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.17327.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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.65
//
[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:

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:

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:

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:

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