Alignments for a candidate for asp-kinase in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Burkholderia phytofirmans PsJN

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate BPHYT_RS12410 BPHYT_RS12410 aspartate kinase

Query= SwissProt::C3JXY0
         (413 letters)



>FitnessBrowser__BFirm:BPHYT_RS12410
          Length = 416

 Score =  511 bits (1316), Expect = e-149
 Identities = 270/416 (64%), Positives = 329/416 (79%), Gaps = 12/416 (2%)

Query: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60
           MALIV K+GGTS+GSVERI+ VA +V K+  AG  +VVV SAMSGETNRL+ LAK I+G 
Sbjct: 1   MALIVHKYGGTSMGSVERIKNVAKRVAKWHKAGHKMVVVPSAMSGETNRLLGLAKEITG- 59

Query: 61  QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120
            QP PRELD+I +TGEQV+  LLA+AL + GV AVSY G QV + TDSA TKARI +ID 
Sbjct: 60  -QPSPRELDMIAATGEQVSSGLLAIALQEAGVDAVSYAGWQVPVKTDSAFTKARISEIDG 118

Query: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180
           +++  DL AG+VVV+ GFQG+D  G+ITTLGRGGSDT+ VA+AAALKADEC IYTDVDGV
Sbjct: 119 ERVLRDLDAGKVVVITGFQGIDPDGHITTLGRGGSDTSAVAVAAALKADECLIYTDVDGV 178

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

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

Query: 292 EVDMIVQNVSHDNTTDFTFTVHRNEYDAAERILQNTAK-EIGAREVVGDTKIAKVSIVGV 350
           +VDMI+QN S +  T FTFTV R +Y  A  IL    K  + A +V+GD K++KVS+VGV
Sbjct: 299 DVDMIIQNQSVEGKTAFTFTVGRGDYQRAMDILTTQVKGHVQAEQVLGDPKVSKVSVVGV 358

Query: 351 GMRSHAGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 406
           GMRSH G+AS MF  L++E INIQMISTSEIK+SV+I+EKY+ELAVRALH AFELD
Sbjct: 359 GMRSHVGIASTMFRTLSEEGINIQMISTSEIKISVLIDEKYMELAVRALHKAFELD 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: 518
Number of extensions: 15
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: 416
Length adjustment: 31
Effective length of query: 382
Effective length of database: 385
Effective search space:   147070
Effective search space used:   147070
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 BPHYT_RS12410 BPHYT_RS12410 (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.28594.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   4.2e-130  420.3   9.7   4.8e-130  420.1   9.7    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS12410  BPHYT_RS12410 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS12410  BPHYT_RS12410 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.1   9.7  4.8e-130  4.8e-130       1     406 [.       1     413 [.       1     414 [. 0.95

  Alignments for each domain:
  == domain 1  score: 420.1 bits;  conditional E-value: 4.8e-130
                                TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 
                                              + liV K+GGts+gs+erik++ak+v k  k g+k+vVV SAms++t++l+ la      + i  ++spr
  lcl|FitnessBrowser__BFirm:BPHYT_RS12410   1 MALIVHKYGGTSMGSVERIKNVAKRVAKWHKAGHKMVVVPSAMSGETNRLLGLA------KEITGQPSPR 64 
                                              579***************************************************......89******** PP

                                TIGR00656  71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvv 140
                                              e d++ ++GE++ss ll+ al+e gv+a+++ g++ ++ Td+ f++A+i+e++  er+l  L+ g++vv+
  lcl|FitnessBrowser__BFirm:BPHYT_RS12410  65 ELDMIAATGEQVSSGLLAIALQEAGVDAVSYAGWQVPVKTDSAFTKARISEIDG-ERVLRDLDAGKVVVI 133
                                              ******************************************************.99************* PP

                                TIGR00656 141 aGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalel 210
                                              +GF+G + +G+iTtLGRGGSD++A+++aaalkAd++ iyTDV+GvyttDPrvveea+++d++++eE+le+
  lcl|FitnessBrowser__BFirm:BPHYT_RS12410 134 TGFQGIDPDGHITTLGRGGSDTSAVAVAAALKADECLIYTDVDGVYTTDPRVVEEARRLDRVTFEEMLEM 203
                                              ********************************************************************** PP

                                TIGR00656 211 AtlGakvlhpralelaveakvpilvrss.........kekeegTlitn....kkensslvkaialeknva 267
                                              A+lG kvl+ r++e+a +++v+ +v ss          e ++gTlit     ++e+  ++++ia++++ a
  lcl|FitnessBrowser__BFirm:BPHYT_RS12410 204 ASLGSKVLQIRSVEFAGKYQVKTRVLSSltdplmpldAEMKSGTLITFeedeTMEK-AVISGIAFQRDEA 272
                                              *************************99843333332234569****9866533444.6************ PP

                                TIGR00656 268 rltvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkees.gaae 333
                                              r++v+  g+ +k+gi+ +i + +a+++i+vd+i+q +s    t+ +++v + d ++a ++L++++ g ++
  lcl|FitnessBrowser__BFirm:BPHYT_RS12410 273 RIAVM--GVPDKPGIAYQILGPVADANIDVDMIIQNQSVegkTAFTFTVGRGDYQRAMDILTTQVkGHVQ 340
                                              *****..9***************************9986677*******************987516778 PP

                                TIGR00656 334 lesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhek 403
                                               e++  + ++ +vs+vg+g++++ G+as +f  l+e++ini mis+se+kisvl+dek++e avr+lh++
  lcl|FitnessBrowser__BFirm:BPHYT_RS12410 341 AEQVLGDPKVSKVSVVGVGMRSHVGIASTMFRTLSEEGINIQMISTSEIKISVLIDEKYMELAVRALHKA 410
                                              9********************************************************************* PP

                                TIGR00656 404 lee 406
                                              +e+
  lcl|FitnessBrowser__BFirm:BPHYT_RS12410 411 FEL 413
                                              *97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 8.50
//
[ok]

This GapMind analysis is from Apr 09 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