GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Flavobacterium glycines Gm-149

Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_066329102.1 BLR17_RS14640 bifunctional aspartate kinase/homoserine dehydrogenase I

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



>NCBI__GCF_900100165.1:WP_066329102.1
          Length = 815

 Score =  768 bits (1982), Expect = 0.0
 Identities = 389/814 (47%), Positives = 570/814 (70%), Gaps = 2/814 (0%)

Query: 1   MKIIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEES 60
           M+++KFGG+S+AN +NI+ V  I+  K++K+   +V SA   VT+ L   A+ A  ++ES
Sbjct: 1   MRVLKFGGTSVANAKNIKLVLDIVLNKAKKDKLIVVVSALSKVTDLLQLAASKAAANDES 60

Query: 61  YHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDYV 120
           Y  I+ E+EK+HL+ +K+L+PV +QS+ L+ +K   N L  +  G +L+ E S RT D +
Sbjct: 61  YKEIVAEIEKKHLDALKELIPVSEQSSLLSHIKRIINHLETILDGCFLLGELSARTSDTI 120

Query: 121 LSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSHD 180
           LSFGE LS++I+A  L+     +SY D+R+L+KT++ +G A VNF+ TN L    F ++D
Sbjct: 121 LSFGELLSSYIIAEALKQNLKNSSYKDSRELIKTNNNYGKAAVNFEVTNSLTTAFFANND 180

Query: 181 -DIKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLVY 239
             + V+ GFI S+     TT+GR GSDYTA+I A AL A+++EIWTDV+G+ TA+P++V 
Sbjct: 181 AQVVVMPGFIASSLDEINTTLGRGGSDYTAAILAGALNADELEIWTDVNGMFTANPKIVK 240

Query: 240 TAFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDS-G 298
            A  I  +SY EAMELSHFGAKV++P T+QP ++++IPI+IKNTF+P+  GT IS  S  
Sbjct: 241 QAQPIATISYQEAMELSHFGAKVLYPPTIQPVLRKNIPIHIKNTFEPEAEGTYISNVSVS 300

Query: 299 EGKIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSICVA 358
            G  ++GIS +DNI+++ ++GPG++ V G S+R F  L+N GIN+I I+QASSEHSIC+ 
Sbjct: 301 NGIPVRGISHIDNITLITLEGPGMIGVSGSSKRLFEVLSNEGINVIFITQASSEHSICIG 360

Query: 359 IASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQALG 418
           I + DA  A++ I + F  EI   ++D   +  ++ +IA+VGENM+++ G SGRMF  LG
Sbjct: 361 ILNSDAEVAENAINKAFEIEIAQNKIDPCIVEQNLCIIALVGENMKNHQGLSGRMFSTLG 420

Query: 419 RNNVNVAAIAQGSSELNISAVITQADLQKALNALHEAFFLSDYKVLHLFLVGVGLIGKAL 478
           +NNVN+ AIAQG+SE NISAVI + D++KALN LHE FF  + K L+LF++GVG +G+  
Sbjct: 421 KNNVNIRAIAQGASERNISAVINERDVKKALNTLHENFFEENTKQLNLFVMGVGNVGEKF 480

Query: 479 TKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEPMDMDKFIGT 538
            + IHQQ K L+E   +++++  ++NSR M F ED  DL +     EN E  + + FI  
Sbjct: 481 IEQIHQQKKFLKENLKINVRVIALSNSRKMLFDEDAIDLNSWQAALENGETANKELFIEK 540

Query: 539 MTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLAGQRG 598
           +  +N  NS+FVD TA+ DVA IYE+ L   VG+VT NK A +   + YK LKKL+ Q  
Sbjct: 541 VAALNLRNSIFVDITANADVAAIYERFLKQSVGVVTCNKIACASAYDNYKNLKKLSRQYN 600

Query: 599 VRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELEKGMPFSEVVAQA 658
             F +ETNV AGLP+I+T+++L+ SGD VH+I+AVLSGS+N+IF+  ++   F +VV +A
Sbjct: 601 APFLFETNVGAGLPIIDTVKNLIASGDKVHKIQAVLSGSLNFIFNNFDENNSFHDVVKEA 660

Query: 659 KEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAASVPEFFK 718
             +G+TEPDP+ DLSG+DVARKILIL RE+G  +  E++E  S +P  C    +  +FFK
Sbjct: 661 GVQGFTEPDPKIDLSGIDVARKILILIRESGYKMEIENIENNSFLPAACMATTNNEDFFK 720

Query: 719 KLQKHDGHFQQLLDEANAKGEKLRFMATLENGKAKVGLNSLDSEHPFFTLKGSDNMILFT 778
            L +++ HF+ +L EA AK  +L+F+A   NGKA VGL  +  +HPF+ L+G DN++LF 
Sbjct: 721 SLIEYNSHFEGILAEAKAKDSRLKFVAEFINGKANVGLQFIPKDHPFYNLEGKDNIVLFY 780

