Alignments for a candidate for trpD_2 in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Marinobacter adhaerens HP15

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate GFF3348 HP15_3290 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8PD71
         (345 letters)



>FitnessBrowser__Marino:GFF3348
          Length = 342

 Score =  300 bits (769), Expect = 3e-86
 Identities = 162/338 (47%), Positives = 218/338 (64%), Gaps = 5/338 (1%)

Query: 6   QQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMR 65
           ++AL R   + ++  +EM D+MR +M GE +DA + A L GLR+K ETI EI GA  VMR
Sbjct: 4   KEALNRIASNLDLSREEMKDVMRIVMNGEATDAQIGAFLMGLRLKSETIDEITGATEVMR 63

Query: 66  EFSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSA 125
           E + +V V     +VDIVGTGGDG++ FN+S+ A FV AA G  VAKHGNR+VSSKSGSA
Sbjct: 64  ELATKVSVK-AEPLVDIVGTGGDGANLFNVSSAASFVVAAAGGFVAKHGNRAVSSKSGSA 122

Query: 126 DALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNILGPL 185
           D LE LG  + ++PE+VA  + + G+GFM+AP HH AMK     R+E+G RTIFNILGP+
Sbjct: 123 DLLEKLGINLSMKPEEVARCVEEIGVGFMFAPAHHGAMKHAIGPRKELGCRTIFNILGPM 182

Query: 186 TNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGELRDG 245
           TNPAG    L+GVF+ +L      VL  LGAE  +VV  +DG+DE+SL + T V EL+DG
Sbjct: 183 TNPAGVKRQLVGVFNRELCRPMTEVLHRLGAEHIMVVCSKDGLDEISLASATHVAELKDG 242

Query: 246 QVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVL----DNVPGPALDIVALNAGAA 301
           +V EY++ PED GI   A   L V  A +S  ++        D +   A D++ALNAGAA
Sbjct: 243 KVTEYDITPEDLGIKSQALVGLTVDTADDSLKLIKAAFGRGHDEMAEKARDLIALNAGAA 302

Query: 302 LYVAGVADSIADGIVRARQVLADGSARACLDAYVAFTQ 339
           +YVAG+A +  +G+  A   +  G A   +     F+Q
Sbjct: 303 IYVAGLAKTPKEGVDMALDAMGSGLAAGKMSELADFSQ 340


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: 328
Number of extensions: 12
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: 342
Length adjustment: 29
Effective length of query: 316
Effective length of database: 313
Effective search space:    98908
Effective search space used:    98908
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 GFF3348 HP15_3290 (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.1320.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   9.8e-125  402.2   3.4   1.1e-124  402.0   3.4    1.0  1  lcl|FitnessBrowser__Marino:GFF3348  HP15_3290 anthranilate phosphori


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3348  HP15_3290 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.0   3.4  1.1e-124  1.1e-124       1     329 [.       7     337 ..       7     338 .. 0.97

  Alignments for each domain:
  == domain 1  score: 402.0 bits;  conditional E-value: 1.1e-124
                           TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDiv 75 
                                         l+++++n dLs+ee++++m+ +m+gea+daqi+A+l+ lr k+et++ei+g+ +++re a+kv+++ +e lvDiv
  lcl|FitnessBrowser__Marino:GFF3348   7 LNRIASNLDLSREEMKDVMRIVMNGEATDAQIGAFLMGLRLKSETIDEITGATEVMRELATKVSVK-AEPLVDIV 80 
                                         5789999**********************************************************5.******** PP

                           TIGR01245  76 GTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPk 150
                                         GTGGDg++ +N+S a+++v+aaaG  vaKhGnr+vssksGsaD+Le+lg+nl ++pe+var++ee g+gF+fAP+
  lcl|FitnessBrowser__Marino:GFF3348  81 GTGGDGANLFNVSSAASFVVAAAGGFVAKHGNRAVSSKSGSADLLEKLGINLSMKPEEVARCVEEIGVGFMFAPA 155
                                         *************************************************************************** PP

                           TIGR01245 151 yhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEisl 225
                                         +h a+k++++ RkeLg rt+fN+LGP++nPa +k+q++Gv++++l++ + evl++lg+++++vv+++dglDEisl
  lcl|FitnessBrowser__Marino:GFF3348 156 HHGAMKHAIGPRKELGCRTIFNILGPMTNPAGVKRQLVGVFNRELCRPMTEVLHRLGAEHIMVVCSKDGLDEISL 230
                                         *************************************************************************** PP

                           TIGR01245 226 tgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevl...egkekkakrdivvlNaaaalyv 297
                                            t+vaelkdg+++ey+++ped+g+k + l  l +++a+++++l+k+++   + ++ +++rd+++lNa+aa+yv
  lcl|FitnessBrowser__Marino:GFF3348 231 ASATHVAELKDGKVTEYDITPEDLGIKSQALVGLTVDTADDSLKLIKAAFgrgHDEMAEKARDLIALNAGAAIYV 305
                                         ***********************************************999422234478899************* PP

                           TIGR01245 298 agkakdlkegvelakeaiksgkalekleelva 329
                                         ag ak+ kegv++a++a+ sg a+ k++el++
  lcl|FitnessBrowser__Marino:GFF3348 306 AGLAKTPKEGVDMALDAMGSGLAAGKMSELAD 337
                                         ***********************999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (342 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.65
//
[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