Alignments for a candidate for asp-kinase in Brevundimonas sp. GW460-12-10-14-LB2

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Brevundimonas sp. GW460-12-10-14-LB2

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_066553906.1 A4249_RS14490 aspartate kinase

Query= BRENDA::O69077
         (412 letters)



>NCBI__GCF_001636925.1:WP_066553906.1
          Length = 424

 Score =  357 bits (916), Expect = e-103
 Identities = 211/418 (50%), Positives = 272/418 (65%), Gaps = 18/418 (4%)

Query: 4   IVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLI----GLANQIME 59
           +V KFGGTS+G +ERI + A  V     AG  V VVVSAM+G+TN L+    G       
Sbjct: 9   LVMKFGGTSMGDLERIRRAARIVAAEVSAGKQVAVVVSAMAGKTNELVAWTDGAGPAAAG 68

Query: 60  QPVPR-ELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDD 118
            P+   E DV+V++GEQVT  LL+  L   G  A S+ G QV ILTD AH +ARI+ I  
Sbjct: 69  LPLSDDEYDVVVASGEQVTSGLLAATLRNMGFNARSWMGWQVPILTDDAHARARIIDIPG 128

Query: 119 THIRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 178
             + A +  G + +V GFQGV  +G ITTLGRGGSDT+ VA+AAAL    C IYTDVDGV
Sbjct: 129 EKLGAAVDGGEIAIVPGFQGVTADGKITTLGRGGSDTSAVAVAAALGCP-CDIYTDVDGV 187

Query: 179 YTTDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGP-- 236
           YTTDPR+  +ARRL K+++EEMLEMASLG+KVLQ R+VE A    VP+RVL SF E    
Sbjct: 188 YTTDPRIENRARRLAKVSYEEMLEMASLGAKVLQTRSVELAMAKQVPVRVLSSFIEPDAN 247

Query: 237 -------GTLITIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAAN 289
                  GTLI   DEEE +E+ I+SG+  +RDEA++T+ G+ D       +   ++ AN
Sbjct: 248 GVMPDKGGTLIC--DEEEIVEKRIVSGVTMSRDEARITLLGLSDRVDAPADVFTRLAEAN 305

Query: 290 VEVDMIVQNVAHD-NTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVG 348
           V VDMIVQ+ +    T + TFT  R D + A +++      +G  E   D ++AKVS+VG
Sbjct: 306 VNVDMIVQSQSRTAGTVNLTFTTGRRDAVRAADLMTAAKEQLGFEEIRVDEDVAKVSVVG 365

Query: 349 VGMRSHAGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDA 406
           VGMRSHAGVA  MF+ALA + +  Q ISTSEIK+SV+I+  Y ELAVRALH+A+ LDA
Sbjct: 366 VGMRSHAGVAQTMFKALADKGVKFQAISTSEIKISVLIDAAYAELAVRALHSAYGLDA 423


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: 462
Number of extensions: 21
Number of successful extensions: 5
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: 424
Length adjustment: 32
Effective length of query: 380
Effective length of database: 392
Effective search space:   148960
Effective search space used:   148960
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 WP_066553906.1 A4249_RS14490 (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.1401860.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-127  412.5   8.3   7.9e-110  353.9   2.3    2.0  2  NCBI__GCF_001636925.1:WP_066553906.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001636925.1:WP_066553906.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.4   2.1e-21   2.1e-21       3      56 ..       8      61 ..       6      68 .. 0.93
   2 !  353.9   2.3  7.9e-110  7.9e-110     103     441 ..      73     420 ..      65     421 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 2.1e-21
                             TIGR00657  3 liVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaek 56
                                          ++V+KFGGtS+g+ eri+++a+iv +e   g+qv+VVvSAmag T++Lv+  + 
  NCBI__GCF_001636925.1:WP_066553906.1  8 RLVMKFGGTSMGDLERIRRAARIVAAEVSAGKQVAVVVSAMAGKTNELVAWTDG 61
                                          78***********************************************98765 PP

  == domain 2  score: 353.9 bits;  conditional E-value: 7.9e-110
                             TIGR00657 103 ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterleklleegiivvva 175
                                           + e+d+++++GE++++ llaa+l++ g +a+s++g++ +iltd+++ rA+ +++i  e+l ++++ g i +v 
  NCBI__GCF_001636925.1:WP_066553906.1  73 DDEYDVVVASGEQVTSGLLAATLRNMGFNARSWMGWQVPILTDDAHARAR-IIDIPGEKLGAAVDGGEIAIVP 144
                                           6799**********************************************.********************** PP

                             TIGR00657 176 GFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslG 248
                                           GF+G+t +g+ittLGRGGSD++A+++Aaal+   ++iytDVdG+yt+DPri + Arrl+++syeE+lE+aslG
  NCBI__GCF_001636925.1:WP_066553906.1 145 GFQGVTADGKITTLGRGGSDTSAVAVAAALGCP-CDIYTDVDGVYTTDPRIENRARRLAKVSYEEMLEMASLG 216
                                           *******************************98.*************************************** PP

                             TIGR00657 249 akvLhprtlepamrakipivvkstf........npeaeGTlivakskseeepavkalsldknqalvsvsgttm 313
                                           akvL+ r++e+am++++p++v s+f         p+++GTli+ +++  e+ +v+++++++++a++++ g ++
  NCBI__GCF_001636925.1:WP_066553906.1 217 AKVLQTRSVELAMAKQVPVRVLSSFiepdangvMPDKGGTLICDEEEIVEKRIVSGVTMSRDEARITLLGLSD 289
                                           *********************999854433333467899********8888********************** PP

                             TIGR00657 314 kpgilaevfgalaeakvnvdlilqsssets....isfvvdkedadkakellkkkvkeekaleevevekklalv 382
                                           ++   a+vf++laea+vnvd+i+qs+s+t     ++f+  ++da +a+ l+ +++ke+  +ee++v++++a+v
  NCBI__GCF_001636925.1:WP_066553906.1 290 RVDAPADVFTRLAEANVNVDMIVQSQSRTAgtvnLTFTTGRRDAVRAADLM-TAAKEQLGFEEIRVDEDVAKV 361
                                           *************************994444556999*************8.689****************** PP

                             TIGR00657 383 slvGagmksapgvaakifeaLaeeniniemissseikisvvvdekdaekavealheklv 441
                                           s+vG gm+s+ gva+++f+aLa+++++ ++is+seikisv++d  +ae av+alh+++ 
  NCBI__GCF_001636925.1:WP_066553906.1 362 SVVGVGMRSHAGVAQTMFKALADKGVKFQAISTSEIKISVLIDAAYAELAVRALHSAYG 420
                                           *******************************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (424 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: 15.20
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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