Alignments for a candidate for asp-kinase in Desulfurobacterium atlanticum DSM 15668

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Desulfurobacterium atlanticum DSM 15668

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_089322638.1 CHB58_RS03055 aspartate kinase

Query= SwissProt::Q88EI9
         (411 letters)



>NCBI__GCF_900188395.1:WP_089322638.1
          Length = 403

 Score =  468 bits (1205), Expect = e-136
 Identities = 242/402 (60%), Positives = 309/402 (76%), Gaps = 1/402 (0%)

Query: 3   LIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQPV 62
           L+VQKFGGTS+GSI+RI+ VA +V + +  G+D+VVV+SAMSGET+RLI L K+IT +P 
Sbjct: 2   LVVQKFGGTSMGSIDRIKHVASRVIEEKSKGNDVVVVVSAMSGETDRLIQLVKEITSEPS 61

Query: 63  PRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQKIR 122
            R++D +V+TGEQV+  LL++ L   G  AVS TG Q  I TD +  KARIL+ID  +IR
Sbjct: 62  ERDMDFVVATGEQVSAGLLSITLNSLGYDAVSLTGWQAGIKTDKAFTKARILEIDTDRIR 121

Query: 123 ADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTD 182
             LK G++VV+ GFQG+ E G ITTLGRGGSDT+ VA+AAALKAD C IYTDVDGVYT D
Sbjct: 122 NYLKNGKIVVITGFQGITEEGDITTLGRGGSDTSAVAIAAALKADRCDIYTDVDGVYTAD 181

Query: 183 PRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLITI 242
           PR+V  AR+++ I++EEMLE+ASLG+KVLQIRSVEFA KY VPLRV  +F    GTLI  
Sbjct: 182 PRIVENARKIDVISYEEMLELASLGAKVLQIRSVEFAMKYKVPLRVRSTFTTDEGTLIK- 240

Query: 243 DEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVAHDN 302
           +E+  ME+ ++ GIA N++EA++T+  VPD PG+A K+   ++ +NI VDMIVQNV+ D 
Sbjct: 241 EEDAEMEKVVVRGIAHNKNEARITVERVPDKPGIAAKLFEALAEANIPVDMIVQNVSVDG 300

Query: 303 TTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASCMFE 362
            TD +FTV +N+  KAQ + E  A EIGAR VI D KIAKVSIVG+GMR+HAGVA  +F+
Sbjct: 301 YTDISFTVDKNDISKAQKITEKVAEEIGARGVITDDKIAKVSIVGLGMRNHAGVAGKVFD 360

Query: 363 ALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404
            LAK  INI MISTSEIK+S ++EEK+ ELAVR LH AF+LD
Sbjct: 361 TLAKYGINILMISTSEIKISCIIEEKFTELAVRVLHEAFNLD 402


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: 474
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: 403
Length adjustment: 31
Effective length of query: 380
Effective length of database: 372
Effective search space:   141360
Effective search space used:   141360
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_089322638.1 CHB58_RS03055 (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.20787.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-151  489.8  16.8   3.8e-151  489.6  16.8    1.0  1  lcl|NCBI__GCF_900188395.1:WP_089322638.1  CHB58_RS03055 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900188395.1:WP_089322638.1  CHB58_RS03055 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  489.6  16.8  3.8e-151  3.8e-151       2     406 ..       1     401 [.       1     402 [. 0.98

  Alignments for each domain:
  == domain 1  score: 489.6 bits;  conditional E-value: 3.8e-151
                                 TIGR00656   2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 
                                               +l+VqKFGGts+gs++rik++a++v++e+++g++vvVVvSAms++td+l++l+      + i +e+s+r
  lcl|NCBI__GCF_900188395.1:WP_089322638.1   1 MLVVQKFGGTSMGSIDRIKHVASRVIEEKSKGNDVVVVVSAMSGETDRLIQLV------KEITSEPSER 63 
                                               79***************************************************......899******* PP

                                 TIGR00656  71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139
                                                +d +v++GE++s+ lls  l+ lg++a++l+g++agi Td+ f++A+i e++t  r+ + L++g+ivv
  lcl|NCBI__GCF_900188395.1:WP_089322638.1  64 DMDFVVATGEQVSAGLLSITLNSLGYDAVSLTGWQAGIKTDKAFTKARILEIDT-DRIRNYLKNGKIVV 131
                                               ******************************************************.************** PP

                                 TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208
                                               ++GF+G teeG+iTtLGRGGSD++A+++aaalkAdr++iyTDV+Gvyt+DPr+ve+a+kid isyeE+l
  lcl|NCBI__GCF_900188395.1:WP_089322638.1 132 ITGFQGITEEGDITTLGRGGSDTSAVAIAAALKADRCDIYTDVDGVYTADPRIVENARKIDVISYEEML 200
                                               ********************************************************************* PP

                                 TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltvege 274
                                               elA+lGakvl+ r++e+a+++kvp++vrs++ ++egTli +   ++e+  +v++ia++kn ar+tve  
  lcl|NCBI__GCF_900188395.1:WP_089322638.1 201 ELASLGAKVLQIRSVEFAMKYKVPLRVRSTFTTDEGTLIKEedaEMEK-VVVRGIAHNKNEARITVE-- 266
                                               ***************************************997544444.59****************.. PP

                                 TIGR00656 275 gmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleve 340
                                                + +k+gi+a++f+aLae++i vd+i+q  s    t+is++vd++d+ +a+k+ +++ ++++ + + ++
  lcl|NCBI__GCF_900188395.1:WP_089322638.1 267 RVPDKPGIAAKLFEALAEANIPVDMIVQNVSVdgyTDISFTVDKNDISKAQKITEKVAEEIGARGVITD 335
                                               ****************************9987889********************************** PP

                                 TIGR00656 341 edlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                                ++a+vsivg g++++ Gva+++f  l++ +inilmis+se+kis +++ek +e avr lhe++ +
  lcl|NCBI__GCF_900188395.1:WP_089322638.1 336 DKIAKVSIVGLGMRNHAGVAGKVFDTLAKYGINILMISTSEIKISCIIEEKFTELAVRVLHEAFNL 401
                                               ***************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (403 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: 00:00:00.01
# Mc/sec: 8.51
//
[ok]

This GapMind analysis is from Apr 10 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