GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Pseudomonas simiae WCS417

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate GFF4227 PS417_21655 aspartate kinase

Query= SwissProt::C3JXY0
         (413 letters)



>FitnessBrowser__WCS417:GFF4227
          Length = 413

 Score =  786 bits (2029), Expect = 0.0
 Identities = 413/413 (100%), Positives = 413/413 (100%)

Query: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60
           MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD
Sbjct: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60

Query: 61  QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120
           QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD
Sbjct: 61  QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120

Query: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180
           QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV
Sbjct: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180

Query: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT 240
           YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT
Sbjct: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT 240

Query: 241 LITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANIEVDMIVQNV 300
           LITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANIEVDMIVQNV
Sbjct: 241 LITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANIEVDMIVQNV 300

Query: 301 SHDNTTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAGVAS 360
           SHDNTTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAGVAS
Sbjct: 301 SHDNTTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAGVAS 360

Query: 361 RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPARQGE 413
           RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPARQGE
Sbjct: 361 RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPARQGE 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: 739
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 GFF4227 PS417_21655 (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.23461.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.7e-136  441.4  13.1   1.9e-136  441.2  13.1    1.0  1  lcl|FitnessBrowser__WCS417:GFF4227  PS417_21655 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4227  PS417_21655 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.2  13.1  1.9e-136  1.9e-136       1     406 [.       1     405 [.       1     406 [. 0.97

  Alignments for each domain:
  == domain 1  score: 441.2 bits;  conditional E-value: 1.9e-136
                           TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerdel 75 
                                         + liVqKFGGtsvgs+eri+++a++v+k    g++ vVV+SAms++t++l++la+    + +  +++ pre d +
  lcl|FitnessBrowser__WCS417:GFF4227   1 MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAK----AISGDQQPLPRELDVI 71 
                                         579***************************************************4....334456789******* PP

                           TIGR00656  76 vsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGateeG 150
                                         vs+GE++++all++al+++gv a++++g +  ilTd+ +++A+i +++  +++   L+ g +vvvaGF+G +e+G
  lcl|FitnessBrowser__WCS417:GFF4227  72 VSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD-QKIRTDLKAGRVVVVAGFQGVDEQG 145
                                         ************************************************9.9************************ PP

                           TIGR00656 151 eiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpralel 225
                                         +iTtLGRGGSD+t ++laaalkAd+++iyTDV+GvyttDPrvv+ a+++dki++eE+le+A+lG kvl+ ra+e+
  lcl|FitnessBrowser__WCS417:GFF4227 146 NITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEF 220
                                         *************************************************************************** PP

                           TIGR00656 226 aveakvpilvrsskekeegTlitn....kkensslvkaialeknvarltvegegmlgkrgilaeifkaLaeeein 296
                                         a +++vp++v +s+++  gTlit     ++e++ ++++ia++++ a+lt++  g+ + +g++ +i + ++ ++i 
  lcl|FitnessBrowser__WCS417:GFF4227 221 AGKYNVPLRVLHSFKEGPGTLITIdeeeSMEQP-IISGIAFNRDEAKLTIR--GVPDTPGVAFKILGPISGANIE 292
                                         **********************98555566666.*****************..9********************* PP

                           TIGR00656 297 vdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvaseifkale 368
                                         vd+i+q  s+   t+ +++v++++ d+a+++L+++ ++++ +++  + ++a+vsivg+g++++ Gvas++f+al+
  lcl|FitnessBrowser__WCS417:GFF4227 293 VDMIVQNVSHdntTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAGVASRMFEALA 367
                                         *******9988999************************************************************* PP

                           TIGR00656 369 ekninilmisssetkisvlvdekdaekavrklheklee 406
                                         ++ ini mis+se+k+sv+++ek++e avr+lh ++e+
  lcl|FitnessBrowser__WCS417:GFF4227 368 KESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFEL 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: 00:00:00.02
# Mc/sec: 7.69
//
[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