GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Lentibacillus jeotgali Grbi

Align Aspartokinase 3; Aspartate kinase 3; Aspartokinase III; EC 2.7.2.4 (characterized)
to candidate WP_010530910.1 ON01_RS10040 aspartate kinase

Query= SwissProt::P94417
         (454 letters)



>NCBI__GCF_000224785.1:WP_010530910.1
          Length = 448

 Score =  500 bits (1287), Expect = e-146
 Identities = 247/449 (55%), Positives = 344/449 (76%), Gaps = 3/449 (0%)

Query: 1   MKVVKFGGSSLASGAQLDKVFHIVTSDPARKAVVVSAPGKHYAEDTKVTDLLIACAEQYL 60
           MKVVKFGGSS+A+ AQ+ K   I+  D  RK VVVSAPGK + +D K+TDLLI  +E  L
Sbjct: 1   MKVVKFGGSSVANDAQIRKAGSIIADDSERKFVVVSAPGKRFKDDVKITDLLIELSELVL 60

Query: 61  ATGSAPELAEAVVERYALIANELQLGQSIIEKIRDDLFTLLEGDKSNPEQY-LDAVKASG 119
              S  +    ++ R++ I N+L+L QSI+  I   +   L  + ++P+Q   D +K+ G
Sbjct: 61  NNKSHEKKFAEIMARFSEIVNDLELPQSILADIEQSIQNTL--NTNSPDQIKADGLKSIG 118

Query: 120 EDNNAKLIAAYFRYKGVKAEYVNPKDAGLFVTNEPGNAQVLPESYQNLYRLRERDGLIIF 179
           ED++AK+++ + + KG+ A YVNPKDAG+ V+NEPGNAQVLPES+  +Y +R RDG+++ 
Sbjct: 119 EDSSAKIVSEHLKTKGLNAHYVNPKDAGIIVSNEPGNAQVLPESFTKIYEMRARDGILVI 178

Query: 180 PGFFGFSKDGDVITFSRSGSDITGSILANGLQADLYENFTDVDAVYSVNPSFVENPKEIS 239
           PGFFGF+K+G ++TFSR GSDITGSI+A G+QADLYENFTDVD+VY+VNP+ V NP++I+
Sbjct: 179 PGFFGFTKNGGLMTFSRGGSDITGSIVAAGVQADLYENFTDVDSVYAVNPAIVSNPEKIT 238

Query: 240 ELTYREMRELSYAGFSVFHDEALIPAFRAGIPVQIKNTNNPSAEGTRVVSKRDNTNGPVV 299
            LTY+EMRELSY+GF VFHDEAL+PAF+A IPV IKNTNNP++ GT +VS ++     VV
Sbjct: 239 TLTYKEMRELSYSGFGVFHDEALMPAFQAEIPVCIKNTNNPASPGTMIVSDKNPHTRCVV 298

Query: 300 GIASDTGFCSIYISKYLMNREIGFGRRALQILEEHGLTYEHVPSGIDDMTIILRQGQMDA 359
           GIASDTGF ++Y+SKYLMNRE+GFGR+ LQILE+ G+++EH PSGID+M++I+R  Q+ A
Sbjct: 299 GIASDTGFSNLYVSKYLMNRELGFGRKLLQILEDEGISFEHAPSGIDNMSVIIRDSQLTA 358

Query: 360 ATERSVIKRIEEDLHADEVIVEHHLALIMVVGEAMRHNVGTTARAAKALSEAQVNIEMIN 419
             E +VI RI+ +L+ + + +++  A+IMVVGE M   VG   ++A A +EA ++IEMIN
Sbjct: 359 EKEINVINRIKSELNPETISIDYGFAMIMVVGEGMMSAVGIAEKSAAAFAEANISIEMIN 418

Query: 420 QGSSEVSMMFGVKEAEERKAVQALYQEFF 448
           QGSSEVS+MFG+++ +   AV++LYQ+FF
Sbjct: 419 QGSSEVSVMFGIRKDKLDLAVKSLYQKFF 447


