Alignments for a candidate for asp-kinase in Arcobacter nitrofigilis DSM 7299

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Arcobacter nitrofigilis DSM 7299

Align Aspartokinase 3; Aspartate kinase 3; Aspartokinase III; EC 2.7.2.4 (characterized)
to candidate WP_013136261.1 ARNIT_RS12310 aspartate kinase

Query= SwissProt::P94417
         (454 letters)



>NCBI__GCF_000092245.1:WP_013136261.1
          Length = 458

 Score =  254 bits (648), Expect = 5e-72
 Identities = 149/455 (32%), Positives = 256/455 (56%), Gaps = 17/455 (3%)

Query: 1   MKVVKFGGSSLASGAQLDKVFHIVTSDPARKAVVVSAPGKHYAEDTKVTDLLIACA---- 56
           +KV KFGGSS+   +Q+ KV  IV  D  R+ +VVSAPG+    D K+TD L+  A    
Sbjct: 3   IKVCKFGGSSVKDASQIKKVLDIVKEDDGRRVIVVSAPGRDDNFDEKITDHLLNVATSGK 62

Query: 57  --EQYLATGSAPELAEAVVERYALIANELQL-GQSIIEKIRDDLF-TLLEGDKSNPEQYL 112
             E++    S  +  +A++++Y  + ++L + G  +I+ +  DL  +LL+G++       
Sbjct: 63  YFEEHFLNISKKQSYDAIIDKYRRLCSDLNVNGDDLIKSLDKDLSNSLLKGERKEA---- 118

Query: 113 DAVKASGEDNNAKLIAAYFRYKGVKAEYVNPKDAGLFVTNEPGNAQVLPESYQNLYRLRE 172
               + GE  NAK+I  YF  +G+  + + P++ G  ++++  + +V   +Y+N+    +
Sbjct: 119 -FFLSRGEHYNAKIIQRYFSNEGLNIKLMLPEEFGFILSDDFRDGKVQKVTYKNIEEKFD 177

Query: 173 --RDGLIIFPGFFGFSKDGDVITFSRSGSDITGSILANGLQADLYENFTDVDAVYSVNPS 230
             +D   + PGF+G +K+ ++   SR GSD+TG  LA  L A+ YEN+TD + VY V+P 
Sbjct: 178 TTKDTKYLVPGFYGVTKNDEIAVMSRGGSDLTGGELAYALDANKYENWTDTNGVYEVDPR 237

Query: 231 FVENPKEISELTYREMRELSYAGFSVFHDEALIPAFRAGIPVQIKNTNNPSAEGTRVVSK 290
            +   K I  LT++E+R LS  GF+VFH  A++   ++ IP+ I+NTNN    GT ++S+
Sbjct: 238 VISGSKVIPRLTFKELRLLSSKGFNVFHFNAMLNCKKSKIPINIRNTNNKEHCGTMILSE 297

Query: 291 RDNTNGPVVGIASDTGFCSIYISKYLMNREIGFGRRALQILEEHGLTYEHVPSGIDDMTI 350
           R      +VGIA      SIY+ K ++  EIGF    L+I  E G+   H P+  DD++I
Sbjct: 298 RVPME-DLVGIAKLDNMASIYLQKDMLADEIGFTAELLKIFSEFGVNTYHYPTDRDDISI 356

Query: 351 ILRQGQMDAATERSVIKRIEEDLHADEVIVEHHLALIMVVGEAMRHNVGTTARAAKALSE 410
           ++ Q  +      ++ + IE+ L  D +IV ++L +I +VG  ++ N      A  AL E
Sbjct: 357 LVEQEDLKGKI-NNLRREIEKRLKTDNIIVSYNLCVITLVGIGLKENTFAIVDAINALKE 415

Query: 411 AQVNIEMINQGSSEVSMMFGVKEAEERKAVQALYQ 445
             ++ +M++   S++S+  GV +     A++ LY+
Sbjct: 416 NNISFDMLDMSPSKISLHIGVSQNIANNALETLYE 450


Lambda     K      H
   0.316    0.134    0.370 

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: 486
Number of extensions: 26
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: 454
Length of database: 458
Length adjustment: 33
Effective length of query: 421
Effective length of database: 425
Effective search space:   178925
Effective search space used:   178925
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: 51 (24.3 bits)

