Alignments for a candidate for asp-kinase in Chlorobaculum parvum NCIB 8327

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Chlorobaculum parvum NCIB 8327

Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_012503132.1 CPAR_RS09690 bifunctional aspartate kinase/homoserine dehydrogenase I

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



>NCBI__GCF_000020505.1:WP_012503132.1
          Length = 818

 Score =  679 bits (1751), Expect = 0.0
 Identities = 356/818 (43%), Positives = 522/818 (63%), Gaps = 7/818 (0%)

Query: 1   MKIIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEES 60
           MK+ KFGGSSIA+  NI    +II ++ E+    +V SA   VT+ L +    A + +E+
Sbjct: 1   MKVFKFGGSSIASAANISNAAAIIRKELERSELIVVVSAIARVTDLLAEAGAQAGKGDEA 60

Query: 61  YHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDYV 120
           +   L  +   H +++++L   ++ +    +++    EL D+ HG+ L++E S++++  +
Sbjct: 61  WRETLDVIGSLHADVIRELFG-EEAAPEEAWLREVVAELNDVLHGVALLRELSDKSLVLI 119

Query: 121 LSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSHD 180
           LS+GERLS  I++  L   G     VDAR+L+ TD+ + +AKV+   T K I++ F+++D
Sbjct: 120 LSYGERLSCRIMSRCLDVSGTPAECVDARELIVTDENYCYAKVDRLATGKRIKERFQTYD 179

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

Query: 241 AFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISK----D 296
           A  +P++SY EAMELSH GAKV+ P  +QP MK  IP+ I+N   P+  GTRI +     
Sbjct: 240 AKVLPEISYAEAMELSHAGAKVLHPLAVQPVMKASIPLLIRNASDPENPGTRIGQLPAST 299

Query: 297 SGEGKIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSIC 356
            G+ + + G++S++ + +LN+ G G+  V G + R F  LA + INII ISQASSE SI 
Sbjct: 300 DGQPRPVTGLTSINRVVLLNLSGSGMAGVPGTASRLFTCLARHSINIIFISQASSEQSIS 359

Query: 357 VAIASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQA 416
           +A+A   AS AK V+EEE+  EI+   +D + +  ++A++A+VG  M  +PG S ++F+ 
Sbjct: 360 LAVAPDQASMAKKVLEEEYSREIKERRIDPVSVRRNLAMVAIVGNKMSGHPGVSAQLFET 419

Query: 417 LGRNNVNVAAIAQGSSELNISAVITQADLQKALNALHEAFFLSDYKVLHLFLVGVGLIGK 476
           LG+N VNV A+AQG++E+NIS VI  +D  KALN +HE+FFLS  KV H+F+ G G I K
Sbjct: 420 LGKNGVNVIAVAQGANEMNISVVIDSSDEDKALNCIHESFFLSMRKV-HVFIAGTGTIAK 478

Query: 477 ALTKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEP-MDMDKF 535
           +L   I      LQ+E  LDI + G+AN+R +    +G DL       +  E    +  +
Sbjct: 479 SLISQIRDHRATLQQEMALDIVVAGLANTRAICIEPEGIDLEHWEESMKTREAHQGIGHY 538

Query: 536 IGTMTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLAG 595
           I  +   N  N++ VDCTAS+ VA+ Y ++L + + + T NK   +G  E Y K+ K   
Sbjct: 539 IKLIRAENLHNTIVVDCTASKQVAESYPELLQANISVATANKLGMAGSGELYGKIMKAER 598

Query: 596 QRGVRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELEKGMPFSEVV 655
               RF YETNV AGLP+I+TL DL  SGD +  IE VLSG+++YIF+EL KG  FSE+V
Sbjct: 599 SSNARFLYETNVGAGLPIISTLNDLKNSGDRIICIEGVLSGTLSYIFNELRKGGRFSEIV 658

Query: 656 AQAKEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAASVPE 715
            +AKE GYTEPDPRDDLSG D ARK+LILGR  G  L ++DVE QS+VPE C+   S  E
Sbjct: 659 RKAKESGYTEPDPRDDLSGADFARKMLILGRALGYQLEYDDVECQSLVPESCQGDMSTAE 718

Query: 716 FFKKLQKHDGHFQQLLDEANAKGEKLRFMATLENGKAKVGLNSLDSEHPFFTLKGSDNMI 775
           F  +L   D  + + ++ A  +G+ + +   L++GKAKVGL  +  E P   L G++N++
Sbjct: 719 FLDRLATIDDWYVEEMESAAKEGKTIAYTGELKDGKAKVGLKRVPLESPVAGLNGTENLV 778

