GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Caldicellulosiruptor kronotskyensis 2002

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013429768.1 CALKRO_RS03695 aspartate kinase

Query= BRENDA::P08495
         (408 letters)



>NCBI__GCF_000166775.1:WP_013429768.1
          Length = 409

 Score =  419 bits (1077), Expect = e-122
 Identities = 224/402 (55%), Positives = 297/402 (73%), Gaps = 2/402 (0%)

Query: 1   MGLIVQKFGGTSVGSVEKIQNAANRAIAEKQKGHQVVVVVSAMGKSTDELVSLAKAISDQ 60
           MG++VQK+GGTSV   E+I  AA RAI+E +KG++VVVVVSA G +TDEL+  AK I++ 
Sbjct: 1   MGIVVQKYGGTSVADKERIFRAARRAISEYEKGNKVVVVVSAQGDTTDELIEKAKEINEN 60

Query: 61  PSKREMDMLLATGEQVTISLLSMALQEKGYDAVSYTGWQAGIRTEAIHGNARITDIDTSV 120
           PSKREMDMLL+TGEQ++I+L++MA+++ GY  +S TGWQAGI+T++ + NARI +ID+  
Sbjct: 61  PSKREMDMLLSTGEQISIALMAMAIEKLGYPVISLTGWQAGIKTDSHYSNARIIEIDSER 120

Query: 121 LADQLEKGKIVIVAGFQGMTEDCEITTLGRGGSDTTAVALAAALKADKCDIYTDVPGVFT 180
           L  +L+K  IV+VAGFQG+ +  +ITTLGRGGSDTTAVALAAALKADKC+IYTDV GV+T
Sbjct: 121 LQRELDKRNIVVVAGFQGINKYDDITTLGRGGSDTTAVALAAALKADKCEIYTDVDGVYT 180

Query: 181 TDPRYVKSARKLEGISYDEMLELANLGAGVLHPRAVEFAKNYQVPLEVRSSTETEAGTLI 240
            DPR V +A KL+ ISYDEMLELA LGA VLH R+VE AK Y +PL VRSS     GT++
Sbjct: 181 ADPRIVPNASKLKEISYDEMLELATLGAKVLHNRSVELAKKYNIPLVVRSSFNDNEGTIV 240

Query: 241 EEESSMEQNLIVRGIAFEDQITRVTIYGLTSGLTTLSTIFTTLAKRNINVDIIIQTQAED 300
           +E +S+E+ L+V G+A +  I RV + G+ +       IF+ LAK NINVDII+Q+   +
Sbjct: 241 KEVNSVEK-LLVSGVACDKDIARVAVIGVENVPGKAFQIFSLLAKENINVDIILQSIGRE 299

Query: 301 KT-GISFSVKTEDADQTVAVLEEYKDALEFEKIETESKLAKVSIVGSGMVSNPGVAAEMF 359
           KT  ISF+V   +  QT+ VL +    +  + I     +AKVSIVG+GMV+NPGVAA MF
Sbjct: 300 KTKDISFTVSKSNLKQTLDVLTKNLHIIGAKDITYADNVAKVSIVGAGMVNNPGVAAMMF 359

Query: 360 AVLAQKNILIKMVSTSEIKVSTVVSENDMVKAVESLHDAFEL 401
             L    I I+M+STSEIK+S ++ E D  KAV ++HD F+L
Sbjct: 360 EALYDAGINIEMISTSEIKISVLIDEKDAEKAVRAIHDKFKL 401


Lambda     K      H
   0.313    0.128    0.337 

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: 407
Number of extensions: 14
Number of successful extensions: 4
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: 408
Length of database: 409
Length adjustment: 31
Effective length of query: 377
Effective length of database: 378
Effective search space:   142506
Effective search space used:   142506
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_013429768.1 CALKRO_RS03695 (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.1916323.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-149  484.0  13.4   2.1e-149  483.8  13.4    1.0  1  NCBI__GCF_000166775.1:WP_013429768.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_013429768.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  483.8  13.4  2.1e-149  2.1e-149       1     406 [.       1     401 [.       1     402 [. 0.99

  Alignments for each domain:
  == domain 1  score: 483.8 bits;  conditional E-value: 2.1e-149
                             TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 
                                           + ++VqK+GGtsv+++eri +aa+++++e+++g+kvvVVvSA + +tdel+e a      + i++++s+re+d
  NCBI__GCF_000166775.1:WP_013429768.1   1 MGIVVQKYGGTSVADKERIFRAARRAISEYEKGNKVVVVVSAQGDTTDELIEKA------KEINENPSKREMD 67 
                                           579***************************************************......9************ PP

                             TIGR00656  74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146
                                           +l+s+GE++s+al+++a+++lg+  ++l+g++agi Td+++ nA+i e++  erL   L++  ivvvaGF+G 
  NCBI__GCF_000166775.1:WP_013429768.1  68 MLLSTGEQISIALMAMAIEKLGYPVISLTGWQAGIKTDSHYSNARIIEIDS-ERLQRELDKRNIVVVAGFQGI 139
                                           ***************************************************.********************* PP

                             TIGR00656 147 teeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlh 219
                                           ++  +iTtLGRGGSD+tA++laaalkAd++eiyTDV+Gvyt+DPr+v++a k+++isy+E+lelAtlGakvlh
  NCBI__GCF_000166775.1:WP_013429768.1 140 NKYDDITTLGRGGSDTTAVALAAALKADKCEIYTDVDGVYTADPRIVPNASKLKEISYDEMLELATLGAKVLH 212
                                           ************************************************************************* PP

                             TIGR00656 220 pralelaveakvpilvrsskekeegTlitn.kkensslvkaialeknvarltvegegmlgkrgilaeifkaLa 291
                                           +r++ela+++++p++vrss++ +egT + + ++ ++ lv+++a +k++ar++v   g+ + +g + +if++La
  NCBI__GCF_000166775.1:WP_013429768.1 213 NRSVELAKKYNIPLVVRSSFNDNEGTIVKEvNSVEKLLVSGVACDKDIARVAVI--GVENVPGKAFQIFSLLA 283
                                           ****************************998777778*****************..99*************** PP

                             TIGR00656 292 eeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvas 361
                                           +e+invd+i q+ ++    +is++v++ +++++ ++L++    ++ +++ +  ++a+vsivgag+v++pGva+
  NCBI__GCF_000166775.1:WP_013429768.1 284 KENINVDIILQSIGRektKDISFTVSKSNLKQTLDVLTKNLHIIGAKDITYADNVAKVSIVGAGMVNNPGVAA 356
                                           *************9989899***************************************************** PP

                             TIGR00656 362 eifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                            +f+al + +ini mis+se+kisvl+dekdaekavr++h+k+++
  NCBI__GCF_000166775.1:WP_013429768.1 357 MMFEALYDAGINIEMISTSEIKISVLIDEKDAEKAVRAIHDKFKL 401
                                           ******************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (409 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: 14.73
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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