GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Pseudomonas fluorescens GW456-L13

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate PfGW456L13_1981 Aspartokinase (EC 2.7.2.4)

Query= SwissProt::C3JXY0
         (413 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1981
          Length = 413

 Score =  745 bits (1924), Expect = 0.0
 Identities = 390/413 (94%), Positives = 401/413 (97%)

Query: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60
           MALIVQKFGGTSVG+VERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAK ISGD
Sbjct: 1   MALIVQKFGGTSVGTVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKQISGD 60

Query: 61  QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120
            QP+PRELDVIVSTGEQVTIALLAMAL KRGVPAVSYTG+QVRILTDSAH KARILQIDD
Sbjct: 61  GQPVPRELDVIVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHNKARILQIDD 120

Query: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180
           QKIR DLKAGRVVVVAGFQGVDE GNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV
Sbjct: 121 QKIRGDLKAGRVVVVAGFQGVDEHGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180

Query: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT 240
           YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT
Sbjct: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT 240

Query: 241 LITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANIEVDMIVQNV 300
           LITIDEEE+MEQPIISGIAFNRDEAKLTIRGVPD PGVAFKILGPIS ANIEVDMIVQNV
Sbjct: 241 LITIDEEETMEQPIISGIAFNRDEAKLTIRGVPDIPGVAFKILGPISAANIEVDMIVQNV 300

Query: 301 SHDNTTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAGVAS 360
           +HDNTTDFTFTVHRN+Y AA+ +L+ TA E+GAREVVGDTKIAKVSIVGVGMRSHAGVAS
Sbjct: 301 AHDNTTDFTFTVHRNDYQAAQAVLEKTAGELGAREVVGDTKIAKVSIVGVGMRSHAGVAS 360

Query: 361 RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPARQGE 413
           RMFE+LAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPARQGE
Sbjct: 361 RMFESLAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPARQGE 413


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: 698
Number of extensions: 23
Number of successful extensions: 1
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: 413
Length adjustment: 31
Effective length of query: 382
Effective length of database: 382
Effective search space:   145924
Effective search space used:   145924
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 PfGW456L13_1981 (Aspartokinase (EC 2.7.2.4))
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.763.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   2.7e-133  430.8  13.4     3e-133  430.7  13.4    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1981  Aspartokinase (EC 2.7.2.4)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1981  Aspartokinase (EC 2.7.2.4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.7  13.4    3e-133    3e-133       1     406 [.       1     405 [.       1     406 [. 0.97

  Alignments for each domain:
  == domain 1  score: 430.7 bits;  conditional E-value: 3e-133
                                               TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelae 55 
                                                             + liVqKFGGtsvg +eri+++a++v+k    g++ vVV+SAms++t++l++la+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1981   1 MALIVQKFGGTSVGTVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAK 55 
                                                             579***************************************************5 PP

                                               TIGR00656  56 llklleaisdeisprerdelvsvGEllssallssalrelgvkaealdgkeagilT 110
                                                                 + +   ++ pre d +vs+GE++++all++al ++gv a++++g++  ilT
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1981  56 ----QISGDGQPVPRELDVIVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILT 106
                                                             ....345567899****************************************** PP

                                               TIGR00656 111 ddefgnAkikelateerLlelLeegiivvvaGFiGateeGeiTtLGRGGSDltAa 165
                                                             d+ +++A+i +++  +++   L+ g +vvvaGF+G +e+G+iTtLGRGGSD+t +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1981 107 DSAHNKARILQIDD-QKIRGDLKAGRVVVVAGFQGVDEHGNITTLGRGGSDTTGV 160
                                                             *************9.**************************************** PP

                                               TIGR00656 166 llaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhp 220
                                                             +laaalkAd+++iyTDV+GvyttDPrvv+ a+++dki++eE+le+A+lG kvl+ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1981 161 ALAAALKADECQIYTDVDGVYTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQI 215
                                                             ******************************************************* PP

                                               TIGR00656 221 ralelaveakvpilvrsskekeegTlitn....kkensslvkaialeknvarltv 271
                                                             ra+e+a +++vp++v +s+++  gTlit     ++e++ ++++ia++++ a+lt+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1981 216 RAVEFAGKYNVPLRVLHSFKEGPGTLITIdeeeTMEQP-IISGIAFNRDEAKLTI 269
                                                             ***************************98665556666.**************** PP

                                               TIGR00656 272 egegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakk 323
                                                             +  g+ + +g++ +i + ++ ++i vd+i+q  ++   t+ +++v+++d ++a++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1981 270 R--GVPDIPGVAFKILGPISAANIEVDMIVQNVAHdntTDFTFTVHRNDYQAAQA 322
                                                             *..9***************************99988889**************** PP

                                               TIGR00656 324 aLkeesgaaelesleveedlavvsivgaglveapGvaseifkaleekninilmis 378
                                                             +L+++ g+++ +++  + ++a+vsivg+g++++ Gvas++f+ l+++ ini mis
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1981 323 VLEKTAGELGAREVVGDTKIAKVSIVGVGMRSHAGVASRMFESLAKESINIQMIS 377
                                                             ******************************************************* PP

                                               TIGR00656 379 ssetkisvlvdekdaekavrklheklee 406
                                                             +se+k+sv+++ek++e avr+lh ++e+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1981 378 TSEIKVSVVIEEKYLELAVRALHTAFEL 405
                                                             *************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (413 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: 9.36
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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