Query: 776 LFTTERYNDFPMIVRGPGAGADVTAAGVFADIIRLGNY 813
           +FTT+RY D P++V+GPGAG +VTA GVFADI+R+ +Y
Sbjct: 779 VFTTDRYLDTPLVVKGPGAGGEVTAGGVFADILRIASY 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: 1322
Number of extensions: 51
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 WP_012503132.1 CPAR_RS09690 (bifunctional aspartate kinase/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.15314.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-126  408.5   0.0   2.7e-126  408.1   0.0    1.2  1  lcl|NCBI__GCF_000020505.1:WP_012503132.1  CPAR_RS09690 bifunctional aspart


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020505.1:WP_012503132.1  CPAR_RS09690 bifunctional aspartate kinase/homoserine dehydrogenase I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.1   0.0  2.7e-126  2.7e-126       5     441 ..       3     460 ..       1     461 [. 0.95

  Alignments for each domain:
  == domain 1  score: 408.1 bits;  conditional E-value: 2.7e-126
                                 TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekire 71 
                                               V KFGG+S++++ +i+++a i+ ke  ++ + +VVvSA+a vTd L e   ++ +++e   e++++i +
  lcl|NCBI__GCF_000020505.1:WP_012503132.1   3 VFKFGGSSIASAANISNAAAIIRKEL-ERSELIVVVSAIARVTDLLAEAGAQAGKGDEawRETLDVIGS 70 
                                               89************************.556************************999999999999999 PP

                                 TIGR00657  72 khlealeela..sqalkeklkallekeleevkk.........ereldlilsvGEklSaallaaaleelg 129
                                                h + + el   + a +e + + + +el+ v +         +++l lils+GE+lS+++++  l   g
  lcl|NCBI__GCF_000020505.1:WP_012503132.1  71 LHADVIRELFgeEAAPEEAWLREVVAELNDVLHgvallrelsDKSLVLILSYGERLSCRIMSRCLDVSG 139
                                               9999999887645556666777777777777778999*9999*************************** PP

                                 TIGR00657 130 vkavsllgaeagiltdsefgrAkvleeikterleklleeg.iivvvaGFiGatekgeittLGRGGSDlt 197
                                                  +++++a++ i+td+++  Akv + ++ +r+++  +    ++vv+GFi++ e+g++t LGRGGSD+t
  lcl|NCBI__GCF_000020505.1:WP_012503132.1 140 -TPAECVDARELIVTDENYCYAKVDRLATGKRIKERFQTYdPVPVVTGFIASAEDGSVTNLGRGGSDFT 207
                                               .999*****************************99999888**************************** PP

                                 TIGR00657 198 AallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakip 266
                                               A++l+aal+A+ev+i+t VdG y+aDP+ vp+A+ l+eisy+Ea+EL++ GakvLhp +++p+m+a+ip
  lcl|NCBI__GCF_000020505.1:WP_012503132.1 208 ATILGAALHAEEVWIWTHVDGFYSADPKRVPDAKVLPEISYAEAMELSHAGAKVLHPLAVQPVMKASIP 276
                                               ********************************************************************* PP

                                 TIGR00657 267 ivvkstfnpeaeGTlivaksk..seeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvn 331
                                               +++++  +pe++GT i++     + ++ +v++l++ +  +l+++sg++m+  pg+++++f++la++++n
  lcl|NCBI__GCF_000020505.1:WP_012503132.1 277 LLIRNASDPENPGTRIGQLPAstDGQPRPVTGLTSINRVVLLNLSGSGMAgvPGTASRLFTCLARHSIN 345
                                               ****************9876655677789**************************************** PP

                                 TIGR00657 332 vdlilqsssetsisfvvdkedadkakellk...kkvkeekaleevevekklalvslvGagmksapgvaa 397
                                               ++ i+q sse+sis++v  ++a+ ak++l+   + + +e+ + +v+v ++la+v++vG++m+++pgv a
  lcl|NCBI__GCF_000020505.1:WP_012503132.1 346 IIFISQASSEQSISLAVAPDQASMAKKVLEeeySREIKERRIDPVSVRRNLAMVAIVGNKMSGHPGVSA 414
                                               ****************************998887789999***************************** PP

                                 TIGR00657 398 kifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441
                                               ++fe+L ++++n+ +++  ++e++isvv+d++d +ka++++he ++
  lcl|NCBI__GCF_000020505.1:WP_012503132.1 415 QLFETLGKNGVNVIAVAqgANEMNISVVIDSSDEDKALNCIHESFF 460
                                               *****************99************************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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.11
//
[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