Alignments for a candidate for asp-kinase in Beijerinckia indica subsp. indica ATCC 9039

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Beijerinckia indica subsp. indica ATCC 9039

Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_012383897.1 BIND_RS04530 aspartate kinase

Query= SwissProt::A4VJB4
         (412 letters)



>NCBI__GCF_000019845.1:WP_012383897.1
          Length = 411

 Score =  399 bits (1026), Expect = e-116
 Identities = 222/412 (53%), Positives = 286/412 (69%), Gaps = 7/412 (1%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60
           M  +V KFGGTSV T++RI  VA  V + R  G DI VVVSAMSG+TN L+   K+ S  
Sbjct: 1   MPRLVMKFGGTSVATIDRIRNVARHVLRERKAGFDIAVVVSAMSGKTNELVGWCKEASPL 60

Query: 61  PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120
             P E D +V++GEQVT  LLA+ L   G+PA S+ G QV I T  AH  ARI+ ID + 
Sbjct: 61  YDPSEYDAVVASGEQVTAGLLALVLRDMGLPARSWQGWQVPIHTSDAHAAARIVSIDGKN 120

Query: 121 IQRDIKAGR-VVVVAGFQGVDEKGN-ITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 178
           +    +A + + V+ GFQG+ E    ITTLGRGGSDT+ VA+AAA+ A+ C IYTDVDGV
Sbjct: 121 LIEGFEARQEIAVITGFQGIHEPTQRITTLGRGGSDTSAVAVAAAIGAERCDIYTDVDGV 180

Query: 179 YTTDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEG--- 235
           YTTDPRVV KA+RLDKI FEEMLEMASLG+KVLQ+R+VE A  + V   V  SF +    
Sbjct: 181 YTTDPRVVPKAKRLDKIAFEEMLEMASLGAKVLQVRSVELAMLHKVKTFVRSSFDDPETP 240

Query: 236 -PGTLITLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMI 294
            PGTLI  DEE+ +EQ +++GIAF+RDEA++T+R V D PGVA  I  P++ AN+ VDMI
Sbjct: 241 RPGTLIC-DEEDIVEQQVVTGIAFSRDEAQITLRRVSDHPGVAAAIFMPLAEANINVDMI 299

Query: 295 VQNVAHDNTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHA 354
           +Q  + D+ TD TFTV   ++  A Q+L    +++G     G T++ KVS +GVGMRSHA
Sbjct: 300 IQVASADHATDITFTVPGTEFERAQQILYKAQSQIGFSNLQGTTDMVKVSAIGVGMRSHA 359

Query: 355 GVASRMFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAP 406
           GVA+R F+AL+ + INI+ I+TSEIK S++IE  Y ELAVR LHT + LD P
Sbjct: 360 GVAARAFKALSDKGINIRAITTSEIKFSILIEAAYTELAVRTLHTLYGLDQP 411


Lambda     K      H
   0.317    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: 418
Number of extensions: 13
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: 411
Length adjustment: 31
Effective length of query: 381
Effective length of database: 380
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_012383897.1 BIND_RS04530 (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.3135547.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-127  412.2   4.6   4.4e-109  351.4   1.2    2.0  2  NCBI__GCF_000019845.1:WP_012383897.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000019845.1:WP_012383897.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.1   1.9e-21   1.9e-21       2      59 ..       2      59 ..       1      62 [. 0.95
   2 !  351.4   1.2  4.4e-109  4.4e-109     103     440 ..      63     406 ..      58     408 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 1.9e-21
                             TIGR00657  2 aliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvss 59
                                           ++V+KFGGtSv++++ri++va++v++e++ g + +VVvSAm+g T++Lv  ++++s+
  NCBI__GCF_000019845.1:WP_012383897.1  2 PRLVMKFGGTSVATIDRIRNVARHVLRERKAGFDIAVVVSAMSGKTNELVGWCKEASP 59
                                          579***************************************************9986 PP

  == domain 2  score: 351.4 bits;  conditional E-value: 4.4e-109
                             TIGR00657 103 ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterleklleeg.iivvv 174
                                           ++e+d+++++GE+++a lla++l++ g  a+s+ g++ +i t++++  A+ +++i+ ++l +  e+   i v+
  NCBI__GCF_000019845.1:WP_012383897.1  63 PSEYDAVVASGEQVTAGLLALVLRDMGLPARSWQGWQVPIHTSDAHAAAR-IVSIDGKNLIEGFEARqEIAVI 134
                                           6899**********************************************.88888888877777777***** PP

                             TIGR00657 175 aGFiGat.ekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELas 246
                                           +GF+G++ ++++ittLGRGGSD++A+++Aaa++A++++iytDVdG+yt+DPr+vp+A+rld+i++eE+lE+as
  NCBI__GCF_000019845.1:WP_012383897.1 135 TGFQGIHePTQRITTLGRGGSDTSAVAVAAAIGAERCDIYTDVDGVYTTDPRVVPKAKRLDKIAFEEMLEMAS 207
                                           ******97899************************************************************** PP

                             TIGR00657 247 lGakvLhprtlepamrakipivvkstfnpe...aeGTlivakskseeepavkalsldknqalvsvsgttmkpg 316
                                           lGakvL+ r++e+am +k++ +v+s+f++     +GTli+ +++  e++ v+++++++++a +++++++++pg
  NCBI__GCF_000019845.1:WP_012383897.1 208 LGAKVLQVRSVELAMLHKVKTFVRSSFDDPetpRPGTLICDEEDIVEQQVVTGIAFSRDEAQITLRRVSDHPG 280
                                           ***************************85312249*********8888************************* PP

                             TIGR00657 317 ilaevfgalaeakvnvdlilqsss..ets..isfvvdkedadkakellkkkvkeekaleevevekklalvslv 385
                                           ++a +f  laea++nvd+i+q++s  +    i+f+v+ ++ ++a+++l  k++++  +++++ ++++ +vs +
  NCBI__GCF_000019845.1:WP_012383897.1 281 VAAAIFMPLAEANINVDMIIQVASadH-AtdITFTVPGTEFERAQQIL-YKAQSQIGFSNLQGTTDMVKVSAI 351
                                           ***********************9652.157****************8.5799******************** PP

                             TIGR00657 386 GagmksapgvaakifeaLaeeniniemissseikisvvvdekdaekavealhekl 440
                                           G gm+s+ gvaa++f+aL++++ini++i +seik s++++  + e av++lh  +
  NCBI__GCF_000019845.1:WP_012383897.1 352 GVGMRSHAGVAARAFKALSDKGINIRAITTSEIKFSILIEAAYTELAVRTLHTLY 406
                                           ****************************************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (411 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 13.29
//
[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