GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Malonomonas rubra DSM 5091

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_072906511.1 BUB13_RS05490 aspartate kinase

Query= BRENDA::O69077
         (412 letters)



>NCBI__GCF_900142125.1:WP_072906511.1
          Length = 411

 Score =  505 bits (1300), Expect = e-147
 Identities = 256/412 (62%), Positives = 326/412 (79%), Gaps = 2/412 (0%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60
           MAL+VQK+GGTSVGTVE+I  VA +V K  + G+DVVV+VSAM+GETNRL+ LA+++ E 
Sbjct: 1   MALVVQKYGGTSVGTVEKIRNVARRVAKTFDDGNDVVVIVSAMAGETNRLVALADEMCEF 60

Query: 61  PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120
           P  RE DV+VSTGEQVTIALLSM L   G  A SY G+Q+ ++TDSAH++ARI  IDD  
Sbjct: 61  PSEREYDVLVSTGEQVTIALLSMCLQSMGYNAKSYLGSQIPVMTDSAHSRARIKSIDDKK 120

Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           +R DLK G +++VAGFQG+D +GN+TTLGRGGSDT+ VA+AAALKAD C+IYTDVDGVYT
Sbjct: 121 VREDLKNGTIIIVAGFQGIDDDGNVTTLGRGGSDTSAVAVAAALKADVCEIYTDVDGVYT 180

Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240
           TDPR+VP+AR+++KI++EEMLEMASLG+KVLQIR+VEFA KYNV + V  +F + PGTL+
Sbjct: 181 TDPRMVPEARKIEKISYEEMLEMASLGAKVLQIRSVEFAKKYNVVVHVRSTFNDKPGTLV 240

Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300
             +D+E  ME  ++SGIA+N+DEAK++I GVPD PG+A +I  P+S AN+ VDMI+QNV+
Sbjct: 241 MKEDQE--METVLVSGIAYNKDEAKISIFGVPDQPGIAAQIFSPLSEANITVDMIIQNVS 298

Query: 301 HDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVASR 360
            D  TD TFTV + D   AL+I++     IGA     + NI+K+SI+GVGMRSH+G+A  
Sbjct: 299 QDGKTDMTFTVLKTDCKKALKIVEDVMGKIGASGVKSNENISKISIIGVGMRSHSGIAQT 358

Query: 361 MFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPARQGE 412
           MFE LAKE INI+MISTSEIKVS +I+ KY ELAVR LH AF LD  A + E
Sbjct: 359 MFETLAKEGINIEMISTSEIKVSCIIDAKYTELAVRVLHEAFGLDKAAVEDE 410


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: 488
Number of extensions: 16
Number of successful extensions: 2
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: 411
Length adjustment: 31
Effective length of query: 381
Effective length of database: 380
Effective search space:   144780
Effective search space used:   144780
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_072906511.1 BUB13_RS05490 (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.521842.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.1e-139  449.7  15.3   5.7e-139  449.5  15.3    1.0  1  NCBI__GCF_900142125.1:WP_072906511.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900142125.1:WP_072906511.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.5  15.3  5.7e-139  5.7e-139       1     405 [.       1     401 [.       1     403 [. 0.98

  Alignments for each domain:
  == domain 1  score: 449.5 bits;  conditional E-value: 5.7e-139
                             TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 
                                           + l+VqK+GGtsvg +e+i+++a++v k+  +g++vvV+vSAm+++t++lv+la      + + + +s+re d
  NCBI__GCF_900142125.1:WP_072906511.1   1 MALVVQKYGGTSVGTVEKIRNVARRVAKTFDDGNDVVVIVSAMAGETNRLVALA------DEMCEFPSEREYD 67 
                                           579***************************************************......6999********* PP

                             TIGR00656  74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146
                                            lvs+GE++++alls+ l+  g++a+++ g + +++Td+ + +A+ik+++  +++ e L++g+i++vaGF+G 
  NCBI__GCF_900142125.1:WP_072906511.1  68 VLVSTGEQVTIALLSMCLQSMGYNAKSYLGSQIPVMTDSAHSRARIKSIDD-KKVREDLKNGTIIIVAGFQGI 139
                                           **************************************************9.9******************** PP

                             TIGR00656 147 teeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlh 219
                                           + +G++TtLGRGGSD++A+++aaalkAd +eiyTDV+GvyttDPr+v+ea+ki+kisyeE+le+A+lGakvl+
  NCBI__GCF_900142125.1:WP_072906511.1 140 DDDGNVTTLGRGGSDTSAVAVAAALKADVCEIYTDVDGVYTTDPRMVPEARKIEKISYEEMLEMASLGAKVLQ 212
                                           ************************************************************************* PP

                             TIGR00656 220 pralelaveakvpilvrsskekeegTlitn.kkens.slvkaialeknvarltvegegmlgkrgilaeifkaL 290
                                            r++e+a++++v + vrs+++ + gTl+++ ++e++  lv++ia++k+ a+++++  g+ +++gi+a+if+ L
  NCBI__GCF_900142125.1:WP_072906511.1 213 IRSVEFAKKYNVVVHVRSTFNDKPGTLVMKeDQEMEtVLVSGIAYNKDEAKISIF--GVPDQPGIAAQIFSPL 283
                                           *****************************974444446*****************..9*************** PP

                             TIGR00656 291 aeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGva 360
                                           +e++i vd+i+q  s+   t+++++v ++d ++a k+ ++++g+++ + ++ +e++ ++si+g+g+++++G+a
  NCBI__GCF_900142125.1:WP_072906511.1 284 SEANITVDMIIQNVSQdgkTDMTFTVLKTDCKKALKIVEDVMGKIGASGVKSNENISKISIIGVGMRSHSGIA 356
                                           ************9988888****************************************************** PP

                             TIGR00656 361 seifkaleekninilmisssetkisvlvdekdaekavrklhekle 405
                                           + +f+ l++++ini mis+se+k+s ++d k++e avr lhe++ 
  NCBI__GCF_900142125.1:WP_072906511.1 357 QTMFETLAKEGINIEMISTSEIKVSCIIDAKYTELAVRVLHEAFG 401
                                           ******************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (411 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 25.71
//
[ok]

This GapMind analysis is from Jul 25 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