Alignments for a candidate for asp-kinase in Pseudomonas fluorescens FW300-N1B4

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Pseudomonas fluorescens FW300-N1B4

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate Pf1N1B4_3451 Aspartokinase (EC 2.7.2.4)

Query= SwissProt::C3JXY0
         (413 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3451
          Length = 413

 Score =  751 bits (1938), Expect = 0.0
 Identities = 392/413 (94%), Positives = 404/413 (97%)

Query: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60
           MALIVQKFGGTSVG+VERIEQVADKVKKFR+AGDDLVVVLSAMSGETNRLIDLAK ISGD
Sbjct: 1   MALIVQKFGGTSVGTVERIEQVADKVKKFREAGDDLVVVLSAMSGETNRLIDLAKQISGD 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+MEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPIS ANIEVDMIVQNV
Sbjct: 241 LITIDEEETMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANIEVDMIVQNV 300

Query: 301 SHDNTTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAGVAS 360
           +HDNTTDFTFTVHRN+Y AA+ +L+NTA+EIGAREVVGDTKIAKVSIVGVGMRSHAGVAS
Sbjct: 301 AHDNTTDFTFTVHRNDYQAAQTVLENTAREIGAREVVGDTKIAKVSIVGVGMRSHAGVAS 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: 708
Number of extensions: 24
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 Pf1N1B4_3451 (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.1390625.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.8e-133  431.4  13.8   2.1e-133  431.2  13.8    1.0  1  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3451  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3451  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.2  13.8  2.1e-133  2.1e-133       1     406 [.       1     405 [.       1     406 [. 0.97

  Alignments for each domain:
  == domain 1  score: 431.2 bits;  conditional E-value: 2.1e-133
                                  TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeis 68 
                                                + liVqKFGGtsvg +eri+++a++v+k  + g++ vVV+SAms++t++l++la+    + +   ++ 
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3451   1 MALIVQKFGGTSVGTVERIEQVADKVKKFREAGDDLVVVLSAMSGETNRLIDLAK----QISGDGQPV 64 
                                                579***************************************************5....345567899 PP

                                  TIGR00656  69 prerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegi 136
                                                pre d +vs+GE++++all++al ++gv a++++g++  ilTd+ +++A+i +++  +++   L+ g 
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3451  65 PRELDVIVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHNKARILQIDD-QKIRGDLKAGR 131
                                                *******************************************************9.*********** PP

                                  TIGR00656 137 ivvvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisy 204
                                                +vvvaGF+G +e+G+iTtLGRGGSD+t ++laaalkAd+++iyTDV+GvyttDPrvv+ a+++dki++
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3451 132 VVVVAGFQGVDEHGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTDPRVVSVAQRLDKITF 199
                                                ******************************************************************** PP

                                  TIGR00656 205 eEalelAtlGakvlhpralelaveakvpilvrsskekeegTlitn....kkensslvkaialeknvar 268
                                                eE+le+A+lG kvl+ ra+e+a +++vp++v +s+++  gTlit     ++e++ ++++ia++++ a+
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3451 200 EEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGTLITIdeeeTMEQP-IISGIAFNRDEAK 266
                                                *******************************************98665556666.************* PP

                                  TIGR00656 269 ltvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaae 333
                                                lt++  g+ + +g++ +i + ++ ++i vd+i+q  ++   t+ +++v+++d ++a+ +L+++  +++
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3451 267 LTIR--GVPDTPGVAFKILGPISAANIEVDMIVQNVAHdntTDFTFTVHRNDYQAAQTVLENTAREIG 332
                                                ****..9***************************99988889************************** PP

                                  TIGR00656 334 lesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklh 401
                                                 +++  + ++a+vsivg+g++++ Gvas++f+ l+++ ini mis+se+k+sv+++ek++e avr+lh
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3451 333 AREVVGDTKIAKVSIVGVGMRSHAGVASRMFESLAKESINIQMISTSEIKVSVVIEEKYLELAVRALH 400
                                                ******************************************************************** PP

                                  TIGR00656 402 eklee 406
                                                 ++e+
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3451 401 TAFEL 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 14.03
//
[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