Alignments for a candidate for thrB in Trichormus variabilis ATCC 29413

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Trichormus variabilis ATCC 29413

Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_011319547.1 AVA_RS14135 homoserine kinase

Query= curated2:B2J7E8
         (304 letters)



>NCBI__GCF_000204075.1:WP_011319547.1
          Length = 302

 Score =  479 bits (1232), Expect = e-140
 Identities = 240/301 (79%), Positives = 265/301 (88%)

Query: 1   MSVVSAITVTVPATTANLGPGFDCIGAALKLYNEFRFTRLEEGGLIIHVSGTEAERVQTD 60
           MSVVS++TV VP TTANLGPGFDCIGAAL +YN+F+FTRLE   LII  +G EAERV TD
Sbjct: 1   MSVVSSVTVKVPGTTANLGPGFDCIGAALTIYNQFQFTRLETSELIIQATGAEAERVPTD 60

Query: 61  ESNLLYQAFVKFYQHIEQTPPTVKIEIKLGVPLARGLGSSATAIVGGLVAANQLEGATLS 120
           ESNLLYQAFVK YQ+I+QTPP VK+EI+LGVPLARGLGSSATAIVGGLVAAN+L G  LS
Sbjct: 61  ESNLLYQAFVKLYQYIDQTPPGVKVEIELGVPLARGLGSSATAIVGGLVAANRLAGEPLS 120

Query: 121 QSQVMELAIAMEGHPDNVVPALLGGCRLAATSGTAWEICDVPWHKDVVPVVAIPNFELST 180
           Q+QVMELAIA+EGHPDNVVPAL+GGCRLAAT    WEICDVPWH D+VPV+AIP+FELST
Sbjct: 121 QAQVMELAIAIEGHPDNVVPALVGGCRLAATGAMGWEICDVPWHGDIVPVLAIPDFELST 180

Query: 181 SEARGVLPTEVSRADAIFNTAHLGLLLRGLETGNGQWLKTALQDKLHQPYRKALIPSYDA 240
           SEAR VLPTE SRADAIFNTAHLGLLLRGL+TG G+WL+ ALQDKLHQPYR+ALIP YDA
Sbjct: 181 SEARRVLPTEYSRADAIFNTAHLGLLLRGLQTGKGEWLRAALQDKLHQPYRQALIPGYDA 240

Query: 241 VNIAAVSAGAYGMVISGAGPTLLALADQLHSEAVEAAMLAAWQEEGITAEVRSLSLDTQG 300
           VN AAV+AGAYGMVISGAGPTLLALAD  H+ AV AAM  AW+E GI A VRSL+LDT G
Sbjct: 241 VNTAAVAAGAYGMVISGAGPTLLALADVSHAAAVAAAMSTAWREAGIKAVVRSLALDTHG 300

Query: 301 A 301
           A
Sbjct: 301 A 301


Lambda     K      H
   0.317    0.132    0.380 

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: 363
Number of extensions: 8
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: 304
Length of database: 302
Length adjustment: 27
Effective length of query: 277
Effective length of database: 275
Effective search space:    76175
Effective search space used:    76175
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: 48 (23.1 bits)

Align candidate WP_011319547.1 AVA_RS14135 (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.19863.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.1e-97  312.5   0.0    1.2e-97  312.3   0.0    1.0  1  lcl|NCBI__GCF_000204075.1:WP_011319547.1  AVA_RS14135 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204075.1:WP_011319547.1  AVA_RS14135 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.3   0.0   1.2e-97   1.2e-97       1     299 [.       7     301 ..       7     302 .] 0.98

  Alignments for each domain:
  == domain 1  score: 312.3 bits;  conditional E-value: 1.2e-97
                                 TIGR00191   1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakk 69 
                                               ++vkvP+++ANlgpGfD++G+al+ ++++  t     e+ +  ++a+g ++e++p++ + Nl+yq+++k
  lcl|NCBI__GCF_000204075.1:WP_011319547.1   7 VTVKVPGTTANLGPGFDCIGAALTIYNQFQFTR---LETSELIIQATGAEAERVPTD-ESNLLYQAFVK 71 
                                               68*****************************99...888888899************.*********** PP

                                 TIGR00191  70 vlkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvap 138
                                               +++  ++ +++vk+++e  +pl+rGLGSSa+aiv++++aan lag++ls++++++la+++EgHpDNv p
  lcl|NCBI__GCF_000204075.1:WP_011319547.1  72 LYQYIDQTPPGVKVEIELGVPLARGLGSSATAIVGGLVAANRLAGEPLSQAQVMELAIAIEGHPDNVVP 140
                                               ********************************************************************* PP

                                 TIGR00191 139 allGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtA 207
                                               al+GG+ la +     e+ +vP + ++  vl+iP +e+sT eaR vLP +ysr+d++fn++hl++l   
  lcl|NCBI__GCF_000204075.1:WP_011319547.1 141 ALVGGCRLAATGAMGWEICDVPWHGDIVPVLAIPDFELSTSEARRVLPTEYSRADAIFNTAHLGLLLRG 209
                                               **********99999****************************************************** PP

                                 TIGR00191 208 lvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek.eekaqe 275
                                               l ++ k ++l+ a++D++hqpyR+ liP+++++++aa ++ga+g+++SGaGpt+lala+ ++ +  a+ 
  lcl|NCBI__GCF_000204075.1:WP_011319547.1 210 LQTG-KGEWLRAALQDKLHQPYRQALIPGYDAVNTAAVAAGAYGMVISGAGPTLLALADVSHaAAVAAA 277
                                               ****.*******************************************************997888888 PP

                                 TIGR00191 276 lleklakegieltvkvleldtdga 299
                                               +   + ++gi++ v+ l ldt+ga
  lcl|NCBI__GCF_000204075.1:WP_011319547.1 278 MSTAWREAGIKAVVRSLALDTHGA 301
                                               889999***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (302 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.87
//
[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