Alignments for a candidate for hom_kinase in Chlorobaculum parvum NCIB 8327

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom_kinase in Chlorobaculum parvum NCIB 8327

Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_012503135.1 CPAR_RS09705 homoserine kinase

Query= reanno::Cola:Echvi_2001
         (311 letters)



>NCBI__GCF_000020505.1:WP_012503135.1
          Length = 324

 Score =  315 bits (808), Expect = 7e-91
 Identities = 168/321 (52%), Positives = 216/321 (67%), Gaps = 12/321 (3%)

Query: 1   MKKVTAFAPATVANVSCGFDILGFAVEEMGDKVTVSLADEPG----VRVVRIEGDGGRLP 56
           MK VT FA ATV NV+CGFD+LGFA+ E GD+V ++L DEP     V +  I GDGG LP
Sbjct: 1   MKTVTGFASATVGNVACGFDVLGFAITEPGDEVILTLHDEPRSGSPVTITSISGDGGALP 60

Query: 57  YEVDKNTCGVALKAFLA------AIDYKGGLEVELYKGLPLGSGMGSSAASSVAALEAAN 110
            +  KNT    +  FL        ID+KG +++EL K LPL SGMGSSAAS+ AAL AAN
Sbjct: 61  LDPKKNTSSFVVLKFLEYIRSTKGIDFKGHIDLELKKHLPLSSGMGSSAASAAAALVAAN 120

Query: 111 QLLGNPLDKKALLPFAMKAEGVACGAEHADNVAPSLLGGFVLIRSYHPLDVTKLHVPKGL 170
           +LLG+P  K  L+ FA++ E VACG+ HADN AP++LG F+LIRSYHPLD+  +  PK L
Sbjct: 121 ELLGSPCSKMELVHFAIEGERVACGSAHADNAAPAMLGNFILIRSYHPLDLITIRPPKDL 180

Query: 171 YCALVHPHLELNTADSRSVLRQQVPLKDAITQSGNIAGLVAGLYQEDMGLISRSLQDVIA 230
           +C LVHPH E+ T+ +RSVL + +PL  AI Q GN+  LV+GL  ED  LI R+L DV+A
Sbjct: 181 FCTLVHPHTEVKTSFARSVLPKSIPLSMAIQQWGNVGALVSGLLMEDYDLIGRALVDVVA 240

Query: 231 EPSRSVLIPGFDEIKSAIKEVGALGVGISGSGPTTFILAPSREVAERASEICQEVF--DK 288
           EP R+ LIPGF+E+K A  + GALG  I+GSGP+ F  + SR  AE      QE F   K
Sbjct: 241 EPKRAPLIPGFNEVKQAALDAGALGCSIAGSGPSVFAFSSSRATAETVGAAMQETFKLSK 300

Query: 289 IGLEVDLYVSAVNTKGTYVIN 309
             L+ D++VS V ++G  VI+
Sbjct: 301 AELDSDMWVSPVCSQGARVIS 321


Lambda     K      H
   0.317    0.136    0.383 

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: 266
Number of extensions: 15
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: 311
Length of database: 324
Length adjustment: 27
Effective length of query: 284
Effective length of database: 297
Effective search space:    84348
Effective search space used:    84348
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_012503135.1 CPAR_RS09705 (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.8389.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
      1e-62  197.7   0.0    1.3e-62  197.3   0.0    1.0  1  lcl|NCBI__GCF_000020505.1:WP_012503135.1  CPAR_RS09705 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020505.1:WP_012503135.1  CPAR_RS09705 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.3   0.0   1.3e-62   1.3e-62       6     283 ..       9     299 ..       5     321 .. 0.83

  Alignments for each domain:
  == domain 1  score: 197.3 bits;  conditional E-value: 1.3e-62
                                 TIGR00191   6 PassANlgpGfDvlGlalslv.lellvtedvaqeskdk.sleaegegvekipkesdkNliyqvakkvlk 72 
                                                a+  N++ GfDvlG a+++  +e+++t + +  s +   +++ + +   +p++++kN    v++k+l+
  lcl|NCBI__GCF_000020505.1:WP_012503135.1   9 SATVGNVACGFDVLGFAITEPgDEVILTLHDEPRSGSPvTITSISGDGGALPLDPKKNTSSFVVLKFLE 77 
                                               58999*************9882455555533333333367888888889*********66666555555 PP

                                 TIGR00191  73 ....klgkr.vkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg..... 131
                                                   + g++    + l+++k++pl++G+GSSaa+ +aa++aanel+g ++sk+el+++a++ E+     
  lcl|NCBI__GCF_000020505.1:WP_012503135.1  78 yirsTKGIDfKGHIDLELKKHLPLSSGMGSSAASAAAALVAANELLGSPCSKMELVHFAIEGERvacgs 146
                                               111056666555689****************************************************** PP

                                 TIGR00191 132 .HpDNvapallGGlqlavkedd.llevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnl 198
                                                H+DN+apa+lG + l  +++   l++++ P  ++l + lv P+ ev+T  aR vLPk+ +++ ++++ 
  lcl|NCBI__GCF_000020505.1:WP_012503135.1 147 aHADNAAPAMLGNFILIRSYHPlDLITIRPP--KDLFCTLVHPHTEVKTSFARSVLPKSIPLSMAIQQW 213
                                               ****************999998445566666..89********************************** PP

                                 TIGR00191 199 shlavlvtAlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaee 267
                                                +++ lv  l ++   dl+  a+ D+v++p+R+ liP+++e+kqaa ++galg  + G+Gp+++a+++ 
  lcl|NCBI__GCF_000020505.1:WP_012503135.1 214 GNVGALVSGLLME-DYDLIGRALVDVVAEPKRAPLIPGFNEVKQAALDAGALGCSIAGSGPSVFAFSSS 281
                                               *************.8999999*********************************************999 PP

                                 TIGR00191 268 ek.eeka.qelleklake 283
                                                  +e + + + e+++  
  lcl|NCBI__GCF_000020505.1:WP_012503135.1 282 RAtAETVgAAMQETFKLS 299
                                               885443303333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (324 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.91
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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