Align candidate WP_013136261.1 ARNIT_RS12310 (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.7356.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-71  228.0   0.0    1.4e-71  227.8   0.0    1.0  1  lcl|NCBI__GCF_000092245.1:WP_013136261.1  ARNIT_RS12310 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092245.1:WP_013136261.1  ARNIT_RS12310 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.8   0.0   1.4e-71   1.4e-71       2     441 ..       2     453 ..       1     454 [. 0.86

  Alignments for each domain:
  == domain 1  score: 227.8 bits;  conditional E-value: 1.4e-71
                                 TIGR00657   2 aliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAm.......agvTdaLvelaekvsseeek 63 
                                               ++ V+KFGG+Sv+++ +ikkv +ivk+++  +   v+VvSA+       +++Td+L+++a + +  ee 
  lcl|NCBI__GCF_000092245.1:WP_013136261.1   2 SIKVCKFGGSSVKDASQIKKVLDIVKEDDGRR---VIVVSAPgrddnfdEKITDHLLNVATSGKYFEE- 66 
                                               5669*************************555...8999**84444444589****999999988884. PP

                                 TIGR00657  64 eliekirekhleal..eela.sqalkeklkallekeleevkk.....ereldlilsvGEklSaallaaa 124
                                               ++++  +++ ++a+  ++++ ++ l+ +  +l+++  + + +     er+++  ls+GE+  a++++ +
  lcl|NCBI__GCF_000092245.1:WP_013136261.1  67 HFLNISKKQSYDAIidKYRRlCSDLNVNGDDLIKSLDKDLSNsllkgERKEAFFLSRGEHYNAKIIQRY 135
                                               45555455554443112233444455555555555555554467778********************** PP

                                 TIGR00657 125 leelgvkavsllgaeagiltdsefgrAkvleeikterleklleeg..iivvvaGFiGatekgeittLGR 191
                                               ++++g +   +l  e g + ++ f++ k +++++ +++e+  +    + ++v GF G+t++ ei ++ R
  lcl|NCBI__GCF_000092245.1:WP_013136261.1 136 FSNEGLNIKLMLPEEFGFILSDDFRDGK-VQKVTYKNIEEKFDTTkdTKYLVPGFYGVTKNDEIAVMSR 203
                                               *****655556677889999********.88888888887766544799******************** PP

                                 TIGR00657 192 GGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepa 260
                                               GGSDlt   lA al+A++ e +tD +G+y  DPr+++  + ++ ++++E   L+s G  v+h +++  +
  lcl|NCBI__GCF_000092245.1:WP_013136261.1 204 GGSDLTGGELAYALDANKYENWTDTNGVYEVDPRVISGSKVIPRLTFKELRLLSSKGFNVFHFNAMLNC 272
                                               ********************************************************************* PP

                                 TIGR00657 261 mrakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalae 327
                                               +++kipi +++t n+e  GT+i ++++++e   + +++  +n+a + +++   +   g+ ae++++ +e
  lcl|NCBI__GCF_000092245.1:WP_013136261.1 273 KKSKIPINIRNTNNKEHCGTMILSERVPME--DLVGIAKLDNMASIYLQKDMLAdeIGFTAELLKIFSE 339
                                               *************************99888..8899999999999999988777779************ PP

                                 TIGR00657 328 akvnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgva 396
                                                +vn       ++++ is+ v++ed++   + l++++++  +  ++ v  +l++++lvG g+k++   +
  lcl|NCBI__GCF_000092245.1:WP_013136261.1 340 FGVNTYHYP--TDRDDISILVEQEDLKGKINNLRREIEKRLKTDNIIVSYNLCVITLVGIGLKENTFAI 406
                                               ***998766..88889**********9999999999********************************* PP

                                 TIGR00657 397 akifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441
                                                 +++aL+e+ni+  m+    s i++ + v+++ a++a+e+l+e l 
  lcl|NCBI__GCF_000092245.1:WP_013136261.1 407 VDAINALKENNISFDMLDmsPSKISLHIGVSQNIANNALETLYESLL 453
                                               ****************983345555556689999********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (458 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.52
//
[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