+  A + +  G+A+A ++
Sbjct: 270 AENAQAFRDLLDGAKNAYRDAVLLNAAAALVVADKAADLRVGVEMAAESIDSGAAKAKVE 329

Query: 333 AYVAFTQQA 341
           A    TQ A
Sbjct: 330 ALARVTQAA 338


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: 363
Number of extensions: 19
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: 338
Length adjustment: 29
Effective length of query: 316
Effective length of database: 309
Effective search space:    97644
Effective search space used:    97644
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_085637395.1 MGEO_RS11335 (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.1796332.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     4e-120  387.0   2.7   4.9e-120  386.7   2.7    1.0  1  NCBI__GCF_002115805.1:WP_085637395.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085637395.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.7   2.7  4.9e-120  4.9e-120       8     329 ..      15     333 ..      10     334 .. 0.98

  Alignments for each domain:
  == domain 1  score: 386.7 bits;  conditional E-value: 4.9e-120
                             TIGR01245   8 kdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDivGTGGD 80 
                                             Ls+ +aeq+++ +++gea++aq++ +l+alr++ge ++e a++a ++r+k + v++   e ++DivGTGGD
  NCBI__GCF_002115805.1:WP_085637395.1  15 GPLSRSQAEQAFELLFDGEATPAQMGGLLMALRARGEAVSEYAAAAAVMRAKCTAVKA--PEGAMDIVGTGGD 85 
                                           579*****************************************************88..79*********** PP

                             TIGR01245  81 glktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPkyhp 153
                                           g+ t+NiSTa+a+v+a+aGv+vaKhGnr  ssksGsaD L ++g+n+ +spe v+r+++evgigF++AP++hp
  NCBI__GCF_002115805.1:WP_085637395.1  86 GMGTLNISTATAFVVAGAGVPVAKHGNRNLSSKSGSADALTEMGINVMVSPEVVERAIAEVGIGFMMAPMHHP 158
                                           ************************************************************************* PP

                             TIGR01245 154 alkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEislt 226
                                           a+k+v+pvR+eLg +t+fN+LGPL+nPa +k+q+ G +  dl+  +ae+lk+lg+++a +vhg dg+DEis+ 
  NCBI__GCF_002115805.1:WP_085637395.1 159 AMKHVMPVRQELGSKTIFNILGPLTNPAGVKRQLTGAFAIDLIFPMAETLKELGSEKAWLVHGGDGTDEISIS 231
                                           ************************************************************************* PP

                             TIGR01245 227 getkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaaalyvag 299
                                           ++t+va l+dg+i+  +++ped gl+ ++ +++ gg+++ena++++++l g + +a rd+v+lNaaaal+va+
  NCBI__GCF_002115805.1:WP_085637395.1 232 APTQVAVLEDGKIRGREVHPEDAGLPVHPFRDILGGTPAENAQAFRDLLDGAK-NAYRDAVLLNAAAALVVAD 303
                                           ***************************************************98.899**************** PP

                             TIGR01245 300 kakdlkegvelakeaiksgkalekleelva 329
                                           ka+dl+ gve+a e+i+sg+a +k+e+l++
  NCBI__GCF_002115805.1:WP_085637395.1 304 KAADLRVGVEMAAESIDSGAAKAKVEALAR 333
                                           ************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (338 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: 00:00:00.00
# Mc/sec: 14.17
//
[ok]

This GapMind analysis is from Jul 26 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