Alignments for a candidate for trpD_2 in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Shewanella loihica PV-4

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate 5209800 Shew_2253 anthranilate phosphoribosyltransferase (RefSeq)

Query= SwissProt::P83827
         (329 letters)



>FitnessBrowser__PV4:5209800
          Length = 349

 Score =  255 bits (651), Expect = 1e-72
 Identities = 141/323 (43%), Positives = 200/323 (61%), Gaps = 10/323 (3%)

Query: 10  GEVLEEEEAYEVMRALMAGEVSPVRAAGLLVALSLRGERPHEIAAMARAMREAARPL--- 66
           G+ +  EE   +   ++ G++ PV  AG+LVA+ +RGE   EI+  A A+ +AA+     
Sbjct: 14  GQTISREETKALFSEIVEGKMDPVAMAGMLVAMKMRGETIDEISGAADALLQAAKAFPAP 73

Query: 67  --RVHRRPLLDIVGTGGDGKGLMNLSTLAALVAAAGGVAVAKHGNRAASSRAGSADLLEA 124
                 + ++DIVGTGGDG   +N+ST +A VAAA G  VAKHGNR+ SS++GS+DLL  
Sbjct: 74  SEATRTQGIVDIVGTGGDGHNTINISTTSAFVAAAAGAKVAKHGNRSVSSKSGSSDLLAQ 133

Query: 125 LGVDLEAPPERVGEAIEELGFGFLFARVFHPAMRHVAPVRAELGVRTVFNLLGPLTNPAG 184
            G+DL   PE   + +++LG  FLFA  +H  +RH  PVR  L  RT+FN+LGPL NPA 
Sbjct: 134 FGIDLTMAPETARDCLDDLGLCFLFAPHYHGGVRHAVPVRQALKTRTLFNVLGPLINPAR 193

Query: 185 ADAYVLGVFSPEWLAPMAEALERLGA-RGLVVHGEGADEL-VLGENRVVEVGKG---AYA 239
            D  +LGV+ P  + P+ + L+ L   R +VVHG G DE+ V GE  V E+ +G    Y 
Sbjct: 194 PDYMLLGVYDPMLVRPICDVLKALDVKRAMVVHGSGLDEVAVHGETLVCELKQGEIVEYY 253

Query: 240 LTPEEVGLKRAPLEALKGGGPEENAALARRLLKGEEKGPLADAVALAAGAGFYAAGKTPS 299
           L+PE +GL RA +  L G GP ENA + R +L+G  +    +AVA  AG   Y +G   S
Sbjct: 254 LSPEALGLSRAAISDLAGAGPAENAEITRAILQGHGELAHTEAVAANAGCALYVSGCCDS 313

Query: 300 LKEGVALAREVLASGEAYLLLER 322
            ++G ALA + LASG+AY+LL++
Sbjct: 314 PQQGTALALQTLASGKAYILLQQ 336


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: 301
Number of extensions: 23
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: 349
Length adjustment: 28
Effective length of query: 301
Effective length of database: 321
Effective search space:    96621
Effective search space used:    96621
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 5209800 Shew_2253 (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.22809.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   2.9e-128  413.8   0.1   3.3e-128  413.6   0.1    1.0  1  lcl|FitnessBrowser__PV4:5209800  Shew_2253 anthranilate phosphori


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209800  Shew_2253 anthranilate phosphoribosyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.6   0.1  3.3e-128  3.3e-128       2     328 ..       9     338 ..       8     340 .. 0.97

  Alignments for each domain:
  == domain 1  score: 413.6 bits;  conditional E-value: 3.3e-128
                        TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkveke....eseelvDiv 75 
                                       +l++++++s+ee ++l++ei++g+++++ +a +lva++++get++ei+g+a al++ ak +++      ++ +vDiv
  lcl|FitnessBrowser__PV4:5209800   9 DRLYQGQTISREETKALFSEIVEGKMDPVAMAGMLVAMKMRGETIDEISGAADALLQAAKAFPAPseatRTQGIVDIV 86 
                                      5899*******************************************************99876422235788***** PP

                        TIGR01245  76 GTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPkyhp 153
                                      GTGGDg +tiNiST+sa+vaaaaG+kvaKhGnrsvssksGs+D+L ++g+ l + pe ++ +l+++g++FlfAP+yh 
  lcl|FitnessBrowser__PV4:5209800  87 GTGGDGHNTINISTTSAFVAAAAGAKVAKHGNRSVSSKSGSSDLLAQFGIDLTMAPETARDCLDDLGLCFLFAPHYHG 164
                                      ****************************************************************************** PP

                        TIGR01245 154 alkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEisltgetkv 231
                                      ++++++pvR+ L++rt+fN+LGPL+nPar+++ +lGvy++ lv+ +  vlk+l vkra+vvhg +glDE++++get v
  lcl|FitnessBrowser__PV4:5209800 165 GVRHAVPVRQALKTRTLFNVLGPLINPARPDYMLLGVYDPMLVRPICDVLKALDVKRAMVVHG-SGLDEVAVHGETLV 241
                                      ***************************************************************.************** PP

                        TIGR01245 232 aelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaaalyvagkakdlkegve 309
                                      +elk+gei ey+lspe +gl ra +++l+g+ ++enae+++++l+g+++ a++++v++Na+ alyv+g  ++ ++g+ 
  lcl|FitnessBrowser__PV4:5209800 242 CELKQGEIVEYYLSPEALGLSRAAISDLAGAGPAENAEITRAILQGHGELAHTEAVAANAGCALYVSGCCDSPQQGTA 319
                                      ****************************************************************************** PP

                        TIGR01245 310 lakeaiksgkalekleelv 328
                                      la++++ sgka+ +l++l+
  lcl|FitnessBrowser__PV4:5209800 320 LALQTLASGKAYILLQQLA 338
                                      ***************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (349 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: 00:00:00.01
# Mc/sec: 9.40
//
[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