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.9621.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.73
//
[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:

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