Alignments for a candidate for thrB in Carboxydothermus pertinax Ug1

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Carboxydothermus pertinax Ug1

Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_075858772.1 cpu_RS04100 homoserine kinase

Query= curated2:Q3AAV5
         (304 letters)



>NCBI__GCF_001950255.1:WP_075858772.1
          Length = 304

 Score =  543 bits (1398), Expect = e-159
 Identities = 274/304 (90%), Positives = 287/304 (94%)

Query: 1   MVCVLIPATSANLGPGFDAVGMALSFYNEVSLGPSPKELEIEVFGDGAELISRDKNNLVY 60
           MV VLIPATSANLGPGFDAVGMALSFYNEV L PSPKELEI+V+GDG+E+I +D+NNLVY
Sbjct: 1   MVRVLIPATSANLGPGFDAVGMALSFYNEVCLKPSPKELEIDVWGDGSEIIPKDRNNLVY 60

Query: 61  VAITKIFERLGKTPRNLKLTLKNRVPLARGLGSSAAAIVGGLVAANAYLGNPLPKDELLR 120
           +A+TK+FE LGK PRNLKL+LKNRVP ARGLGSSAAAIVGGLVAANAYLGNPLP DELLR
Sbjct: 61  IAVTKVFESLGKIPRNLKLSLKNRVPFARGLGSSAAAIVGGLVAANAYLGNPLPTDELLR 120

Query: 121 LATELEGHPDNVAPALLGGVVVSGFDRDKVKYLKLPVPEVEVVVAIPKFQLKTADSRQIL 180
           LATELEGHPDNVAPALLGGVVVSGFDRDKVKYLKLPVPEVEVVVAIPKFQLKT DSRQIL
Sbjct: 121 LATELEGHPDNVAPALLGGVVVSGFDRDKVKYLKLPVPEVEVVVAIPKFQLKTVDSRQIL 180

Query: 181 PAEIPFSQAVLNVNRVSFLIAAFCLKKYEYLQIGMEDYLHQPYRSQLIPGFYQVVEEAKK 240
           P EIPFSQAVLNVNRVSFLIAAFCLKKYEYLQIGMEDYLHQPYRSQLIPGFYQV+EEAKK
Sbjct: 181 PVEIPFSQAVLNVNRVSFLIAAFCLKKYEYLQIGMEDYLHQPYRSQLIPGFYQVMEEAKK 240

Query: 241 AGAYGVALSGSGPTVIALAREGKAVGRAIEETFLNFGVEAEIIYTRPEERGAIDLINYKG 300
           AGAYGVALSGSGPTVIA ARE +AVGRAI E FLNF VEAEIIYTRPE RGAIDLI +KG
Sbjct: 241 AGAYGVALSGSGPTVIAFARESEAVGRAIREAFLNFNVEAEIIYTRPENRGAIDLIMHKG 300

Query: 301 EGDC 304
           EGDC
Sbjct: 301 EGDC 304


Lambda     K      H
   0.318    0.139    0.396 

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: 420
Number of extensions: 7
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: 304
Length adjustment: 27
Effective length of query: 277
Effective length of database: 277
Effective search space:    76729
Effective search space used:    76729
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_075858772.1 cpu_RS04100 (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.34822.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    3.9e-90  287.7   0.0    4.7e-90  287.5   0.0    1.0  1  NCBI__GCF_001950255.1:WP_075858772.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001950255.1:WP_075858772.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.5   0.0   4.7e-90   4.7e-90       1     294 [.       2     287 ..       2     294 .. 0.93

  Alignments for each domain:
  == domain 1  score: 287.5 bits;  conditional E-value: 4.7e-90
                             TIGR00191   1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakkvlkk 73 
                                           ++v +Pa+sANlgpGfD +G+als ++e+ +++    + k+ ++   g+g e ipk+ ++Nl+y +++kv+++
  NCBI__GCF_001950255.1:WP_075858772.1   2 VRVLIPATSANLGPGFDAVGMALSFYNEVCLKP----SPKELEIDVWGDGSEIIPKD-RNNLVYIAVTKVFES 69 
                                           6899*****************************....88888999************.*************** PP

                             TIGR00191  74 lgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvapallGGlql 146
                                           lgk +  +kl +++ +p +rGLGSSaaaiv++++aan+ +g++l + ell la++lEgHpDNvapallGG+++
  NCBI__GCF_001950255.1:WP_075858772.1  70 LGKIPRNLKLSLKNRVPFARGLGSSAAAIVGGLVAANAYLGNPLPTDELLRLATELEGHPDNVAPALLGGVVV 142
                                           **********************************************************************999 PP

                             TIGR00191 147 avkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtAlvskdkadllai 219
                                           +  + d+++ lk+P  ++++vv++iP+++++T ++R++LP + + +++v n+++++ l++A+  k k ++l+i
  NCBI__GCF_001950255.1:WP_075858772.1 143 SGFDRDKVKYLKLPV-PEVEVVVAIPKFQLKTVDSRQILPVEIPFSQAVLNVNRVSFLIAAFCLK-KYEYLQI 213
                                           86655559******6.9************************************************.******* PP

                             TIGR00191 220 amkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeekeekaqelleklakegieltvkvl 292
                                            m+D +hqpyR++liP++ ++ ++ak++ga+g++lSG+Gpt++a+a+e++      + e + + + e+++   
  NCBI__GCF_001950255.1:WP_075858772.1 214 GMEDYLHQPYRSQLIPGFYQVMEEAKKAGAYGVALSGSGPTVIAFARESE-AVGRAIREAFLNFNVEAEIIYT 285
                                           ************************************************99.4444455555555555555555 PP

                             TIGR00191 293 el 294
                                           ++
  NCBI__GCF_001950255.1:WP_075858772.1 286 RP 287
                                           55 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (304 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: 14.45
//
[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 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