Alignments for a candidate for asp-kinase in Sulfurimonas denitrificans DSM 1251

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Sulfurimonas denitrificans DSM 1251

Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_011373268.1 SUDEN_RS08595 aspartate kinase

Query= SwissProt::A4VJB4
         (412 letters)



>NCBI__GCF_000012965.1:WP_011373268.1
          Length = 403

 Score =  429 bits (1102), Expect = e-124
 Identities = 222/402 (55%), Positives = 299/402 (74%), Gaps = 1/402 (0%)

Query: 3   LIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQPV 62
           LIVQKFGGTSVG +ERI+ VA +V + +  G+D+VVVVSAMSGETN+L+  A+  S+ P 
Sbjct: 2   LIVQKFGGTSVGDLERIQNVASRVCETKKAGNDVVVVVSAMSGETNKLLAYAEHFSKNPQ 61

Query: 63  PRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQRIQ 122
             E+D+++S+GE+VT +LLA+AL + G  AVS TG +  I+TD+ HTKARI +ID   + 
Sbjct: 62  RAEVDMLLSSGERVTASLLAIALSEMGCEAVSMTGRKAGIVTDNIHTKARIEEIDPTAMN 121

Query: 123 RDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTD 182
           + IK G++VVVAGFQG+ + GN+TTLGRGGSD + VA+A A+KAD C+IYTDV G++TTD
Sbjct: 122 KAIKDGKIVVVAGFQGISQDGNVTTLGRGGSDLSAVAIAGAIKADLCEIYTDVSGIFTTD 181

Query: 183 PRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGTLITL 242
           PR+  +A++LDKI+++EMLE+ASLG+KVLQ R+VE A K +V L    SF    GTLIT 
Sbjct: 182 PRIEPRAKKLDKISYDEMLELASLGAKVLQNRSVELAKKLNVNLVTRTSFSNEEGTLIT- 240

Query: 243 DEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVAHDN 302
            EE  ME+P++SGIA ++++A++++ GV D PG+A  I   +S  +V +DMI+QNV HD 
Sbjct: 241 KEENIMEKPLVSGIALDKNQARVSLVGVKDRPGIASDIFTKLSNNSVNIDMIIQNVGHDG 300

Query: 303 TTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAGVASRMFE 362
             +  FTV  ND  +A +V+     E    E   D NI KVSIVGVGM+SH GVA++ F 
Sbjct: 301 KANIDFTVPVNDLADAKKVMDSFVKESEVDEVSYDENICKVSIVGVGMKSHTGVAAKAFS 360

Query: 363 ALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 404
            +A ENINI MISTSEIK+S++I EKY ELAVRALH+A+ELD
Sbjct: 361 VMAAENININMISTSEIKISMIIAEKYAELAVRALHSAYELD 402


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: 459
Number of extensions: 15
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: 412
Length of database: 403
Length adjustment: 31
Effective length of query: 381
Effective length of database: 372
Effective search space:   141732
Effective search space used:   141732
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_011373268.1 SUDEN_RS08595 (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.5411.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-144  468.2  16.7   1.4e-144  468.0  16.7    1.0  1  lcl|NCBI__GCF_000012965.1:WP_011373268.1  SUDEN_RS08595 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000012965.1:WP_011373268.1  SUDEN_RS08595 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.0  16.7  1.4e-144  1.4e-144       2     406 ..       1     401 [.       1     402 [. 0.98

  Alignments for each domain:
  == domain 1  score: 468.0 bits;  conditional E-value: 1.4e-144
                                 TIGR00656   2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 
                                               +liVqKFGGtsvg+ eri+++a++v +++k g++vvVVvSAms++t++l++ a      e +s+++ ++
  lcl|NCBI__GCF_000012965.1:WP_011373268.1   1 MLIVQKFGGTSVGDLERIQNVASRVCETKKAGNDVVVVVSAMSGETNKLLAYA------EHFSKNPQRA 63 
                                               79***************************************************......7********* PP

                                 TIGR00656  71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139
                                               e d+l+s GE+++++ll+ al e g +a++++g +agi+Td+ +++A+i+e+++   + + +++g+ivv
  lcl|NCBI__GCF_000012965.1:WP_011373268.1  64 EVDMLLSSGERVTASLLAIALSEMGCEAVSMTGRKAGIVTDNIHTKARIEEIDP-TAMNKAIKDGKIVV 131
                                               ******************************************************.9************* PP

                                 TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208
                                               vaGF+G  ++G++TtLGRGGSDl+A+++a a+kAd +eiyTDV+G++ttDPr+ ++akk+dkisy+E+l
  lcl|NCBI__GCF_000012965.1:WP_011373268.1 132 VAGFQGISQDGNVTTLGRGGSDLSAVAIAGAIKADLCEIYTDVSGIFTTDPRIEPRAKKLDKISYDEML 200
                                               ********************************************************************* PP

                                 TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitn...kkensslvkaialeknvarltvege 274
                                               elA+lGakvl++r++ela++ +v++++r s+++eegTlit+    +e++ lv++ial+kn+ar++++  
  lcl|NCBI__GCF_000012965.1:WP_011373268.1 201 ELASLGAKVLQNRSVELAKKLNVNLVTRTSFSNEEGTLITKeenIMEKP-LVSGIALDKNQARVSLV-- 266
                                               ****************************************966455666.*****************.. PP

                                 TIGR00656 275 gmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleve 340
                                               g+ +++gi++ if+ L+++++n+d+i+q  ++    +i+++v  +d+ +akk++ +++++ e+++++++
  lcl|NCBI__GCF_000012965.1:WP_011373268.1 267 GVKDRPGIASDIFTKLSNNSVNIDMIIQNVGHdgkANIDFTVPVNDLADAKKVMDSFVKESEVDEVSYD 335
                                               99**************************9877777********************************** PP

                                 TIGR00656 341 edlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                               e++++vsivg+g+++++Gva+++f++++ +nini mis+se+kis+++ ek+ae avr+lh+++e+
  lcl|NCBI__GCF_000012965.1:WP_011373268.1 336 ENICKVSIVGVGMKSHTGVAAKAFSVMAAENININMISTSEIKISMIIAEKYAELAVRALHSAYEL 401
                                               ***************************************************************997 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.09
//
[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