Alignments for a candidate for asp-kinase in Nocardiopsis lucentensis DSM 44048

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Nocardiopsis lucentensis DSM 44048

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_083924279.1 D471_RS0121390 aspartate kinase

Query= BRENDA::P26512
         (421 letters)



>NCBI__GCF_000341125.1:WP_083924279.1
          Length = 435

 Score =  280 bits (716), Expect = 6e-80
 Identities = 178/416 (42%), Positives = 238/416 (57%), Gaps = 25/416 (6%)

Query: 5   VQKYGGSSLESAERIRNVAERIVATKKAGNDVVVVCSAMGDTTDELLELAAAVNPVPPAR 64
           V K+GGSSL + ER+R  A R  A  ++G  + VV SA GDTTD LL  AA V      R
Sbjct: 29  VWKFGGSSLATTERVRAAARRAGAAYRSGGPLAVVVSAQGDTTDALLSRAADVGSTAAGR 88

Query: 65  EMDMLLTAGERISNALVAMAIESLGAEAQSFTGSQAGVLTTERHGNARIVDVTPGRVREA 124
           E+D LL  GE  S AL+A+A++ LG  A + TGSQ+G+L T RHG   +V V P R+   
Sbjct: 89  ELDQLLATGENASAALMAIALQGLGVPAVAVTGSQSGILATGRHGTGVVVAVDPERILRV 148

Query: 125 LDEGKICIVAGFQGVNKETRDVTTLGRGGSDTTAVALAAALNADVCEIYSDVDGVYTADP 184
           LD GK+ +VAGFQG N+E  DV TLGRGGSD++A ALAA L A  C+I +DV GVYTADP
Sbjct: 149 LDGGKVAVVAGFQGTNEE-GDVITLGRGGSDSSAAALAAGLGAHDCDILTDVAGVYTADP 207

Query: 185 RIVPNAQKLEKLSFEEMLELAAVGSKILVLRSVEYARAFNVPLRVRSSYSNDPGTLI--- 241
           RI P+AQ +  +  + M E+A  G++++  R+VE A   +V LRVRSS+   PGT I   
Sbjct: 208 RICPSAQLMPVVPNDVMAEMAFAGARVMHTRAVEIAALHDVELRVRSSFEQTPGTRIPLR 267

Query: 242 --AGSMEDIPVEEAVLTGVATDKSEAKVTVLGISDKPGEAAKVFRALADAEINIDMVLQN 299
              G +E +P   AV+     D   A+V +          A ++R LA   I +DM    
Sbjct: 268 GDGGMVETVPAAWAVV----HDLDVARVELSAGGAGGATVADLYRRLARRGITVDM---- 319

Query: 300 VSSVEDGTTDIT--FTCPRSD---GRRAMEILKKLQVQG-NWTNVLYDDQVGKVSLVGAG 353
           V S  DG   +T   T  RSD    RRA+E     +V G +   V+ D++V +VS+VG G
Sbjct: 320 VGSARDGRGGLTSGMTVRRSDVPEVRRALE-----RVAGPSRGRVVVDEEVARVSVVGTG 374

Query: 354 MKSHPGVTAEFMEALRDVNVNIELISTSEIRISVLIREDDLDAAARALHEQFQLGG 409
           + S P  TA  +  LR   +    +STS+ RI V +       A R LH++F L G
Sbjct: 375 LLSRPEYTARMLSCLRTAGIEASALSTSQARICVTVPSASATLAVRRLHQEFGLDG 430


Lambda     K      H
   0.314    0.131    0.355 

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: 403
Number of extensions: 16
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: 421
Length of database: 435
Length adjustment: 32
Effective length of query: 389
Effective length of database: 403
Effective search space:   156767
Effective search space used:   156767
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: 42 (22.0 bits)
S2: 51 (24.3 bits)

Align candidate WP_083924279.1 D471_RS0121390 (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.3355.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.3e-96  310.4   0.2    4.8e-84  268.9   0.1    2.0  2  lcl|NCBI__GCF_000341125.1:WP_083924279.1  D471_RS0121390 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000341125.1:WP_083924279.1  D471_RS0121390 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   1.2e-14   1.2e-14       5      57 ..      29      81 ..      26      86 .. 0.93
   2 !  268.9   0.1   4.8e-84   4.8e-84     103     441 ..      87     427 ..      78     428 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.2e-14
                                 TIGR00657  5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekv 57
                                              V KFGG+S+++ er++++a++  +++++g + +VVvSA +++TdaL++ a  v
  lcl|NCBI__GCF_000341125.1:WP_083924279.1 29 VWKFGGSSLATTERVRAAARRAGAAYRSGGPLAVVVSAQGDTTDALLSRAADV 81
                                              89********************************************9987665 PP

  == domain 2  score: 268.9 bits;  conditional E-value: 4.8e-84
                                 TIGR00657 103 ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterleklleegii 171
                                                reld +l++GE+ Saal+a al+ lgv av+++g+++gil+++++g  + ++ ++ er++ +l+ g++
  lcl|NCBI__GCF_000341125.1:WP_083924279.1  87 GRELDQLLATGENASAALMAIALQGLGVPAVAVTGSQSGILATGRHGTGV-VVAVDPERILRVLDGGKV 154
                                               689***********************************************.****************** PP

                                 TIGR00657 172 vvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeE 240
                                                vvaGF+G++e+g++ tLGRGGSD +Aa+lAa l+A+ ++i tDV G+ytaDPri p+A++++ +  + 
  lcl|NCBI__GCF_000341125.1:WP_083924279.1 155 AVVAGFQGTNEEGDVITLGRGGSDSSAAALAAGLGAHDCDILTDVAGVYTADPRICPSAQLMPVVPNDV 223
                                               ********************************************************************* PP

                                 TIGR00657 241 alELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivaksk...seeepavkalsldknqalv 306
                                               ++E+a  Ga+v+h r++e+a+ ++++++v+s+f+++ +GT i    +   +e  pa  a+ +d + a+v
  lcl|NCBI__GCF_000341125.1:WP_083924279.1 224 MAEMAFAGARVMHTRAVEIAALHDVELRVRSSFEQT-PGTRIPLRGDggmVETVPAAWAVVHDLDVARV 291
                                               ***********************************9.*****999889988888999************ PP

                                 TIGR00657 307 svsgttmkpgilaevfgalaeakvnvdlilqsss.ets...isfvvdkedadkakellkkkvkeekale 371
                                               ++s  +    ++a++ ++la++++ vd++    + + +     ++v ++d+++  ++l++   +    +
  lcl|NCBI__GCF_000341125.1:WP_083924279.1 292 ELSAGGAGGATVADLYRRLARRGITVDMVGSARDgR-GgltSGMTVRRSDVPEVRRALER--VAGPSRG 357
                                               *****************************9665542.244458**************964..5566667 PP

                                 TIGR00657 372 evevekklalvslvGagmksapgvaakifeaLaeeniniemissseikisvvvdekdaekavealhekl 440
                                               +v v++++a vs+vG g+ s+p  +a++++ L+ ++i   ++s+s+ +i+v v++  a+ av+ lh+++
  lcl|NCBI__GCF_000341125.1:WP_083924279.1 358 RVVVDEEVARVSVVGTGLLSRPEYTARMLSCLRTAGIEASALSTSQARICVTVPSASATLAVRRLHQEF 426
                                               8******************************************************************99 PP

                                 TIGR00657 441 v 441
                                                
  lcl|NCBI__GCF_000341125.1:WP_083924279.1 427 G 427
                                               6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (435 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: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 3.23
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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