GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Desulfarculus baarsii DSM 2075

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_013257768.1 DEBA_RS04735 aspartate kinase

Query= SwissProt::Q88EI9
         (411 letters)



>NCBI__GCF_000143965.1:WP_013257768.1
          Length = 414

 Score =  459 bits (1181), Expect = e-134
 Identities = 234/412 (56%), Positives = 321/412 (77%), Gaps = 2/412 (0%)

Query: 1   MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60
           MA+IVQKFGGTSVGSIE+I+ VA KVK   + G+ +VVVLSAM+G T++LI LAK+++ +
Sbjct: 1   MAIIVQKFGGTSVGSIEKIKNVARKVKARADQGNKMVVVLSAMAGVTDKLIALAKEVSPE 60

Query: 61  PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120
           P  RE+DV+++TGEQ ++AL  +A  + G+PA S  G Q  ILTD+   KARI  ++ Q+
Sbjct: 61  PDAREMDVLLATGEQQSVALFCIAARQMGLPAHSLLGFQAAILTDNVFGKARIKDVEAQR 120

Query: 121 IRADLKEGRVVVVAGFQGVD-EHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVY 179
           I   L +G+VVVVAGFQG+D + G +TTLGRGGSDTT VALAAA+KAD C+I+TDVDGVY
Sbjct: 121 ISEMLDQGQVVVVAGFQGLDWDSGDVTTLGRGGSDTTAVALAAAIKADVCEIFTDVDGVY 180

Query: 180 TTDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTL 239
           TTDP +VPQAR+L  I+++EMLEMASLG+KVL+IRSV FA ++ V + V  +F +  GT+
Sbjct: 181 TTDPNIVPQARKLAAISYDEMLEMASLGAKVLEIRSVAFAKQFGVKIHVRSTFTDQEGTM 240

Query: 240 ITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVA 299
           + + EE+  E+ ++SG+A+N++EA++TI+GV D PGVA K+  PI A+NI VD+I+QN +
Sbjct: 241 V-VSEEQITEKLVVSGVAYNKNEARITIKGVVDQPGVASKVFTPIGAANIVVDVIIQNTS 299

Query: 300 HDNTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASC 359
            D  TD +FTV + +Y++A  V++ TA+E+GA++VIGD  +AKVSI+G GMR+HAGVA+ 
Sbjct: 300 EDGKTDISFTVPKTDYDQAMRVVQATAKELGAKQVIGDPNVAKVSIIGTGMRNHAGVATK 359

Query: 360 MFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLDAPARQGE 411
           MF+ LA E INI+ I+TSEIK+S V++EKY ELAVRALH AF L   A + E
Sbjct: 360 MFQVLAGEGINIETINTSEIKISCVIKEKYTELAVRALHEAFHLAGDAPKAE 411


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: 490
Number of extensions: 19
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: 414
Length adjustment: 31
Effective length of query: 380
Effective length of database: 383
Effective search space:   145540
Effective search space used:   145540
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_013257768.1 DEBA_RS04735 (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.28148.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-134  434.6  18.1   2.2e-134  434.4  18.1    1.0  1  NCBI__GCF_000143965.1:WP_013257768.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000143965.1:WP_013257768.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.4  18.1  2.2e-134  2.2e-134       1     406 [.       1     403 [.       1     404 [. 0.98

  Alignments for each domain:
  == domain 1  score: 434.4 bits;  conditional E-value: 2.2e-134
                             TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 
                                           + +iVqKFGGtsvgs+e+ik++a++v+++  +g+k+vVV+SAm++vtd+l++la      + +s e+  re+d
  NCBI__GCF_000143965.1:WP_013257768.1   1 MAIIVQKFGGTSVGSIEKIKNVARKVKARADQGNKMVVVLSAMAGVTDKLIALA------KEVSPEPDAREMD 67 
                                           579***************************************************......9************ PP

                             TIGR00656  74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146
                                            l+++GE+ s+al+  a r+ g  a++l g +a+ilTd+ fg+A+ik+++  +r+ e+L++g++vvvaGF+G 
  NCBI__GCF_000143965.1:WP_013257768.1  68 VLLATGEQQSVALFCIAARQMGLPAHSLLGFQAAILTDNVFGKARIKDVEA-QRISEMLDQGQVVVVAGFQGL 139
                                           ***************************************************.********************* PP

                             TIGR00656 147 t.eeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvl 218
                                           +   G++TtLGRGGSD+tA++laaa+kAd +ei+TDV+GvyttDP++v++a+k++ isy+E+le+A+lGakvl
  NCBI__GCF_000143965.1:WP_013257768.1 140 DwDSGDVTTLGRGGSDTTAVALAAAIKADVCEIFTDVDGVYTTDPNIVPQARKLAAISYDEMLEMASLGAKVL 212
                                           9457********************************************************************* PP

                             TIGR00656 219 hpralelaveakvpilvrsskekeegTlitn..kkensslvkaialeknvarltvegegmlgkrgilaeifka 289
                                             r++ +a++ +v+i vrs++  +egT +++  +  ++ +v+++a++kn ar+t++  g+++++g+++++f+ 
  NCBI__GCF_000143965.1:WP_013257768.1 213 EIRSVAFAKQFGVKIHVRSTFTDQEGTMVVSeeQITEKLVVSGVAYNKNEARITIK--GVVDQPGVASKVFTP 283
                                           ******************************9544455589****************..*************** PP

                             TIGR00656 290 Laeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGv 359
                                           ++ ++i vd+i+q +se   t+is++v ++d d+a ++ +++ ++++ +++  + ++a+vsi+g+g++++ Gv
  NCBI__GCF_000143965.1:WP_013257768.1 284 IGAANIVVDVIIQNTSEdgkTDISFTVPKTDYDQAMRVVQATAKELGAKQVIGDPNVAKVSIIGTGMRNHAGV 356
                                           ***************99999***************************************************** PP

                             TIGR00656 360 aseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                           a+++f++l+ ++ini +i +se+kis +++ek++e avr+lhe++ +
  NCBI__GCF_000143965.1:WP_013257768.1 357 ATKMFQVLAGEGINIETINTSEIKISCVIKEKYTELAVRALHEAFHL 403
                                           *******************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (414 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: 00:00:00.00
# Mc/sec: 28.77
//
[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