Alignments for a candidate for asp-kinase in Desulfotomaculum ruminis DSM 2154

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Desulfotomaculum ruminis DSM 2154

Align aspartate kinase 1; EC 2.7.2.4 (characterized)
to candidate WP_013841940.1 DESRU_RS09750 aspartate kinase

Query= CharProtDB::CH_090816
         (404 letters)



>NCBI__GCF_000215085.1:WP_013841940.1
          Length = 411

 Score =  409 bits (1051), Expect = e-119
 Identities = 214/404 (52%), Positives = 283/404 (70%), Gaps = 2/404 (0%)

Query: 1   MKIIVQKFGGTSVKDDKGRKLALGHIKEAISEGYKVVVVVSAMGRKGDPYATDSLLGLLY 60
           M+ +VQKFGGTS+   + R      I EA+ EGY  VVVVSA+GR G+PYATD+LL    
Sbjct: 1   MRFLVQKFGGTSLLTQELRDRVATRIAEAVDEGYAPVVVVSAIGRAGEPYATDTLLNFAL 60

Query: 61  GDQSAISPREQDLLLSCGETISSVVFTSMLLDNGVKAAALTGAQAGFLTNDQHTNAKIIE 120
                +  RE D+L+SCGE IS VV  + L   G +A  LTGAQAG +T+  H +A+I+ 
Sbjct: 61  AAGRDLPARELDILMSCGEVISGVVMVNTLQRMGRQAVFLTGAQAGIITDHNHNDARILR 120

Query: 121 MKPERLFSVLANHDAVVVAGFQGATEKGDTTTIGRGGSDTSAAALGAAVDAEYIDIFTDV 180
           + P+ + S       V+VAGFQG +E+G+ TT+GRGGSDT+AAALG A++AE IDIFTDV
Sbjct: 121 VDPKNVISQAKEGKIVIVAGFQGISEEGEITTLGRGGSDTTAAALGVALNAECIDIFTDV 180

Query: 181 EGVMTADPRVVENAKPLPVVTYTEICNLAYQGAKVISPRAVEIAMQAKVPIRVRSTYSND 240
           EG+MTADPR+VE+A+ L  VTY EIC LA++GAKVI PRAVEIAMQ  +PIRVRST++N 
Sbjct: 181 EGIMTADPRIVEDARILDNVTYNEICQLAHEGAKVIHPRAVEIAMQKNIPIRVRSTFTNS 240

Query: 241 KGTLVTSHHSSKVGSDV-FERLITGIAHVKDVTQFKVP-AKIGQYNVQTEVFKAMANAGI 298
            GTLV SH+      D+  +RL +G+AH+  VTQFK+  +++   N    +FKA+A A I
Sbjct: 241 PGTLVASHNQVYGTIDITTDRLASGVAHIAGVTQFKLTVSEVNIDNPALRIFKALALADI 300

Query: 299 SVDFFNITPSEIVYTVAGNKTETAQRILMDMGYDPMVTRNCAKVSAVGAGIMGVPGVTSK 358
           S+DF N++P  I++TV     + A  +L ++G  P +  NCAK+S VGAGI GVPGV S 
Sbjct: 301 SIDFINVSPELIMFTVKDEVAKKATAVLQNLGIHPQIRPNCAKISTVGAGIHGVPGVMSH 360

Query: 359 IVSALSEKEIPILQSADSHTTIWVLVHEADMVPAVNALHEEFEL 402
           IV AL+E+++ ILQS+DSHTTIWVLV +  M  A+ ALH +FEL
Sbjct: 361 IVEALAEEQVEILQSSDSHTTIWVLVQQDQMHKAIQALHRKFEL 404


Lambda     K      H
   0.316    0.131    0.364 

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: 436
Number of extensions: 16
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: 404
Length of database: 411
Length adjustment: 31
Effective length of query: 373
Effective length of database: 380
Effective search space:   141740
Effective search space used:   141740
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: 50 (23.9 bits)

