GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Novosphingobium barchaimii LL02

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_059152208.1 V474_RS14540 aspartate kinase

Query= SwissProt::Q88EI9
         (411 letters)



>NCBI__GCF_001046635.1:WP_059152208.1
          Length = 419

 Score =  407 bits (1047), Expect = e-118
 Identities = 227/419 (54%), Positives = 290/419 (69%), Gaps = 12/419 (2%)

Query: 1   MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60
           MA IV KFGGTS+   ERI +VA  VK+ +EAG ++ VV+SAMSGET+RL++  ++    
Sbjct: 1   MARIVMKFGGTSMAGSERIRRVAGIVKRQQEAGHEVAVVVSAMSGETDRLVNFCREANAL 60

Query: 61  PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120
             P E DV+V++GEQVT  LL + L   G  A S+ G QV I TD +H KARI +ID   
Sbjct: 61  YDPAEYDVVVASGEQVTSGLLALTLQAIGCKARSWQGWQVPIKTDDAHAKARIEEIDADA 120

Query: 121 IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           + A +  G + V+ GFQGV   G +TTLGRGGSDT+ VA+AAA+KAD C IYTDVDGVYT
Sbjct: 121 LIASMAAGEIAVIPGFQGVSPEGRVTTLGRGGSDTSAVAVAAAVKADRCDIYTDVDGVYT 180

Query: 181 TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEG----- 235
           TDPR+V +AR+L  +T+EEMLE+AS+GSKVLQ RSV  A K  V ++VL SF +      
Sbjct: 181 TDPRIVAKARKLPLVTYEEMLELASVGSKVLQTRSVSLAMKEKVRVQVLSSFIDETAPAA 240

Query: 236 ---PGTLITIDEE---ESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNI 289
              PGTLI  DEE     ME+ +I+GIA +++EAK+T+  VPD PG    I  P++ SNI
Sbjct: 241 DTIPGTLIVSDEELEGSDMERQLITGIAADKNEAKVTLTRVPDRPGAVASIFAPLAESNI 300

Query: 290 EVDMIVQNVAHD-NTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGV 348
            VDMI+QNVA D   TD TFTV +++  +AQ++LE     IG   +I D  +AK+S+VGV
Sbjct: 301 NVDMIIQNVAKDKGETDVTFTVPQSDLARAQAMLEERKDSIGYYRLIADGNVAKISVVGV 360

Query: 349 GMRSHAGVASCMFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLDAPA 407
           GMRSHAGVAS MF+ LA   INI  ISTSEIKVSV+++    ELAVR LHTA+ LDA A
Sbjct: 361 GMRSHAGVASTMFKTLADRGINIIAISTSEIKVSVLIDTDETELAVRVLHTAYGLDAAA 419


Lambda     K      H
   0.316    0.133    0.358 

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: 406
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: 411
Length of database: 419
Length adjustment: 31
Effective length of query: 380
Effective length of database: 388
Effective search space:   147440
Effective search space used:   147440
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_059152208.1 V474_RS14540 (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.1807183.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-126  408.3  11.8   2.2e-126  408.1  11.8    1.0  1  NCBI__GCF_001046635.1:WP_059152208.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001046635.1:WP_059152208.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.1  11.8  2.2e-126  2.2e-126       3     405 ..       3     414 ..       1     416 [. 0.95

  Alignments for each domain:
  == domain 1  score: 408.1 bits;  conditional E-value: 2.2e-126
                             TIGR00656   3 liVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerdel 75 
                                            iV+KFGGts+++seri+++a iv+++ + g++v VVvSAms++td+lv++       +  +    p+e d +
  NCBI__GCF_001046635.1:WP_059152208.1   3 RIVMKFGGTSMAGSERIRRVAGIVKRQQEAGHEVAVVVSAMSGETDRLVNFC------REANALYDPAEYDVV 69 
                                           59*************************************************9......67888889******* PP

                             TIGR00656  76 vsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGate 148
                                           v+ GE+++s ll+  l++ g ka++ +g++ +i Tdd + +A+i+e++    L+  ++ g i v+ GF+G   
  NCBI__GCF_001046635.1:WP_059152208.1  70 VASGEQVTSGLLALTLQAIGCKARSWQGWQVPIKTDDAHAKARIEEIDA-DALIASMAAGEIAVIPGFQGVSP 141
                                           *************************************************.999******************** PP

                             TIGR00656 149 eGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpr 221
                                           eG++TtLGRGGSD++A+++aaa+kAdr++iyTDV+GvyttDPr+v +a+k++ ++yeE+lelA++G kvl+ r
  NCBI__GCF_001046635.1:WP_059152208.1 142 EGRVTTLGRGGSDTSAVAVAAAVKADRCDIYTDVDGVYTTDPRIVAKARKLPLVTYEEMLELASVGSKVLQTR 214
                                           ************************************************************************* PP

                             TIGR00656 222 alelaveakvpilvrssk........ekeegTlitn.......kkensslvkaialeknvarltvegegmlgk 279
                                           ++ la++ kv + v ss+        ++  gTli++       ++e + l+++ia +kn a++t++   + ++
  NCBI__GCF_001046635.1:WP_059152208.1 215 SVSLAMKEKVRVQVLSSFidetapaaDTIPGTLIVSdeelegsDMERQ-LITGIAADKNEAKVTLT--RVPDR 284
                                           **************99973333332133379****9887776555555.*****************..***** PP

                             TIGR00656 280 rgilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsi 348
                                           +g  a if  Lae++invd+i+q  ++    t+++++v + d+ +a+++L+e+++ +++ +l  + ++a++s+
  NCBI__GCF_001046635.1:WP_059152208.1 285 PGAVASIFAPLAESNINVDMIIQNVAKdkgeTDVTFTVPQSDLARAQAMLEERKDSIGYYRLIADGNVAKISV 357
                                           **********************997766677****************************************** PP

                             TIGR00656 349 vgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405
                                           vg+g++++ Gvas +fk l++++ini+ is+se+k+svl+d+ ++e avr lh ++ 
  NCBI__GCF_001046635.1:WP_059152208.1 358 VGVGMRSHAGVASTMFKTLADRGINIIAISTSEIKVSVLIDTDETELAVRVLHTAYG 414
                                           *****************************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 16.36
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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