Alignments for a candidate for trpD_2 in Shewanella sp. ANA-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Shewanella sp. ANA-3

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate 7024326 Shewana3_1518 anthranilate phosphoribosyltransferase (RefSeq)

Query= SwissProt::P83827
         (329 letters)



>FitnessBrowser__ANA3:7024326
          Length = 347

 Score =  251 bits (640), Expect = 2e-71
 Identities = 140/323 (43%), Positives = 195/323 (60%), Gaps = 9/323 (2%)

Query: 9   LGEVLEEEEAYEVMRALMAGEVSPVRAAGLLVALSLRGERPHEIAAMARAMREAARPLRV 68
           LG+ L  E+   +   L+ GE++    A +L+AL +RGE   EI+  A AMR AA+P   
Sbjct: 15  LGKALTREQTASLFSTLIQGEMNEAVMAAMLMALKIRGETIAEISGAADAMRAAAKPFPY 74

Query: 69  ----HRRPLLDIVGTGGDGKGLMNLSTLAALVAAAGGVAVAKHGNRAASSRAGSADLLEA 124
                 + ++DIVGTGGDG   +N+ST AA VAAA G  VAKHGNR+ SS++GS+DLL  
Sbjct: 75  PASSRSQGIIDIVGTGGDGFNTINISTTAAFVAAAAGAKVAKHGNRSVSSKSGSSDLLAQ 134

Query: 125 LGVDLEAPPERVGEAIEELGFGFLFARVFHPAMRHVAPVRAELGVRTVFNLLGPLTNPAG 184
            G+DL   PE     +E L   FLFA  +H  ++H  PVR  L  RT+FN+LGPL NPA 
Sbjct: 135 FGIDLTMSPELASRCLESLNLCFLFAPHYHGGVKHAVPVRQALKTRTLFNVLGPLINPAR 194

Query: 185 ADAYVLGVFSPEWLAPMAEALERLGA-RGLVVHGEGADELVL-GENRVVEVGKG---AYA 239
            +  +LGV+SPE + P+A  L+ LG  R +VVHG G DE+ L G  +V E+  G    Y 
Sbjct: 195 PEFMLLGVYSPELVTPIARVLQALGTQRAMVVHGSGLDEVALHGSTQVAELKDGEIIEYQ 254

Query: 240 LTPEEVGLKRAPLEALKGGGPEENAALARRLLKGEEKGPLADAVALAAGAGFYAAGKTPS 299
           LTP + G+ +A +  L+GG P +NA + + +L+G+       AVA+ AG   Y  G + S
Sbjct: 255 LTPADFGVPQAQISELEGGEPAQNAQITQSILQGQGSDAHTHAVAINAGCALYLCGLSDS 314

Query: 300 LKEGVALAREVLASGEAYLLLER 322
           +K G ALA   + SG+A+ LL +
Sbjct: 315 VKAGTALALNTIKSGKAFELLNQ 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: 265
Number of extensions: 17
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 7024326 Shewana3_1518 (anthranilate phosphoribosyltransferase (RefSeq))
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.16749.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     2e-132  427.4   0.5   2.3e-132  427.2   0.5    1.0  1  lcl|FitnessBrowser__ANA3:7024326  Shewana3_1518 anthranilate phosp


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7024326  Shewana3_1518 anthranilate phosphoribosyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.2   0.5  2.3e-132  2.3e-132       6     329 ..      15     340 ..      10     341 .. 0.97

  Alignments for each domain:
  == domain 1  score: 427.2 bits;  conditional E-value: 2.3e-132
                         TIGR01245   6 dnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkveke...eseelvDivGTGG 79 
                                        +k L++e+ ++l++++++ge+++a +aA+l+al+++get+ ei+g+a a+r+ ak ++      s+ ++DivGTGG
  lcl|FitnessBrowser__ANA3:7024326  15 LGKALTREQTASLFSTLIQGEMNEAVMAAMLMALKIRGETIAEISGAADAMRAAAKPFPYPassRSQGIIDIVGTGG 91 
                                       5789****************************************************998643336789********* PP

                         TIGR01245  80 DglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPkyhpalk 156
                                       Dg++tiNiST++a+vaaaaG+kvaKhGnrsvssksGs+D+L ++g+ l +spe + r+le+++++FlfAP+yh ++k
  lcl|FitnessBrowser__ANA3:7024326  92 DGFNTINISTTAAFVAAAAGAKVAKHGNRSVSSKSGSSDLLAQFGIDLTMSPELASRCLESLNLCFLFAPHYHGGVK 168
                                       ***************************************************************************** PP

                         TIGR01245 157 evapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEisltgetkvae 233
                                       +++pvR+ L++rt+fN+LGPL+nPar+++ +lGvys++lv+ +a+vl++lg++ra+vvhg +glDE++l+g+t+vae
  lcl|FitnessBrowser__ANA3:7024326 169 HAVPVRQALKTRTLFNVLGPLINPARPEFMLLGVYSPELVTPIARVLQALGTQRAMVVHG-SGLDEVALHGSTQVAE 244
                                       ************************************************************.**************** PP

                         TIGR01245 234 lkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaaalyvagkakdlkegvel 310
                                       lkdgei ey+l+p+dfg+++a+++el+gg++++na++++++l+g++++a++++v++Na+ aly+ g  +++k+g+ l
  lcl|FitnessBrowser__ANA3:7024326 245 LKDGEIIEYQLTPADFGVPQAQISELEGGEPAQNAQITQSILQGQGSDAHTHAVAINAGCALYLCGLSDSVKAGTAL 321
                                       ***************************************************************************** PP

                         TIGR01245 311 akeaiksgkalekleelva 329
                                       a+++iksgka e+l++l++
  lcl|FitnessBrowser__ANA3:7024326 322 ALNTIKSGKAFELLNQLAK 340
                                       **************99876 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.73
//
[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