Alignments for a candidate for asp-kinase in Clostridium acetobutylicum ATCC 824

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Clostridium acetobutylicum ATCC 824

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate NP_346919.1 CA_C0278 aspartate kinase

Query= BRENDA::Q97MC0
         (437 letters)



>NCBI__GCF_000008765.1:NP_346919.1
          Length = 437

 Score =  863 bits (2229), Expect = 0.0
 Identities = 437/437 (100%), Positives = 437/437 (100%)

Query: 1   MKIVVTKFGGSSLADSNQFKKVKGIIDSDANRKYIIPSAPGKRTNKDYKITDLLYLCNAH 60
           MKIVVTKFGGSSLADSNQFKKVKGIIDSDANRKYIIPSAPGKRTNKDYKITDLLYLCNAH
Sbjct: 1   MKIVVTKFGGSSLADSNQFKKVKGIIDSDANRKYIIPSAPGKRTNKDYKITDLLYLCNAH 60

Query: 61  VKNGIPFDDVFKLISQRYTEIVSELNIDMDIAYYLEKVKKNIENGASSDYAASRGEYLNG 120
           VKNGIPFDDVFKLISQRYTEIVSELNIDMDIAYYLEKVKKNIENGASSDYAASRGEYLNG
Sbjct: 61  VKNGIPFDDVFKLISQRYTEIVSELNIDMDIAYYLEKVKKNIENGASSDYAASRGEYLNG 120

Query: 121 VILAKYLNAEFIDAAEVIFFDKSGCFDEKKSYEKIKEKVLSCNKAVIPGFYGSSFNGDVK 180
           VILAKYLNAEFIDAAEVIFFDKSGCFDEKKSYEKIKEKVLSCNKAVIPGFYGSSFNGDVK
Sbjct: 121 VILAKYLNAEFIDAAEVIFFDKSGCFDEKKSYEKIKEKVLSCNKAVIPGFYGSSFNGDVK 180

Query: 181 TFSRGGSDVTGSIISAGVNADLYENWTDVSGFLMADPRIVENPKTISKISYKELRELSYM 240
           TFSRGGSDVTGSIISAGVNADLYENWTDVSGFLMADPRIVENPKTISKISYKELRELSYM
Sbjct: 181 TFSRGGSDVTGSIISAGVNADLYENWTDVSGFLMADPRIVENPKTISKISYKELRELSYM 240

Query: 241 GATVLHEEAIFPVKDSGIPINIKNTNKPSDPGTLILSDTHKEINLGTITGIAGKKNFTVI 300
           GATVLHEEAIFPVKDSGIPINIKNTNKPSDPGTLILSDTHKEINLGTITGIAGKKNFTVI
Sbjct: 241 GATVLHEEAIFPVKDSGIPINIKNTNKPSDPGTLILSDTHKEINLGTITGIAGKKNFTVI 300

Query: 301 AIEKALLNSEVGFCRKILSILEMYGVSFEHMPSGVDSVSLVIEDCKLDGKCDKIIEEIKK 360
           AIEKALLNSEVGFCRKILSILEMYGVSFEHMPSGVDSVSLVIEDCKLDGKCDKIIEEIKK
Sbjct: 301 AIEKALLNSEVGFCRKILSILEMYGVSFEHMPSGVDSVSLVIEDCKLDGKCDKIIEEIKK 360

Query: 361 QCNPDSIEIHPNMALVATVGTGMAKTKGIANKIFTALSKENVNIRMIDQGSSEINVIVGV 420
           QCNPDSIEIHPNMALVATVGTGMAKTKGIANKIFTALSKENVNIRMIDQGSSEINVIVGV
Sbjct: 361 QCNPDSIEIHPNMALVATVGTGMAKTKGIANKIFTALSKENVNIRMIDQGSSEINVIVGV 420

Query: 421 ETVDFEKAVKSIYNAFN 437
           ETVDFEKAVKSIYNAFN
Sbjct: 421 ETVDFEKAVKSIYNAFN 437


Lambda     K      H
   0.316    0.135    0.379 

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: 823
Number of extensions: 17
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: 437
Length of database: 437
Length adjustment: 32
Effective length of query: 405
Effective length of database: 405
Effective search space:   164025
Effective search space used:   164025
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: 51 (24.3 bits)

