Alignments for a candidate for asp-kinase in Thermomonospora curvata DSM 43183

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Thermomonospora curvata DSM 43183

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_012855184.1 TCUR_RS23935 aspartate kinase

Query= BRENDA::P9WPX3
         (421 letters)



>NCBI__GCF_000024385.1:WP_012855184.1
          Length = 422

 Score =  577 bits (1487), Expect = e-169
 Identities = 293/422 (69%), Positives = 350/422 (82%), Gaps = 1/422 (0%)

Query: 1   MALVVQKYGGSSVADAERIRRVAERIVATKKQGNDVVVVVSAMGDTTDDLLDLAQQVCPA 60
           MALVVQKYGGSSVADAE ++RVA+RIVATKK GN VVVVVSAMGDTTD+L+DLA+QV P 
Sbjct: 1   MALVVQKYGGSSVADAECVKRVAQRIVATKKAGNSVVVVVSAMGDTTDELIDLAEQVSPL 60

Query: 61  PPPRELDMLLTAGERISNALVAMAIESLGAHARSFTGSQAGVITTGTHGNAKIIDVTPGR 120
           PP RELDMLLTAGERIS AL+AMAI +LG  ARSFTGSQAGVIT G+HG A+IIDVTPGR
Sbjct: 61  PPARELDMLLTAGERISMALLAMAIANLGHEARSFTGSQAGVITDGSHGKARIIDVTPGR 120

Query: 121 LQTALEEGRVVLVAGFQGVSQDTKDVTTLGRGGSDTTAVAMAAALGADVCEIYTDVDGIF 180
           +++AL+EG + +VAGFQGVSQDTKD+TTLGRGGSDTTAVA+AAALGADVCEIYTDVDG+F
Sbjct: 121 IRSALDEGAIAIVAGFQGVSQDTKDITTLGRGGSDTTAVALAAALGADVCEIYTDVDGVF 180

Query: 181 SADPRIVRNARKLDTVTFEEMLEMAACGAKVLMLRCVEYARRHNIPVHVRSSYSDRPGTV 240
           +ADPRIV  AR++  +++EEMLEMAACGAK+L LRCVEYARR++IP+HVRSS+S +PGT 
Sbjct: 181 TADPRIVPTARRIPRISYEEMLEMAACGAKILHLRCVEYARRYDIPIHVRSSFSQKPGTW 240

Query: 241 VVGSIKDVPMEDPILTGVAHDRSEAKVTIVGLPDIPGYAAKVFRAVADADVNIDMVLQNV 300
           +  S +   ME PI++GVAHDRSEAKVT+VG+PD  G AA +F  ++DA +N+DM++QNV
Sbjct: 241 ITDSTEGSEMEQPIISGVAHDRSEAKVTVVGVPDKVGVAATIFSVLSDAGINLDMIVQNV 300

Query: 301 SKVEDGKTDITFTCSRDVGPAAVEKLDSLRNEIGFSQLLYDDHIGKVSLIGAGMRSHPGV 360
           S    G+TDI+FT     G  A+  L+  +++IGF  LLYDD IGKVSLIGAGMRSHPGV
Sbjct: 301 SAAATGRTDISFTLPGTDGQTALTALNKAKDQIGFESLLYDDRIGKVSLIGAGMRSHPGV 360

Query: 361 TATFCEALAAVGVNIELISTSEIRISVLCRDTELDKAVVALHEAFGLGGDE-EATVYAGT 419
           TA F  ALA  GVNIE+ISTSEIRISV+    +++ AV A H AF L  D+ EA VY GT
Sbjct: 361 TAKFFTALADAGVNIEMISTSEIRISVIVSQDDVEAAVNAAHRAFDLDADQIEAVVYGGT 420

