Alignments for a candidate for asp-kinase in Nitratifractor salsuginis DSM 16511

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Nitratifractor salsuginis DSM 16511

Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_013553601.1 NITSA_RS03245 aspartate kinase

Query= SwissProt::A4VJB4
         (412 letters)



>NCBI__GCF_000186245.1:WP_013553601.1
          Length = 401

 Score =  428 bits (1100), Expect = e-124
 Identities = 216/402 (53%), Positives = 303/402 (75%), Gaps = 3/402 (0%)

Query: 3   LIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQPV 62
           LIVQK+GGTSVG++ERIE VA++V K R+ G+D+VVVVSAMSGETN+LID A   S+ P 
Sbjct: 2   LIVQKYGGTSVGSLERIENVAKRVAKAREEGNDLVVVVSAMSGETNKLIDYAHHFSKTPS 61

Query: 63  PRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQRIQ 122
            RE+D+++S+GE+VT +LLA+AL + G  A++ TG Q  I TD  HT ARI  ID   I+
Sbjct: 62  KREMDILLSSGERVTASLLAIALQEMGYDAIAMTGRQAGIKTDGTHTYARIESIDTSAIE 121

Query: 123 RDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTD 182
             IK G++V+VAGFQG++EKG +TTLGRGGSD + VALA AL AD C+IY+DVDG+YTTD
Sbjct: 122 ERIKEGKIVIVAGFQGINEKGEVTTLGRGGSDLSAVALAGALHADACEIYSDVDGIYTTD 181

Query: 183 PRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGTLITL 242
           PR+  KA++LD I+++EMLE++SLG+KVLQ R+VE A K  V +    SF +GPGT+I  
Sbjct: 182 PRIEPKAKKLDYISYDEMLELSSLGAKVLQNRSVELAKKMGVKIIAKSSFSDGPGTIIA- 240

Query: 243 DEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVAHDN 302
           +E E+ME  ++SGIA ++++A++++R V D PG+A +I   ++   + VDMI+QN + + 
Sbjct: 241 EENEAMEAVLVSGIALDKNQARVSLRDVEDRPGIAAEIFNRLADEQINVDMIIQNASKEG 300

Query: 303 TTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAGVASRMFE 362
            T+  FTV +++   A +V+     + G  EA  D N+ KVSIVGVGM+SH+G+A++ F 
Sbjct: 301 KTNLGFTVPQSELEAAKKVIGSFEKDFG--EADYDENVCKVSIVGVGMKSHSGIAAKAFS 358

Query: 363 ALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 404
           A+A+ NINI+MISTSEIK+S++++EKY ELAVR LH  +ELD
Sbjct: 359 AMAENNINIEMISTSEIKISMIVDEKYGELAVRVLHETYELD 400


Lambda     K      H
   0.317    0.133    0.357 

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: 457
Number of extensions: 15
Number of successful extensions: 4
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: 401
Length adjustment: 31
Effective length of query: 381
Effective length of database: 370
Effective search space:   140970
Effective search space used:   140970
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_013553601.1 NITSA_RS03245 (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.1376996.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.2e-146  473.4  12.0   3.6e-146  473.2  12.0    1.0  1  NCBI__GCF_000186245.1:WP_013553601.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000186245.1:WP_013553601.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  473.2  12.0  3.6e-146  3.6e-146       2     406 ..       1     399 [.       1     400 [. 0.98

  Alignments for each domain:
  == domain 1  score: 473.2 bits;  conditional E-value: 3.6e-146
                             TIGR00656   2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerde 74 
                                           +liVqK+GGtsvgs eri+++ak+v k+ +eg++ vVVvSAms++t++l++ a      + +s+ +s+re+d 
  NCBI__GCF_000186245.1:WP_013553601.1   1 MLIVQKYGGTSVGSLERIENVAKRVAKAREEGNDLVVVVSAMSGETNKLIDYA------HHFSKTPSKREMDI 67 
                                           79***************************************************......8************* PP

                             TIGR00656  75 lvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGat 147
                                           l+s GE+++++ll+ al+e g++a+a++g +agi Td++++ A+i++++t + ++e+++eg+iv+vaGF+G +
  NCBI__GCF_000186245.1:WP_013553601.1  68 LLSSGERVTASLLAIALQEMGYDAIAMTGRQAGIKTDGTHTYARIESIDT-SAIEERIKEGKIVIVAGFQGIN 139
                                           **************************************************.********************** PP

                             TIGR00656 148 eeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhp 220
                                           e+Ge+TtLGRGGSDl+A++la al+Ad +eiy DV+G+yttDPr+ ++akk+d+isy+E+lel +lGakvl++
  NCBI__GCF_000186245.1:WP_013553601.1 140 EKGEVTTLGRGGSDLSAVALAGALHADACEIYSDVDGIYTTDPRIEPKAKKLDYISYDEMLELSSLGAKVLQN 212
                                           ************************************************************************* PP

                             TIGR00656 221 ralelaveakvpilvrsskekeegTlitnkkens..slvkaialeknvarltvegegmlgkrgilaeifkaLa 291
                                           r++ela++++v+i+ +ss++   gT i +++e     lv++ial+kn+ar++++  ++ +++gi+aeif++La
  NCBI__GCF_000186245.1:WP_013553601.1 213 RSVELAKKMGVKIIAKSSFSDGPGTIIAEENEAMeaVLVSGIALDKNQARVSLR--DVEDRPGIAAEIFNRLA 283
                                           ****************************965554457*****************..***************** PP

                             TIGR00656 292 eeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvas 361
                                           +e+invd+i+q  s+   t++ ++v + ++++akk++ ++ ++++  + +++e++++vsivg+g+++++G+a+
  NCBI__GCF_000186245.1:WP_013553601.1 284 DEQINVDMIIQNASKegkTNLGFTVPQSELEAAKKVIGSFEKDFG--EADYDENVCKVSIVGVGMKSHSGIAA 354
                                           ***********9998888**********************86666..9************************* PP

                             TIGR00656 362 eifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                           ++f+a++e+nini mis+se+kis++vdek+ e avr lhe++e+
  NCBI__GCF_000186245.1:WP_013553601.1 355 KAFSAMAENNINIEMISTSEIKISMIVDEKYGELAVRVLHETYEL 399
                                           ******************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (401 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: 00:00:00.01
# Mc/sec: 14.08
//
[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