Alignments for a candidate for asp-kinase in Prosthecochloris aestuarii DSM 271

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Prosthecochloris aestuarii DSM 271

Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_012504858.1 PAES_RS01305 bifunctional aspartate kinase/homoserine dehydrogenase I

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



>NCBI__GCF_000020625.1:WP_012504858.1
          Length = 819

 Score =  666 bits (1719), Expect = 0.0
 Identities = 349/820 (42%), Positives = 517/820 (63%), Gaps = 10/820 (1%)

Query: 1   MKIIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEES 60
           M ++KFGG+SI N + I+ V +II          +V SA   VT+ LL  A  A +    
Sbjct: 1   MNVLKFGGTSIENGKRIRNVLNIIRDAMHDGPVIVVVSAIRKVTDLLLDAALTACRGGGD 60

Query: 61  YHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDYV 120
           Y   L ++E+ H  +V+ L+  ++      ++    +ELGD+ HG+ L++E S ++   +
Sbjct: 61  YKEKLVDIERLHTALVEDLLTGEKAEDVQRYLCGVLSELGDVLHGVSLLRELSEKSSALI 120

Query: 121 LSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSHD 180
           +SFGER S +I+++ L  +G+  SYVDAR ++ TD   G A+V+ + +   I++   + D
Sbjct: 121 MSFGERFSAYIISSYLSQEGVAASYVDARGMIVTDTSHGDARVDMEASALQIRERLNNAD 180

Query: 181 DIKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLVYT 240
            I V+TG+IGS   G  TT+GR GSDYTA+I  + LGA +++IWTDV G  +ADP+ V  
Sbjct: 181 SIPVVTGYIGSAPDGTVTTLGRGGSDYTATIIGSVLGAGEIQIWTDVDGFFSADPKRVRD 240

Query: 241 AFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDSGEG 300
           A+ +P +SY EAMELSH GAKV+ P  + PAMK  IPI I+N+  P   GTRI K S E 
Sbjct: 241 AYALPFISYAEAMELSHAGAKVLHPYAVHPAMKAGIPITIRNSMNPGAPGTRIEKLSSEE 300

Query: 301 KI----IKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSIC 356
            +    + G+SS+ +I +LN+ G G+V V G++ R F  LA + INII ISQASSE SI 
Sbjct: 301 AVSARPVTGLSSISDIVLLNISGSGMVGVPGIASRLFSCLARHMINIIFISQASSEQSIS 360

Query: 357 VAIASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQA 416
           +AI +  AS+A+  +++EF  E+ S +++ + +  D+++IAVVG++M  +PG S  +F+ 
Sbjct: 361 LAINALQASKAQMALDDEFAVELGSRQIESLTVRQDISMIAVVGKSMSGHPGVSAHLFET 420

Query: 417 LGRNNVNVAAIAQGSSELNISAVITQADLQKALNALHEAFFLSDYKVLHLFLVGVGLIGK 476
           LG+N +NV A+AQG++E+NIS VI   D  KALN +HE+FFLS  KV H+F+ G G I  
Sbjct: 421 LGKNGINVIAVAQGANEMNISFVIDSHDEDKALNCVHESFFLSRRKV-HVFIAGTGTISS 479

Query: 477 ALTKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDL---ATVGPPDENDEPMDMD 533
           +L   I    + L     LDI + GMAN+R M  + +G DL    +   P E +  +   
Sbjct: 480 SLIGQIRDHHETLSVGKNLDIVVCGMANTRMMALNNEGIDLNDWQSALQPREGERTIG-- 537

Query: 534 KFIGTMTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKL 593
            ++  +   N  N++FVDCTAS DVA  Y ++L S + +VT NK   +G  + Y+ +   
Sbjct: 538 DYLARIRSRNLHNTIFVDCTASADVAAAYPELLRSNISVVTANKLGMAGSWDLYETINDA 597

Query: 594 AGQRGVRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELEKGMPFSE 653
                 +F YETNV AGLP+INTL DL  SGD + +IE VLSG+++YIF+EL KG  FS 
Sbjct: 598 LNSSNAKFLYETNVGAGLPIINTLNDLRNSGDKILKIEGVLSGTLSYIFNELRKGGAFSR 657

Query: 654 VVAQAKEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAASV 713
           +V QA++ G+TEPDPR+DLSG D ARK LILGRE G  +++ED++ +S+VP+       V
Sbjct: 658 IVRQARDAGFTEPDPREDLSGADFARKFLILGRELGFRINYEDIQCESLVPDHLMGQMPV 717

Query: 714 PEFFKKLQKHDGHFQQLLDEANAKGEKLRFMATLENGKAKVGLNSLDSEHPFFTLKGSDN 773
            EF +KL   D  +  +  +A A+G  + +   +  GKAK+ +  L   +P   L G++N
Sbjct: 718 EEFLEKLACVDEEYDDMNRKAAAEGMTIAYAGEINGGKAKISVKMLPLSNPVAGLNGTEN 777

