Alignments for a candidate for asp-kinase in Chlorobaculum tepidum TLS

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Chlorobaculum tepidum TLS

Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate NP_662905.1 CT2030 bifunctional aspartokinase I/homoserine dehydrogenase I

Query= reanno::Cola:Echvi_2000
         (815 letters)



>NCBI__GCF_000006985.1:NP_662905.1
          Length = 818

 Score =  679 bits (1753), Expect = 0.0
 Identities = 368/821 (44%), Positives = 521/821 (63%), Gaps = 13/821 (1%)

Query: 1   MKIIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEES 60
           M++ KFGGSSIA+   I  V  II ++ +     +V SA G VT+ L + A +A   + +
Sbjct: 1   MRVFKFGGSSIASAAKISNVAGIIRRELKSTPLVVVVSAIGKVTDMLAETAALAGNGDAA 60

Query: 61  YHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDYV 120
           Y   L+ +   H  I+++L   +  S   T++     EL D+ HG++L++E S++++  V
Sbjct: 61  YRDKLEGIASLHGGIIRELFGTEA-SAEETWLGEMMAELNDVLHGVFLLRELSDKSLALV 119

Query: 121 LSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSHD 180
           LS+GERLS  I++  +   G     VDAR ++ TDD    AKV+   T KLI + F+S D
Sbjct: 120 LSYGERLSCRIVSRYMHVSGTPAECVDARSVIVTDDNHCFAKVDRLATGKLIHERFRSFD 179

Query: 181 DIKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLVYT 240
            + V+TGFI S   G  T +GR GSD+TA+I  AAL AE+V IWTDV G  +ADP+ V  
Sbjct: 180 VLPVVTGFIASAPDGSVTNLGRGGSDFTATILGAALHAEEVWIWTDVDGFYSADPKRVPD 239

Query: 241 AFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDSGEG 300
           A  IP++SY EAMELSH GAKV+ P  +QP MK  IP+ IKN+F P++ GTRI  ++   
Sbjct: 240 ARVIPEISYAEAMELSHAGAKVLHPLAVQPVMKAGIPLRIKNSFNPEKPGTRIGIEAAGA 299

Query: 301 KI----IKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSIC 356
           +     + G++S++++ +L++ G G+  V G + R F  LA + INII ISQASSE SI 
Sbjct: 300 EALPGTVTGLTSINHVVLLSLSGSGMAGVPGTASRLFTCLARHSINIIFISQASSEQSIS 359

Query: 357 VAIASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQA 416
           +AIA   AS AK V+EEEF  EI+   +D + +  ++A++AVVG  M  +PG S ++F+ 
Sbjct: 360 LAIAPGQASMAKKVLEEEFAREIEERRIDPVSVRRNLAMVAVVGNKMLGHPGVSAQLFET 419

Query: 417 LGRNNVNVAAIAQGSSELNISAVITQADLQKALNALHEAFFLSDYKVLHLFLVGVGLIGK 476
           LG+N VNV A+AQG++E+NIS VI  AD  KALN +HE+FFLS  KV H+F+VG G I K
Sbjct: 420 LGKNGVNVIAVAQGANEMNISLVIDSADENKALNCVHESFFLSMRKV-HVFIVGTGTIAK 478

Query: 477 ALTKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLA----TVGPPDENDEPMDM 532
           +L   I +    LQ+E  LD+ + G+AN+R M     G DL     ++ P + ++    +
Sbjct: 479 SLISQIRRHRATLQKELGLDVVVAGLANTRSMCIEPAGIDLEHWHDSLKPRESHE---GI 535

Query: 533 DKFIGTMTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKK 592
            ++I  + E N  N++ VDCTAS+ VA+ Y  +L + + + T NK   +GP + Y+K+  
Sbjct: 536 GQYIRLIQERNLHNTIVVDCTASRQVAECYPALLRANISVATANKLGMAGPWDLYRKIMD 595

Query: 593 LAGQRGVRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELEKGMPFS 652
                  +F YETNV AGLPVINTL DL  SGD +  IE VLSG++++IF+EL KG  FS
Sbjct: 596 ALRSSNAKFLYETNVGAGLPVINTLNDLKNSGDKIVCIEGVLSGTLSFIFNELRKGGRFS 655

Query: 653 EVVAQAKEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAAS 712
           E+V +AKE GYTEPDPRDDLSG D ARK+LILGRE G  L + DVE QS+VPE      S
Sbjct: 656 EIVRKAKESGYTEPDPRDDLSGADFARKLLILGRELGYQLEYADVECQSLVPEPLRGEMS 715

Query: 713 VPEFFKKLQKHDGHFQQLLDEANAKGEKLRFMATLENGKAKVGLNSLDSEHPFFTLKGSD 772
             EF  +L   D  +   +  A ++G  + +   L +GKAKVGL  +  E P   L GS+
Sbjct: 716 PAEFLDQLSSIDDWYVDEMASAASEGMTIAYTGELRDGKAKVGLKRVPLESPVAGLNGSE 775

