Alignments for a candidate for thrC in Heliobacterium modesticaldum Ice1; ATCC 51547

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Heliobacterium modesticaldum Ice1; ATCC 51547

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_012282996.1 HM1_RS08715 threonine synthase

Query= BRENDA::O66740
         (352 letters)



>NCBI__GCF_000019165.1:WP_012282996.1
          Length = 349

 Score =  429 bits (1103), Expect = e-125
 Identities = 216/349 (61%), Positives = 274/349 (78%), Gaps = 4/349 (1%)

Query: 1   MNRWQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTG 60
           MNR QGII  +K +LPV E TP+V+L EGNTPLI A  L++ IG   ++Y KYEGLNPTG
Sbjct: 1   MNR-QGIIPTFKDFLPVTEKTPMVSLCEGNTPLIAAPRLSQQIG--AELYFKYEGLNPTG 57

Query: 61  SFKDRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLS 120
           SFKDRGM +A++KAVE G +A++CASTGNTSA+AAAYAAR G++  V++P+G +A+GKL+
Sbjct: 58  SFKDRGMVMAVAKAVEEGAQAIMCASTGNTSAAAAAYAARCGIKCIVIIPEGKIALGKLA 117

Query: 121 QAMIYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEA 180
           QA+IYGAKV+AI+G FD+AL IVR I    P+ +VNSVNPYRIEGQKTAAFE+C  LG+A
Sbjct: 118 QALIYGAKVIAIEGNFDEALKIVRDICAKHPITLVNSVNPYRIEGQKTAAFEVCQQLGDA 177

Query: 181 PDYHFIPVGNAGNITAYWKGFKIYYEEGKITKLPRMMGWQAEGAAPIVKGYPIKNPQTIA 240
           PDY  IPVGNAGNITAYWKGF  + + GK+ K P+M+G++AEGAA IV    I+ P+T+A
Sbjct: 178 PDYLAIPVGNAGNITAYWKGFVEWKQAGKVDKTPKMIGFEAEGAAAIVFDRVIEKPETVA 237

Query: 241 TAIKIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAGLI 300
           TAI+IGNP SW+ A+ AA++SGG ID V+D EIL AY+L+AS EG+FCEPASAAS+AG+I
Sbjct: 238 TAIRIGNPASWQGAVAAARDSGGFIDYVTDEEILEAYRLLASQEGIFCEPASAASLAGVI 297

Query: 301 KLVREGFFKGGEVVTCTLTGNGLKDPDTAIK-VCEEPITVPPDFDEVVK 348
           K  + G    G  + C LTG+GLKDPD AIK V   PI VP   + V++
Sbjct: 298 KKRQAGILPEGAKIVCVLTGHGLKDPDNAIKTVSGGPIMVPATEEAVLR 346


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: 476
Number of extensions: 15
Number of successful extensions: 3
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: 349
Length adjustment: 29
Effective length of query: 323
Effective length of database: 320
Effective search space:   103360
Effective search space used:   103360
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_012282996.1 HM1_RS08715 (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.26016.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.1e-108  346.9   0.0     7e-108  346.7   0.0    1.0  1  lcl|NCBI__GCF_000019165.1:WP_012282996.1  HM1_RS08715 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019165.1:WP_012282996.1  HM1_RS08715 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.7   0.0    7e-108    7e-108       4     340 .]      10     324 ..       7     324 .. 0.97

  Alignments for each domain:
  == domain 1  score: 346.7 bits;  conditional E-value: 7e-108
                                 TIGR00260   4 yreilevt.ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalel 71 
                                                + +l+vt ++++v+l+eg+t+l+++p+l++++ga +ly k ++++Pt++FKDrg   + ++++ka e+
  lcl|NCBI__GCF_000019165.1:WP_012282996.1  10 FKDFLPVTeKTPMVSLCEGNTPLIAAPRLSQQIGA-ELYFKYEGLNPTGSFKDRG---MVMAVAKAVEE 74 
                                               5789****99*************************.*******************...*********** PP

                                 TIGR00260  72 gnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlv 140
                                               g+++++cA++G+t+aaaa a+a++ ++k++v++P+gki+   +kl++al+++akv+ai+G+FD+a+++v
  lcl|NCBI__GCF_000019165.1:WP_012282996.1  75 GAQAIMCASTGNTSAAAA-AYAARCGIKCIVIIPEGKIA--LGKLAQALIYGAKVIAIEGNFDEALKIV 140
                                               ******************.********************..**************************** PP

                                 TIGR00260 141 keifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekkelg 208
                                               ++i+ +++++++nsvN   p+rie+qkt+afe+++qlg ++pd +++pv+ +gn++a++kGf+e k++g
  lcl|NCBI__GCF_000019165.1:WP_012282996.1 141 RDICAKHPITLVNSVN---PYRIEGQKTAAFEVCQQLG-DAPDYLAIPVGnAGNITAYWKGFVEWKQAG 205
                                               ****999999999999...*******************.****************************** PP

                                 TIGR00260 209 ....lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnledlk 273
                                                    p ++++++aegaa iv           +e++eT++tA++ignp++++ a+++ar s+g ++ + 
  lcl|NCBI__GCF_000019165.1:WP_012282996.1 206 kvdkTP-KMIGFEAEGAAAIVFDR-------VIEKPETVATAIRIGNPASWQGAVAAARDSGGFIDYV- 265
                                               ***999.**********9988544.......7999*********************************. PP

                                 TIGR00260 274 esvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkdpe 340
                                                  +deeilea+++la +eg+++ep++a+++a+++k  ++g    ++++  +++v++ltg++lkdp+
  lcl|NCBI__GCF_000019165.1:WP_012282996.1 266 ---TDEEILEAYRLLASQEGIFCEPASAASLAGVIKKRQAG---ILPEG--AKIVCVLTGHGLKDPD 324
                                               ...**************************************...88888..**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.53
//
[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