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

GapMind for Amino acid biosynthesis

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

Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_012676051.1 PERMA_RS05395 homoserine kinase

Query= curated2:C0QQC5
         (300 letters)



>NCBI__GCF_000021565.1:WP_012676051.1
          Length = 300

 Score =  588 bits (1517), Expect = e-173
 Identities = 300/300 (100%), Positives = 300/300 (100%)

Query: 1   MKVLKVKVPATTANLGAGFDTLGLALTLYNEFIVEEHDGVVIETEPKNEFLEIPENNLFI 60
           MKVLKVKVPATTANLGAGFDTLGLALTLYNEFIVEEHDGVVIETEPKNEFLEIPENNLFI
Sbjct: 1   MKVLKVKVPATTANLGAGFDTLGLALTLYNEFIVEEHDGVVIETEPKNEFLEIPENNLFI 60

Query: 61  QVIKYACERRGKTFHGAKLKQINRVPVARGLGSSATAIVGAIVVSSAVSKTELTDDIFFD 120
           QVIKYACERRGKTFHGAKLKQINRVPVARGLGSSATAIVGAIVVSSAVSKTELTDDIFFD
Sbjct: 61  QVIKYACERRGKTFHGAKLKQINRVPVARGLGSSATAIVGAIVVSSAVSKTELTDDIFFD 120

Query: 121 IAYRFEPHPDNLIPAWKGGFITALKDREKTYYNSIDFPEDIKAVVVIPEFELSTEKARSV 180
           IAYRFEPHPDNLIPAWKGGFITALKDREKTYYNSIDFPEDIKAVVVIPEFELSTEKARSV
Sbjct: 121 IAYRFEPHPDNLIPAWKGGFITALKDREKTYYNSIDFPEDIKAVVVIPEFELSTEKARSV 180

Query: 181 LPERIPLRDGIFNVQRVSLFLSALQNRRYDLLRVAMEDRFHQPYRKKLIPNFDRVVQNGY 240
           LPERIPLRDGIFNVQRVSLFLSALQNRRYDLLRVAMEDRFHQPYRKKLIPNFDRVVQNGY
Sbjct: 181 LPERIPLRDGIFNVQRVSLFLSALQNRRYDLLRVAMEDRFHQPYRKKLIPNFDRVVQNGY 240

Query: 241 DAGALGVSLSGAGSAILALADRNFEEIGKAMTEGFSEAGIRSEYKILDIDREGANLEILE 300
           DAGALGVSLSGAGSAILALADRNFEEIGKAMTEGFSEAGIRSEYKILDIDREGANLEILE
Sbjct: 241 DAGALGVSLSGAGSAILALADRNFEEIGKAMTEGFSEAGIRSEYKILDIDREGANLEILE 300


Lambda     K      H
   0.320    0.138    0.392 

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: 445
Number of extensions: 13
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: 300
Length of database: 300
Length adjustment: 27
Effective length of query: 273
Effective length of database: 273
Effective search space:    74529
Effective search space used:    74529
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: 48 (23.1 bits)

Align candidate WP_012676051.1 PERMA_RS05395 (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.1530.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.7e-87  278.4   0.0    3.3e-87  278.1   0.0    1.0  1  lcl|NCBI__GCF_000021565.1:WP_012676051.1  PERMA_RS05395 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021565.1:WP_012676051.1  PERMA_RS05395 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.1   0.0   3.3e-87   3.3e-87       1     301 [.       4     296 ..       4     298 .. 0.94

  Alignments for each domain:
  == domain 1  score: 278.1 bits;  conditional E-value: 3.3e-87
                                 TIGR00191   1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakk 69 
                                               lkvkvPa++ANlg GfD+lGlal+l++e++v+e       ++ + +e+e  ++  + +++Nl+ qv+k+
  lcl|NCBI__GCF_000021565.1:WP_012676051.1   4 LKVKVPATTANLGAGFDTLGLALTLYNEFIVEE-------HDGVVIETEPKNEFLEIPENNLFIQVIKY 65 
                                               69*****************************99.......22244444444555555667********* PP

                                 TIGR00191  70 vlkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvap 138
                                                +++ gk  ++ kl+  + +p++rGLGSSa+aiv+a++   ++ +++l++    d+a   E HpDN  p
  lcl|NCBI__GCF_000021565.1:WP_012676051.1  66 ACERRGKTFHGAKLKQINRVPVARGLGSSATAIVGAIVVSSAVSKTELTDDIFFDIAYRFEPHPDNLIP 134
                                               ********************************************************************* PP

                                 TIGR00191 139 allGGlqlavkedd..llevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlv 205
                                               a  GG+ +a+k+ +     +++ P  +++k+v+viP++e+sT++aR vLP++ +++d +fn+++++++ 
  lcl|NCBI__GCF_000021565.1:WP_012676051.1 135 AWKGGFITALKDREktYYNSIDFP--EDIKAVVVIPEFELSTEKARSVLPERIPLRDGIFNVQRVSLFL 201
                                               **********99883445566666..9****************************************** PP

                                 TIGR00191 206 tAlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeekeekaq 274
                                                Al ++ + dll++am+Dr+hqpyR+kliP+++++ q   ++galg+ lSGaG++ilala+ ++ee+ +
  lcl|NCBI__GCF_000021565.1:WP_012676051.1 202 SALQNR-RYDLLRVAMEDRFHQPYRKKLIPNFDRVVQNGYDAGALGVSLSGAGSAILALADRNFEEIGK 269
                                               ******.************************************************************** PP

                                 TIGR00191 275 elleklakegieltvkvleldtdgaev 301
                                                + e ++++gi+ + k+l++d +ga++
  lcl|NCBI__GCF_000021565.1:WP_012676051.1 270 AMTEGFSEAGIRSEYKILDIDREGANL 296
                                               ************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (300 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: 10.03
//
[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