Align candidate NP_346919.1 CA_C0278 (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.8597.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
    5.3e-81  258.9   0.5    6.7e-81  258.5   0.5    1.1  1  lcl|NCBI__GCF_000008765.1:NP_346919.1  CA_C0278 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008765.1:NP_346919.1  CA_C0278 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.5   0.5   6.7e-81   6.7e-81       1     440 [.       1     436 [.       1     437 [] 0.89

  Alignments for each domain:
  == domain 1  score: 258.5 bits;  conditional E-value: 6.7e-81
                              TIGR00657   1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee........ke 64 
                                            m+++V KFGG+S+++ +++kkv  i+ +++   n   ++ SA+++ T++  ++ + +  ++          +
  lcl|NCBI__GCF_000008765.1:NP_346919.1   1 MKIVVTKFGGSSLADSNQFKKVKGIIDSDA---NRKYIIPSAPGKRTNKDYKITDLLYLCNAhvkngipfDD 69 
                                            789**************************9...456999**************9999888887888888777 PP

                              TIGR00657  65 liekirekhlealeela.sqalkeklkallekeleevkkereldlilsvGEklSaallaaaleelgvkavsl 135
                                            + + i ++  e+++el+        +   lek  +++++ ++ d+  s+GE l   +la +l+++ ++a+++
  lcl|NCBI__GCF_000008765.1:NP_346919.1  70 VFKLISQRYTEIVSELNiD----MDIAYYLEKVKKNIENGASSDYAASRGEYLNGVILAKYLNAEFIDAAEV 137
                                            7788888888888887744....56667777777778889**********************9988555554 PP

                              TIGR00657 136 lgaeagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkA 207
                                            +  +++    + f++ k  +e ++e++++        v+ GF G++ +g++ t  RGGSD+t +++ a ++A
  lcl|NCBI__GCF_000008765.1:NP_346919.1 138 IFFDKS----GCFDEKK-SYEKIKEKVLSCN----KAVIPGFYGSSFNGDVKTFSRGGSDVTGSIISAGVNA 200
                                            444432....3455555.4444444444433....45899******************************** PP

                              TIGR00657 208 deveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeG 279
                                            d  e +tDV+G + aDPriv++++ + +isy+E  EL+++Ga vLh +++ p++ ++ipi +k+t  p+ +G
  lcl|NCBI__GCF_000008765.1:NP_346919.1 201 DLYENWTDVSGFLMADPRIVENPKTISKISYKELRELSYMGATVLHEEAIFPVKDSGIPINIKNTNKPSDPG 272
                                            ************************************************************************ PP

                              TIGR00657 280 Tlivakskseee.pavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvv 348
                                            Tli +++++e +   +++++ +kn ++++++++  +  +g+  +++++l+  +v+ + +   ++  s+s+v+
  lcl|NCBI__GCF_000008765.1:NP_346919.1 273 TLILSDTHKEINlGTITGIAGKKNFTVIAIEKALLNseVGFCRKILSILEMYGVSFEHMPSGVD--SVSLVI 342
                                            ******99554415899**************9999999*********************95555..89**** PP

                              TIGR00657 349 dkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..ssei 418
                                            ++ ++d    +  +++k++ +  ++e++ ++alv+ vG gm++++g+a kif+aL++en+ni+mi   ssei
  lcl|NCBI__GCF_000008765.1:NP_346919.1 343 EDCKLDGKCDKIIEEIKKQCNPDSIEIHPNMALVATVGTGMAKTKGIANKIFTALSKENVNIRMIDqgSSEI 414
                                            ****99888888889**************************************************9999*** PP

                              TIGR00657 419 kisvvvdekdaekavealhekl 440
                                            ++ v v+  d ekav+ +++++
  lcl|NCBI__GCF_000008765.1:NP_346919.1 415 NVIVGVETVDFEKAVKSIYNAF 436
                                            *******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (437 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: 00:00:00.02
# Mc/sec: 9.19
//
[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