Alignments for a candidate for asp-kinase in Archaeoglobus veneficus SNP6

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Archaeoglobus veneficus SNP6

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013684026.1 ARCVE_RS06785 aspartate kinase, monofunctional class

Query= BRENDA::Q57991
         (473 letters)



>NCBI__GCF_000194625.1:WP_013684026.1
          Length = 462

 Score =  420 bits (1079), Expect = e-122
 Identities = 231/472 (48%), Positives = 323/472 (68%), Gaps = 20/472 (4%)

Query: 1   MTTVMKFGGTSVGSGERIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVR 60
           M  VMKFGG SV  G  I H AK+V KR   D+++VVVVSAM+ VT++LV  +++    +
Sbjct: 1   MRIVMKFGGASVKDGNSILHCAKLV-KRFSTDNEIVVVVSAMAGVTDSLVHAARKCYTEQ 59

Query: 61  DIAKVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGELTPK 120
               +  FI  + ++HY A+  A+ +E  ++ V   ID  I+ELEKVL+G++YLGELT +
Sbjct: 60  SPGFIKMFIAELAKRHYDAVNTAV-AEPHRQRVIAHIDRLIDELEKVLLGISYLGELTRR 118

Query: 121 SRDYILSFGERLSSPILSGAIRDLGEKSIALEGGEAGIITDNNFGSAR----VKRLEVKE 176
           S DYILSFGERLS+PI+S A+  +G  S+AL GG+AGI+T+ NFG A+    V  + +K 
Sbjct: 119 SEDYILSFGERLSAPIVSAALLSIGVDSLALTGGDAGIVTNRNFGRAKPIPGVYSI-IKS 177

Query: 177 RLLPLLK-EGIIPVVTGFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVSGV 235
           RL PLL  +  +PVVTGFIG TE+G ITTLGRGGSD +A LI   LDAD + +W +V GV
Sbjct: 178 RLEPLLTIKHTVPVVTGFIGATEDGNITTLGRGGSDLTATLIAAALDADEVWLWKEVDGV 237

Query: 236 YTTDPRLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPESEG 295
            TTDP++VP AR IP++SY EAMEL++FGAK+LHPR +EP M K IP+ +KNTF PE+ G
Sbjct: 238 LTTDPKIVPEARVIPEISYQEAMELSHFGAKILHPRALEPVMLKKIPVRIKNTFNPEAPG 297

Query: 296 TLITNDMEMSDSIVKAISTIKNVALINIFGAGMVGVSGTAARIFKALGEEEVNVILISQG 355
           T+I++  E +  IVKA+S I+ VA++N+ GAG    +   A +F+ L  E VNVI++SQ 
Sbjct: 298 TVISDGCESTKDIVKALSLIEKVAIVNVSGAGF-DFAEVMADVFRRLANERVNVIMVSQS 356

Query: 356 SSETNISLVVSEEDVDKALKALKREFGDFGKKSFLNNNLIRDVSVDKDVCVISVVGAGMR 415
           SSE N+S+VV E DV +A++ LK           +N  +   +S  +DV V+S VGAGM 
Sbjct: 357 SSELNLSIVVDESDVGRAMRVLKH---------MVNGTI--SISKLEDVAVVSAVGAGMA 405

Query: 416 GAKGIAGKIFTAVSESGANIKMIAQGSSEVNISFVIDEKDLLNCVRKLHEKF 467
           G  G+AG+IF+A+ ++G N+ MI+Q  SE N+SF + + D    V+ LH++F
Sbjct: 406 GTPGVAGRIFSALGKNGINVIMISQSCSEYNVSFAVSKADGRKAVKILHDEF 457


Lambda     K      H
   0.316    0.135    0.364 

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: 569
Number of extensions: 28
Number of successful extensions: 8
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: 473
Length of database: 462
Length adjustment: 33
Effective length of query: 440
Effective length of database: 429
Effective search space:   188760
Effective search space used:   188760
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: 51 (24.3 bits)

