Alignments for a candidate for asp-kinase in Desulfuromusa kysingii DSM 7343

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Desulfuromusa kysingii DSM 7343

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_092344162.1 BLU87_RS01505 aspartate kinase

Query= BRENDA::Q97MC0
         (437 letters)



>NCBI__GCF_900107645.1:WP_092344162.1
          Length = 433

 Score =  317 bits (811), Expect = 6e-91
 Identities = 175/427 (40%), Positives = 262/427 (61%), Gaps = 5/427 (1%)

Query: 5   VTKFGGSSLADSNQFKKVKGIIDSDANRKYIIPSAPGKRTNKDYKITDLLYLCNAHVKNG 64
           V KFGG+SLA + Q KK   II +D  R+ ++ SAPGKR N+D KITDLL   +     G
Sbjct: 3   VVKFGGTSLASAAQIKKAVEIIQADDQRQAVVLSAPGKRDNQDTKITDLLINTHKQKTAG 62

Query: 65  IPFDDVFKLISQRYTEIVSELNIDMDIAYYLEKVKKNIENGASSDYAASRGEYLNGVILA 124
             +   F+ I  R+ E+   L +D++IA  L+ +++ I  G + D+  SRGEYLN +I+A
Sbjct: 63  EEYLPTFEKIRARFVELSELLEVDVNIAAELDVIEQKITAGTTLDFVESRGEYLNSLIIA 122

Query: 125 KYLNAEFIDAAEVIFFDKSGCFDEKKSYEKIKEKVLSCN-KAVIPGFYGSSFNGDVKTFS 183
           KYL AEF+DAA V+     G  D + SYE I +++ +   + V+PGFYG+  +G++KTFS
Sbjct: 123 KYLGAEFVDAANVVRLTIDGRVDPE-SYELISKQLGNATGRFVVPGFYGTGPDGEIKTFS 181

Query: 184 RGGSDVTGSIISAGVNADLYENWTDVSGFLMADPRIVENPKTISKISYKELRELSYMGAT 243
           RGGSD+TG+I++ GVNAD+YENWTDVSG L ADPRIV   ++I +I+Y E+REL+  GA+
Sbjct: 182 RGGSDITGAIVARGVNADVYENWTDVSGILQADPRIVPAAQSIPEITYAEVRELASCGAS 241

Query: 244 VLHEEAIFPVKDSGIPINIKNTNKPSDPGTLILSDTHKEINLGTITGIAGKKNFTVIAIE 303
           V HEEAI PV+D+ IPINIKNTN P+D GT+I     +      + G++GKK + ++  E
Sbjct: 242 VFHEEAIAPVRDAKIPINIKNTNSPADCGTMI--QPTRSAEKMPVVGVSGKKPYRILNAE 299

Query: 304 KALLNSEVGFCRKILSILEMYGVSFEHMPSGVDSVSLVIEDCKLDGKCDKIIEEIKKQCN 363
           K +LN       +I   L    ++ E    G DS +L++ D   +   + I + I ++  
Sbjct: 300 KFMLNRYPELPGQIKEALTQQDLAVEFDMKGFDSFALMV-DSSSNFDENAICKYILEKTE 358

Query: 364 PDSIEIHPNMALVATVGTGMAKTKGIANKIFTALSKENVNIRMIDQGSSEINVIVGVETV 423
            D+      +ALV  VG G+    G+  ++ +AL +  + IR I  G S++  ++ +   
Sbjct: 359 VDACSFGMTVALVGIVGAGLQSQTGLLGRMLSALDQAEIGIRSISYGGSQLTALLAINLE 418