Align candidate WP_013841940.1 DESRU_RS09750 (aspartate kinase)
to HMM TIGR00656 (aspartate kinase, monofunctional class (EC 2.7.2.4))

# 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/TIGR00656.hmm
# target sequence database:        /tmp/gapView.10823.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00656  [M=407]
Accession:   TIGR00656
Description: asp_kin_monofn: aspartate kinase, monofunctional class
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-125  405.3   7.5   1.7e-125  405.1   7.5    1.0  1  lcl|NCBI__GCF_000215085.1:WP_013841940.1  DESRU_RS09750 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000215085.1:WP_013841940.1  DESRU_RS09750 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.1   7.5  1.7e-125  1.7e-125       2     406 ..       2     404 ..       1     405 [. 0.97

  Alignments for each domain:
  == domain 1  score: 405.1 bits;  conditional E-value: 1.7e-125
                                 TIGR00656   2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 
                                                  VqKFGGts+  +e + ++a ++ +++ eg+ +vVVvSA+++ ++ +++ + ll+++ a   +   r
  lcl|NCBI__GCF_000215085.1:WP_013841940.1   2 RFLVQKFGGTSLLTQELRDRVATRIAEAVDEGYAPVVVVSAIGRAGEPYATDT-LLNFALAAGRDLPAR 69 
                                               568**************************************************.9****999999999* PP

                                 TIGR00656  71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139
                                               e d l+s+GE +s +++++ l++ g +a+ l+g++agi+Td ++++A+i ++++ ++++++ +eg+iv+
  lcl|NCBI__GCF_000215085.1:WP_013841940.1  70 ELDILMSCGEVISGVVMVNTLQRMGRQAVFLTGAQAGIITDHNHNDARILRVDP-KNVISQAKEGKIVI 137
                                               ******************************************************.99999********* PP

                                 TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208
                                               vaGF+G  eeGeiTtLGRGGSD+tAa+l+ al+A+ ++i+TDVeG++t+DPr+ve+a+ +d+++y+E++
  lcl|NCBI__GCF_000215085.1:WP_013841940.1 138 VAGFQGISEEGEITTLGRGGSDTTAAALGVALNAECIDIFTDVEGIMTADPRIVEDARILDNVTYNEIC 206
                                               ********************************************************************* PP

                                 TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitn........kkensslvkaialeknvarl 269
                                               +lA+ Gakv+hpra+e+a+++++pi+vrs++ ++ gTl+ +        +  +++l +++a+  +v+++
  lcl|NCBI__GCF_000215085.1:WP_013841940.1 207 QLAHEGAKVIHPRAVEIAMQKNIPIRVRSTFTNSPGTLVAShnqvygtiDITTDRLASGVAHIAGVTQF 275
                                               ****************************************988888877777779************** PP

                                 TIGR00656 270 tvegegmlgkrgilaeifkaLaeeeinvdlisqtesetsislvvdeedvdeakkaLkeesgaaelesle 338
                                               +++  + ++  + + +ifkaLa ++i++d+i+ ++    i ++v++e +++a+++L++  +  +     
  lcl|NCBI__GCF_000215085.1:WP_013841940.1 276 KLT-VSEVNIDNPALRIFKALALADISIDFINVSP--ELIMFTVKDEVAKKATAVLQNLGIHPQ----- 336
                                               **9.88889999999********************..99*******************986666..... PP

                                 TIGR00656 339 veedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                               ++ ++a++s vgag+ ++pGv+s+i++al+e++++il++s+s+t+i+vlv++ +++ka+++lh+k+e+
  lcl|NCBI__GCF_000215085.1:WP_013841940.1 337 IRPNCAKISTVGAGIHGVPGVMSHIVEALAEEQVEILQSSDSHTTIWVLVQQDQMHKAIQALHRKFEL 404
                                               7889**************************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (411 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: 9.44
//
[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