Alignments for a candidate for asp-kinase in Methanococcus aeolicus Nankai-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Methanococcus aeolicus Nankai-3

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011973392.1 MAEO_RS03365 aspartate kinase, monofunctional class

Query= BRENDA::Q57991
         (473 letters)



>NCBI__GCF_000017185.1:WP_011973392.1
          Length = 468

 Score =  622 bits (1604), Expect = 0.0
 Identities = 310/476 (65%), Positives = 399/476 (83%), Gaps = 11/476 (2%)

Query: 1   MTTVMKFGGTSVGSGERIRHVAKIVT-KRKKEDDDVVVVVSAMSEVTNALVEISQQALDV 59
           M TVMKFGGTSVG G+RIR+VAKI+  K  KE+ D+VVV SAMS++TNALV +S+QAL+V
Sbjct: 1   MITVMKFGGTSVGDGQRIRNVAKIIVDKSNKENTDIVVVTSAMSQITNALVNMSKQALNV 60

Query: 60  RDIAKVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGELTP 119
           RDIAK+ +F++ ++EKH  AI+EA+K+++I+ EV+ +I+S I+EL KVL+GV+YLGELTP
Sbjct: 61  RDIAKINNFVEELKEKHAIAIDEAVKNDDIRTEVRHVINSSIDELGKVLVGVSYLGELTP 120

Query: 120 KSRDYILSFGERLSSPILSGAIRDLGEKSIALEGGEAGIITDNNFGSARVKRLEVKERLL 179
           KS+DYILSFGERLS+PILSGA+RDLG+ S+ L GGEAG+ITD N+G AR  ++++KE++ 
Sbjct: 121 KSKDYILSFGERLSAPILSGAVRDLGKNSLFLLGGEAGLITDENYGCARPIKIKIKEKVN 180

Query: 180 PLLKEGIIPVVTGFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVSGVYTTD 239
           PLL+E IIP++TGF+  TE G ITT GRGGSDYSAAL+G GLDAD +EIWTDVSG+ T+D
Sbjct: 181 PLLEENIIPIITGFVAGTENGDITTFGRGGSDYSAALVGAGLDADTVEIWTDVSGILTSD 240

Query: 240 PRLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPESEGTLIT 299
           PR+V   +RIPK+SYIEAMELAYFGAKVLHPRT+EP MEK IP+ +KNTFEPE+EGT IT
Sbjct: 241 PRIVKNVKRIPKMSYIEAMELAYFGAKVLHPRTVEPLMEKNIPLRIKNTFEPENEGTFIT 300

Query: 300 NDMEMSDSIVKAISTIKNVALINIFGAGMVGVSGTAARIFKALGEEEVNVILISQGSSET 359
           N  E+S+S++KA+S I++V LINIFGAGMVGVSGTAARIF ALG  + NV+LI+QGSSET
Sbjct: 301 NCKELSNSVMKAVSAIRDVFLINIFGAGMVGVSGTAARIFSALGRADANVLLITQGSSET 360

Query: 360 NISLVV--SEEDVDKALKALKREFGDFGKKSFLNNNLIRDVSVDKDVCVISVVGAGMRGA 417
           N+S+V+   E D +  +K L++E        F N+NL++D+S+D++V VIS VG GM+G+
Sbjct: 361 NVSVVIYGDEVDANNCMKELRKE--------FKNSNLVKDISIDENVAVISAVGVGMKGS 412

Query: 418 KGIAGKIFTAVSESGANIKMIAQGSSEVNISFVIDEKDLLNCVRKLHEKFIEKTNS 473
           KGIAGK+F AV+ESGANIKMIAQGSSEVNISFVI E++L NC+R LH +FIE   +
Sbjct: 413 KGIAGKLFGAVAESGANIKMIAQGSSEVNISFVIGEEELENCLRILHGRFIENAEN 468


Lambda     K      H
   0.316    0.135    0.364 

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: 778
Number of extensions: 28
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: 473
Length of database: 468
Length adjustment: 33
Effective length of query: 440
Effective length of database: 435
Effective search space:   191400
Effective search space used:   191400
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_011973392.1 MAEO_RS03365 (aspartate kinase, monofunctional class)
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.28179.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-145  471.7   6.9   1.5e-145  471.5   6.9    1.0  1  lcl|NCBI__GCF_000017185.1:WP_011973392.1  MAEO_RS03365 aspartate kinase, m


