Alignments for a candidate for trpD_2 in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Bacteroides thetaiotaomicron VPI-5482

Align anthranilate phosphoribosyltransferase (EC 2.4.2.18) (characterized)
to candidate 350058 BT0530 anthranilate phosphoribosyltransferase (NCBI ptt file)

Query= reanno::Btheta:350058
         (332 letters)



>FitnessBrowser__Btheta:350058
          Length = 332

 Score =  658 bits (1698), Expect = 0.0
 Identities = 332/332 (100%), Positives = 332/332 (100%)

Query: 1   MKQILYKLFEHQYLGRDEARTILQNIAQGKYNDVQVASLITVFLMRNISVEELCGFRDAL 60
           MKQILYKLFEHQYLGRDEARTILQNIAQGKYNDVQVASLITVFLMRNISVEELCGFRDAL
Sbjct: 1   MKQILYKLFEHQYLGRDEARTILQNIAQGKYNDVQVASLITVFLMRNISVEELCGFRDAL 60

Query: 61  LEMRVPVDLSEFAPIDIVGTGGDGKNTFNISTAACFTVAGAGIPVVKHGNYGATSVSGAS 120
           LEMRVPVDLSEFAPIDIVGTGGDGKNTFNISTAACFTVAGAGIPVVKHGNYGATSVSGAS
Sbjct: 61  LEMRVPVDLSEFAPIDIVGTGGDGKNTFNISTAACFTVAGAGIPVVKHGNYGATSVSGAS 120

Query: 121 NVMEQHGVKFTSDVDQMRRSMEQCNIAYLHAPLFNPALKAVAPIRKGLAVRTFFNMLGPL 180
           NVMEQHGVKFTSDVDQMRRSMEQCNIAYLHAPLFNPALKAVAPIRKGLAVRTFFNMLGPL
Sbjct: 121 NVMEQHGVKFTSDVDQMRRSMEQCNIAYLHAPLFNPALKAVAPIRKGLAVRTFFNMLGPL 180

Query: 181 VNPVLPTYQLLGVYNLPLLRLYTYTYQESKTKFAVVHSLDGYDEISLTNEFKVATCGNEK 240
           VNPVLPTYQLLGVYNLPLLRLYTYTYQESKTKFAVVHSLDGYDEISLTNEFKVATCGNEK
Sbjct: 181 VNPVLPTYQLLGVYNLPLLRLYTYTYQESKTKFAVVHSLDGYDEISLTNEFKVATCGNEK 240

Query: 241 IYTPEGLGFARYQDTDLDGGQTPEDAAKIFDNIMNNTATEAQKNVVVINAAFAIQVVRPE 300
           IYTPEGLGFARYQDTDLDGGQTPEDAAKIFDNIMNNTATEAQKNVVVINAAFAIQVVRPE
Sbjct: 241 IYTPEGLGFARYQDTDLDGGQTPEDAAKIFDNIMNNTATEAQKNVVVINAAFAIQVVRPE 300

Query: 301 KTIEECIALAKESLESGRALATLKKFIELNNK 332
           KTIEECIALAKESLESGRALATLKKFIELNNK
Sbjct: 301 KTIEECIALAKESLESGRALATLKKFIELNNK 332


Lambda     K      H
   0.319    0.135    0.387 

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: 554
Number of extensions: 19
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: 332
Length of database: 332
Length adjustment: 28
Effective length of query: 304
Effective length of database: 304
Effective search space:    92416
Effective search space used:    92416
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 350058 BT0530 (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.32581.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    8.3e-95  303.8   0.0    9.5e-95  303.6   0.0    1.0  1  lcl|FitnessBrowser__Btheta:350058  BT0530 anthranilate phosphoribos


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350058  BT0530 anthranilate phosphoribosyltransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.6   0.0   9.5e-95   9.5e-95       3     329 ..       7     328 ..       5     329 .. 0.97

  Alignments for each domain:
  == domain 1  score: 303.6 bits;  conditional E-value: 9.5e-95
                          TIGR01245   3 klldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDivGTG 78 
                                        kl++++ L ++ea+++++ i++g+++d+q+a++++++ ++  ++ee+ g+  al+e  + v+ + +   +DivGTG
  lcl|FitnessBrowser__Btheta:350058   7 KLFEHQYLGRDEARTILQNIAQGKYNDVQVASLITVFLMRNISVEELCGFRDALLEMRVPVDLS-EFAPIDIVGTG 81 
                                        89999********************************************************995.88899****** PP

                          TIGR01245  79 GDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPkyhpa 154
                                        GDg +t+NiSTa+ + +a+aG++v+KhGn  ++s sG+++v+e+ gv++  + ++++rs+e+ +i++l+AP + pa
  lcl|FitnessBrowser__Btheta:350058  82 GDGKNTFNISTAACFTVAGAGIPVVKHGNYGATSVSGASNVMEQHGVKFTSDVDQMRRSMEQCNIAYLHAPLFNPA 157
                                        **************************************************************************** PP

                          TIGR01245 155 lkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEisltgetk 230
                                        lk+vap+Rk L+vrt fN+LGPL+nP+ +++q+lGvy+  l++++  + ++ ++k   vvh+ dg DEislt+e k
  lcl|FitnessBrowser__Btheta:350058 158 LKAVAPIRKGLAVRTFFNMLGPLVNPVLPTYQLLGVYNLPLLRLYTYTYQESKTK-FAVVHSLDGYDEISLTNEFK 232
                                        ******************************************************9.7899**************** PP

                          TIGR01245 231 vaelkdgeieeytlspedfglkraeleelkggsa.eenaellkevlegkekkakrdivvlNaaaalyvagkakdlk 305
                                        va   +++i     +pe +g++r++ ++l gg++ e+ a+++ +++++ +++a++++vv+Naa+a++v   +k+++
  lcl|FitnessBrowser__Btheta:350058 233 VATCGNEKIY----TPEGLGFARYQDTDLDGGQTpEDAAKIFDNIMNNTATEAQKNVVVINAAFAIQVVRPEKTIE 304
                                        *****99985....7***************98764889999*********************************** PP

                          TIGR01245 306 egvelakeaiksgkalekleelva 329
                                        e + lake+++sg+al++l+++++
  lcl|FitnessBrowser__Btheta:350058 305 ECIALAKESLESGRALATLKKFIE 328
                                        *********************986 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: 7.75
//
[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