Query: 420 GR 421
           GR
Sbjct: 421 GR 422


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: 560
Number of extensions: 21
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: 422
Length adjustment: 32
Effective length of query: 389
Effective length of database: 390
Effective search space:   151710
Effective search space used:   151710
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_012855184.1 TCUR_RS23935 (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.11878.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.6e-135  436.4   8.2   6.3e-135  436.2   8.2    1.0  1  lcl|NCBI__GCF_000024385.1:WP_012855184.1  TCUR_RS23935 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024385.1:WP_012855184.1  TCUR_RS23935 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.2   8.2  6.3e-135  6.3e-135       1     406 [.       1     407 [.       1     408 [. 0.97

  Alignments for each domain:
  == domain 1  score: 436.2 bits;  conditional E-value: 6.3e-135
                                 TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 
                                               + l+VqK+GG+sv++ e +k++a+++++++k g++vvVVvSAm+ +tdel++la      e++s  +  
  lcl|NCBI__GCF_000024385.1:WP_012855184.1   1 MALVVQKYGGSSVADAECVKRVAQRIVATKKAGNSVVVVVSAMGDTTDELIDLA------EQVSPLPPA 63 
                                               579***************************************************......79******* PP

                                 TIGR00656  70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138
                                               re d+l+  GE++s+all++a+ +lg++a++++g +ag++Td+++g+A+i ++ +  r+ + L+eg i 
  lcl|NCBI__GCF_000024385.1:WP_012855184.1  64 RELDMLLTAGERISMALLAMAIANLGHEARSFTGSQAGVITDGSHGKARIIDVTP-GRIRSALDEGAIA 131
                                               *******************************************************.************* PP

                                 TIGR00656 139 vvaGFiGateeG.eiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeE 206
                                               +vaGF+G  ++  +iTtLGRGGSD+tA++laaal Ad +eiyTDV+Gv+t+DPr+v++a++i++isyeE
  lcl|NCBI__GCF_000024385.1:WP_012855184.1 132 IVAGFQGVSQDTkDITTLGRGGSDTTAVALAAALGADVCEIYTDVDGVFTADPRIVPTARRIPRISYEE 200
                                               *******9887638******************************************************* PP

                                 TIGR00656 207 alelAtlGakvlhpralelaveakvpilvrsskekeegTlitn.....kkensslvkaialeknvarlt 270
                                               +le+A  Gak+lh r +e+a ++++pi vrss++++ gT it+     ++e+ ++++++a+++  a++t
  lcl|NCBI__GCF_000024385.1:WP_012855184.1 201 MLEMAACGAKILHLRCVEYARRYDIPIHVRSSFSQKPGTWITDstegsEMEQ-PIISGVAHDRSEAKVT 268
                                               *******************************************555544555.5*************** PP

                                 TIGR00656 271 vegegmlgkrgilaeifkaLaeeeinvdlisqtese.....tsislvvdeedvdeakkaLkeesgaael 334
                                               v+  g+ +k g++a+if++L++++in+d+i+q  s      t+is+++  +d ++a  aL++ ++++++
  lcl|NCBI__GCF_000024385.1:WP_012855184.1 269 VV--GVPDKVGVAATIFSVLSDAGINLDMIVQNVSAaatgrTDISFTLPGTDGQTALTALNKAKDQIGF 335
                                               **..9***************************887667777**************************** PP

                                 TIGR00656 335 esleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhek 403
                                               esl ++  + +vs++gag++++pGv+++ f+al++ ++ni mis+se++isv+v++ d+e av++ h++
  lcl|NCBI__GCF_000024385.1:WP_012855184.1 336 ESLLYDDRIGKVSLIGAGMRSHPGVTAKFFTALADAGVNIEMISTSEIRISVIVSQDDVEAAVNAAHRA 404
                                               ********************************************************************9 PP

                                 TIGR00656 404 lee 406
                                               + +
  lcl|NCBI__GCF_000024385.1:WP_012855184.1 405 FDL 407
                                               976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (422 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 8.51
//
[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