Alignments for a candidate for asp-kinase in Nitratiruptor tergarcus DSM 16512

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Nitratiruptor tergarcus DSM 16512

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_084276585.1 B8779_RS05980 aspartate kinase

Query= SwissProt::Q88EI9
         (411 letters)



>NCBI__GCF_900176045.1:WP_084276585.1
          Length = 401

 Score =  448 bits (1153), Expect = e-130
 Identities = 229/402 (56%), Positives = 313/402 (77%), Gaps = 3/402 (0%)

Query: 3   LIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQPV 62
           LIVQK+GGTSVGS+ERIE VA++V K +EAG+D+VVV+SAMSGETN+LID AK  +  P 
Sbjct: 2   LIVQKYGGTSVGSLERIENVAKRVAKTKEAGNDVVVVVSAMSGETNKLIDYAKHFSPTPS 61

Query: 63  PRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQKIR 122
            R++D+++S+GE+VT ALL++AL + G P V+ TG Q  I+TD SH  ARI +I+ + ++
Sbjct: 62  RRDMDLLLSSGERVTAALLSIALNEMGFPTVAMTGRQAGIVTDKSHTVARIEKINPEPMQ 121

Query: 123 ADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTD 182
             LKEG+++VVAGFQG+ E G +TTLGRGGSD T VA+A AL AD+C+IY+DVDGVYTTD
Sbjct: 122 NALKEGKIIVVAGFQGITEDGQVTTLGRGGSDLTAVAIAGALGADKCEIYSDVDGVYTTD 181

Query: 183 PRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLITI 242
           PR+ P+A++L+KI+++EMLE+ASLG+KVLQ RSVE A K  V +    SF + PGT+IT 
Sbjct: 182 PRIEPKAKKLDKISYDEMLELASLGAKVLQNRSVELAKKLGVVIEARSSFNDNPGTIIT- 240

Query: 243 DEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVAHDN 302
            EE+ ME+P++SGIA ++++A++++RGV D PG+A +I   ++  NI VDMIVQ +  D 
Sbjct: 241 KEEDIMEKPLVSGIALDKNQARVSLRGVKDRPGIAAEIFKALANENINVDMIVQTIGEDG 300

Query: 303 TTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASCMFE 362
            T+  FTV +NE E  + V+E    E    +V  D  +AKVSIVGVGM+SH+GVAS  FE
Sbjct: 301 KTNLDFTVPQNELELVKKVMEQFKDEY--EKVEYDPDVAKVSIVGVGMKSHSGVASKAFE 358

Query: 363 ALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404
            +AKE+INI+MISTSEIK+S++++EKY ELAVRALH A++LD
Sbjct: 359 TMAKENINIEMISTSEIKISMIIDEKYGELAVRALHAAYELD 400


Lambda     K      H
   0.316    0.133    0.358 

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: 467
Number of extensions: 16
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: 411
Length of database: 401
Length adjustment: 31
Effective length of query: 380
Effective length of database: 370
Effective search space:   140600
Effective search space used:   140600
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: 50 (23.9 bits)

Align candidate WP_084276585.1 B8779_RS05980 (aspartate kinase)
to HMM TIGR00656 (aspartate kinase, monofunctional class (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/TIGR00656.hmm
# target sequence database:        /tmp/gapView.7215.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00656  [M=407]
Accession:   TIGR00656
Description: asp_kin_monofn: aspartate kinase, monofunctional class
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.4e-148  479.5  10.2     5e-148  479.4  10.2    1.0  1  lcl|NCBI__GCF_900176045.1:WP_084276585.1  B8779_RS05980 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900176045.1:WP_084276585.1  B8779_RS05980 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.4  10.2    5e-148    5e-148       2     406 ..       1     399 [.       1     400 [. 0.98

  Alignments for each domain:
  == domain 1  score: 479.4 bits;  conditional E-value: 5e-148
                                 TIGR00656   2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 
                                               +liVqK+GGtsvgs eri+++ak+v k+++ g++vvVVvSAms++t++l++ a      + +s  +s+r
  lcl|NCBI__GCF_900176045.1:WP_084276585.1   1 MLIVQKYGGTSVGSLERIENVAKRVAKTKEAGNDVVVVVSAMSGETNKLIDYA------KHFSPTPSRR 63 
                                               79***************************************************......9********* PP

                                 TIGR00656  71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139
                                                +d+l+s GE++++alls al+e g  ++a++g +agi+Td++++ A+i+++++ e + + L+eg+i+v
  lcl|NCBI__GCF_900176045.1:WP_084276585.1  64 DMDLLLSSGERVTAALLSIALNEMGFPTVAMTGRQAGIVTDKSHTVARIEKINP-EPMQNALKEGKIIV 131
                                               ******************************************************.9************* PP

                                 TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208
                                               vaGF+G te+G++TtLGRGGSDltA+++a al Ad++eiy DV+GvyttDPr+ ++akk+dkisy+E+l
  lcl|NCBI__GCF_900176045.1:WP_084276585.1 132 VAGFQGITEDGQVTTLGRGGSDLTAVAIAGALGADKCEIYSDVDGVYTTDPRIEPKAKKLDKISYDEML 200
                                               ********************************************************************* PP

                                 TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltvege 274
                                               elA+lGakvl++r++ela++ +v i+ rss++ + gT it+    +e++ lv++ial+kn+ar++++  
  lcl|NCBI__GCF_900176045.1:WP_084276585.1 201 ELASLGAKVLQNRSVELAKKLGVVIEARSSFNDNPGTIITKeedIMEKP-LVSGIALDKNQARVSLR-- 266
                                               ****************************************976445666.*****************.. PP

                                 TIGR00656 275 gmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleve 340
                                               g+ +++gi+aeifkaLa+e+invd+i+qt +e   t+++++v +++++  kk++++++  +e+e++e++
  lcl|NCBI__GCF_900176045.1:WP_084276585.1 267 GVKDRPGIAAEIFKALANENINVDMIVQTIGEdgkTNLDFTVPQNELELVKKVMEQFK--DEYEKVEYD 333
                                               99****************************99999*******************9996..7888***** PP

                                 TIGR00656 341 edlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                                d+a+vsivg+g+++++Gvas++f+ ++++nini mis+se+kis+++dek+ e avr+lh+++e+
  lcl|NCBI__GCF_900176045.1:WP_084276585.1 334 PDVAKVSIVGVGMKSHSGVASKAFETMAKENINIEMISTSEIKISMIIDEKYGELAVRALHAAYEL 399
                                               ***************************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (401 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: 10.44
//
[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