Query: 779 TERYNDFPMIVRGPGAGADVTAAGVFADIIRLGN 812
           T+RY D P++++G GAGA VTA+G+FAD+IR+GN
Sbjct: 781 TDRYVDQPLLIKGAGAGAAVTASGIFADVIRIGN 814


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: 1443
Number of extensions: 67
Number of successful extensions: 5
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: 815
Length adjustment: 41
Effective length of query: 774
Effective length of database: 774
Effective search space:   599076
Effective search space used:   599076
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_066329102.1 BLR17_RS14640 (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.2442477.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.7e-128  413.9   7.1   4.7e-128  413.9   7.1    1.7  2  NCBI__GCF_900100165.1:WP_066329102.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066329102.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.9   7.1  4.7e-128  4.7e-128       5     442 .]       3     460 ..       1     460 [. 0.94
   2 ?   -1.6   0.2     0.056     0.056     314     361 ..     476     527 ..     462     563 .. 0.59

  Alignments for each domain:
  == domain 1  score: 413.9 bits;  conditional E-value: 4.7e-128
                             TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekirekhle 75 
                                           V+KFGGtSv+n+++ik v +iv+++++k+ + +VVvSA ++vTd L   a+k+  ++e  ke++++i++khl+
  NCBI__GCF_900100165.1:WP_066329102.1   3 VLKFGGTSVANAKNIKLVLDIVLNKAKKD-KLIVVVSALSKVTDLLQLAASKAAANDEsyKEIVAEIEKKHLD 74 
                                           99************************777.****************999999999888899************ PP

                             TIGR00657  76 aleelasqalkeklkallekeleevkk............ereldlilsvGEklSaallaaaleelgvkavsll 136
                                           al+el++ + +  l + +++ ++++++             r+ d+ils+GE lS+ ++a+al++   k+ s+ 
  NCBI__GCF_900100165.1:WP_066329102.1  75 ALKELIPVSEQSSLLSHIKRIINHLETildgcfllgelsARTSDTILSFGELLSSYIIAEALKQNL-KNSSYK 146
                                           ******989999999999999999888999********************************9998.****** PP

                             TIGR00657 137 gaeagiltdsefgrAkvleeikterlek.lleeg..iivvvaGFiGatekgeittLGRGGSDltAallAaalk 206
                                           ++++ i t++++g+A  ++ + t+ l++ +  ++  ++vv+ GFi+++ +   ttLGRGGSD+tAa+lA al+
  NCBI__GCF_900100165.1:WP_066329102.1 147 DSRELIKTNNNYGKAA-VNFEVTNSLTTaFFANNdaQVVVMPGFIASSLDEINTTLGRGGSDYTAAILAGALN 218
                                           ****************.55555555555144444689************************************ PP

                             TIGR00657 207 AdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeG 279
                                           Ade+ei+tDV+G +ta P+iv++A+ +++isy+Ea+EL+++GakvL+p t++p+ r++ipi++k+tf+peaeG
  NCBI__GCF_900100165.1:WP_066329102.1 219 ADELEIWTDVNGMFTANPKIVKQAQPIATISYQEAMELSHFGAKVLYPPTIQPVLRKNIPIHIKNTFEPEAEG 291
                                           ************************************************************************* PP

                             TIGR00657 280 Tlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdk 350
                                           T i + s+ ++  +v+++s+ +n +l++++g++m   +g  +++f+ l+++++nv+ i+q sse+si + + +
  NCBI__GCF_900100165.1:WP_066329102.1 292 TYISNVSV-SNGIPVRGISHIDNITLITLEGPGMIgvSGSSKRLFEVLSNEGINVIFITQASSEHSICIGILN 363
                                           ******88.555***********************99*****************************9999999 PP

                             TIGR00657 351 edadkakellk...kkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..ssei 418
                                           +da+ a+++ +   + + +++++ +  ve++l++++lvG++mk++ g+ +++f++L ++n+ni++i+  +se+
  NCBI__GCF_900100165.1:WP_066329102.1 364 SDAEVAENAINkafEIEIAQNKIDPCIVEQNLCIIALVGENMKNHQGLSGRMFSTLGKNNVNIRAIAqgASER 436
                                           999999999986666677889999999****************************************9***** PP

                             TIGR00657 419 kisvvvdekdaekavealheklve 442
                                           +is v++e+d++ka+++lhe+++e
  NCBI__GCF_900100165.1:WP_066329102.1 437 NISAVINERDVKKALNTLHENFFE 460
                                           **********************85 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.056
                             TIGR00657 314 k.pgilaevfgalaeak....vnvdlilqsssetsisfvvdkedadkakellk 361
                                              +++++++++ +  k    +nv +i++s+s+  + f  d  d+++ +++l+
  NCBI__GCF_900100165.1:WP_066329102.1 476 VgEKFIEQIHQQKKFLKenlkINVRVIALSNSR-KMLFDEDAIDLNSWQAALE 527
                                           336677777766554444455999999988874.3334334444555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (815 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: 34.70
//
[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