Alignments for a candidate for asp-kinase in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Marinobacter adhaerens HP15

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate GFF1350 HP15_1320 aspartate kinase: aspartate kinase, monofunctional class

Query= BRENDA::O69077
         (412 letters)



>FitnessBrowser__Marino:GFF1350
          Length = 412

 Score =  623 bits (1606), Expect = 0.0
 Identities = 324/408 (79%), Positives = 360/408 (88%), Gaps = 1/408 (0%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60
           MAL+VQKFGGTSVGT ERIE VAEKV +FR+ G DVVVVVSAMSGETNRLI LAN IME+
Sbjct: 1   MALLVQKFGGTSVGTTERIEAVAEKVSRFRKEGHDVVVVVSAMSGETNRLIALANNIMEE 60

Query: 61  PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120
           P PRE+DV+VSTGEQVTIALLSMAL K G  A SYTG+QVRILTDS+HTKARI  ID+  
Sbjct: 61  PTPREMDVLVSTGEQVTIALLSMALQKLGCEARSYTGSQVRILTDSSHTKARIKQIDEQR 120

Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           +R DL AGRVVVVAGFQG+D +GNITTLGRGGSDTT VALAAAL+ADECQIYTDVDGVYT
Sbjct: 121 MREDLDAGRVVVVAGFQGIDESGNITTLGRGGSDTTAVALAAALRADECQIYTDVDGVYT 180

Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240
           TDPRVV  ARRL++ITFEEMLEMASLGSKVLQIR+VEFAGKYNVPLRVL SFQEG GTLI
Sbjct: 181 TDPRVVDTARRLERITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLSSFQEGEGTLI 240

Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300
           T++D E +MEQP++SGIAFNRDEAKLTI GVPDTPG A +IL P+S AN+EVDMIVQNV 
Sbjct: 241 TLED-ENAMEQPVVSGIAFNRDEAKLTIAGVPDTPGSALRILKPVSDANIEVDMIVQNVG 299

Query: 301 HDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVASR 360
            DN T FTFTVHRND+  A E+L++ A  +GARE  GD+ IAKVSIVGVGMRSHAGVA++
Sbjct: 300 EDNRTAFTFTVHRNDFKRAKEVLQRVADELGAREVAGDSKIAKVSIVGVGMRSHAGVATQ 359

Query: 361 MFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPA 408
           MFEAL+ E INIQMISTSEIK+SVVI+EKYLELAVRALH+AFELD PA
Sbjct: 360 MFEALSNEGINIQMISTSEIKISVVIDEKYLELAVRALHSAFELDKPA 407


Lambda     K      H
   0.317    0.133    0.362 

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: 573
Number of extensions: 14
Number of successful extensions: 3
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: 412
Length of database: 412
Length adjustment: 31
Effective length of query: 381
Effective length of database: 381
Effective search space:   145161
Effective search space used:   145161
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate GFF1350 HP15_1320 (aspartate kinase: aspartate kinase, monofunctional class)
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.31457.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.3e-142  460.7  12.7   2.6e-142  460.5  12.7    1.0  1  lcl|FitnessBrowser__Marino:GFF1350  HP15_1320 aspartate kinase: aspa


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1350  HP15_1320 aspartate kinase: aspartate kinase, monofunctional class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  460.5  12.7  2.6e-142  2.6e-142       1     406 [.       1     403 [.       1     404 [. 0.98

  Alignments for each domain:
  == domain 1  score: 460.5 bits;  conditional E-value: 2.6e-142
                           TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerdel 75 
                                         + l VqKFGGtsvg +eri+++a++v +  keg++vvVVvSAms++t++l++la      ++i +e++pre+d l
  lcl|FitnessBrowser__Marino:GFF1350   1 MALLVQKFGGTSVGTTERIEAVAEKVSRFRKEGHDVVVVVSAMSGETNRLIALA------NNIMEEPTPREMDVL 69 
                                         5799**************************************************......8999*********** PP

                           TIGR00656  76 vsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGateeG 150
                                         vs+GE++++alls+al++lg +a++++g +  ilTd+++++A+ik+++  +r+ e L+ g +vvvaGF+G +e G
  lcl|FitnessBrowser__Marino:GFF1350  70 VSTGEQVTIALLSMALQKLGCEARSYTGSQVRILTDSSHTKARIKQIDE-QRMREDLDAGRVVVVAGFQGIDESG 143
                                         ************************************************9.************************* PP

                           TIGR00656 151 eiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpralel 225
                                         +iTtLGRGGSD+tA++laaal Ad+++iyTDV+GvyttDPrvv++a+++++i++eE+le+A+lG kvl+ r++e+
  lcl|FitnessBrowser__Marino:GFF1350 144 NITTLGRGGSDTTAVALAAALRADECQIYTDVDGVYTTDPRVVDTARRLERITFEEMLEMASLGSKVLQIRSVEF 218
                                         *************************************************************************** PP

                           TIGR00656 226 aveakvpilvrsskekeegTlitn....kkensslvkaialeknvarltvegegmlgkrgilaeifkaLaeeein 296
                                         a +++vp++v ss+++ egTlit      +e++ +v++ia++++ a+lt+   g+ + +g + +i k +++++i 
  lcl|FitnessBrowser__Marino:GFF1350 219 AGKYNVPLRVLSSFQEGEGTLITLedenAMEQP-VVSGIAFNRDEAKLTIA--GVPDTPGSALRILKPVSDANIE 290
                                         **********************98555466666.*****************..9********************* PP

                           TIGR00656 297 vdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvaseifkale 368
                                         vd+i+q  +e   t+ +++v+++d ++ak++L+++ ++++ +++  ++++a+vsivg+g++++ Gva+++f+al+
  lcl|FitnessBrowser__Marino:GFF1350 291 VDMIVQNVGEdnrTAFTFTVHRNDFKRAKEVLQRVADELGAREVAGDSKIAKVSIVGVGMRSHAGVATQMFEALS 365
                                         *******999889************************************************************** PP

                           TIGR00656 369 ekninilmisssetkisvlvdekdaekavrklheklee 406
                                         +++ini mis+se+kisv++dek++e avr+lh+++e+
  lcl|FitnessBrowser__Marino:GFF1350 366 NEGINIQMISTSEIKISVVIDEKYLELAVRALHSAFEL 403
                                         ************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (412 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: 10.54
//
[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:

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