Alignments for a candidate for asp-kinase in Saccharomonospora cyanea NA-134

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Saccharomonospora cyanea NA-134

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_005459952.1 SACCYDRAFT_RS23295 aspartate kinase

Query= BRENDA::P9WPX3
         (421 letters)



>NCBI__GCF_000244975.1:WP_005459952.1
          Length = 420

 Score =  615 bits (1587), Expect = 0.0
 Identities = 308/421 (73%), Positives = 364/421 (86%), Gaps = 1/421 (0%)

Query: 1   MALVVQKYGGSSVADAERIRRVAERIVATKKQGNDVVVVVSAMGDTTDDLLDLAQQVCPA 60
           MALVVQKYGGSS+  A+RI+RVAERIVATKK GN VVVV SAMGDTTD+LLDLAQQV P 
Sbjct: 1   MALVVQKYGGSSLESADRIKRVAERIVATKKAGNQVVVVCSAMGDTTDELLDLAQQVNPV 60

Query: 61  PPPRELDMLLTAGERISNALVAMAIESLGAHARSFTGSQAGVITTGTHGNAKIIDVTPGR 120
           PP RE+DMLLTAGERISNALVAMAI + GA A SFTGSQAGV+TT  HGNA+IIDVTP R
Sbjct: 61  PPEREMDMLLTAGERISNALVAMAISAQGAEAWSFTGSQAGVVTTSVHGNARIIDVTPSR 120

Query: 121 LQTALEEGRVVLVAGFQGVSQDTKDVTTLGRGGSDTTAVAMAAALGADVCEIYTDVDGIF 180
           +  ALE+G + LVAGFQGVSQDTKD+TTLGRGGSDTTAVA+AAAL ADVCEIY+DVDG++
Sbjct: 121 VTEALEQGYIALVAGFQGVSQDTKDITTLGRGGSDTTAVAVAAALDADVCEIYSDVDGVY 180

Query: 181 SADPRIVRNARKLDTVTFEEMLEMAACGAKVLMLRCVEYARRHNIPVHVRSSYSDRPGTV 240
           +ADPRIV NARKLDT+ +EEMLE+AA G+K+L LR VEYARR+ +P+ VRSSYSD+PGT 
Sbjct: 181 TADPRIVSNARKLDTIPYEEMLELAASGSKILHLRSVEYARRYGVPIRVRSSYSDKPGTT 240

Query: 241 VVGSIKDVPMEDPILTGVAHDRSEAKVTIVGLPDIPGYAAKVFRAVADADVNIDMVLQNV 300
           V GSI+++P+E  ++TGVAHDRSEAK+T+ G+PD  G A ++FRAVADA+++IDMVLQN+
Sbjct: 241 VTGSIEEIPVEQALITGVAHDRSEAKITVTGVPDHAGAAGRIFRAVADAEIDIDMVLQNI 300

Query: 301 SKVEDGKTDITFTCSRDVGPAAVEKLDSLRNEIGFSQLLYDDHIGKVSLIGAGMRSHPGV 360
           S    G+TDITFT S+  GP AV +L+ ++ E+ FS +LYDDH+GKVSL+GAGMRSHPGV
Sbjct: 301 SNT-TGRTDITFTLSKANGPKAVSELEKIKAELDFSAVLYDDHVGKVSLVGAGMRSHPGV 359

Query: 361 TATFCEALAAVGVNIELISTSEIRISVLCRDTELDKAVVALHEAFGLGGDEEATVYAGTG 420
           TATFCEALA  GVNIE+I+TSEIRISVL RD +LD AV A+HEAF LGGDEEA VYAG+G
Sbjct: 360 TATFCEALAKAGVNIEIINTSEIRISVLIRDEQLDDAVRAIHEAFELGGDEEAVVYAGSG 419

