Alignments for a candidate for asp-kinase in Anaerobutyricum hallii DSM 3353

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Anaerobutyricum hallii DSM 3353

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_005350179.1 EUBHAL_RS12075 aspartate kinase

Query= BRENDA::P08495
         (408 letters)



>NCBI__GCF_000173975.1:WP_005350179.1
          Length = 402

 Score =  401 bits (1031), Expect = e-116
 Identities = 213/400 (53%), Positives = 287/400 (71%), Gaps = 2/400 (0%)

Query: 3   LIVQKFGGTSVGSVEKIQNAANRAIAEKQKGHQVVVVVSAMGKSTDELVSLAKAISDQPS 62
           LIV+KFGGTSVG+ E+I N A R I + QKG+ VVVV+SAMGKSTDEL+ +AK I+  PS
Sbjct: 2   LIVKKFGGTSVGNKERILNVAKRCIEDYQKGNDVVVVLSAMGKSTDELIDMAKDINPTPS 61

Query: 63  KREMDMLLATGEQVTISLLSMALQEKGYDAVSYTGWQAGIRTEAIHGNARITDIDTSVLA 122
           KREMDML+ TGEQV++SL++MA+   G  A+S   +Q  + T   +GNA++  IDT  + 
Sbjct: 62  KREMDMLMTTGEQVSVSLMAMAMGSLGVPAISLNAFQVAMHTTHRYGNAQLKRIDTDRIR 121

Query: 123 DQLEKGKIVIVAGFQGMTEDCEITTLGRGGSDTTAVALAAALKADKCDIYTDVPGVFTTD 182
           ++LE+ KIV+V GFQG+ +   +TTLGRGGSDTTAVALAAAL AD C+IYTDV GV+T D
Sbjct: 122 NELEQRKIVLVTGFQGIDKFDNVTTLGRGGSDTTAVALAAALHADACEIYTDVDGVYTAD 181

Query: 183 PRYVKSARKLEGISYDEMLELANLGAGVLHPRAVEFAKNYQVPLEVRSSTETEAGTLIEE 242
           PRYVK ARKL  I+YDEML+LA+LGAGVLH R+VE AK Y V L VRSS     GT++ E
Sbjct: 182 PRYVKKARKLAEITYDEMLDLASLGAGVLHNRSVEMAKKYGVQLVVRSSLNNHEGTIVRE 241

Query: 243 ESSMEQNLIVRGIAFEDQITRVTIYGLTSGLTTLSTIFTTLAKRNINVDIIIQTQAEDKT 302
           E +ME+ ++V G+A +   TR+ + GL         +F  LAK NINVDII+Q+   + T
Sbjct: 242 EVNMEK-MLVSGVAADKNATRIAVIGLKDEPGIAFHLFNALAKYNINVDIILQSVGRNGT 300

Query: 303 -GISFSVKTEDADQTVAVLEEYKDALEFEKIETESKLAKVSIVGSGMVSNPGVAAEMFAV 361
             ISF+V  ++AD+ VA++++     E+ KI+ E  +AK+SIVG+GM+++PGVAA MF  
Sbjct: 301 KDISFTVAEDEADEAVAIIQKSFPKSEYNKIDEEKDVAKISIVGAGMMTHPGVAASMFEA 360

Query: 362 LAQKNILIKMVSTSEIKVSTVVSENDMVKAVESLHDAFEL 401
           L    + IKM+STSEI+V+ ++ E    KA+ ++HD F L
Sbjct: 361 LYDAGVNIKMISTSEIRVTVLIDEKYTEKALNAVHDKFAL 400


Lambda     K      H
   0.313    0.128    0.337 

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: 386
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: 408
Length of database: 402
Length adjustment: 31
Effective length of query: 377
Effective length of database: 371
Effective search space:   139867
Effective search space used:   139867
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_005350179.1 EUBHAL_RS12075 (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.2974556.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.4e-141  455.9  11.8   7.2e-141  455.8  11.8    1.0  1  NCBI__GCF_000173975.1:WP_005350179.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000173975.1:WP_005350179.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.8  11.8  7.2e-141  7.2e-141       2     405 ..       1     399 [.       1     401 [. 0.98

  Alignments for each domain:
  == domain 1  score: 455.8 bits;  conditional E-value: 7.2e-141
                             TIGR00656   2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerde 74 
                                           +liV+KFGGtsvg++eri ++ak+ ++++++g++vvVV+SAm+k+tdel+++a      + i+  +s+re+d+
  NCBI__GCF_000173975.1:WP_005350179.1   1 MLIVKKFGGTSVGNKERILNVAKRCIEDYQKGNDVVVVLSAMGKSTDELIDMA------KDINPTPSKREMDM 67 
                                           79***************************************************......8************* PP

                             TIGR00656  75 lvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGat 147
                                           l+ +GE++s++l+++a+  lgv a++l+  + ++ T  ++gnA+ k+++t  r+ + Le+ +iv+v+GF+G +
  NCBI__GCF_000173975.1:WP_005350179.1  68 LMTTGEQVSVSLMAMAMGSLGVPAISLNAFQVAMHTTHRYGNAQLKRIDT-DRIRNELEQRKIVLVTGFQGID 139
                                           **************************************************.********************** PP

                             TIGR00656 148 eeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhp 220
                                           +  ++TtLGRGGSD+tA++laaal+Ad +eiyTDV+Gvyt+DPr+v++a+k+++i+y+E+l+lA+lGa vlh+
  NCBI__GCF_000173975.1:WP_005350179.1 140 KFDNVTTLGRGGSDTTAVALAAALHADACEIYTDVDGVYTADPRYVKKARKLAEITYDEMLDLASLGAGVLHN 212
                                           ************************************************************************* PP

                             TIGR00656 221 ralelaveakvpilvrsskekeegTlitnkkens.slvkaialeknvarltvegegmlgkrgilaeifkaLae 292
                                           r++e+a++++v+++vrss +++egT + ++ +++  lv+++a +kn +r++v   g+ +++gi+ ++f+aLa+
  NCBI__GCF_000173975.1:WP_005350179.1 213 RSVEMAKKYGVQLVVRSSLNNHEGTIVREEVNMEkMLVSGVAADKNATRIAVI--GLKDEPGIAFHLFNALAK 283
                                           *****************************66655469****************..999*************** PP

                             TIGR00656 293 eeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvase 362
                                           ++invd+i q+ ++    +is++v+e ++dea++++++ + + e+++++ e+d+a++sivgag++ +pGva+ 
  NCBI__GCF_000173975.1:WP_005350179.1 284 YNINVDIILQSVGRngtKDISFTVAEDEADEAVAIIQKSFPKSEYNKIDEEKDVAKISIVGAGMMTHPGVAAS 356
                                           ***********99988889****************************************************** PP

                             TIGR00656 363 ifkaleekninilmisssetkisvlvdekdaekavrklhekle 405
                                           +f+al + ++ni+mis+se++++vl+dek++eka +++h+k+ 
  NCBI__GCF_000173975.1:WP_005350179.1 357 MFEALYDAGVNIKMISTSEIRVTVLIDEKYTEKALNAVHDKFA 399
                                           *****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (402 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: 17.24
//
[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:

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