Alignments for a candidate for thrC in Persephonella marina EX-H1

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Persephonella marina EX-H1

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_012676942.1 PERMA_RS01265 threonine synthase

Query= BRENDA::O66740
         (352 letters)



>NCBI__GCF_000021565.1:WP_012676942.1
          Length = 356

 Score =  553 bits (1426), Expect = e-162
 Identities = 268/351 (76%), Positives = 310/351 (88%), Gaps = 2/351 (0%)

Query: 3   RWQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKG--KIYLKYEGLNPTG 60
           +W+GII  Y+++LPV + TP+VTLYEGNTPLI+A NL++ I      KIYLKYEGLNPTG
Sbjct: 5   KWRGIITAYREFLPVTDKTPVVTLYEGNTPLIDAPNLSKKIAPDKDLKIYLKYEGLNPTG 64

Query: 61  SFKDRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLS 120
           SFKDRGMT+AISKA E+GK AVICASTGNTSASAAAYAARAG+ AYV+LPKGAVA+GKLS
Sbjct: 65  SFKDRGMTMAISKAKESGKTAVICASTGNTSASAAAYAARAGMDAYVILPKGAVALGKLS 124

Query: 121 QAMIYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEA 180
           QAM+YGAK++A+ G FDDAL+IVR+IGE +PVE+VNSVNPYRIEGQKTA+FEI D LG+A
Sbjct: 125 QAMVYGAKIIALMGNFDDALSIVREIGEKYPVEVVNSVNPYRIEGQKTASFEIIDALGDA 184

Query: 181 PDYHFIPVGNAGNITAYWKGFKIYYEEGKITKLPRMMGWQAEGAAPIVKGYPIKNPQTIA 240
           PDYHFIPVGNAGNITAYWKG+K Y E G+ TKLPRM+GWQAEGAAPIVKG+PIKNPQTIA
Sbjct: 185 PDYHFIPVGNAGNITAYWKGYKEYKEAGRSTKLPRMIGWQAEGAAPIVKGFPIKNPQTIA 244

Query: 241 TAIKIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAGLI 300
           TAIKIGNPYSW+ AL+AA+ES G IDAVSD EIL AY+L+ASTEGVFCEPASAASVAG+I
Sbjct: 245 TAIKIGNPYSWQPALQAAKESNGFIDAVSDEEILEAYRLVASTEGVFCEPASAASVAGVI 304

Query: 301 KLVREGFFKGGEVVTCTLTGNGLKDPDTAIKVCEEPITVPPDFDEVVKVLG 351
           K  R+G FKGGE V CTLTGNGLKDPDT IK  E+P+ +PPD +E+ + LG
Sbjct: 305 KAYRKGLFKGGETVVCTLTGNGLKDPDTVIKASEKPVEMPPDINEIARYLG 355


Lambda     K      H
   0.317    0.136    0.400 

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: 572
Number of extensions: 22
Number of successful extensions: 2
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: 352
Length of database: 356
Length adjustment: 29
Effective length of query: 323
Effective length of database: 327
Effective search space:   105621
Effective search space used:   105621
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_012676942.1 PERMA_RS01265 (threonine synthase)
to HMM TIGR00260 (thrC: threonine synthase (EC 4.2.3.1))

# 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/TIGR00260.hmm
# target sequence database:        /tmp/gapView.28871.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00260  [M=340]
Accession:   TIGR00260
Description: thrC: threonine synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-106  342.1   0.0     2e-106  341.9   0.0    1.0  1  lcl|NCBI__GCF_000021565.1:WP_012676942.1  PERMA_RS01265 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021565.1:WP_012676942.1  PERMA_RS01265 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.9   0.0    2e-106    2e-106       1     340 []      10     331 ..      10     331 .. 0.98

  Alignments for each domain:
  == domain 1  score: 341.9 bits;  conditional E-value: 2e-106
                                 TIGR00260   1 vvryreilevt.ekdlvdlaegstelfrspklaeevga...enlyvkelfhgPtlaFKDrglqfvavll 65 
                                               ++ yre+l+vt ++++v+l eg+t+l+++p+l++++      ++y+k ++++Pt++FKDrg   +++++
  lcl|NCBI__GCF_000021565.1:WP_012676942.1  10 ITAYREFLPVTdKTPVVTLYEGNTPLIDAPNLSKKIAPdkdLKIYLKYEGLNPTGSFKDRG---MTMAI 75 
                                               678********99***********************98856678*****************...***** PP

                                 TIGR00260  66 tkalelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFD 134
                                               +ka+e g+++v+cA++G+t+a+aa a+a++a+++++v++Pkg ++   +kl +a++++ak++a  G+FD
  lcl|NCBI__GCF_000021565.1:WP_012676942.1  76 SKAKESGKTAVICASTGNTSASAA-AYAARAGMDAYVILPKGAVA--LGKLSQAMVYGAKIIALMGNFD 141
                                               ************************.********************..********************** PP

                                 TIGR00260 135 daqdlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGfl 202
                                               da+ +v+ei    ek+ + +vNs+np+rie+qkt+ fei+++lg ++pd   +pv+ +gn++a++kG++
  lcl|NCBI__GCF_000021565.1:WP_012676942.1 142 DALSIVREIG---EKYPVEVVNSVNPYRIEGQKTASFEIIDALG-DAPDYHFIPVGnAGNITAYWKGYK 206
                                               *********9...677889999999*******************.************************ PP

                                 TIGR00260 203 ekkelg....lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslg 267
                                               e+ke+g    lp ++++ +aegaa+iv+ f       p+++++T++tA++ignp +++ al++a++s+g
  lcl|NCBI__GCF_000021565.1:WP_012676942.1 207 EYKEAGrstkLP-RMIGWQAEGAAPIVKGF-------PIKNPQTIATAIKIGNPYSWQPALQAAKESNG 267
                                               ************.*****************.......******************************** PP

                                 TIGR00260 268 nledlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnkl 336
                                                ++++    sdeeilea++++a +eg+++ep++a++va+++k   kg     + +  e+vv+ ltgn+l
  lcl|NCBI__GCF_000021565.1:WP_012676942.1 268 FIDAV----SDEEILEAYRLVASTEGVFCEPASAASVAGVIKAYRKG---LFKGG--ETVVCTLTGNGL 327
                                               *****....**************************************...88888..************ PP

                                 TIGR00260 337 kdpe 340
                                               kdp+
  lcl|NCBI__GCF_000021565.1:WP_012676942.1 328 KDPD 331
                                               **97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (356 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: 10.89
//
[ok]

This GapMind analysis is from Apr 10 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