Query: 421 R 421
           R
Sbjct: 420 R 420


Lambda     K      H
   0.318    0.134    0.376 

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: 572
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: 421
Length of database: 420
Length adjustment: 32
Effective length of query: 389
Effective length of database: 388
Effective search space:   150932
Effective search space used:   150932
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_005459952.1 SACCYDRAFT_RS23295 (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.24276.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-139  451.6   9.8   2.2e-136  441.4   9.8    2.0  1  lcl|NCBI__GCF_000244975.1:WP_005459952.1  SACCYDRAFT_RS23295 aspartate kin


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000244975.1:WP_005459952.1  SACCYDRAFT_RS23295 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.4   9.8  2.2e-136  2.2e-136       1     441 [.       1     405 [.       1     406 [. 0.98

  Alignments for each domain:
  == domain 1  score: 441.4 bits;  conditional E-value: 2.2e-136
                                 TIGR00657   1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekelieki 69 
                                               mal+VqK+GG+S+ +++rik+va++++++k+ gnqvvVV+SAm+++Td+L++la++v++ +        
  lcl|NCBI__GCF_000244975.1:WP_005459952.1   1 MALVVQKYGGSSLESADRIKRVAERIVATKKAGNQVVVVCSAMGDTTDELLDLAQQVNPVP-------- 61 
                                               899**********************************************************........ PP

                                 TIGR00657  70 rekhlealeelasqalkeklkallekeleevkkereldlilsvGEklSaallaaaleelgvkavsllga 138
                                                           +                    ere+d++l+ GE++S al+a+a++++g++a s++g+
  lcl|NCBI__GCF_000244975.1:WP_005459952.1  62 ------------P--------------------EREMDMLLTAGERISNALVAMAISAQGAEAWSFTGS 98 
                                               ............7....................8*********************************** PP

                                 TIGR00657 139 eagiltdsefgrAkvleeikterleklleegiivvvaGFiGat.ekgeittLGRGGSDltAallAaalk 206
                                               +ag++t+s +g+A+ +++++ +r++++le+g+i +vaGF+G++ ++++ittLGRGGSD+tA+++Aaal+
  lcl|NCBI__GCF_000244975.1:WP_005459952.1  99 QAGVVTTSVHGNAR-IIDVTPSRVTEALEQGYIALVAGFQGVSqDTKDITTLGRGGSDTTAVAVAAALD 166
                                               **************.**************************9968899********************* PP

                                 TIGR00657 207 AdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnp 275
                                               Ad++eiy DVdG+ytaDPriv++Ar+ld+i yeE+lELa +G+k+Lh r++e+a+r+++pi+v+s++++
  lcl|NCBI__GCF_000244975.1:WP_005459952.1 167 ADVCEIYSDVDGVYTADPRIVSNARKLDTIPYEEMLELAASGSKILHLRSVEYARRYGVPIRVRSSYSD 235
                                               ********************************************************************* PP

                                 TIGR00657 276 eaeGTlivaksk..seeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlilqssset 342
                                               + +GT ++++ +  + e+  ++++++d+++a+++v g+++++g + ++f+a+a+a++++d++lq++s+t
  lcl|NCBI__GCF_000244975.1:WP_005459952.1 236 K-PGTTVTGSIEeiPVEQALITGVAHDRSEAKITVTGVPDHAGAAGRIFRAVADAEIDIDMVLQNISNT 303
                                               9.********999977779************************************************66 PP

                                 TIGR00657 343 s....isfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeen 407
                                               +    i+f+++k + +ka+++l +k+k+e +++ v +++++ +vslvGagm+s+pgv+a+++eaLa+++
  lcl|NCBI__GCF_000244975.1:WP_005459952.1 304 TgrtdITFTLSKANGPKAVSEL-EKIKAELDFSAVLYDDHVGKVSLVGAGMRSHPGVTATFCEALAKAG 371
                                               66889****************8.57******************************************** PP

                                 TIGR00657 408 iniemissseikisvvvdekdaekavealheklv 441
                                               +nie+i +sei+isv++++++ + av+a+he+++
  lcl|NCBI__GCF_000244975.1:WP_005459952.1 372 VNIEIINTSEIRISVLIRDEQLDDAVRAIHEAFE 405
                                               *******************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (420 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 4.28
//
[ok]

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