Alignments for a candidate for asp-kinase in Geobacter lovleyi SZ

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Geobacter lovleyi SZ

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_012468657.1 GLOV_RS02785 aspartate kinase

Query= SwissProt::Q88EI9
         (411 letters)



>NCBI__GCF_000020385.1:WP_012468657.1
          Length = 407

 Score =  406 bits (1043), Expect = e-118
 Identities = 207/404 (51%), Positives = 292/404 (72%), Gaps = 1/404 (0%)

Query: 1   MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60
           MA +VQK+GG++V S E+I ++AE++ +     +D+VVV+SA +GETNRLI++A+++  +
Sbjct: 1   MASVVQKYGGSAVTSPEQIRKIAERIIQSYNDRNDVVVVISARAGETNRLIEMAQEMCPR 60

Query: 61  PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120
               E D+++S GEQV+I LL + +   G    +Y G QV I+TDS H +A I  ID  K
Sbjct: 61  QTGSEYDLLISAGEQVSIGLLALCISSLGYKVRTYLGWQVPIITDSLHTRASIEYIDPAK 120

Query: 121 IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           IRADL  G +V+VAGFQG+D  G+ITTLGRGG DT+ VALA AL A+ C++Y+DVDG++T
Sbjct: 121 IRADLNHGAIVLVAGFQGIDRSGTITTLGRGGGDTSAVALAHALGAEVCELYSDVDGIFT 180

Query: 181 TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLI 240
            DP +   AR++EKI+++EMLE+AS G++ +QIR++E+A K+NV + V  +F    GTL+
Sbjct: 181 ADPAICDDARKIEKISYDEMLELASQGARGVQIRAIEYAKKHNVTIHVRSAFTAERGTLV 240

Query: 241 TIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVAH 300
            + E   ME  +++GI  +++EAK+ + GVPD PG A KIL  ++  +I VDMIVQNV  
Sbjct: 241 -VKEHMPMEGVVVTGIVADKNEAKIAVLGVPDKPGSAAKILTGLADKDISVDMIVQNVGQ 299

Query: 301 DNTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASCM 360
           D   D TF++ + + EKA  +    A+E+ AREV+ D  I+KVSIVG+GM++HAGVA+ M
Sbjct: 300 DGLADITFSISKTDLEKAHQITTQIAKEVNAREVLADRNISKVSIVGLGMKNHAGVAARM 359

Query: 361 FEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404
           F ALA  +INIQMISTSEIKVSV +EEKY ELAVR LH AF +D
Sbjct: 360 FTALAYNNINIQMISTSEIKVSVAIEEKYTELAVRVLHEAFKVD 403


Lambda     K      H
   0.316    0.133    0.358 

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: 454
Number of extensions: 17
Number of successful extensions: 2
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: 411
Length of database: 407
Length adjustment: 31
Effective length of query: 380
Effective length of database: 376
Effective search space:   142880
Effective search space used:   142880
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_012468657.1 GLOV_RS02785 (aspartate kinase)
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.12269.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.8e-130  421.2   9.7   1.3e-112  363.1   6.8    2.0  2  lcl|NCBI__GCF_000020385.1:WP_012468657.1  GLOV_RS02785 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020385.1:WP_012468657.1  GLOV_RS02785 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.1   1.4e-20   1.4e-20       1      61 [.       1      61 [.       1      65 [. 0.96
   2 !  363.1   6.8  1.3e-112  1.3e-112     104     441 ..      64     401 ..      61     402 .. 0.99

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 1.4e-20
                                 TIGR00657  1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvssee 61
                                              ma +VqK+GG+ v + e+i+k+a++++++++ +n+vvVV+SA+ag T++L+e+a+++++++
  lcl|NCBI__GCF_000020385.1:WP_012468657.1  1 MASVVQKYGGSAVTSPEQIRKIAERIIQSYNDRNDVVVVISARAGETNRLIEMAQEMCPRQ 61
                                              789*******************************************************988 PP

  == domain 2  score: 363.1 bits;  conditional E-value: 1.3e-112
                                 TIGR00657 104 reldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterleklleegiiv 172
                                               +e+dl++s GE++S+ lla+ +++lg+k +++lg++ +i+tds ++rA+ +e i+ +++ + l++g iv
  lcl|NCBI__GCF_000020385.1:WP_012468657.1  64 SEYDLLISAGEQVSIGLLALCISSLGYKVRTYLGWQVPIITDSLHTRAS-IEYIDPAKIRADLNHGAIV 131
                                               589**********************************************.******************* PP

                                 TIGR00657 173 vvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEa 241
                                               +vaGF+G++++g ittLGRGG D++A++lA+al+A+++e+y DVdGi+taDP i  +Ar++++isy+E+
  lcl|NCBI__GCF_000020385.1:WP_012468657.1 132 LVAGFQGIDRSGTITTLGRGGGDTSAVALAHALGAEVCELYSDVDGIFTADPAICDDARKIEKISYDEM 200
                                               ********************************************************************* PP

                                 TIGR00657 242 lELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsg 310
                                               lELas Ga+  + r++e+a+++++ i+v+s f  e  GTl+v+++ ++e + v+++  dkn+a+++v g
  lcl|NCBI__GCF_000020385.1:WP_012468657.1 201 LELASQGARGVQIRAIEYAKKHNVTIHVRSAFTAE-RGTLVVKEHMPMEGVVVTGIVADKNEAKIAVLG 268
                                               ***********************************.********************************* PP

                                 TIGR00657 311 ttmkpgilaevfgalaeakvnvdlilqsssets...isfvvdkedadkakellkkkvkeekaleeveve 376
                                               +++kpg +a++++ la+++++vd+i+q++++++   i+f ++k+d++ka++++ +++ +e + +ev  +
  lcl|NCBI__GCF_000020385.1:WP_012468657.1 269 VPDKPGSAAKILTGLADKDISVDMIVQNVGQDGladITFSISKTDLEKAHQIT-TQIAKEVNAREVLAD 336
                                               ******************************999999****************8.5699999999***** PP

                                 TIGR00657 377 kklalvslvGagmksapgvaakifeaLaeeniniemissseikisvvvdekdaekavealheklv 441
                                               +++++vs+vG gmk++ gvaa++f+aLa +nini+mis+seik+sv ++ek+ e av++lhe+++
  lcl|NCBI__GCF_000020385.1:WP_012468657.1 337 RNISKVSIVGLGMKNHAGVAARMFTALAYNNINIQMISTSEIKVSVAIEEKYTELAVRVLHEAFK 401
                                               **************************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (407 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: 0.07u 0.00s 00:00:00.07 Elapsed: 00:00:00.07
# Mc/sec: 2.44
//
[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