Lambda     K      H
   0.316    0.134    0.370 

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: 619
Number of extensions: 19
Number of successful extensions: 2
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: 454
Length of database: 448
Length adjustment: 33
Effective length of query: 421
Effective length of database: 415
Effective search space:   174715
Effective search space used:   174715
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 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate WP_010530910.1 ON01_RS10040 (aspartate kinase)
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.4048514.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.8e-85  273.6   0.8      2e-85  273.4   0.8    1.0  1  NCBI__GCF_000224785.1:WP_010530910.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010530910.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  273.4   0.8     2e-85     2e-85       5     441 ..       3     447 ..       1     448 [] 0.92

  Alignments for each domain:
  == domain 1  score: 273.4 bits;  conditional E-value: 2e-85
                             TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAma.......gvTdaLvelaekvsseee.kelieki 69 
                                           V+KFGG+Sv+n  +i+k+  i+  ++e +   +VVvSA++       ++Td L+el+e v ++++ +++ ++i
  NCBI__GCF_000224785.1:WP_010530910.1   3 VVKFGGSSVANDAQIRKAGSIIADDSERK---FVVVSAPGkrfkddvKITDLLIELSELVLNNKShEKKFAEI 72 
                                           89**********************99555...******98333344459************9999888999** PP

                             TIGR00657  70 rekhlealeela.sqalkeklkallekeleevkk.ereldlilsvGEklSaallaaaleelgvkavsllgaea 140
                                           +++  e+++ l+ +q++ + +++ +++ l+     + + d + s+GE+ Sa+++++ l+++g +a  +  ++a
  NCBI__GCF_000224785.1:WP_010530910.1  73 MARFSEIVNDLElPQSILADIEQSIQNTLNTNSPdQIKADGLKSIGEDSSAKIVSEHLKTKGLNAHYVNPKDA 145
                                           ***********************99999988766577899**********************99999999*** PP

                             TIGR00657 141 giltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiy 213
                                           gi+ ++e g+A+ +  ++  ++ ++   + i v+ GF+G t++g + t  RGGSD+t +++Aa ++Ad  e +
  NCBI__GCF_000224785.1:WP_010530910.1 146 GIIVSNEPGNAQ-VLPESFTKIYEMRARDGILVIPGFFGFTKNGGLMTFSRGGSDITGSIVAAGVQADLYENF 217
                                           ************.66666667777777777******************************************* PP

                             TIGR00657 214 tDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivaks 286
                                           tDVd +y   P iv+++ ++ +++y+E+ EL+++G  v+h ++l pa +a+ip+ +k+t np ++GT+iv+++
  NCBI__GCF_000224785.1:WP_010530910.1 218 TDVDSVYAVNPAIVSNPEKITTLTYKEMRELSYSGFGVFHDEALMPAFQAEIPVCIKNTNNPASPGTMIVSDK 290
                                           ************************************************************************8 PP

                             TIGR00657 287 kseeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkak 357
                                           +  ++  v ++++d+  + + vs+  m+   g+  +++++l++++++ +     ++  ++s ++ ++++ ++k
  NCBI__GCF_000224785.1:WP_010530910.1 291 N-PHTRCVVGIASDTGFSNLYVSKYLMNreLGFGRKLLQILEDEGISFEHAPSGID--NMSVIIRDSQLTAEK 360
                                           8.6679*********************9999******************9985555..677888888765555 PP

                             TIGR00657 358 ellk.kkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..sseikisvvvdek 427
                                           e+   + +k+e + e+++++ ++a++ +vG+gm sa g+a k ++a ae+ni+iemi   sse+++ + ++++
  NCBI__GCF_000224785.1:WP_010530910.1 361 EINViNRIKSELNPETISIDYGFAMIMVVGEGMMSAVGIAEKSAAAFAEANISIEMINqgSSEVSVMFGIRKD 433
                                           553357899*************************************************99************* PP

                             TIGR00657 428 daekavealheklv 441
                                           + + av+ l++k++
  NCBI__GCF_000224785.1:WP_010530910.1 434 KLDLAVKSLYQKFF 447
                                           ************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (448 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 28.31
//
[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