Alignments for a candidate for asp-kinase in Burkholderia vietnamiensis G4

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Burkholderia vietnamiensis G4

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_011885194.1 aspartate kinase

Query= SwissProt::C3JXY0
         (413 letters)



>NCBI__GCF_000016205.1:WP_011885194.1
          Length = 417

 Score =  517 bits (1332), Expect = e-151
 Identities = 272/416 (65%), Positives = 330/416 (79%), Gaps = 12/416 (2%)

Query: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60
           MALIV K+GGTS+GSVERI+ VA +V K+  AG  +VVV SAMSGETNRL+ LAK IS  
Sbjct: 1   MALIVHKYGGTSMGSVERIKNVAKRVAKWHQAGHQMVVVPSAMSGETNRLLGLAKEISS- 59

Query: 61  QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120
            QP PRELD+I STGEQV++ LL++AL + GV AVSY G QV I TDSA TKARI  IDD
Sbjct: 60  -QPSPRELDMIASTGEQVSVGLLSIALQEIGVEAVSYAGWQVPIKTDSAFTKARIHSIDD 118

Query: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180
           ++++ DL AG+VV++ GFQGVD  G+ITTLGRGGSDT+ VA+AAAL A+EC IYTDVDGV
Sbjct: 119 ERVKADLNAGKVVIITGFQGVDPDGHITTLGRGGSDTSAVAVAAALGAEECLIYTDVDGV 178

Query: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKE---- 236
           YTTDPRVV  A+RLD++TFEEMLEMASLGSKVLQIR+VEFAGKY V  RVL S  +    
Sbjct: 179 YTTDPRVVEEARRLDRVTFEEMLEMASLGSKVLQIRSVEFAGKYQVKTRVLSSLTDPLIA 238

Query: 237 -----GPGTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANI 291
                  GTLIT +E+E+ME+ +ISGIAF RDEA++ + GVPD PG+A++ILGP++ AN+
Sbjct: 239 LDEEMRSGTLITFEEDETMEKAVISGIAFQRDEARIAVMGVPDKPGIAYQILGPVADANV 298

Query: 292 EVDMIVQNVSHDNTTDFTFTVHRNEYDAAERILQNTAK-EIGAREVVGDTKIAKVSIVGV 350
           +VDMI+QN S +  TDFTFTV R +Y  A  IL N  K  + A  V GD K++KVS+VGV
Sbjct: 299 DVDMIIQNQSVEGKTDFTFTVGRGDYQKAMDILTNQVKGHVNAERVQGDPKVSKVSVVGV 358

Query: 351 GMRSHAGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 406
           GMRSH GVAS+MF  L++E INIQMISTSEIK+SV+I+EKY+ELAVRALH AFELD
Sbjct: 359 GMRSHVGVASKMFRTLSEEGINIQMISTSEIKISVLIDEKYMELAVRALHKAFELD 414


Lambda     K      H
   0.316    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: 529
Number of extensions: 20
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: 413
Length of database: 417
Length adjustment: 31
Effective length of query: 382
Effective length of database: 386
Effective search space:   147452
Effective search space used:   147452
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_011885194.1 (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.1055857.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-132  427.8  10.7   2.5e-132  427.7  10.7    1.0  1  NCBI__GCF_000016205.1:WP_011885194.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016205.1:WP_011885194.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.7  10.7  2.5e-132  2.5e-132       1     406 [.       1     413 [.       1     414 [. 0.95

  Alignments for each domain:
  == domain 1  score: 427.7 bits;  conditional E-value: 2.5e-132
                             TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 
                                           + liV K+GGts+gs+erik++ak+v k  + g+++vVV SAms++t++l+ la      + is+++spre d
  NCBI__GCF_000016205.1:WP_011885194.1   1 MALIVHKYGGTSMGSVERIKNVAKRVAKWHQAGHQMVVVPSAMSGETNRLLGLA------KEISSQPSPRELD 67 
                                           579***************************************************......9************ PP

                             TIGR00656  74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146
                                           ++ s+GE++s+ lls al+e gv+a+++ g++ +i Td+ f++A+i++++  er+   L+ g++v+++GF+G 
  NCBI__GCF_000016205.1:WP_011885194.1  68 MIASTGEQVSVGLLSIALQEIGVEAVSYAGWQVPIKTDSAFTKARIHSIDD-ERVKADLNAGKVVIITGFQGV 139
                                           **************************************************9.********************* PP

                             TIGR00656 147 teeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlh 219
                                           + +G+iTtLGRGGSD++A+++aaal A+++ iyTDV+GvyttDPrvveea+++d++++eE+le+A+lG kvl+
  NCBI__GCF_000016205.1:WP_011885194.1 140 DPDGHITTLGRGGSDTSAVAVAAALGAEECLIYTDVDGVYTTDPRVVEEARRLDRVTFEEMLEMASLGSKVLQ 212
                                           ************************************************************************* PP

                             TIGR00656 220 pralelaveakvpilvrss.........kekeegTlitn....kkensslvkaialeknvarltvegegmlgk 279
                                            r++e+a +++v+ +v ss         +e ++gTlit     ++e+  ++++ia++++ ar++v+  g+ +k
  NCBI__GCF_000016205.1:WP_011885194.1 213 IRSVEFAGKYQVKTRVLSSltdplialdEEMRSGTLITFeedeTMEK-AVISGIAFQRDEARIAVM--GVPDK 282
                                           ****************99844444443234459****9866533444.6*****************..9**** PP

                             TIGR00656 280 rgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkees.gaaelesleveedlavvsi 348
                                           +gi+ +i + +a+++++vd+i+q +s    t+ +++v + d ++a ++L++++ g ++ e+++ + ++ +vs+
  NCBI__GCF_000016205.1:WP_011885194.1 283 PGIAYQILGPVADANVDVDMIIQNQSVegkTDFTFTVGRGDYQKAMDILTNQVkGHVNAERVQGDPKVSKVSV 355
                                           ***********************9986677*******************987515677*************** PP

                             TIGR00656 349 vgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                           vg+g++++ Gvas++f  l+e++ini mis+se+kisvl+dek++e avr+lh+++e+
  NCBI__GCF_000016205.1:WP_011885194.1 356 VGVGMRSHVGVASKMFRTLSEEGINIQMISTSEIKISVLIDEKYMELAVRALHKAFEL 413
                                           ********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (417 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 14.83
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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