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.3030495.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 23.35
//
[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:

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:

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:

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:

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