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017185.1:WP_011973392.1  MAEO_RS03365 aspartate kinase, monofunctional class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  471.5   6.9  1.5e-145  1.5e-145       2     441 ..       1     463 [.       1     464 [. 0.96

  Alignments for each domain:
  == domain 1  score: 471.5 bits;  conditional E-value: 1.5e-145
                                 TIGR00657   2 aliVqKFGGtSvgnverikkvakivkkeke.kgnqvvVVvSAmagvTdaLvelaekvsseee....kel 65 
                                               ++ V+KFGGtSvg+++ri++vaki++ +++ ++ + vVV SAm+++T+aLv++++++ + ++    +++
  lcl|NCBI__GCF_000017185.1:WP_011973392.1   1 MITVMKFGGTSVGDGQRIRNVAKIIVDKSNkENTDIVVVTSAMSQITNALVNMSKQALNVRDiakiNNF 69 
                                               578********************99876650566889999**********************9999999 PP

                                 TIGR00657  66 iekirekhlealeela.sqalkeklkallekeleevkk............ereldlilsvGEklSaall 121
                                               +e+++ekh  a++e+  ++ +++++++++++ ++e+ k            ++++d+ils+GE+lSa++l
  lcl|NCBI__GCF_000017185.1:WP_011973392.1  70 VEELKEKHAIAIDEAVkNDDIRTEVRHVINSSIDELGKvlvgvsylgeltPKSKDYILSFGERLSAPIL 138
                                               **************999*******************99******************************* PP

                                 TIGR00657 122 aaaleelgvkavsllgaeagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLG 190
                                               ++a+++lg +++ llg+eag++td+++g A+ ++  ++e++++llee+ii++++GF++ te+g+itt G
  lcl|NCBI__GCF_000017185.1:WP_011973392.1 139 SGAVRDLGKNSLFLLGGEAGLITDENYGCARPIKIKIKEKVNPLLEENIIPIITGFVAGTENGDITTFG 207
                                               *******************************8888899******************************* PP

                                 TIGR00657 191 RGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlep 259
                                               RGGSD++Aal++a l+Ad vei+tDV+Gi+t DPriv++ +r++++sy Ea+ELa++GakvLhprt+ep
  lcl|NCBI__GCF_000017185.1:WP_011973392.1 208 RGGSDYSAALVGAGLDADTVEIWTDVSGILTSDPRIVKNVKRIPKMSYIEAMELAYFGAKVLHPRTVEP 276
                                               ********************************************************************* PP

                                 TIGR00657 260 amrakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgala 326
                                               +m+++ip+++k+tf+pe+eGT i++ ++ ++ + +ka+s  ++  l+++ g++m   +g++a++f+al 
  lcl|NCBI__GCF_000017185.1:WP_011973392.1 277 LMEKNIPLRIKNTFEPENEGTFITNCKELSN-SVMKAVSAIRDVFLINIFGAGMVgvSGTAARIFSALG 344
                                               **************************98666.9************************************ PP

                                 TIGR00657 327 eakvnvdlilqsssetsisfvvdked..adkakellkkkvkeekaleevevekklalvslvGagmksap 393
                                               +a+ nv li+q sset++s v+  ++  a++  ++l+k++k+ + ++++++++++a++s vG gmk+ +
  lcl|NCBI__GCF_000017185.1:WP_011973392.1 345 RADANVLLITQGSSETNVSVVIYGDEvdANNCMKELRKEFKNSNLVKDISIDENVAVISAVGVGMKGSK 413
                                               ***************99887775555227777777789******************************* PP

                                 TIGR00657 394 gvaakifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441
                                               g+a+k+f a+ae++ ni+mi+  sse++is+v+ e++ e++++ lh +++
  lcl|NCBI__GCF_000017185.1:WP_011973392.1 414 GIAGKLFGAVAESGANIKMIAqgSSEVNISFVIGEEELENCLRILHGRFI 463
                                               ***********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (468 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: 10.38
//
[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