Alignments for a candidate for asp-kinase in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Dinoroseobacter shibae DFL-12

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 3608668 Dshi_2061 aspartate kinase (RefSeq)

Query= BRENDA::O69077
         (412 letters)



>FitnessBrowser__Dino:3608668
          Length = 412

 Score =  415 bits (1067), Expect = e-120
 Identities = 222/412 (53%), Positives = 293/412 (71%), Gaps = 4/412 (0%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60
           M+++V KFGGTSV  +++I+  AEKV++    G  V+V+VSAMSG+TN L+G   +    
Sbjct: 1   MSILVMKFGGTSVADLDKIKNAAEKVQREVARGHKVIVIVSAMSGKTNELVGWVGKTSPL 60

Query: 61  PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120
              RE D +VS+GE VT  LL++ L +  +PA S+ G QV + T+SAH  ARI  I   +
Sbjct: 61  YDAREYDAVVSSGENVTAGLLALTLQEMEIPARSWQGWQVPLRTNSAHAAARIEEIPRAN 120

Query: 121 IRADLKAG-RVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVY 179
           + A    G +V V+AGFQG+   G ITTLGRGGSDTT VA AAA  A  C IYTDVDGVY
Sbjct: 121 LDAKFDEGMQVAVIAGFQGISPEGRITTLGRGGSDTTAVAFAAAFGAVRCDIYTDVDGVY 180

Query: 180 TTDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTL 239
           TTDPR+  +AR+LD+I +EEMLE+ASLG+KVLQ R+VE A ++ VPLRVL SF+E   T 
Sbjct: 181 TTDPRIEDKARKLDRIAYEEMLELASLGAKVLQTRSVELAMRFKVPLRVLSSFEENTDTS 240

Query: 240 IT-IDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQN 298
            T + DE+E ME  ++SG+A++RDEAK+T+  V D PG+A  I GP+S A V VDMIVQN
Sbjct: 241 GTLVCDEDEIMESNVVSGVAYSRDEAKMTLISVADRPGIAAAIFGPLSEAGVNVDMIVQN 300

Query: 299 VAHDNTTDFTFTVHRNDYLNALEILKQT--AANIGAREAIGDTNIAKVSIVGVGMRSHAG 356
           ++ D  TD TF+   +  L A   +K+      I  +E + DT++AKVS+VG+GMRSHAG
Sbjct: 301 ISEDGRTDMTFSCPTDQVLRAERAIKEAKELGEINFQELVADTDVAKVSVVGIGMRSHAG 360

Query: 357 VASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPA 408
           VA+RMF+AL  E INI++I+TSEIK+SV+IE KY+ELAV+ALH AFELD  A
Sbjct: 361 VAARMFQALRDEGINIRVITTSEIKISVLIERKYMELAVQALHDAFELDRAA 412


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: 424
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: 412
Length of database: 412
Length adjustment: 31
Effective length of query: 381
Effective length of database: 381
Effective search space:   145161
Effective search space used:   145161
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 3608668 Dshi_2061 (aspartate kinase (RefSeq))
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.31056.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.5e-127  410.7   6.5   3.9e-127  410.5   6.5    1.0  1  lcl|FitnessBrowser__Dino:3608668  Dshi_2061 aspartate kinase (RefS


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608668  Dshi_2061 aspartate kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.5   6.5  3.9e-127  3.9e-127       1     406 [.       1     408 [.       1     409 [. 0.96

  Alignments for each domain:
  == domain 1  score: 410.5 bits;  conditional E-value: 3.9e-127
                         TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerdelvs 77 
                                       +++ V+KFGGtsv++ ++ik+aa++v +e+ +g+kv+V+vSAms++t+elv  +       ++s     re d +vs
  lcl|FitnessBrowser__Dino:3608668   1 MSILVMKFGGTSVADLDKIKNAAEKVQREVARGHKVIVIVSAMSGKTNELVGWV------GKTSPLYDAREYDAVVS 71 
                                       5799**************************************************......68899999********* PP

                         TIGR00656  78 vGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegi.ivvvaGFiGateeGeiT 153
                                        GE +++ ll+  l+e +  a++ +g++ +++T++ +  A+i+e+    +L    +eg+ + v+aGF+G   eG+iT
  lcl|FitnessBrowser__Dino:3608668  72 SGENVTAGLLALTLQEMEIPARSWQGWQVPLRTNSAHAAARIEEIPR-ANLDAKFDEGMqVAVIAGFQGISPEGRIT 147
                                       *********************************************99.99*****9996388*************** PP

                         TIGR00656 154 tLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpralelaveak 230
                                       tLGRGGSD+tA++ aaa  A r++iyTDV+GvyttDPr+ ++a+k+d+i+yeE+lelA+lGakvl+ r++ela++ k
  lcl|FitnessBrowser__Dino:3608668 148 TLGRGGSDTTAVAFAAAFGAVRCDIYTDVDGVYTTDPRIEDKARKLDRIAYEEMLELASLGAKVLQTRSVELAMRFK 224
                                       ***************************************************************************** PP

                         TIGR00656 231 vpilvrsskeke...egTlitn...kkensslvkaialeknvarltvegegmlgkrgilaeifkaLaeeeinvdlis 301
                                       vp++v ss+e++   +gTl+++    +e  ++v+++a++++ a++t+   ++++++gi+a if+ L+e+++nvd+i+
  lcl|FitnessBrowser__Dino:3608668 225 VPLRVLSSFEENtdtSGTLVCDedeIMES-NVVSGVAYSRDEAKMTLI--SVADRPGIAAAIFGPLSEAGVNVDMIV 298
                                       ********98654478*****96533334.6*****************..9************************** PP

                         TIGR00656 302 qtese...tsislvvdeedvdeakkaLkeesgaae..lesleveedlavvsivgaglveapGvaseifkaleeknin 373
                                       q  se   t+++++  + +v +a++a+ke +++ e  +++l  + d+a+vs+vg g++++ Gva+++f+al++++in
  lcl|FitnessBrowser__Dino:3608668 299 QNISEdgrTDMTFSCPTDQVLRAERAIKEAKELGEinFQELVADTDVAKVSVVGIGMRSHAGVAARMFQALRDEGIN 375
                                       ***99999*********************998777779*************************************** PP

                         TIGR00656 374 ilmisssetkisvlvdekdaekavrklheklee 406
                                       i  i++se+kisvl++ k++e av++lh+++e+
  lcl|FitnessBrowser__Dino:3608668 376 IRVITTSEIKISVLIERKYMELAVQALHDAFEL 408
                                       *******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (412 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: 7.63
//
[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