Alignments for a candidate for hom_kinase in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom_kinase in Echinicola vietnamensis KMM 6221, DSM 17526

Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate Echvi_2001 Echvi_2001 homoserine kinase

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



>FitnessBrowser__Cola:Echvi_2001
          Length = 311

 Score =  605 bits (1561), Expect = e-178
 Identities = 311/311 (100%), Positives = 311/311 (100%)

Query: 1   MKKVTAFAPATVANVSCGFDILGFAVEEMGDKVTVSLADEPGVRVVRIEGDGGRLPYEVD 60
           MKKVTAFAPATVANVSCGFDILGFAVEEMGDKVTVSLADEPGVRVVRIEGDGGRLPYEVD
Sbjct: 1   MKKVTAFAPATVANVSCGFDILGFAVEEMGDKVTVSLADEPGVRVVRIEGDGGRLPYEVD 60

Query: 61  KNTCGVALKAFLAAIDYKGGLEVELYKGLPLGSGMGSSAASSVAALEAANQLLGNPLDKK 120
           KNTCGVALKAFLAAIDYKGGLEVELYKGLPLGSGMGSSAASSVAALEAANQLLGNPLDKK
Sbjct: 61  KNTCGVALKAFLAAIDYKGGLEVELYKGLPLGSGMGSSAASSVAALEAANQLLGNPLDKK 120

Query: 121 ALLPFAMKAEGVACGAEHADNVAPSLLGGFVLIRSYHPLDVTKLHVPKGLYCALVHPHLE 180
           ALLPFAMKAEGVACGAEHADNVAPSLLGGFVLIRSYHPLDVTKLHVPKGLYCALVHPHLE
Sbjct: 121 ALLPFAMKAEGVACGAEHADNVAPSLLGGFVLIRSYHPLDVTKLHVPKGLYCALVHPHLE 180

Query: 181 LNTADSRSVLRQQVPLKDAITQSGNIAGLVAGLYQEDMGLISRSLQDVIAEPSRSVLIPG 240
           LNTADSRSVLRQQVPLKDAITQSGNIAGLVAGLYQEDMGLISRSLQDVIAEPSRSVLIPG
Sbjct: 181 LNTADSRSVLRQQVPLKDAITQSGNIAGLVAGLYQEDMGLISRSLQDVIAEPSRSVLIPG 240

Query: 241 FDEIKSAIKEVGALGVGISGSGPTTFILAPSREVAERASEICQEVFDKIGLEVDLYVSAV 300
           FDEIKSAIKEVGALGVGISGSGPTTFILAPSREVAERASEICQEVFDKIGLEVDLYVSAV
Sbjct: 241 FDEIKSAIKEVGALGVGISGSGPTTFILAPSREVAERASEICQEVFDKIGLEVDLYVSAV 300

Query: 301 NTKGTYVINKA 311
           NTKGTYVINKA
Sbjct: 301 NTKGTYVINKA 311


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: 468
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: 311
Length of database: 311
Length adjustment: 27
Effective length of query: 284
Effective length of database: 284
Effective search space:    80656
Effective search space used:    80656
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 Echvi_2001 Echvi_2001 (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.7645.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-73  232.0   0.0    4.5e-73  231.7   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2001  Echvi_2001 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2001  Echvi_2001 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.7   0.0   4.5e-73   4.5e-73       4     302 ..       7     308 ..       4     310 .. 0.92

  Alignments for each domain:
  == domain 1  score: 231.7 bits;  conditional E-value: 4.5e-73
                            TIGR00191   4 kvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakkvlkklgkr 77 
                                           +Pa+ AN++ GfD+lG a++++ + + +   a e     +++eg+g  ++p e dkN    ++k +l   + +
  lcl|FitnessBrowser__Cola:Echvi_2001   7 FAPATVANVSCGFDILGFAVEEMGDKVTVS-LADEPGVRVVRIEGDG-GRLPYEVDKNTCGVALKAFLAAIDYK 78 
                                          58*******************997665555.3455555569999999.99************************ PP

                            TIGR00191  78 vkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg......HpDNvapallGGlq 145
                                            ++++++ k +plg+G+GSSaa++vaa+ aan+l+g++l+k+ ll +a+  Eg      H+DNvap+llGG++
  lcl|FitnessBrowser__Cola:Echvi_2001  79 -GGLEVELYKGLPLGSGMGSSAASSVAALEAANQLLGNPLDKKALLPFAMKAEGvacgaeHADNVAPSLLGGFV 151
                                          .************************************************************************* PP

                            TIGR00191 146 lavkedd.llevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtAlvskdkadlla 218
                                          l  +++   + +l+vP  + l++ lv P++e++Ta++R vL ++++++d++ ++ + a+lv+ l+++    l+ 
  lcl|FitnessBrowser__Cola:Echvi_2001 152 LIRSYHPlDVTKLHVP--KGLYCALVHPHLELNTADSRSVLRQQVPLKDAITQSGNIAGLVAGLYQE-DMGLIS 222
                                          *999988567889999..89***********************************************.788999 PP

                            TIGR00191 219 iamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek.eekaqelleklake.gieltvk 290
                                            ++D++++p R+ liP+++eik a ke galg+++SG+Gpt + la   + +e+a+e+ +++ ++ g e+ + 
  lcl|FitnessBrowser__Cola:Echvi_2001 223 RSLQDVIAEPSRSVLIPGFDEIKSAIKEVGALGVGISGSGPTTFILAPSREvAERASEICQEVFDKiGLEVDLY 296
                                          99***********************************************9999999999887655426788899 PP

                            TIGR00191 291 vleldtdgaeve 302
                                          v  ++t+g+ v+
  lcl|FitnessBrowser__Cola:Echvi_2001 297 VSAVNTKGTYVI 308
                                          999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (311 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: 10.44
//
[ok]

This GapMind analysis is from Apr 09 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