Alignments for a candidate for thrB in Nitratiruptor tergarcus DSM 16512

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Nitratiruptor tergarcus DSM 16512

Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_084275346.1 B8779_RS04430 homoserine kinase

Query= curated2:A8EWD5
         (293 letters)



>NCBI__GCF_900176045.1:WP_084275346.1
          Length = 293

 Score =  362 bits (928), Expect = e-105
 Identities = 183/292 (62%), Positives = 229/292 (78%)

Query: 1   MKVSVPATSANLGPGFDCLGLAVSLKNQVIIRPSKFHSVSLKGEGANNPALKDNNMFISI 60
           M +SVPATSANLGPGFD LG+A+ L+N+V I+ S+F S+S+KGEG+ +  LK NN+FISI
Sbjct: 1   MFISVPATSANLGPGFDTLGVALDLRNEVSIKRSRFFSISIKGEGSKSFRLKGNNIFISI 60

Query: 61  FNDFYQNLSHKKRFFRFEFQNEIPLSRGLGSSSAVIVSAIASAYAIEGIKLERDKLLNLA 120
           FN+ Y+NL  KK  FRF F N+IPLSRGLGSSSAVIVSAIA+AYA+ GI L   +LL+LA
Sbjct: 61  FNEHYRNLVDKKEKFRFTFYNKIPLSRGLGSSSAVIVSAIAAAYAMAGIPLSSQRLLSLA 120

Query: 121 LAYESHPDNITPAVMGGFNVACVQENEVKYINKPIPKSLKAVIVVPNRAISTAMSRKTLP 180
           L+YE HPDNITPAVMGGFN A V+ + V  I K +P++LKAVIV+PNR IST+ SR  LP
Sbjct: 121 LSYEPHPDNITPAVMGGFNAAVVENSRVYSIKKEMPQNLKAVIVIPNRPISTSHSRTKLP 180

Query: 181 FKYSKEDTIFNISHSSLLTAAFMSENWEMLKYASNDQVHQKYRMKQMPELFEVQKTALKE 240
            K S  D +FNISHSSLLTAA  +E W++L+ AS D++HQ  RM+ MPELFEVQK AL+ 
Sbjct: 181 RKLSLSDAVFNISHSSLLTAAIFNEEWDLLRIASKDKLHQDIRMRAMPELFEVQKLALQN 240

Query: 241 GALMSTLSGSGSTLFSMAYTDDSRNLEKALKNKFPHFRVFVVDFDNTGVKIE 292
           GALMSTLSGSGST F+M Y +D++ L   L+N+F  F + ++DFDN G+ IE
Sbjct: 241 GALMSTLSGSGSTFFNMVYAEDAKPLAYKLQNRFSKFAIKILDFDNQGIIIE 292


Lambda     K      H
   0.318    0.132    0.371 

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: 282
Number of extensions: 9
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: 293
Length of database: 293
Length adjustment: 26
Effective length of query: 267
Effective length of database: 267
Effective search space:    71289
Effective search space used:    71289
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: 48 (23.1 bits)

Align candidate WP_084275346.1 B8779_RS04430 (homoserine kinase)
to HMM TIGR00191 (thrB: homoserine kinase (EC 2.7.1.39))

# 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/TIGR00191.hmm
# target sequence database:        /tmp/gapView.25764.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00191  [M=304]
Accession:   TIGR00191
Description: thrB: homoserine kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    7.6e-87  276.9   0.0    8.4e-87  276.8   0.0    1.0  1  lcl|NCBI__GCF_900176045.1:WP_084275346.1  B8779_RS04430 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900176045.1:WP_084275346.1  B8779_RS04430 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.8   0.0   8.4e-87   8.4e-87       3     302 ..       3     292 ..       1     293 [] 0.95

  Alignments for each domain:
  == domain 1  score: 276.8 bits;  conditional E-value: 8.4e-87
                                 TIGR00191   3 vkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakkvl 71 
                                               ++vPa+sANlgpGfD+lG+al l++e+ ++     + + + + ++geg +   ++  +N++  ++++ +
  lcl|NCBI__GCF_900176045.1:WP_084275346.1   3 ISVPATSANLGPGFDTLGVALDLRNEVSIKR----SRFFS-ISIKGEGSKSFRLK-GNNIFISIFNEHY 65 
                                               89***************************99....66665.99999998888888.9************ PP

                                 TIGR00191  72 kklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvapal 140
                                               ++l  + + +++t  ++ipl+rGLGSS+a iv+a++aa ++ag +ls ++ll lal +E HpDN++pa+
  lcl|NCBI__GCF_900176045.1:WP_084275346.1  66 RNLVDKKEKFRFTFYNKIPLSRGLGSSSAVIVSAIAAAYAMAGIPLSSQRLLSLALSYEPHPDNITPAV 134
                                               **99999************************************************************** PP

                                 TIGR00191 141 lGGlqlavkedd..llevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtA 207
                                               +GG+++av e+    +++ ++P  ++lk+v+viPn+ +sT  +R  LP++ s++d+vfn sh+++l++A
  lcl|NCBI__GCF_900176045.1:WP_084275346.1 135 MGGFNAAVVENSrvYSIKKEMP--QNLKAVIVIPNRPISTSHSRTKLPRKLSLSDAVFNISHSSLLTAA 201
                                               ***********96667777788..8******************************************** PP

                                 TIGR00191 208 lvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeekeekaqel 276
                                               + ++ ++dll+ia+kD++hq  R++ +Pel+e+++ a ++gal++tlSG+G+t++++ + e+   a+ l
  lcl|NCBI__GCF_900176045.1:WP_084275346.1 202 IFNE-EWDLLRIASKDKLHQDIRMRAMPELFEVQKLALQNGALMSTLSGSGSTFFNMVYAED---AKPL 266
                                               ****.*******************************************************99...7788 PP

                                 TIGR00191 277 leklakegieltvkvleldtdgaeve 302
                                                 kl++ + ++ +k+l++d++g  +e
  lcl|NCBI__GCF_900176045.1:WP_084275346.1 267 AYKLQNRFSKFAIKILDFDNQGIIIE 292
                                               88999999*************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (293 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: 00:00:00.00
# Mc/sec: 10.38
//
[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