Query: 424 DFEKAVK 430
           D+E  +K
Sbjct: 419 DYENTLK 425


Lambda     K      H
   0.316    0.135    0.379 

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: 458
Number of extensions: 15
Number of successful extensions: 3
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: 437
Length of database: 433
Length adjustment: 32
Effective length of query: 405
Effective length of database: 401
Effective search space:   162405
Effective search space used:   162405
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_092344162.1 BLU87_RS01505 (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.2256394.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.6e-73  232.7   0.1    1.4e-72  231.1   0.1    1.6  1  NCBI__GCF_900107645.1:WP_092344162.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900107645.1:WP_092344162.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.1   0.1   1.4e-72   1.4e-72       5     441 ..       3     432 ..       1     433 [] 0.83

  Alignments for each domain:
  == domain 1  score: 231.1 bits;  conditional E-value: 1.4e-72
                             TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmag.......vTdaLvelaekvsseee.kelieki 69 
                                           V+KFGGtS++++ +ikk+++i++++++ +   +VV+SA+++       +Td L+++ ++   +ee   + eki
  NCBI__GCF_900107645.1:WP_092344162.1   3 VVKFGGTSLASAAQIKKAVEIIQADDQRQ---AVVLSAPGKrdnqdtkITDLLINTHKQKTAGEEyLPTFEKI 72 
                                           89************************665...******98622222226666666666655555455556677 PP

                             TIGR00657  70 rekhlealeela.sqalkeklkallekeleevkkereldlilsvGEklSaallaaaleelgvkavsllgaeag 141
                                           r++ +e  e l+   +++    a l+   +++ +  +ld + s+GE l + ++a +l ++ v+a++++     
  NCBI__GCF_900107645.1:WP_092344162.1  73 RARFVELSELLEvDVNIA----AELDVIEQKITAGTTLDFVESRGEYLNSLIIAKYLGAEFVDAANVVR---- 137
                                           776666666555444344....44444444455579*********************999866665554.... PP

                             TIGR00657 142 iltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiyt 214
                                            lt +   + +  +e ++++l ++       vv GF G+ ++gei t  RGGSD+t a++A  ++Ad+ e +t
  NCBI__GCF_900107645.1:WP_092344162.1 138 -LTIDGRVDPE-SYELISKQLGNAT---GRFVVPGFYGTGPDGEIKTFSRGGSDITGAIVARGVNADVYENWT 205
                                           .4444333333.3455555555544...45799**************************************** PP

                             TIGR00657 215 DVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivaksk 287
                                           DV+Gi+ aDPrivp A+ ++ei+y+E  ELas+Ga v+h +++ p++ akipi +k+t +p   GT+i ++++
  NCBI__GCF_900107645.1:WP_092344162.1 206 DVSGILQADPRIVPAAQSIPEITYAEVRELASCGASVFHEEAIAPVRDAKIPINIKNTNSPADCGTMIQPTRS 278
                                           ***********************************************************************88 PP

                             TIGR00657 288 seeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkake 358
                                             e+ +v ++s +k   ++++++   +  p+   ++ +al++++  v+  ++  +  s +++vd ++   +++
  NCBI__GCF_900107645.1:WP_092344162.1 279 A-EKMPVVGVSGKKPYRILNAEKFMLNryPELPGQIKEALTQQDLAVEFDMKGFD--SFALMVDSSSNFDENA 348
                                           5.5588999999999999999999999999999***********99998886666..7889999887555555 PP

                             TIGR00657 359 llkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..sseikisvvvdekda 429
                                           +  k ++e+ ++   ++   +alv +vGag++s+ g+++++++aL +++i i+ is   s+    + ++ +d 
  NCBI__GCF_900107645.1:WP_092344162.1 349 I-CKYILEKTEVDACSFGMTVALVGIVGAGLQSQTGLLGRMLSALDQAEIGIRSISygGSQLTALLAINLEDY 420
                                           5.4789**************************************************98899999999****** PP

                             TIGR00657 430 ekavealheklv 441
                                           e+++++l ++l+
  NCBI__GCF_900107645.1:WP_092344162.1 421 ENTLKVLVAQLQ 432
                                           *****9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (433 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 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 11.47
//
[ok]

This GapMind analysis is from Jul 25 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:

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