Alignments for a candidate for trpD_2 in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Desulfovibrio vulgaris Hildenborough

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate 209403 DVU0467 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8PD71
         (345 letters)



>MicrobesOnline__882:209403
          Length = 332

 Score =  209 bits (532), Expect = 8e-59
 Identities = 128/316 (40%), Positives = 174/316 (55%), Gaps = 3/316 (0%)

Query: 20  HDEMVDL-MRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMREFSRRVEVTDRRH 78
           H EM       +M G+++ A   + L GLR+K ET  E+  A       +  V   D   
Sbjct: 18  HPEMAGAGFASLMDGDMTPAQAGSFLMGLRMKGETADEMTEAVRAALARAVTVRGVDAPS 77

Query: 79  MVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSADALEALGAVIELQ 138
            +DIVGTGGDG  +FN ST      A  G KV KHGNR+VSS  GSADA+E LG  +E+ 
Sbjct: 78  -IDIVGTGGDGRSSFNCSTATALTLAGMGHKVVKHGNRAVSSSCGSADAIEGLGLPLEVD 136

Query: 139 PEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNILGPLTNPAGSPNILMGV 198
              V A L + G  F++AP  HPA + V P+RRE+GVRT+FN+LGPL NPA   ++L+GV
Sbjct: 137 AADVPAMLHERGFAFLFAPRFHPAFRHVMPIRRELGVRTLFNLLGPLLNPARPTHMLLGV 196

Query: 199 FHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGELRDGQVHEYEVHPEDFG 258
               L+ + A  L+  GA RA VV+G  G DEL+      V  LRDG V E+EV P  +G
Sbjct: 197 ARESLMPLMAETLRRTGAARAAVVFGAGGYDELTPLGPARVLFLRDGIVSEHEVDPARYG 256

Query: 259 IAMSASRNLKVADAAESRAMLLQVLDNV-PGPALDIVALNAGAALYVAGVADSIADGIVR 317
           IA     +L V D  E+  +L ++L    P    D++  N G AL++      + D +  
Sbjct: 257 IAPCTPEDLVVRDREEAVRVLRELLSGAGPQAMRDMLVFNVGMALHLLHDDRPLEDCMNE 316

Query: 318 ARQVLADGSARACLDA 333
           AR+ +  G+ R  L A
Sbjct: 317 ARRAVHAGAGRKVLHA 332


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: 341
Number of extensions: 10
Number of successful extensions: 1
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: 332
Length adjustment: 28
Effective length of query: 317
Effective length of database: 304
Effective search space:    96368
Effective search space used:    96368
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 209403 DVU0467 (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.28937.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.8e-105  338.8   0.0   2.1e-105  338.7   0.0    1.0  1  lcl|MicrobesOnline__882:209403  DVU0467 anthranilate phosphoribo


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:209403  DVU0467 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  338.7   0.0  2.1e-105  2.1e-105       2     324 ..       9     330 ..       8     332 .] 0.98

  Alignments for each domain:
  == domain 1  score: 338.7 bits;  conditional E-value: 2.1e-105
                       TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDivGTGGD 80 
                                     e+l+++ dL+ e a + +  +m+g++++aq +++l+ lr+kget++e++++++a +++a++v+   ++  +DivGTGGD
  lcl|MicrobesOnline__882:209403   9 ETLATGCDLHPEMAGAGFASLMDGDMTPAQAGSFLMGLRMKGETADEMTEAVRAALARAVTVRG-VDAPSIDIVGTGGD 86 
                                     7788999999999*************************************************99.79************ PP

                       TIGR01245  81 glktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPkyhpalkeva 159
                                     g +++N STa+al +a++G kv+KhGnr+vss++GsaD +e lg+ le++++ v ++l+e g++FlfAP++hpa+++v+
  lcl|MicrobesOnline__882:209403  87 GRSSFNCSTATALTLAGMGHKVVKHGNRAVSSSCGSADAIEGLGLPLEVDAADVPAMLHERGFAFLFAPRFHPAFRHVM 165
                                     ******************************************************************************* PP

                       TIGR01245 160 pvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEisltgetkvaelkdge 238
                                     p+R+eLgvrt+fNlLGPLlnPar+++ +lGv++++l+ ++ae+l++ g+ ra vv g++g DE+++ g+++v+ l+dg 
  lcl|MicrobesOnline__882:209403 166 PIRRELGVRTLFNLLGPLLNPARPTHMLLGVARESLMPLMAETLRRTGAARAAVVFGAGGYDELTPLGPARVLFLRDGI 244
                                     ******************************************************************************* PP

                       TIGR01245 239 ieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaaalyvagkakdlkegvelakeaiks 317
                                     ++e +++p+ +g+++++ e+l + + ee +++l+e+l+g + +a rd++v+N+++al + +  + l++ ++ a++a++ 
  lcl|MicrobesOnline__882:209403 245 VSEHEVDPARYGIAPCTPEDLVVRDREEAVRVLRELLSGAGPQAMRDMLVFNVGMALHLLHDDRPLEDCMNEARRAVHA 323
                                     ******************************************************************************* PP

                       TIGR01245 318 gkalekl 324
                                     g+  ++l
  lcl|MicrobesOnline__882:209403 324 GAGRKVL 330
                                     *998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (332 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: 00:00:00.01
# Mc/sec: 9.22
//
[ok]

This GapMind analysis is from Apr 09 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