Alignments for a candidate for asp-kinase in Clostridium kluyveri DSM 555

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Clostridium kluyveri DSM 555

Align aspartate kinase 1; EC 2.7.2.4 (characterized)
to candidate WP_012101829.1 CKL_RS07090 aspartate kinase

Query= CharProtDB::CH_090816
         (404 letters)



>NCBI__GCF_000016505.1:WP_012101829.1
          Length = 399

 Score =  335 bits (858), Expect = 2e-96
 Identities = 179/406 (44%), Positives = 265/406 (65%), Gaps = 14/406 (3%)

Query: 1   MKIIVQKFGGTSVKDDKGRKLALGHIKEAISEGYKVVVVVSAMGRKGDPYATDSLLGLLY 60
           MKI++QKFGGTSV   + R+  +  I +A  +G+  VVVVSAMGRKG PYATD+LL L+ 
Sbjct: 1   MKIVIQKFGGTSVSTHERREQVVNKILKAKDKGFCPVVVVSAMGRKGQPYATDTLLSLIK 60

Query: 61  GDQSAISPREQDLLLSCGETISSVVFTSMLLDNGVKAAALTGAQAGFLTNDQHTNAKIIE 120
            D    +P   DLL+SCGE IS+VV    LL  GVKA  LTG QAG +T+D + NA I++
Sbjct: 61  EDFKIKNPLGVDLLISCGEIISTVVLADELLSQGVKAVPLTGGQAGIITDDTYNNASILK 120

Query: 121 MKPERLFSVLANHDAVVVAGFQGATEKGDTTTIGRGGSDTSAAALGAAVDAEYIDIFTDV 180
           +K ERL +++      +VAGFQG +E G  TT+GRGGSD +A+ LG A+D+E I+I+TDV
Sbjct: 121 VKKERLLNLINEGKIPIVAGFQGESESGHITTLGRGGSDVTASILGVALDSESIEIYTDV 180

Query: 181 EGVMTADPRVVENAKPLPVVTYTEICNLAYQGAKVISPRAVEIAMQAKVPIRVRSTYSND 240
           +G+MTADP +V  A  +  ++Y E+   A QGAKVI PRAV+IAM   VP+ V++T ++ 
Sbjct: 181 DGIMTADPGIVSEAFLIEQISYNEVFQFADQGAKVIHPRAVKIAMSGNVPLVVKNTLNDC 240

Query: 241 KGTLVTSHHSSKVGSDVFERLITGIAHVKDVTQFKVPAKIGQYNVQTEVF----KAMANA 296
           KGT++T   +S +G    +++I+GI  + +  Q  V      YN   +++    + MAN 
Sbjct: 241 KGTIIT---NSVIGES--DKVISGITSMDNRIQVTV-----NYNENNKIYNTLLEEMANN 290

Query: 297 GISVDFFNITPSEIVYTVAGNKTETAQRILMDMGYDPMVTRNCAKVSAVGAGIMGVPGVT 356
            IS+D  N+ PS+ ++T+        + +  ++     +  NC+K++ +G+G+ G+PGV 
Sbjct: 291 SISIDLINVFPSKQIFTIDNKDIGNFKIVAGNLALVYSLIENCSKIALIGSGMRGIPGVM 350

Query: 357 SKIVSALSEKEIPILQSADSHTTIWVLVHEADMVPAVNALHEEFEL 402
           ++I+  L E+ I +LQ+ADSHTTIW LV  ++   A+NALH+EF L
Sbjct: 351 ARILKVLYEEGIEVLQTADSHTTIWCLVKSSETKRAINALHKEFLL 396