Query: 773 NMILFTTERYNDFPMIVRGPGAGADVTAAGVFADIIRLGNY 813
           N+++FTTERY   P++V+GPGAG +VTA GVFADI+R+ +Y
Sbjct: 776 NLVVFTTERYLKTPLVVKGPGAGGEVTAGGVFADILRIASY 816


Lambda     K      H
   0.317    0.134    0.375 

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: 1326
Number of extensions: 53
Number of successful extensions: 7
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: 815
Length of database: 818
Length adjustment: 41
Effective length of query: 774
Effective length of database: 777
Effective search space:   601398
Effective search space used:   601398
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 (21.7 bits)
S2: 56 (26.2 bits)

Align candidate NP_662905.1 CT2030 (bifunctional aspartokinase I/homoserine dehydrogenase I)
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.21912.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   9.3e-125  403.1   0.0   1.2e-124  402.7   0.0    1.1  1  lcl|NCBI__GCF_000006985.1:NP_662905.1  CT2030 bifunctional aspartokinas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000006985.1:NP_662905.1  CT2030 bifunctional aspartokinase I/homoserine dehydrogenase I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.7   0.0  1.2e-124  1.2e-124       5     441 ..       3     460 ..       1     461 [. 0.93

  Alignments for each domain:
  == domain 1  score: 402.7 bits;  conditional E-value: 1.2e-124
                              TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekirekhl 74 
                                            V KFGG+S++++ +i++va i+ +e ++  + vVVvSA+++vTd L e+a  + +++    +++e i + h 
  lcl|NCBI__GCF_000006985.1:NP_662905.1   3 VFKFGGSSIASAAKISNVAGIIRRELKST-PLVVVVSAIGKVTDMLAETAALAGNGDAayRDKLEGIASLHG 73 
                                            89************************555.***********************9999989999********9 PP

                              TIGR00657  75 ealeela.sqalk.eklkallekeleevkk.........ereldlilsvGEklSaallaaaleelgvkavsl 135
                                             ++ el   +a++ e++   + +el+ v +         +++l+l+ls+GE+lS+++++ +++  g   +++
  lcl|NCBI__GCF_000006985.1:NP_662905.1  74 GIIRELFgTEASAeETWLGEMMAELNDVLHgvfllrelsDKSLALVLSYGERLSCRIVSRYMHVSG-TPAEC 144
                                            9999988755444044555666666666668999********************************.999** PP

                              TIGR00657 136 lgaeagiltdsefgrAkvleeikterlek.lleegiivvvaGFiGatekgeittLGRGGSDltAallAaalk 206
                                            ++a+++i+td+++  Akv + ++ + + + + + ++++vv+GFi++ ++g++t LGRGGSD+tA++l+aal+
  lcl|NCBI__GCF_000006985.1:NP_662905.1 145 VDARSVIVTDDNHCFAKVDRLATGKLIHErFRSFDVLPVVTGFIASAPDGSVTNLGRGGSDFTATILGAALH 216
                                            *****************666666665554055556************************************* PP

                              TIGR00657 207 AdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeae 278
                                            A+ev+i+tDVdG y+aDP+ vp+Ar ++eisy+Ea+EL++ GakvLhp +++p+m+a+ip+++k++fnpe++
  lcl|NCBI__GCF_000006985.1:NP_662905.1 217 AEEVWIWTDVDGFYSADPKRVPDARVIPEISYAEAMELSHAGAKVLHPLAVQPVMKAGIPLRIKNSFNPEKP 288
                                            ************************************************************************ PP

                              TIGR00657 279 GTlivaksk..seeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisf 346
                                            GT i+ +    +  +  v++l++ ++ +l+s+sg++m+  pg+++++f++la++++n++ i+q sse+sis+
  lcl|NCBI__GCF_000006985.1:NP_662905.1 289 GTRIGIEAAgaEALPGTVTGLTSINHVVLLSLSGSGMAgvPGTASRLFTCLARHSINIIFISQASSEQSISL 360
                                            *****999976556678******************************************************* PP

                              TIGR00657 347 vvdkedadkakellk...kkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis. 414
                                            ++   +a+ ak++l+     + ee+ + +v+v ++la+v++vG++m ++pgv a++fe+L ++++n+ +++ 
  lcl|NCBI__GCF_000006985.1:NP_662905.1 361 AIAPGQASMAKKVLEeefAREIEERRIDPVSVRRNLAMVAVVGNKMLGHPGVSAQLFETLGKNGVNVIAVAq 432
                                            *************9977766789999*********************************************9 PP

                              TIGR00657 415 .sseikisvvvdekdaekavealheklv 441
                                             ++e++is+v+d+ d +ka++++he ++
  lcl|NCBI__GCF_000006985.1:NP_662905.1 433 gANEMNISLVIDSADENKALNCVHESFF 460
                                            9************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (818 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: 19.57
//
[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