Alignments for a candidate for asp-kinase in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Paraburkholderia bryophila 376MFSha3.1

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate H281DRAFT_00550 H281DRAFT_00550 aspartate kinase

Query= SwissProt::C3JXY0
         (413 letters)



>FitnessBrowser__Burk376:H281DRAFT_00550
          Length = 416

 Score =  513 bits (1320), Expect = e-150
 Identities = 271/416 (65%), Positives = 329/416 (79%), Gaps = 12/416 (2%)

Query: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60
           MALIV K+GGTS+GSVERI+ VA +V K+  AG  +VVV SAMSGETNRL+ LAK I+  
Sbjct: 1   MALIVHKYGGTSMGSVERIKNVAKRVAKWHKAGHKMVVVPSAMSGETNRLLGLAKEIT-- 58

Query: 61  QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120
            QP PRELD+I +TGEQV+  LLA+AL + GV AVSY G QV + TDSA TKARI +ID 
Sbjct: 59  TQPSPRELDMIAATGEQVSSGLLAIALQEAGVDAVSYAGWQVPVRTDSAFTKARISEIDG 118

Query: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180
           +++  DL AG+VVV+ GFQG+D  GNITTLGRGGSDT+ VA+AAALKADEC IYTDVDGV
Sbjct: 119 ERVLRDLDAGKVVVITGFQGIDPDGNITTLGRGGSDTSAVAVAAALKADECLIYTDVDGV 178

Query: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKE---- 236
           YTTDPRVV  A+RLD++TFEEMLEMASLGSKVLQIR+VEFAGKY V  RVL S  +    
Sbjct: 179 YTTDPRVVEEARRLDRVTFEEMLEMASLGSKVLQIRSVEFAGKYQVKTRVLSSLTDPLIP 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 N  K  + A +V+GD K++KVS+VGV
Sbjct: 299 DVDMIIQNQSVEGKTAFTFTVGRGDYQRAMDILTNQVKGHVQAEQVLGDPKVSKVSVVGV 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: 519
Number of extensions: 13
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 H281DRAFT_00550 H281DRAFT_00550 (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.6570.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   7.6e-131  422.8   9.7   8.6e-131  422.6   9.7    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_00550  H281DRAFT_00550 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00550  H281DRAFT_00550 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.6   9.7  8.6e-131  8.6e-131       1     406 [.       1     413 [.       1     414 [. 0.95

  Alignments for each domain:
  == domain 1  score: 422.6 bits;  conditional E-value: 8.6e-131
                                    TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisde 66 
                                                  + liV K+GGts+gs+erik++ak+v k  k g+k+vVV SAms++t++l+ la      + i  +
  lcl|FitnessBrowser__Burk376:H281DRAFT_00550   1 MALIVHKYGGTSMGSVERIKNVAKRVAKWHKAGHKMVVVPSAMSGETNRLLGLA------KEITTQ 60 
                                                  579***************************************************......89**** PP

                                    TIGR00656  67 isprerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelL 132
                                                  +spre d++ ++GE++ss ll+ al+e gv+a+++ g++ +++Td+ f++A+i+e++  er+l  L
  lcl|FitnessBrowser__Burk376:H281DRAFT_00550  61 PSPRELDMIAATGEQVSSGLLAIALQEAGVDAVSYAGWQVPVRTDSAFTKARISEIDG-ERVLRDL 125
                                                  **********************************************************.99***** PP

                                    TIGR00656 133 eegiivvvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakk 198
                                                  + g++vv++GF+G + +G+iTtLGRGGSD++A+++aaalkAd++ iyTDV+GvyttDPrvveea++
  lcl|FitnessBrowser__Burk376:H281DRAFT_00550 126 DAGKVVVITGFQGIDPDGNITTLGRGGSDTSAVAVAAALKADECLIYTDVDGVYTTDPRVVEEARR 191
                                                  ****************************************************************** PP

                                    TIGR00656 199 idkisyeEalelAtlGakvlhpralelaveakvpilvrss.........kekeegTlitn....kk 251
                                                  +d++++eE+le+A+lG kvl+ r++e+a +++v+ +v ss          e ++gTlit     ++
  lcl|FitnessBrowser__Burk376:H281DRAFT_00550 192 LDRVTFEEMLEMASLGSKVLQIRSVEFAGKYQVKTRVLSSltdplipldAEMKSGTLITFeedeTM 257
                                                  *************************************99843333333234569****98665334 PP

                                    TIGR00656 252 ensslvkaialeknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvd 314
                                                  e+  ++++ia++++ ar++v+  g+ +k+gi+ +i + +a+++i+vd+i+q +s    t+ +++v 
  lcl|FitnessBrowser__Burk376:H281DRAFT_00550 258 EK-AVISGIAFQRDEARIAVM--GVPDKPGIAYQILGPVADANIDVDMIIQNQSVegkTAFTFTVG 320
                                                  44.6*****************..9***************************9986677******** PP

                                    TIGR00656 315 eedvdeakkaLkees.gaaelesleveedlavvsivgaglveapGvaseifkaleekninilmiss 379
                                                  + d ++a ++L++++ g ++ e++  + ++ +vs+vg+g++++ G+as +f  l+e++ini mis+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00550 321 RGDYQRAMDILTNQVkGHVQAEQVLGDPKVSKVSVVGVGMRSHVGIASTMFRTLSEEGINIQMIST 386
                                                  ***********9875167789********************************************* PP

                                    TIGR00656 380 setkisvlvdekdaekavrklheklee 406
                                                  se+kisvl+dek++e avr+lh+++e+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00550 387 SEIKISVLIDEKYMELAVRALHKAFEL 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.35
//
[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