Alignments for a candidate for trpD_2 in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Shewanella oneidensis MR-1

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate 202143 SO3021 anthranilate phosphoribosyltransferase (NCBI ptt file)

Query= SwissProt::P83827
         (329 letters)



>FitnessBrowser__MR1:202143
          Length = 347

 Score =  246 bits (629), Expect = 5e-70
 Identities = 139/322 (43%), Positives = 193/322 (59%), Gaps = 9/322 (2%)

Query: 10  GEVLEEEEAYEVMRALMAGEVSPVRAAGLLVALSLRGERPHEIAAMARAMREAARPLRV- 68
           G+ L  E+   +   L+ GE++    AG+L+AL +RGE   EI+  A AMR AA+P    
Sbjct: 16  GKALTREQTASLFSVLIQGEMNETVMAGMLMALKIRGETIEEISGAADAMRAAAKPFPYP 75

Query: 69  ---HRRPLLDIVGTGGDGKGLMNLSTLAALVAAAGGVAVAKHGNRAASSRAGSADLLEAL 125
                + ++DIVGTGGDG   +N+ST AA VAAA G  VAKHGNR+ SS++GS+DLL   
Sbjct: 76  ESSRSQGVIDIVGTGGDGFNTINISTTAAFVAAAAGAKVAKHGNRSVSSKSGSSDLLAQF 135

Query: 126 GVDLEAPPERVGEAIEELGFGFLFARVFHPAMRHVAPVRAELGVRTVFNLLGPLTNPAGA 185
           G+DL   PE     +E L   FLFA  +H  ++H  PVR  L  RT+FN+LGPL NPA  
Sbjct: 136 GIDLTMSPELASHCLEALNLCFLFAPHYHGGVKHAVPVRQTLKTRTLFNVLGPLINPARP 195

Query: 186 DAYVLGVFSPEWLAPMAEALERLGA-RGLVVHGEGADELVL-GENRVVEVGKG---AYAL 240
           +  +LGV+S E + P+A  L+ LG  R +VVHG G DE+ L G  +V E+  G    Y L
Sbjct: 196 EFMLLGVYSAELVTPIARVLQALGTQRAMVVHGSGLDEVALHGSTQVAELKDGEIIEYQL 255

Query: 241 TPEEVGLKRAPLEALKGGGPEENAALARRLLKGEEKGPLADAVALAAGAGFYAAGKTPSL 300
           TP + G+ +A +  L+GG P  NA + +++L+G        AVA+ AG   Y  G + S+
Sbjct: 256 TPADFGVPQAHISELEGGEPAHNALITQQILQGHGCDAHTHAVAINAGCALYLCGLSESV 315

Query: 301 KEGVALAREVLASGEAYLLLER 322
           K G ALA   + +G+AY LL +
Sbjct: 316 KMGTALALSTIKTGKAYELLHK 337


Lambda     K      H
   0.317    0.136    0.380 

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: 270
Number of extensions: 19
Number of successful extensions: 4
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: 329
Length of database: 347
Length adjustment: 28
Effective length of query: 301
Effective length of database: 319
Effective search space:    96019
Effective search space used:    96019
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate 202143 SO3021 (anthranilate phosphoribosyltransferase (NCBI ptt file))
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.27565.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   5.1e-130  419.5   0.4   5.8e-130  419.3   0.4    1.0  1  lcl|FitnessBrowser__MR1:202143  SO3021 anthranilate phosphoribos


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:202143  SO3021 anthranilate phosphoribosyltransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.3   0.4  5.8e-130  5.8e-130       4     328 ..      13     339 ..      10     341 .. 0.98

  Alignments for each domain:
  == domain 1  score: 419.3 bits;  conditional E-value: 5.8e-130
                       TIGR01245   4 lldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkveke...eseelvDivGTGG 79 
                                     l+++k L++e+ ++l++ +++ge++++ +a +l+al+++get+eei+g+a a+r+ ak ++      s+ ++DivGTGG
  lcl|FitnessBrowser__MR1:202143  13 LFQGKALTREQTASLFSVLIQGEMNETVMAGMLMALKIRGETIEEISGAADAMRAAAKPFPYPessRSQGVIDIVGTGG 91 
                                     7899******************************************************997642236789********* PP

                       TIGR01245  80 DglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPkyhpalkev 158
                                     Dg++tiNiST++a+vaaaaG+kvaKhGnrsvssksGs+D+L ++g+ l +spe + ++le ++++FlfAP+yh ++k++
  lcl|FitnessBrowser__MR1:202143  92 DGFNTINISTTAAFVAAAAGAKVAKHGNRSVSSKSGSSDLLAQFGIDLTMSPELASHCLEALNLCFLFAPHYHGGVKHA 170
                                     ******************************************************************************* PP

                       TIGR01245 159 apvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEisltgetkvaelkdg 237
                                     +pvR++L++rt+fN+LGPL+nPar+++ +lGvys++lv+ +a+vl++lg++ra+vvhg +glDE++l+g+t+vaelkdg
  lcl|FitnessBrowser__MR1:202143 171 VPVRQTLKTRTLFNVLGPLINPARPEFMLLGVYSAELVTPIARVLQALGTQRAMVVHG-SGLDEVALHGSTQVAELKDG 248
                                     **********************************************************.******************** PP

                       TIGR01245 238 eieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaaalyvagkakdlkegvelakeaik 316
                                     ei ey+l+p+dfg+++a+++el+gg++++na +++++l+g++ +a++++v++Na+ aly+ g  +++k g+ la+ +ik
  lcl|FitnessBrowser__MR1:202143 249 EIIEYQLTPADFGVPQAHISELEGGEPAHNALITQQILQGHGCDAHTHAVAINAGCALYLCGLSESVKMGTALALSTIK 327
                                     ******************************************************************************* PP

                       TIGR01245 317 sgkalekleelv 328
                                     +gka+e+l++l+
  lcl|FitnessBrowser__MR1:202143 328 TGKAYELLHKLA 339
                                     ********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (347 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: 9.52
//
[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