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: 427
Number of extensions: 18
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: 399
Length adjustment: 31
Effective length of query: 373
Effective length of database: 368
Effective search space:   137264
Effective search space used:   137264
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_012101829.1 CKL_RS07090 (aspartate kinase)
to HMM TIGR00657 (aspartate kinase (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/TIGR00657.hmm
# target sequence database:        /tmp/gapView.9784.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00657  [M=442]
Accession:   TIGR00657
Description: asp_kinases: aspartate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-104  335.3  10.7    3.5e-93  299.0   3.8    2.0  2  lcl|NCBI__GCF_000016505.1:WP_012101829.1  CKL_RS07090 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016505.1:WP_012101829.1  CKL_RS07090 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.4     3e-15     3e-15       1      55 [.       1      60 [.       1      62 [. 0.87
   2 !  299.0   3.8   3.5e-93   3.5e-93      95     441 ..      60     395 ..      48     396 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 3e-15
                                 TIGR00657  1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmag.....vTdaLvelae 55
                                              m++++qKFGGtSv + er ++v++ ++k+k kg  +vVVvSAm+       Td L++l++
  lcl|NCBI__GCF_000016505.1:WP_012101829.1  1 MKIVIQKFGGTSVSTHERREQVVNKILKAKDKGFCPVVVVSAMGRkgqpyATDTLLSLIK 60
                                              789****************************************86333335888887766 PP

  == domain 2  score: 299.0 bits;  conditional E-value: 3.5e-93
                                 TIGR00657  95 keleevkkereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterle 163
                                               ke  ++k++  +dl++s+GE +S+ +la  l ++gvkav l+g++agi+td+++++A+ + ++k+erl+
  lcl|NCBI__GCF_000016505.1:WP_012101829.1  60 KEDFKIKNPLGVDLLISCGEIISTVVLADELLSQGVKAVPLTGGQAGIITDDTYNNAS-ILKVKKERLL 127
                                               45556777999***********************************************.********** PP

                                 TIGR00657 164 klleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArr 232
                                               +l++eg+i++vaGF+G +e+g+ittLGRGGSD+tA++l+ al+ + +eiytDVdGi+taDP iv+eA +
  lcl|NCBI__GCF_000016505.1:WP_012101829.1 128 NLINEGKIPIVAGFQGESESGHITTLGRGGSDVTASILGVALDSESIEIYTDVDGIMTADPGIVSEAFL 196
                                               ********************************************************************* PP

                                 TIGR00657 233 ldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseeepavkalsldk 301
                                               +++isy+E    a  Gakv+hpr++++am  ++p+vvk+t n+  +GT+i+++   e+++ ++++++ +
  lcl|NCBI__GCF_000016505.1:WP_012101829.1 197 IEQISYNEVFQFADQGAKVIHPRAVKIAMSGNVPLVVKNTLNDC-KGTIITNSVIGESDKVISGITSMD 264
                                               *******************************************9.********999999********** PP

                                 TIGR00657 302 nqalvsvsgttmkpgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellkkkvkeekal 370
                                               n++ v+v++++ + +i +++++ +a++++++dli    s++   f++d++d+ + k +      +++  
  lcl|NCBI__GCF_000016505.1:WP_012101829.1 265 NRIQVTVNYNENN-KIYNTLLEEMANNSISIDLINVFPSKQI--FTIDNKDIGNFKIVAG----NLAL- 325
                                               *********9998.999******************7777654..********99999842....3333. PP

                                 TIGR00657 371 eevevekklalvslvGagmksapgvaakifeaLaeeniniemissseikisvvvdekdaekavealhek 439
                                                  ++ ++ ++++l+G+gm++ pgv+a+i+++L ee+i +   + s + i ++v++++ ++a++alh++
  lcl|NCBI__GCF_000016505.1:WP_012101829.1 326 -VYSLIENCSKIALIGSGMRGIPGVMARILKVLYEEGIEVLQTADSHTTIWCLVKSSETKRAINALHKE 393
                                               .478999*************************************************************9 PP

                                 TIGR00657 440 lv 441
                                               + 
  lcl|NCBI__GCF_000016505.1:WP_012101829.1 394 FL 395
                                               96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (399 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: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 3.28
//
[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