Align candidate WP_013684026.1 ARCVE_RS06785 (aspartate kinase, monofunctional class)
to HMM TIGR00657 (aspartate kinase (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/TIGR00657.hmm
# target sequence database:        /tmp/gapView.30181.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00657  [M=442]
Accession:   TIGR00657
Description: asp_kinases: aspartate kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-153  497.3   1.7   2.7e-153  497.1   1.7    1.0  1  lcl|NCBI__GCF_000194625.1:WP_013684026.1  ARCVE_RS06785 aspartate kinase, 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000194625.1:WP_013684026.1  ARCVE_RS06785 aspartate kinase, monofunctional class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  497.1   1.7  2.7e-153  2.7e-153       2     440 ..       1     457 [.       1     459 [. 0.97

  Alignments for each domain:
  == domain 1  score: 497.1 bits;  conditional E-value: 2.7e-153
                                 TIGR00657   2 aliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee....keli 66 
                                               ++iV+KFGG Sv+++++i ++ak+vk+ +  +n+ vVVvSAmagvTd+Lv+ a+k+  e++    k++i
  lcl|NCBI__GCF_000194625.1:WP_013684026.1   1 MRIVMKFGGASVKDGNSILHCAKLVKRFS-TDNEIVVVVSAMAGVTDSLVHAARKCYTEQSpgfiKMFI 68 
                                               68**************************9.666********************************9*** PP

                                 TIGR00657  67 ekirekhlealeelasqalkeklkallekeleevkk............ereldlilsvGEklSaallaa 123
                                               +++ ++h++a++++  +  ++ + a +++ ++e++k            +r++d+ils+GE+lSa++++a
  lcl|NCBI__GCF_000194625.1:WP_013684026.1  69 AELAKRHYDAVNTAVAEPHRQRVIAHIDRLIDELEKvllgisylgeltRRSEDYILSFGERLSAPIVSA 137
                                               ***************8899************************************************** PP

                                 TIGR00657 124 aleelgvkavsllgaeagiltdsefgrAk...vleeikterleklleeg.iivvvaGFiGatekgeitt 188
                                               al + gv++++l+g++agi+t+++fgrAk    +++i+++rle+ll+ + +++vv+GFiGate+g+itt
  lcl|NCBI__GCF_000194625.1:WP_013684026.1 138 ALLSIGVDSLALTGGDAGIVTNRNFGRAKpipGVYSIIKSRLEPLLTIKhTVPVVTGFIGATEDGNITT 206
                                               *******************************99****************9******************* PP

                                 TIGR00657 189 LGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtl 257
                                               LGRGGSDltA+l+Aaal+Adev+++++VdG++t+DP+ivpeAr ++eisy+Ea+EL+++Gak+Lhpr+l
  lcl|NCBI__GCF_000194625.1:WP_013684026.1 207 LGRGGSDLTATLIAAALDADEVWLWKEVDGVLTTDPKIVPEARVIPEISYQEAMELSHFGAKILHPRAL 275
                                               ********************************************************************* PP

                                 TIGR00657 258 epamrakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk.pgilaevfgal 325
                                               ep+m +kip+++k+tfnpea+GT+i    +s++  +vkalsl ++ a+v+vsg++ + ++++a+vf++l
  lcl|NCBI__GCF_000194625.1:WP_013684026.1 276 EPVMLKKIPVRIKNTFNPEAPGTVISDGCESTK-DIVKALSLIEKVAIVNVSGAGFDfAEVMADVFRRL 343
                                               ****************************99555.9********************************** PP

                                 TIGR00657 326 aeakvnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapg 394
                                               a+++vnv++++qssse ++s+vvd++d+ +a ++lk   + +  + +++  +++a+vs vGagm+++pg
  lcl|NCBI__GCF_000194625.1:WP_013684026.1 344 ANERVNVIMVSQSSSELNLSIVVDESDVGRAMRVLK--HMVNGTI-SISKLEDVAVVSAVGAGMAGTPG 409
                                               **********************************95..4666666.489999***************** PP

                                 TIGR00657 395 vaakifeaLaeeniniemis..sseikisvvvdekdaekavealhekl 440
                                               va++if+aL +++in+ mis  +se+++s+ v++ d+ kav+ lh+++
  lcl|NCBI__GCF_000194625.1:WP_013684026.1 410 VAGRIFSALGKNGINVIMISqsCSEYNVSFAVSKADGRKAVKILHDEF 457
                                               ********************999***********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (462 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.33
//
[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