Query: 774 MILFTTERYNDFPMIVRGPGAGADVTAAGVFADIIRLGNY 813
           M++FTT+RY D P++V+GPGAG +VTA GVFADI+R+ +Y
Sbjct: 778 MVVFTTDRYFDTPLVVKGPGAGGEVTAGGVFADILRIASY 817


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: 1404
Number of extensions: 61
Number of successful extensions: 6
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: 819
Length adjustment: 41
Effective length of query: 774
Effective length of database: 778
Effective search space:   602172
Effective search space used:   602172
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_012504858.1 PAES_RS01305 (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.11167.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-125  405.9   0.4   1.6e-125  405.6   0.4    1.1  1  lcl|NCBI__GCF_000020625.1:WP_012504858.1  PAES_RS01305 bifunctional aspart


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020625.1:WP_012504858.1  PAES_RS01305 bifunctional aspartate kinase/homoserine dehydrogenase I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.6   0.4  1.6e-125  1.6e-125       5     441 ..       3     461 ..       1     462 [. 0.95

  Alignments for each domain:
  == domain 1  score: 405.6 bits;  conditional E-value: 1.6e-125
                                 TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekire 71 
                                               V+KFGGtS+ n++ri++v +i+  + + g +v+VVvSA+ +vTd L++ a  ++++    ke++ +i++
  lcl|NCBI__GCF_000020625.1:WP_012504858.1   3 VLKFGGTSIENGKRIRNVLNIIRDAMHDG-PVIVVVSAIRKVTDLLLDAALTACRGGGdyKEKLVDIER 70 
                                               89*********************999888.********************9999988888999****** PP

                                 TIGR00657  72 khlealeelasqalkeklkallekeleevkk............ereldlilsvGEklSaallaaaleel 128
                                                h + +e l   + +e +++ l   l e+              e++ +li+s+GE+ Sa +++++l+++
  lcl|NCBI__GCF_000020625.1:WP_012504858.1  71 LHTALVEDLLTGEKAEDVQRYLCGVLSELGDvlhgvsllrelsEKSSALIMSFGERFSAYIISSYLSQE 139
                                               **999999998788888888887777776668889********************************** PP

                                 TIGR00657 129 gvkavsllgaeagiltdsefgrAkvleeikterleklleeg.iivvvaGFiGatekgeittLGRGGSDl 196
                                               g  a+s+++a+  i+td ++g+A+v  e+++ ++ + l++   i+vv+G+iG+ ++g +ttLGRGGSD+
  lcl|NCBI__GCF_000020625.1:WP_012504858.1 140 G-VAASYVDARGMIVTDTSHGDARVDMEASALQIRERLNNAdSIPVVTGYIGSAPDGTVTTLGRGGSDY 207
                                               *.99********************999999999999998888*************************** PP

                                 TIGR00657 197 tAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamraki 265
                                               tA+++++ l+A e++i+tDVdG ++aDP+ v++A  l+ isy+Ea+EL++ GakvLhp +++pam+a+i
  lcl|NCBI__GCF_000020625.1:WP_012504858.1 208 TATIIGSVLGAGEIQIWTDVDGFFSADPKRVRDAYALPFISYAEAMELSHAGAKVLHPYAVHPAMKAGI 276
                                               ********************************************************************* PP

                                 TIGR00657 266 pivvkstfnpeaeGTlivaksk..seeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakv 330
                                               pi +++++np a+GT i + s+    ++ +v++ls+ ++ +l+++sg++m   pgi++++f++la++ +
  lcl|NCBI__GCF_000020625.1:WP_012504858.1 277 PITIRNSMNPGAPGTRIEKLSSeeAVSARPVTGLSSISDIVLLNISGSGMVgvPGIASRLFSCLARHMI 345
                                               *****************9887766556699*************************************** PP

                                 TIGR00657 331 nvdlilqsssetsisfvvdkedadkakellk...kkvkeekaleevevekklalvslvGagmksapgva 396
                                               n++ i+q sse+sis++++  +a+ka+ +l+     ++  +++e+++v ++++++++vG+ m+++pgv 
  lcl|NCBI__GCF_000020625.1:WP_012504858.1 346 NIIFISQASSEQSISLAINALQASKAQMALDdefAVELGSRQIESLTVRQDISMIAVVGKSMSGHPGVS 414
                                               *****************************997776678889**************************** PP

                                 TIGR00657 397 akifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441
                                               a++fe+L +++in+ +++  ++e++is+v+d++d +ka++++he ++
  lcl|NCBI__GCF_000020625.1:WP_012504858.1 415 AHLFETLGKNGINVIAVAqgANEMNISFVIDSHDEDKALNCVHESFF 461
                                               ******************99************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (819 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: 15.89
//
[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