Alignments for a candidate for asp-kinase in Alicycliphilus denitrificans K601

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Alicycliphilus denitrificans K601

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_013518959.1 ALIDE2_RS11525 aspartate kinase

Query= SwissProt::C3JXY0
         (413 letters)



>NCBI__GCF_000204645.1:WP_013518959.1
          Length = 423

 Score =  513 bits (1322), Expect = e-150
 Identities = 268/421 (63%), Positives = 332/421 (78%), Gaps = 12/421 (2%)

Query: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60
           MAL V K+GGTS+GS ERI  VA +V K+  AG  +VVV SAMSGETNRL+ LAK ++  
Sbjct: 1   MALFVHKYGGTSMGSTERIRNVAKRVAKWARAGHQVVVVPSAMSGETNRLLALAKDLAPA 60

Query: 61  QQPLP--RELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQI 118
           +      RE D++ +TGEQ + ALLA+AL   G+ AVSY G QV I TDS++TKARI  I
Sbjct: 61  RASAAFHREQDMLAATGEQASSALLAIALQAEGMEAVSYAGWQVPIRTDSSYTKARIESI 120

Query: 119 DDQKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVD 178
           DD+++R DL AGRVV++ GFQG+D++GNITTLGRGGSDT+ VA+AAA+KADEC IYTDVD
Sbjct: 121 DDKRVRADLDAGRVVIITGFQGIDDEGNITTLGRGGSDTSAVAVAAAMKADECLIYTDVD 180

Query: 179 GVYTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSF---- 234
           GVYTTDPRVVS A+RL  ++FEEMLEMASLGSKVLQIR+VEFAGKY VP+RVL SF    
Sbjct: 181 GVYTTDPRVVSQARRLKSVSFEEMLEMASLGSKVLQIRSVEFAGKYKVPMRVLSSFTPWD 240

Query: 235 -----KEGPGTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGA 289
                +   GTLIT +E+E MEQ ++SGIAFNRDE K+++ GVPD PG+A++ILGP++ A
Sbjct: 241 IDINEEAKSGTLITFEEDEQMEQAVVSGIAFNRDETKISVLGVPDKPGIAYQILGPVADA 300

Query: 290 NIEVDMIVQNVSHDNTTDFTFTVHRNEY-DAAERILQNTAKEIGAREVVGDTKIAKVSIV 348
           NIEVD+I+QN+S D  TDF+FTV+ N++    E + +     +GA+EVVGDT I KVSIV
Sbjct: 301 NIEVDVIIQNISKDGRTDFSFTVNHNDHARTLELLREKVVPALGAQEVVGDTAICKVSIV 360

Query: 349 GVGMRSHAGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAP 408
           G+GMRSH GVA++MF  L++E INIQMISTSEIK SVVIE+KYLELAVRALH AF+LD P
Sbjct: 361 GIGMRSHVGVAAKMFRVLSEEGINIQMISTSEIKTSVVIEDKYLELAVRALHKAFDLDQP 420

Query: 409 A 409
           A
Sbjct: 421 A 421


Lambda     K      H
   0.316    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: 528
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: 413
Length of database: 423
Length adjustment: 32
Effective length of query: 381
Effective length of database: 391
Effective search space:   148971
Effective search space used:   148971
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_013518959.1 ALIDE2_RS11525 (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.6663.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     3e-128  414.2   7.8   3.4e-128  414.0   7.8    1.0  1  lcl|NCBI__GCF_000204645.1:WP_013518959.1  ALIDE2_RS11525 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204645.1:WP_013518959.1  ALIDE2_RS11525 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.0   7.8  3.4e-128  3.4e-128       2     406 ..       2     417 ..       1     418 [. 0.95

  Alignments for each domain:
  == domain 1  score: 414.0 bits;  conditional E-value: 3.4e-128
                                 TIGR00656   2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 
                                                l V K+GGts+gs+eri+++ak+v k  + g++vvVV SAms++t++l++la   +l+ a  ++  +r
  lcl|NCBI__GCF_000204645.1:WP_013518959.1   2 ALFVHKYGGTSMGSTERIRNVAKRVAKWARAGHQVVVVPSAMSGETNRLLALA--KDLAPARASAAFHR 68 
                                               689**************************************************..69************ PP

                                 TIGR00656  71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139
                                               e+d+l ++GE+ ssall+ al+++g++a+++ g++ +i+Td+++++A+i++++  +r+   L+ g +v+
  lcl|NCBI__GCF_000204645.1:WP_013518959.1  69 EQDMLAATGEQASSALLAIALQAEGMEAVSYAGWQVPIRTDSSYTKARIESIDD-KRVRADLDAGRVVI 136
                                               *****************************************************9.************** PP

                                 TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208
                                               ++GF+G + eG+iTtLGRGGSD++A+++aaa+kAd++ iyTDV+GvyttDPrvv++a++++++s+eE+l
  lcl|NCBI__GCF_000204645.1:WP_013518959.1 137 ITGFQGIDDEGNITTLGRGGSDTSAVAVAAAMKADECLIYTDVDGVYTTDPRVVSQARRLKSVSFEEML 205
                                               ********************************************************************* PP

                                 TIGR00656 209 elAtlGakvlhpralelaveakvpilvrssk.........ekeegTlitn....kkensslvkaialek 264
                                               e+A+lG kvl+ r++e+a ++kvp++v ss+         e ++gTlit     ++e+  +v++ia+++
  lcl|NCBI__GCF_000204645.1:WP_013518959.1 206 EMASLGSKVLQIRSVEFAGKYKVPMRVLSSFtpwdidineEAKSGTLITFeedeQMEQA-VVSGIAFNR 273
                                               *****************************973333333213349****98666555555.********* PP

                                 TIGR00656 265 nvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesg 330
                                               + ++++v   g+ +k+gi+ +i + +a+++i vd+i+q  s+   t+ s++v+++d  ++ ++L+e++ 
  lcl|NCBI__GCF_000204645.1:WP_013518959.1 274 DETKISVL--GVPDKPGIAYQILGPVADANIEVDVIIQNISKdgrTDFSFTVNHNDHARTLELLREKVV 340
                                               ********..9****************************998888*******************98765 PP

                                 TIGR00656 331 .aaelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavr 398
                                                a++ +++  +  +++vsivg g++++ Gva+++f +l+e++ini mis+se+k sv+++ k++e avr
  lcl|NCBI__GCF_000204645.1:WP_013518959.1 341 pALGAQEVVGDTAICKVSIVGIGMRSHVGVAAKMFRVLSEEGINIQMISTSEIKTSVVIEDKYLELAVR 409
                                               2778***************************************************************** PP

                                 TIGR00656 399 klheklee 406
                                               +lh+++ +
  lcl|NCBI__GCF_000204645.1:WP_013518959.1 410 ALHKAFDL 417
                                               ****9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (423 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: 10.27
//
[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