Alignments for a candidate for trpD_2 in Phyllobacterium endophyticum PEPV15

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Phyllobacterium endophyticum PEPV15

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_106716616.1 CU100_RS10980 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8PD71
         (345 letters)



>NCBI__GCF_003010935.1:WP_106716616.1
          Length = 339

 Score =  274 bits (701), Expect = 2e-78
 Identities = 151/310 (48%), Positives = 196/310 (63%), Gaps = 3/310 (0%)

Query: 22  EMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMREFSRRVEVTDRRHMVD 81
           E V+    +M G+ + A + A+L  LRV+ E I EI+GA + MR  S+ + V      +D
Sbjct: 21  EAVEAFDIMMSGQATPAQIGALLMALRVRGENIDEISGAVSAMR--SKMLRVVTSADAID 78

Query: 82  IVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSADALEALGAVIELQPEQ 141
           IVGTGGD S ++N+STCA FVAA  G  VAKHGNR++SS+SG+AD L ALG  IE+ PE 
Sbjct: 79  IVGTGGDQSGSYNVSTCAAFVAAGAGVPVAKHGNRALSSRSGAADTLAALGINIEISPEL 138

Query: 142 VAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNILGPLTNPAGSPNILMGVFHP 201
           +A  + Q GIGFM+AP+HHPAMK V P R E+G RTIFN+LGPLTNPAG    L+GVF P
Sbjct: 139 IATCIEQAGIGFMFAPMHHPAMKHVGPARVELGTRTIFNLLGPLTNPAGVKRQLVGVFAP 198

Query: 202 DLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGELRDGQVHEYEVHPEDFGIAM 261
           + V   A VL++LG+E   VV G DG+DE++    T V  L +G V  +E+ PE FG+ +
Sbjct: 199 EWVEPIAHVLKKLGSEAVWVVHG-DGLDEITTAGVTKVSALENGNVRSFEIDPESFGLRL 257

Query: 262 SASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGAALYVAGVADSIADGIVRARQV 321
               +LK   A E+   LL VLD   G   DI   NAGA L +AGVA  +  GI  A   
Sbjct: 258 VNPDDLKGGTADENAVSLLSVLDGAHGAYRDITLFNAGAGLVIAGVAADLKVGIEMAAHS 317

Query: 322 LADGSARACL 331
           +  G+AR  L
Sbjct: 318 IDSGAARNVL 327


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: 337
Number of extensions: 18
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: 345
Length of database: 339
Length adjustment: 29
Effective length of query: 316
Effective length of database: 310
Effective search space:    97960
Effective search space used:    97960
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_106716616.1 CU100_RS10980 (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.72709.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.1e-124  400.5   1.9   3.7e-124  400.3   1.9    1.0  1  NCBI__GCF_003010935.1:WP_106716616.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106716616.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.3   1.9  3.7e-124  3.7e-124       6     329 ..      13     332 ..       9     333 .. 0.98

  Alignments for each domain:
  == domain 1  score: 400.3 bits;  conditional E-value: 3.7e-124
                             TIGR01245   6 dnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDivGTG 78 
                                            +k Ls++ea ++++ +msg+a++aqi+A+l+alrv+ge+++ei+g++ a+r+k+ +v +  s++++DivGTG
  NCBI__GCF_003010935.1:WP_106716616.1  13 AGKALSQGEAVEAFDIMMSGQATPAQIGALLMALRVRGENIDEISGAVSAMRSKMLRVVT--SADAIDIVGTG 83 
                                           5799******************************************************77..59********* PP

                             TIGR01245  79 GDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPky 151
                                           GD++ ++N+ST +a+vaa+aGv+vaKhGnr+ ss+sG+aD+L alg+n+e+spe +a ++e+ gigF+fAP++
  NCBI__GCF_003010935.1:WP_106716616.1  84 GDQSGSYNVSTCAAFVAAGAGVPVAKHGNRALSSRSGAADTLAALGINIEISPELIATCIEQAGIGFMFAPMH 156
                                           ************************************************************************* PP

                             TIGR01245 152 hpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEis 224
                                           hpa+k+v p R eLg+rt+fNlLGPL+nPa +k+q++Gv+ ++ ve +a+vlk+lg++ + vvhg dglDEi+
  NCBI__GCF_003010935.1:WP_106716616.1 157 HPAMKHVGPARVELGTRTIFNLLGPLTNPAGVKRQLVGVFAPEWVEPIAHVLKKLGSEAVWVVHG-DGLDEIT 228
                                           *****************************************************************.******* PP

                             TIGR01245 225 ltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaaalyv 297
                                           + g tkv+ l++g++++++++pe+fgl   + ++lkgg+a+ena  l +vl g + +a rdi ++Na+a l++
  NCBI__GCF_003010935.1:WP_106716616.1 229 TAGVTKVSALENGNVRSFEIDPESFGLRLVNPDDLKGGTADENAVSLLSVLDGAH-GAYRDITLFNAGAGLVI 300
                                           *****************************************************98.99*************** PP

                             TIGR01245 298 agkakdlkegvelakeaiksgkalekleelva 329
                                           ag+a+dlk g+e+a ++i+sg+a ++l++lv+
  NCBI__GCF_003010935.1:WP_106716616.1 301 AGVAADLKVGIEMAAHSIDSGAARNVLRKLVH 332
                                           ****************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (339 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: 21.32
//
[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:

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 2024 update 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 original 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