Alignments for a candidate for asp-kinase in Azohydromonas australica DSM 1124

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Azohydromonas australica DSM 1124

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_029001770.1 H537_RS0136235 aspartate kinase

Query= SwissProt::C3JXY0
         (413 letters)



>NCBI__GCF_000430725.1:WP_029001770.1
          Length = 424

 Score =  532 bits (1371), Expect = e-156
 Identities = 276/418 (66%), Positives = 338/418 (80%), Gaps = 12/418 (2%)

Query: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60
           MALIV K+GGTS+GS ERI  VA +V K+  AG  +VVV SAMSGETNRL+ LAK +S  
Sbjct: 1   MALIVHKYGGTSMGSTERIRNVAKRVAKWARAGHQMVVVPSAMSGETNRLLGLAKELSPK 60

Query: 61  Q--QPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQI 118
           Q    L RELD+I +TGEQV++ LLA+AL   G+ A+SYTG QV + TDSA+TKARI  I
Sbjct: 61  QTSSALLRELDMIAATGEQVSVGLLAIALQAEGMEAISYTGWQVPVQTDSAYTKARIESI 120

Query: 119 DDQKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVD 178
           DD ++R DL AG+VV++ GFQG+D +G+ITTLGRGGSDT+ VA+AAA+KADEC IYTDVD
Sbjct: 121 DDARVRADLAAGKVVIITGFQGIDAEGHITTLGRGGSDTSAVAVAAAMKADECLIYTDVD 180

Query: 179 GVYTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSF---- 234
           GVYTTDPRVV+ A+RL  ++FEEMLEMASLGSKVLQIR+VEFAGKY VPLRVL SF    
Sbjct: 181 GVYTTDPRVVAEARRLSTVSFEEMLEMASLGSKVLQIRSVEFAGKYRVPLRVLSSFTPWD 240

Query: 235 -----KEGPGTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGA 289
                +   GTLIT +E+E MEQ ++SGIAFNRDEAK+T+ GVPD PG+A++ILG ++ A
Sbjct: 241 IDIEEEARSGTLITFEEDEKMEQAVVSGIAFNRDEAKITVMGVPDKPGIAYQILGAVAEA 300

Query: 290 NIEVDMIVQNVSHDNTTDFTFTVHRNEYDAAERILQN-TAKEIGAREVVGDTKIAKVSIV 348
           NI+VD+I+QNVSHD  TDF+FTVHRN+Y     +LQ+     +GA+E++GDTKI KVSIV
Sbjct: 301 NIDVDVIIQNVSHDGKTDFSFTVHRNDYQRTVDLLQSQVLPALGAKEILGDTKICKVSIV 360

Query: 349 GVGMRSHAGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 406
           G+GMRSHAGVAS+MF +L+ E INIQMI+TSEIK SVVI+EKY+ELAVRALH AFELD
Sbjct: 361 GIGMRSHAGVASKMFRSLSDEGINIQMITTSEIKTSVVIDEKYMELAVRALHRAFELD 418


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: 548
Number of extensions: 16
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: 424
Length adjustment: 32
Effective length of query: 381
Effective length of database: 392
Effective search space:   149352
Effective search space used:   149352
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_029001770.1 H537_RS0136235 (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.21844.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.5e-128  412.9   9.7   8.7e-128  412.7   9.7    1.0  1  lcl|NCBI__GCF_000430725.1:WP_029001770.1  H537_RS0136235 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000430725.1:WP_029001770.1  H537_RS0136235 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.7   9.7  8.7e-128  8.7e-128       1     406 [.       1     417 [.       1     418 [. 0.95

  Alignments for each domain:
  == domain 1  score: 412.7 bits;  conditional E-value: 8.7e-128
                                 TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 
                                               + liV K+GGts+gs+eri+++ak+v k  + g+++vVV SAms++t++l+ la   +l  +  +    
  lcl|NCBI__GCF_000430725.1:WP_029001770.1   1 MALIVHKYGGTSMGSTERIRNVAKRVAKWARAGHQMVVVPSAMSGETNRLLGLA--KELSPKQTSSALL 67 
                                               579***************************************************..5888888888889 PP

                                 TIGR00656  70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138
                                               re d++ ++GE++s+ ll+ al+++g++a++++g++ ++ Td+ +++A+i++++   r+   L+ g++v
  lcl|NCBI__GCF_000430725.1:WP_029001770.1  68 RELDMIAATGEQVSVGLLAIALQAEGMEAISYTGWQVPVQTDSAYTKARIESIDD-ARVRADLAAGKVV 135
                                               ******************************************************9.9************ PP

                                 TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207
                                               +++GF+G + eG+iTtLGRGGSD++A+++aaa+kAd++ iyTDV+GvyttDPrvv ea+++ ++s+eE+
  lcl|NCBI__GCF_000430725.1:WP_029001770.1 136 IITGFQGIDAEGHITTLGRGGSDTSAVAVAAAMKADECLIYTDVDGVYTTDPRVVAEARRLSTVSFEEM 204
                                               ********************************************************************* PP

                                 TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrssk.........ekeegTlitn....kkensslvkaiale 263
                                               le+A+lG kvl+ r++e+a ++ vp++v ss+         e ++gTlit     k+e+  +v++ia++
  lcl|NCBI__GCF_000430725.1:WP_029001770.1 205 LEMASLGSKVLQIRSVEFAGKYRVPLRVLSSFtpwdidieeEARSGTLITFeedeKMEQA-VVSGIAFN 272
                                               ******************************973333333213349****98666555555.******** PP

                                 TIGR00656 264 knvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkees 329
                                               ++ a++tv+  g+ +k+gi+ +i +a+ae++i+vd+i+q  s+   t+ s++v+++d ++++++L++++
  lcl|NCBI__GCF_000430725.1:WP_029001770.1 273 RDEAKITVM--GVPDKPGIAYQILGAVAEANIDVDVIIQNVSHdgkTDFSFTVHRNDYQRTVDLLQSQV 339
                                               *********..9***************************9988888********************998 PP

                                 TIGR00656 330 g.aaelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekav 397
                                               + a++ +++  + ++++vsivg g++++ Gvas++f  l++++ini mi++se+k sv++dek++e av
  lcl|NCBI__GCF_000430725.1:WP_029001770.1 340 LpALGAKEILGDTKICKVSIVGIGMRSHAGVASKMFRSLSDEGINIQMITTSEIKTSVVIDEKYMELAV 408
                                               63667**************************************************************** PP

                                 TIGR00656 398 rklheklee 406
                                               r+lh+++e+
  lcl|NCBI__GCF_000430725.1:WP_029001770.1 409 RALHRAFEL 417
                                               *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 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: 12.52
//
[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