Alignments for a candidate for asp-kinase in Pseudomonas benzenivorans DSM 8628

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Pseudomonas benzenivorans DSM 8628

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_090447420.1 BLS63_RS19300 aspartate kinase

Query= SwissProt::Q88EI9
         (411 letters)



>NCBI__GCF_900100495.1:WP_090447420.1
          Length = 412

 Score =  733 bits (1892), Expect = 0.0
 Identities = 379/412 (91%), Positives = 401/412 (97%), Gaps = 1/412 (0%)

Query: 1   MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITD- 59
           MALIVQKFGGTSVG++ERI+QVAEKVKK RE GDD+VVV+SAMSGETNRLIDLAKQ++D 
Sbjct: 1   MALIVQKFGGTSVGTVERIQQVAEKVKKFRENGDDIVVVVSAMSGETNRLIDLAKQVSDD 60

Query: 60  QPVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQ 119
           QPVPRELDV+VSTGEQVTIALL MALIKRGVPAVSYTGNQVRILTDS+HNKARILQIDD 
Sbjct: 61  QPVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHNKARILQIDDH 120

Query: 120 KIRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVY 179
           K+RADLK GRVVVVAGFQGVDEHG+ITTLGRGGSDTTGVALAAALKADECQIYTDVDGVY
Sbjct: 121 KLRADLKAGRVVVVAGFQGVDEHGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVY 180

Query: 180 TTDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTL 239
           TTDPRVVPQA+RLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSF+EGPGTL
Sbjct: 181 TTDPRVVPQAQRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFQEGPGTL 240

Query: 240 ITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVA 299
           IT+DEEESMEQPIISGIAFNRDEAKLTIRGVPD PGVAFKILGPISA+NIEVDMIVQNVA
Sbjct: 241 ITLDEEESMEQPIISGIAFNRDEAKLTIRGVPDIPGVAFKILGPISAANIEVDMIVQNVA 300

Query: 300 HDNTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASC 359
           HDNTTDFTFTVHRN+Y+ A  VLENTARE+GAREVIGDTKIAKVSIVGVGMRSHAGVAS 
Sbjct: 301 HDNTTDFTFTVHRNDYQSAHQVLENTARELGAREVIGDTKIAKVSIVGVGMRSHAGVASR 360

Query: 360 MFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLDAPARQGE 411
           MFEALAKE+INIQMISTSEIKVSVV+EEKYLELAVRALHTAF+LDAPARQG+
Sbjct: 361 MFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPARQGD 412


Lambda     K      H
   0.316    0.133    0.358 

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: 667
Number of extensions: 19
Number of successful extensions: 2
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: 411
Length of database: 412
Length adjustment: 31
Effective length of query: 380
Effective length of database: 381
Effective search space:   144780
Effective search space used:   144780
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 WP_090447420.1 BLS63_RS19300 (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.20640.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-137  445.3  11.6   1.2e-137  445.1  11.6    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090447420.1  BLS63_RS19300 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090447420.1  BLS63_RS19300 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  445.1  11.6  1.2e-137  1.2e-137       1     406 [.       1     404 [.       1     405 [. 0.98

  Alignments for each domain:
  == domain 1  score: 445.1 bits;  conditional E-value: 1.2e-137
                                 TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 
                                               + liVqKFGGtsvg +eri+++a++v+k  ++g++ vVVvSAms++t++l++la+     ++  d++ p
  lcl|NCBI__GCF_900100495.1:WP_090447420.1   1 MALIVQKFGGTSVGTVERIQQVAEKVKKFRENGDDIVVVVSAMSGETNRLIDLAK-----QVSDDQPVP 64 
                                               579***************************************************5.....99999**** PP

                                 TIGR00656  70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138
                                               re d +vs+GE++++all++al ++gv a++++g++  ilTd+ +++A+i +++  ++L   L+ g +v
  lcl|NCBI__GCF_900100495.1:WP_090447420.1  65 RELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHNKARILQIDD-HKLRADLKAGRVV 132
                                               ******************************************************9.************* PP

                                 TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207
                                               vvaGF+G +e+G+iTtLGRGGSD+t ++laaalkAd+++iyTDV+GvyttDPrvv++a++++ki++eE+
  lcl|NCBI__GCF_900100495.1:WP_090447420.1 133 VVAGFQGVDEHGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTDPRVVPQAQRLEKITFEEM 201
                                               ********************************************************************* PP

                                 TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn....kkensslvkaialeknvarltve 272
                                               le+A+lG kvl+ r++e+a +++vp++v +s+++  gTlit     ++e++ ++++ia++++ a+lt++
  lcl|NCBI__GCF_900100495.1:WP_090447420.1 202 LEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFQEGPGTLITLdeeeSMEQP-IISGIAFNRDEAKLTIR 269
                                               ****************************************98555566666.***************** PP

                                 TIGR00656 273 gegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesle 338
                                                 g+ + +g++ +i + ++ ++i vd+i+q  ++   t+ +++v+++d ++a+++L+++  +++ +++ 
  lcl|NCBI__GCF_900100495.1:WP_090447420.1 270 --GVPDIPGVAFKILGPISAANIEVDMIVQNVAHdntTDFTFTVHRNDYQSAHQVLENTARELGAREVI 336
                                               ..9***************************99988889******************************* PP

                                 TIGR00656 339 veedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                                + ++a+vsivg+g++++ Gvas++f+al+++nini mis+se+k+sv+++ek++e avr+lh ++e+
  lcl|NCBI__GCF_900100495.1:WP_090447420.1 337 GDTKIAKVSIVGVGMRSHAGVASRMFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFEL 404
                                               *****************************************************************997 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.08
//
[ok]

This GapMind analysis is from Apr 10 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