Alignments for a candidate for asp-kinase in Paraburkholderia sp. CCGE1002

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Paraburkholderia sp. CCGE1002

Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_013089748.1 BC1002_RS09065 aspartate kinase

Query= SwissProt::A4VJB4
         (412 letters)



>NCBI__GCF_000092885.1:WP_013089748.1
          Length = 416

 Score =  516 bits (1329), Expect = e-151
 Identities = 264/414 (63%), Positives = 334/414 (80%), Gaps = 10/414 (2%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60
           MALIV K+GGTS+G+VERI+ VA++V K+   G  +VVV SAMSGETNRL+ LAK+I+ Q
Sbjct: 1   MALIVHKYGGTSMGSVERIKNVAKRVAKWHKAGHQMVVVPSAMSGETNRLLGLAKEITTQ 60

Query: 61  PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120
           P PRELD++ +TGEQV+  LLA+AL + GV AVSY G QV + TDSA TKARI  ID +R
Sbjct: 61  PSPRELDMIAATGEQVSSGLLAIALQEAGVEAVSYAGWQVPVRTDSAFTKARISDIDGER 120

Query: 121 IQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           +++D+ AGRVVV+ GFQG+D  G+ITTLGRGGSDT+ VA+AAALKADEC IYTDVDGVYT
Sbjct: 121 VKQDLAAGRVVVITGFQGIDPDGHITTLGRGGSDTSAVAVAAALKADECLIYTDVDGVYT 180

Query: 181 TDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQE------ 234
           TDPRVV +A+RLD++TFEEMLEMASLGSKVLQIR+VEFAGKY V  RVL S  +      
Sbjct: 181 TDPRVVEEARRLDRVTFEEMLEMASLGSKVLQIRSVEFAGKYQVKTRVLSSLTDPLMPLD 240

Query: 235 ---GPGTLITLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEV 291
                GTLIT +E+E+ME+ +ISGIAF RDEA++ + GVPD PG+A++ILGP++ AN++V
Sbjct: 241 DEMKSGTLITFEEDETMEKAVISGIAFQRDEARIAVMGVPDKPGIAYQILGPVADANIDV 300

Query: 292 DMIVQNVAHDNTTDFTFTVHRNDYNNALQVLQG-IAAEMGAREAIGDTNIAKVSIVGVGM 350
           DMI+QN + +  T FTFTV R DY  A+++L G + A + A + +GD  ++KVS+VGVGM
Sbjct: 301 DMIIQNQSVEGKTAFTFTVGRGDYARAMEILTGTVKAHVQAEQVLGDPKVSKVSVVGVGM 360

Query: 351 RSHAGVASRMFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 404
           RSH G+AS+MF  L++E INIQMISTSEIK+SV+I+EKY+ELAVRALH AFELD
Sbjct: 361 RSHVGIASKMFRTLSEEGINIQMISTSEIKISVLIDEKYMELAVRALHKAFELD 414


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: 518
Number of extensions: 12
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: 416
Length adjustment: 31
Effective length of query: 381
Effective length of database: 385
Effective search space:   146685
Effective search space used:   146685
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_013089748.1 BC1002_RS09065 (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.14585.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.2e-136  439.5   8.3   1.1e-132  429.2   8.3    2.0  1  lcl|NCBI__GCF_000092885.1:WP_013089748.1  BC1002_RS09065 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092885.1:WP_013089748.1  BC1002_RS09065 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  429.2   8.3  1.1e-132  1.1e-132       1     441 [.       1     412 [.       1     413 [. 0.96

  Alignments for each domain:
  == domain 1  score: 429.2 bits;  conditional E-value: 1.1e-132
                                 TIGR00657   1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekelieki 69 
                                               maliV K+GGtS+g+verik+vak+v k ++ g+q+vVV SAm+g T++L+ la+++  ++        
  lcl|NCBI__GCF_000092885.1:WP_013089748.1   1 MALIVHKYGGTSMGSVERIKNVAKRVAKWHKAGHQMVVVPSAMSGETNRLLGLAKEITTQP-------- 61 
                                               899**********************************************************........ PP

                                 TIGR00657  70 rekhlealeelasqalkeklkallekeleevkkereldlilsvGEklSaallaaaleelgvkavsllga 138
                                                           s                    +reld+i ++GE++S+ lla al+e gv+avs+ g+
  lcl|NCBI__GCF_000092885.1:WP_013089748.1  62 ------------S--------------------PRELDMIAATGEQVSSGLLAIALQEAGVEAVSYAGW 98 
                                               ............5....................8*********************************** PP

                                 TIGR00657 139 eagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkA 207
                                               + +++tds+f++A+ + +i+ er+++ l +g +vv++GF+G++++g+ittLGRGGSD++A+++AaalkA
  lcl|NCBI__GCF_000092885.1:WP_013089748.1  99 QVPVRTDSAFTKAR-ISDIDGERVKQDLAAGRVVVITGFQGIDPDGHITTLGRGGSDTSAVAVAAALKA 166
                                               **************.****************************************************** PP

                                 TIGR00657 208 deveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstf... 273
                                               de+ iytDVdG+yt+DPr+v+eArrld +++eE+lE+aslG+kvL+ r++e+a +++++ +v s+    
  lcl|NCBI__GCF_000092885.1:WP_013089748.1 167 DECLIYTDVDGVYTTDPRVVEEARRLDRVTFEEMLEMASLGSKVLQIRSVEFAGKYQVKTRVLSSLtdp 235
                                               **************************************************************9975323 PP

                                 TIGR00657 274 .....npeaeGTlivaksk.seeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlil 336
                                                    ++ + GTli+ +++  +e+  ++++++++++a+++v g+++kpgi+ +++g +a+a+++vd+i+
  lcl|NCBI__GCF_000092885.1:WP_013089748.1 236 lmpldDEMKSGTLITFEEDeTMEKAVISGIAFQRDEARIAVMGVPDKPGIAYQILGPVADANIDVDMII 304
                                               3333256789****9887779999********************************************* PP

                                 TIGR00657 337 qsss...etsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifea 402
                                               q++s   +t  +f+v + d+ +a e+l+ +vk++ + e+v  + k+++vs+vG gm+s+ g+a+k+f +
  lcl|NCBI__GCF_000092885.1:WP_013089748.1 305 QNQSvegKTAFTFTVGRGDYARAMEILTGTVKAHVQAEQVLGDPKVSKVSVVGVGMRSHVGIASKMFRT 373
                                               9999655555******************99*************************************** PP

                                 TIGR00657 403 Laeeniniemissseikisvvvdekdaekavealheklv 441
                                               L+ee+ini+mis+seikisv++dek++e av+alh++++
  lcl|NCBI__GCF_000092885.1:WP_013089748.1 374 LSEEGINIQMISTSEIKISVLIDEKYMELAVRALHKAFE 412
                                               ************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (416 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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 2.85
//
[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