GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Pseudomonas fluorescens FW300-N2E2

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate Pf6N2E2_5676 Aspartokinase (EC 2.7.2.4)

Query= SwissProt::C3JXY0
         (413 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676
          Length = 413

 Score =  745 bits (1923), Expect = 0.0
 Identities = 392/413 (94%), Positives = 401/413 (97%)

Query: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60
           MALIVQKFGGTSVG+VERIEQVADKVKKFR+AGDDLVVVLSAMSGETNRLIDLAK ISGD
Sbjct: 1   MALIVQKFGGTSVGTVERIEQVADKVKKFREAGDDLVVVLSAMSGETNRLIDLAKQISGD 60

Query: 61  QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120
           QQP+PRELDVIVSTGEQVTIALLAMAL KRGVPAVSYTG+QVRILTDSAH KARILQIDD
Sbjct: 61  QQPVPRELDVIVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHNKARILQIDD 120

Query: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180
           QKIR DLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV
Sbjct: 121 QKIRGDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180

Query: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT 240
           YTTDPRVV VAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT
Sbjct: 181 YTTDPRVVPVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT 240

Query: 241 LITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANIEVDMIVQNV 300
           LITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPIS ANIEVDMIVQNV
Sbjct: 241 LITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANIEVDMIVQNV 300

Query: 301 SHDNTTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAGVAS 360
           SHDNTTDFTFTVHRN+Y +AE IL+ TA EIGAREVVGDTKIAKVSIVGVGMRSHAGVAS
Sbjct: 301 SHDNTTDFTFTVHRNDYQSAEAILKKTAGEIGAREVVGDTKIAKVSIVGVGMRSHAGVAS 360

Query: 361 RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPARQGE 413
           RMFE+LAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDA A+ GE
Sbjct: 361 RMFESLAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAAAQPGE 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: 700
Number of extensions: 22
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 Pf6N2E2_5676 (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.11945.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   3.8e-135  436.9  12.8   4.3e-135  436.8  12.8    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676  Aspartokinase (EC 2.7.2.4)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676  Aspartokinase (EC 2.7.2.4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.8  12.8  4.3e-135  4.3e-135       1     406 [.       1     405 [.       1     406 [. 0.97

  Alignments for each domain:
  == domain 1  score: 436.8 bits;  conditional E-value: 4.3e-135
                                      TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleais 64 
                                                    + liVqKFGGtsvg +eri+++a++v+k  + g++ vVV+SAms++t++l++la+    + +  
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676   1 MALIVQKFGGTSVGTVERIEQVADKVKKFREAGDDLVVVLSAMSGETNRLIDLAK----QISGD 60 
                                                    579***************************************************5....44556 PP

                                      TIGR00656  65 deisprerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerL 128
                                                    +++ pre d +vs+GE++++all++al ++gv a++++g++  ilTd+ +++A+i +++  +++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676  61 QQPVPRELDVIVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHNKARILQIDD-QKI 123
                                                    7889*******************************************************9.*** PP

                                      TIGR00656 129 lelLeegiivvvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrv 192
                                                       L+ g +vvvaGF+G +e+G+iTtLGRGGSD+t ++laaalkAd+++iyTDV+GvyttDPrv
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676 124 RGDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTDPRV 187
                                                    **************************************************************** PP

                                      TIGR00656 193 veeakkidkisyeEalelAtlGakvlhpralelaveakvpilvrsskekeegTlitn....kke 252
                                                    v+ a+++dki++eE+le+A+lG kvl+ ra+e+a +++vp++v +s+++  gTlit     ++e
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676 188 VPVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGTLITIdeeeSME 251
                                                    *******************************************************985555666 PP

                                      TIGR00656 253 nsslvkaialeknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvv 313
                                                    ++ ++++ia++++ a+lt++  g+ + +g++ +i + ++ ++i vd+i+q  s+   t+ +++v
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676 252 QP-IISGIAFNRDEAKLTIR--GVPDTPGVAFKILGPISAANIEVDMIVQNVSHdntTDFTFTV 312
                                                    66.*****************..9****************************9988999****** PP

                                      TIGR00656 314 deedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvaseifkaleekninilmi 377
                                                    +++d ++a+++Lk++ g+++ +++  + ++a+vsivg+g++++ Gvas++f+ l+++ ini mi
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676 313 HRNDYQSAEAILKKTAGEIGAREVVGDTKIAKVSIVGVGMRSHAGVASRMFESLAKESINIQMI 376
                                                    **************************************************************** PP

                                      TIGR00656 378 sssetkisvlvdekdaekavrklheklee 406
                                                    s+se+k+sv+++ek++e avr+lh ++e+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5676 377 STSEIKVSVVIEEKYLELAVRALHTAFEL 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: 10.61
//
[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