Alignments for a candidate for thrC in Thermocrinis albus DSM 14484

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Thermocrinis albus DSM 14484

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_012991597.1 THAL_RS02775 threonine synthase

Query= BRENDA::O66740
         (352 letters)



>NCBI__GCF_000025605.1:WP_012991597.1
          Length = 352

 Score =  609 bits (1570), Expect = e-179
 Identities = 292/350 (83%), Positives = 327/350 (93%)

Query: 1   MNRWQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTG 60
           MN WQGII +Y+++LPV + TP+VTLYEGNTPLI+ADNLAR +GF+G++YLKYEGLNPTG
Sbjct: 1   MNCWQGIIHRYREFLPVSDKTPVVTLYEGNTPLIKADNLARLVGFRGELYLKYEGLNPTG 60

Query: 61  SFKDRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLS 120
           SFKDRGMT+AISKA+E GKRAVICASTGNTSASAAAYAARAGL+AYVLLP+GAVA+GKLS
Sbjct: 61  SFKDRGMTVAISKALEEGKRAVICASTGNTSASAAAYAARAGLKAYVLLPRGAVALGKLS 120

Query: 121 QAMIYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEA 180
           QA++YGAKVLA++GTFDDAL IVRKIG+  PVE+VNSVNPYRIEGQKTAAFEICD LGEA
Sbjct: 121 QAVMYGAKVLAVKGTFDDALYIVRKIGQMLPVEVVNSVNPYRIEGQKTAAFEICDALGEA 180

Query: 181 PDYHFIPVGNAGNITAYWKGFKIYYEEGKITKLPRMMGWQAEGAAPIVKGYPIKNPQTIA 240
           PDYHF+PVGNAGNITAYWKG+K YY+ GKI KLPRMMGWQAEGAAPIVKGYPIKNPQTIA
Sbjct: 181 PDYHFLPVGNAGNITAYWKGYKEYYQMGKIRKLPRMMGWQAEGAAPIVKGYPIKNPQTIA 240

Query: 241 TAIKIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAGLI 300
           +AI+IGNPYSW+SAL+AAQESGGKIDAV+D EILYAYKL+ASTEGVFCEPASAASVAG I
Sbjct: 241 SAIRIGNPYSWQSALEAAQESGGKIDAVTDEEILYAYKLVASTEGVFCEPASAASVAGFI 300

Query: 301 KLVREGFFKGGEVVTCTLTGNGLKDPDTAIKVCEEPITVPPDFDEVVKVL 350
           KLVREGFF GGEVV CTLTGNGLKDPDTA+KVCE+P  VPPD + V K +
Sbjct: 301 KLVREGFFSGGEVVVCTLTGNGLKDPDTALKVCEQPTNVPPDAEVVAKFI 350


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: 596
Number of extensions: 23
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: 352
Length of database: 352
Length adjustment: 29
Effective length of query: 323
Effective length of database: 323
Effective search space:   104329
Effective search space used:   104329
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_012991597.1 THAL_RS02775 (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.3155462.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.8e-108  348.0   0.0   3.3e-108  347.8   0.0    1.0  1  NCBI__GCF_000025605.1:WP_012991597.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025605.1:WP_012991597.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  347.8   0.0  3.3e-108  3.3e-108       1     340 []       8     327 ..       8     327 .. 0.98

  Alignments for each domain:
  == domain 1  score: 347.8 bits;  conditional E-value: 3.3e-108
                             TIGR00260   1 vvryreilevt.ekdlvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltkalel 71 
                                           ++ryre+l+v+ ++++v+l eg+t+l+++++la+ vg   +ly+k ++++Pt++FKDrg   ++v+++kale+
  NCBI__GCF_000025605.1:WP_012991597.1   8 IHRYREFLPVSdKTPVVTLYEGNTPLIKADNLARLVGFrGELYLKYEGLNPTGSFKDRG---MTVAISKALEE 77 
                                           79*********99************************999*******************...*********** PP

                             TIGR00260  72 gnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeif 144
                                           g+ +v+cA++G+t+a+aa a+a++a++k++vL+P+g ++   +kl +a++++akvla+kG+FDda+ +v++i 
  NCBI__GCF_000025605.1:WP_012991597.1  78 GKRAVICASTGNTSASAA-AYAARAGLKAYVLLPRGAVA--LGKLSQAVMYGAKVLAVKGTFDDALYIVRKIG 147
                                           ******************.********************..*******************************9 PP

                             TIGR00260 145 edkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekkelg....lpie 212
                                              + l + +vNs+np+rie+qkt+afei+++lg e+pd   +pv+ +gn++a++kG++e+ ++g    lp +
  NCBI__GCF_000025605.1:WP_012991597.1 148 ---QMLPVEVVNSVNPYRIEGQKTAAFEICDALG-EAPDYHFLPVGnAGNITAYWKGYKEYYQMGkirkLP-R 215
                                           ...778899999999*******************.************************************.* PP

                             TIGR00260 213 klaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnledlkesvsdeeileai 285
                                           +++ +aegaa+iv+ +       p+++++T++ A++ignp +++ ale+a++s+g+++++    +deeil a+
  NCBI__GCF_000025605.1:WP_012991597.1 216 MMGWQAEGAAPIVKGY-------PIKNPQTIASAIRIGNPYSWQSALEAAQESGGKIDAV----TDEEILYAY 277
                                           *************999.......*************************************....********* PP

                             TIGR00260 286 kklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkdpe 340
                                           k++a +eg+++ep++a++va+ +klv +g     + +  e vv+ ltgn+lkdp+
  NCBI__GCF_000025605.1:WP_012991597.1 278 KLVASTEGVFCEPASAASVAGFIKLVREG---FFSGG--EVVVCTLTGNGLKDPD 327
                                           *****************************...99999..999***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (352 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: 00:00:00.00
# Mc/sec: 14.80
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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