Alignments for a candidate for asp-kinase in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Sphingomonas koreensis DSMZ 15582

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate Ga0059261_2519 Ga0059261_2519 aspartate kinase (EC 2.7.2.4)

Query= BRENDA::O69077
         (412 letters)



>FitnessBrowser__Korea:Ga0059261_2519
          Length = 419

 Score =  414 bits (1064), Expect = e-120
 Identities = 229/414 (55%), Positives = 291/414 (70%), Gaps = 7/414 (1%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60
           MA IV KFGGTS+  +ERI  VA +VK   EAG+ V VVVSAM+GET+RL+G   +    
Sbjct: 1   MARIVMKFGGTSMAGIERIRNVANRVKAEWEAGNQVAVVVSAMAGETDRLVGFCREASPL 60

Query: 61  PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120
              RE D +VS GEQVT  LL++AL   GVPA S+ G Q+ I T SAH  ARI  ID T 
Sbjct: 61  YDLREYDTVVSAGEQVTSGLLAIALQAIGVPARSWLGWQLPIHTSSAHASARIGTIDTTE 120

Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           + A L  G V V+ GFQG+  +  +TTLGRGGSDT+ VA+AAA+KAD C IYTDVDGVYT
Sbjct: 121 LNASLADGNVAVIPGFQGLAEDNRVTTLGRGGSDTSAVAVAAAMKADRCDIYTDVDGVYT 180

Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEG----- 235
           TDPR+VP+AR+L K+T+EEMLE+AS+G+KVLQ R+V  A K  V +RVL S ++      
Sbjct: 181 TDPRIVPRARKLSKVTYEEMLELASVGAKVLQTRSVGLAMKEGVRVRVLSSLEDNRDEEG 240

Query: 236 -PGTLITIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDM 294
             GTLI  ++E   +E+ +I+GIA +++EAK+T+  VPD PG    I  P++ A + VDM
Sbjct: 241 HRGTLIVGEEEINDVERQLITGIAADKNEAKVTLTNVPDRPGAVGHIFTPLAEAGINVDM 300

Query: 295 IVQNVAH-DNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRS 353
           IVQNVAH   +TD TFTV R +   AL++L+++ A IG    I DT +AK+S+VGVGMRS
Sbjct: 301 IVQNVAHATGSTDVTFTVPRAELARALDVLEKSKAPIGYDALIHDTKVAKISVVGVGMRS 360

Query: 354 HAGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAP 407
           HAGVA+ MFE L +  INI  I+TSEIKVSV+I E   ELAVR LHTA+ LDAP
Sbjct: 361 HAGVAATMFETLGERRINILAITTSEIKVSVLIHEDETELAVRVLHTAYGLDAP 414


Lambda     K      H
   0.317    0.133    0.362 

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: 468
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: 412
Length of database: 419
Length adjustment: 31
Effective length of query: 381
Effective length of database: 388
Effective search space:   147828
Effective search space used:   147828
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 Ga0059261_2519 Ga0059261_2519 (aspartate kinase (EC 2.7.2.4))
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.10339.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-132  427.9   8.1   4.2e-111  358.1   3.5    2.0  2  lcl|FitnessBrowser__Korea:Ga0059261_2519  Ga0059261_2519 aspartate kinase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_2519  Ga0059261_2519 aspartate kinase (EC 2.7.2.4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.1   1.8e-24   1.8e-24       1      59 [.       1      59 [.       1      62 [. 0.97
   2 !  358.1   3.5  4.2e-111  4.2e-111     104     440 ..      64     409 ..      60     411 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 1.8e-24
                                 TIGR00657  1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvss 59
                                              ma+iV+KFGGtS++ +eri++va++vk+e e gnqv+VVvSAmag Td+Lv +++++s+
  lcl|FitnessBrowser__Korea:Ga0059261_2519  1 MARIVMKFGGTSMAGIERIRNVANRVKAEWEAGNQVAVVVSAMAGETDRLVGFCREASP 59
                                              799****************************************************9986 PP

  == domain 2  score: 358.1 bits;  conditional E-value: 4.2e-111
                                 TIGR00657 104 reldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterleklleegiiv 172
                                               re+d+++s GE++++ lla al++ gv a+s+lg++ +i t+s++ +A+ + +i+t +l++ l  g + 
  lcl|FitnessBrowser__Korea:Ga0059261_2519  64 REYDTVVSAGEQVTSGLLAIALQAIGVPARSWLGWQLPIHTSSAHASAR-IGTIDTTELNASLADGNVA 131
                                               89***********************************************.******************* PP

                                 TIGR00657 173 vvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEa 241
                                               v+ GF+G+ e++++ttLGRGGSD++A+++Aaa+kAd+++iytDVdG+yt+DPrivp Ar+l +++yeE+
  lcl|FitnessBrowser__Korea:Ga0059261_2519 132 VIPGFQGLAEDNRVTTLGRGGSDTSAVAVAAAMKADRCDIYTDVDGVYTTDPRIVPRARKLSKVTYEEM 200
                                               ********************************************************************* PP

                                 TIGR00657 242 lELaslGakvLhprtlepamrakipivvkstfnpe.....aeGTlivaksk..seeepavkalsldknq 303
                                               lELas+GakvL+ r++ +am+ +++++v s+ +++       GTliv++++  + e++ +++++ dkn+
  lcl|FitnessBrowser__Korea:Ga0059261_2519 201 LELASVGAKVLQTRSVGLAMKEGVRVRVLSSLEDNrdeegHRGTLIVGEEEinDVERQLITGIAADKNE 269
                                               ****************************999876522222469******9998667799********** PP

                                 TIGR00657 304 alvsvsgttmkpgilaevfgalaeakvnvdlilqsssets....isfvvdkedadkakellkkkvkeek 368
                                               a+v++  ++++pg + ++f+ laea++nvd+i+q++ + +    ++f+v++ ++ +a  +l +k k+  
  lcl|FitnessBrowser__Korea:Ga0059261_2519 270 AKVTLTNVPDRPGAVGHIFTPLAEAGINVDMIVQNVAHATgstdVTFTVPRAELARALDVL-EKSKAPI 337
                                               ***********************************994444678****************8.5699999 PP

                                 TIGR00657 369 aleevevekklalvslvGagmksapgvaakifeaLaeeniniemissseikisvvvdekdaekavealh 437
                                                   +  ++k+a++s+vG gm+s+ gvaa++fe+L e+ ini +i +seik+sv+++e++ e av++lh
  lcl|FitnessBrowser__Korea:Ga0059261_2519 338 GYDALIHDTKVAKISVVGVGMRSHAGVAATMFETLGERRINILAITTSEIKVSVLIHEDETELAVRVLH 406
                                               ********************************************************************* PP

                                 TIGR00657 438 ekl 440
                                                ++
  lcl|FitnessBrowser__Korea:Ga0059261_2519 407 TAY 409
                                               998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (419 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 4.08
//
[ok]

This GapMind analysis is from Apr 09 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