Alignments for a candidate for asp-kinase in Polaromonas naphthalenivorans CJ2

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Polaromonas naphthalenivorans CJ2

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_011802264.1 PNAP_RS14430 aspartate kinase

Query= SwissProt::Q88EI9
         (411 letters)



>NCBI__GCF_000015505.1:WP_011802264.1
          Length = 422

 Score =  519 bits (1336), Expect = e-152
 Identities = 268/420 (63%), Positives = 334/420 (79%), Gaps = 14/420 (3%)

Query: 1   MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQI--- 57
           MALIV K+GGTS+GS ERI  VA++V K   AG  +VVV SAMSGETNRL+ LAK++   
Sbjct: 1   MALIVHKYGGTSMGSTERIRNVAKRVAKWARAGHQMVVVPSAMSGETNRLLGLAKELAPA 60

Query: 58  -TDQPVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQI 116
            +D    RELD + +TGEQ + ALL +AL   G+PAVSY G QV I T+S++ KARI  I
Sbjct: 61  QSDDTYSRELDALAATGEQASSALLAIALQAEGMPAVSYAGWQVTIKTNSAYTKARIESI 120

Query: 117 DDQKIRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVD 176
           DD+K+RADL  G+VV++ GFQG+DE G++TTLGRGGSDT+ VA+AAALKA EC IYTDVD
Sbjct: 121 DDEKVRADLDAGKVVIITGFQGMDEGGNVTTLGRGGSDTSAVAIAAALKAHECLIYTDVD 180

Query: 177 GVYTTDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKE-- 234
           GVYTTDPRVVP+ARRL+ ++FEEMLEMAS+GSKVLQIRSVEFAGKY VPLRVL SF +  
Sbjct: 181 GVYTTDPRVVPEARRLQTVSFEEMLEMASMGSKVLQIRSVEFAGKYKVPLRVLSSFTDWN 240

Query: 235 -------GPGTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAS 287
                    GTLI+ +E+E ME+ I+SGIAFNRDEAK+++ GVPDTPG+A++ILG ++ +
Sbjct: 241 IDINEEARSGTLISFEEDEKMEKAIVSGIAFNRDEAKISVLGVPDTPGIAYQILGAVADA 300

Query: 288 NIEVDMIVQNVAHDNTTDFTFTVHRNEYEKAQSVLEN-TAREIGAREVIGDTKIAKVSIV 346
           NIEVD+I+QN++ D  TDF+FTVHRN++ K   +L++     +GA+EV GD +I KVSIV
Sbjct: 301 NIEVDVIIQNISKDGKTDFSFTVHRNDFAKTLDLLKSKVVPALGAQEVTGDARICKVSIV 360

Query: 347 GVGMRSHAGVASCMFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLDAP 406
           G+GMRSH G+AS MF  LA+E INIQMISTSEIK SVV++EKY+ELAVRALH AFDLD P
Sbjct: 361 GIGMRSHVGIASKMFRVLAEEGINIQMISTSEIKTSVVIDEKYMELAVRALHKAFDLDQP 420


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: 553
Number of extensions: 19
Number of successful extensions: 4
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: 422
Length adjustment: 31
Effective length of query: 380
Effective length of database: 391
Effective search space:   148580
Effective search space used:   148580
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_011802264.1 PNAP_RS14430 (aspartate kinase)
to HMM TIGR00657 (aspartate kinase (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/TIGR00657.hmm
# target sequence database:        /tmp/gapView.8228.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00657  [M=442]
Accession:   TIGR00657
Description: asp_kinases: aspartate kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.2e-135  436.4   7.4   2.9e-132  427.8   7.4    2.0  1  lcl|NCBI__GCF_000015505.1:WP_011802264.1  PNAP_RS14430 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015505.1:WP_011802264.1  PNAP_RS14430 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.8   7.4  2.9e-132  2.9e-132       1     440 [.       1     415 [.       1     417 [. 0.95

  Alignments for each domain:
  == domain 1  score: 427.8 bits;  conditional E-value: 2.9e-132
                                 TIGR00657   1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekelieki 69 
                                               maliV K+GGtS+g+ eri++vak+v k ++ g+q+vVV SAm+g T++L+ la+++ + ++       
  lcl|NCBI__GCF_000015505.1:WP_011802264.1   1 MALIVHKYGGTSMGSTERIRNVAKRVAKWARAGHQMVVVPSAMSGETNRLLGLAKELAPAQSD------ 63 
                                               899**********************************************************31...... PP

                                 TIGR00657  70 rekhlealeelasqalkeklkallekeleevkkereldlilsvGEklSaallaaaleelgvkavsllga 138
                                                                                +reld++ ++GE+ S+alla al+++g+ avs+ g+
  lcl|NCBI__GCF_000015505.1:WP_011802264.1  64 ------------------------------DTYSRELDALAATGEQASSALLAIALQAEGMPAVSYAGW 102
                                               ..............................12389********************************** PP

                                 TIGR00657 139 eagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkA 207
                                               +  i t+s++++A+ +e+i+ e++ + l++g++v+++GF+G++e g++ttLGRGGSD++A+++AaalkA
  lcl|NCBI__GCF_000015505.1:WP_011802264.1 103 QVTIKTNSAYTKAR-IESIDDEKVRADLDAGKVVIITGFQGMDEGGNVTTLGRGGSDTSAVAIAAALKA 170
                                               **************.****************************************************** PP

                                 TIGR00657 208 deveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstf... 273
                                               +e+ iytDVdG+yt+DPr+vpeArrl+++s+eE+lE+as+G+kvL+ r++e+a ++k+p++v s+f   
  lcl|NCBI__GCF_000015505.1:WP_011802264.1 171 HECLIYTDVDGVYTTDPRVVPEARRLQTVSFEEMLEMASMGSKVLQIRSVEFAGKYKVPLRVLSSFtdw 239
                                               ****************************************************************98444 PP

                                 TIGR00657 274 .....npeaeGTlivaksk.seeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlil 336
                                                    ++   GTli  +++ ++e+ +v+++++++++a++sv g+++ pgi+ +++ga+a+a+++vd+i+
  lcl|NCBI__GCF_000015505.1:WP_011802264.1 240 nidinEEARSGTLISFEEDeKMEKAIVSGIAFNRDEAKISVLGVPDTPGIAYQILGAVADANIEVDVII 308
                                               4444234568****9877779999********************************************* PP

                                 TIGR00657 337 qsssets...isfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifea 402
                                               q++s+++    sf+v+++d  k+  llk+kv  +   +ev+ + ++++vs+vG gm+s+ g+a+k+f +
  lcl|NCBI__GCF_000015505.1:WP_011802264.1 309 QNISKDGktdFSFTVHRNDFAKTLDLLKSKVVPALGAQEVTGDARICKVSIVGIGMRSHVGIASKMFRV 377
                                               ****666667******************999999999******************************** PP

                                 TIGR00657 403 Laeeniniemissseikisvvvdekdaekavealhekl 440
                                               Laee+ini+mis+seik svv+dek++e av+alh+++
  lcl|NCBI__GCF_000015505.1:WP_011802264.1 378 LAEEGINIQMISTSEIKTSVVIDEKYMELAVRALHKAF 415
                                               ************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (422 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 3.53
//
[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