Alignments for a candidate for hom_kinase in Pyrolobus fumarii 1A

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom_kinase in Pyrolobus fumarii 1A

Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_014026250.1 PYRFU_RS03470 homoserine kinase

Query= curated2:Q9YA72
         (313 letters)



>NCBI__GCF_000223395.1:WP_014026250.1
          Length = 318

 Score =  162 bits (409), Expect = 1e-44
 Identities = 108/296 (36%), Positives = 152/296 (51%), Gaps = 13/296 (4%)

Query: 4   SRARARAYSSAANLGPGFDALAVALDAYYDEVEVRVCSG-GNSVYVDEVEGKFSSGVLQG 62
           +R R +A +S ANLGP FD  A+A+D  YD VEV V    G+ + VD       SG    
Sbjct: 5   NRVRVKAPASIANLGPLFDLAALAIDYAYDVVEVEVVEELGDGIRVDVEAAGAPSGEA-- 62

Query: 63  PNTAAEAVRGLLNMEGVEAEVGIRVYKGVPPGRGLGSSGASAAAAVAAVSHALALEVPVD 122
            NTA  A   +L   G    + IRV KGVPP  G+G SGASAAAA  AV+  L      +
Sbjct: 63  -NTAYTAAYKILEYLGETLHLRIRVVKGVPPRMGMGGSGASAAAAAYAVNLLLGEPFTKE 121

Query: 123 RLVFYAGLGERAAAGQPHFDNAAASILGGLAVVASDAAGKLRVFRVPFKAWFAVVTPMN- 181
            LV +AG  E  AAG PH+DN AAS+LGGL ++   +   +    +P   +  +  P   
Sbjct: 122 ELVKFAGEAEAVAAGTPHYDNVAASLLGGLVILLDRSRPWVARLNIPEDVYIILFIPKRE 181

Query: 182 ----PVPQGKTGVMRKVLPENVSFRDAVRNFSRAAGIVAAAVNGDLKSMGALMMSDEIVE 237
               P  +GKT VMR+VLP  +    ++    +A  +          ++ A       VE
Sbjct: 182 VVKVPPGKGKTEVMREVLPREIPLATSIAWMEKALALTLGLQLDPYTALKAANYGGP-VE 240

Query: 238 PRRRSYVPCYTQVRKAALQAGALGFSLSGAGPSMIAL---APSSEAAREIAAAMEE 290
             R   +P Y + ++ AL+AGAL F++SGAGP++ A+       E AR +A  +E+
Sbjct: 241 EARSKLIPGYAEAKREALEAGALAFNISGAGPTLFAIVREGDEDEVARRVAKILEK 296


Lambda     K      H
   0.317    0.131    0.377 

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: 200
Number of extensions: 9
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: 313
Length of database: 318
Length adjustment: 27
Effective length of query: 286
Effective length of database: 291
Effective search space:    83226
Effective search space used:    83226
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_014026250.1 PYRFU_RS03470 (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.28673.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    3.8e-56  176.1   0.0    4.4e-56  175.9   0.0    1.0  1  lcl|NCBI__GCF_000223395.1:WP_014026250.1  PYRFU_RS03470 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000223395.1:WP_014026250.1  PYRFU_RS03470 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.9   0.0   4.4e-56   4.4e-56       1     302 [.       7     316 ..       7     318 .] 0.91

  Alignments for each domain:
  == domain 1  score: 175.9 bits;  conditional E-value: 4.4e-56
                                 TIGR00191   1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakk 69 
                                               ++vk+Pas ANlgp fD   la+   ++++ +e+   e  d  ++  +e  ++ p+  ++N +y +a+k
  lcl|NCBI__GCF_000223395.1:WP_014026250.1   7 VRVKAPASIANLGPLFDLAALAIDYAYDVVEVEV-VEELGDG-IRVDVEA-AGAPSG-EANTAYTAAYK 71 
                                               69*************************9999993.3444444.8888888.889999.9********** PP

                                 TIGR00191  70 vlkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg......H 132
                                               +l+ lg+    ++++v k +p   G+G S+a+ +aa++a+n l+g++++keel+++a++ E       H
  lcl|NCBI__GCF_000223395.1:WP_014026250.1  72 ILEYLGET-LHLRIRVVKGVPPRMGMGGSGASAAAAAYAVNLLLGEPFTKEELVKFAGEAEAvaagtpH 139
                                               *******9.99********************************************************** PP

                                 TIGR00191 133 pDNvapallGGlqlavkedd.llevlkvPsgsklkvvlviPniev........sTaeaRavLPkaysrq 192
                                               +DNva++llGGl++ + +    +  l++P  ++++++l iP++ev        +T+  R+vLP++ +++
  lcl|NCBI__GCF_000223395.1:WP_014026250.1 140 YDNVAASLLGGLVILLDRSRpWVARLNIP--EDVYIILFIPKREVvkvppgkgKTEVMREVLPREIPLA 206
                                               ****************9998678889999..89**********996656665569************** PP

                                 TIGR00191 193 dlvfnlshlavlvtAlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGpti 261
                                                +++ ++++  l+  l  ++ + l a        +  R+kliP+++e k++a e+gal+  +SGaGpt+
  lcl|NCBI__GCF_000223395.1:WP_014026250.1 207 TSIAWMEKALALTLGLQLDPYTALKAANYGG-PVEEARSKLIPGYAEAKREALEAGALAFNISGAGPTL 274
                                               *******************776666655555.55778******************************** PP

                                 TIGR00191 262 lalaeeek.eekaqelleklakegieltvkvleldtdgaeve 302
                                               +a+ +e + +e a ++ + l k+  el+ +v+++d +ga+++
  lcl|NCBI__GCF_000223395.1:WP_014026250.1 275 FAIVREGDeDEVARRVAKILEKHWGELETRVVNIDREGARIT 316
                                               ********66666667777788899**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (318 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: 8.18
//
[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