Alignments for a candidate for asp-kinase in Kyrpidia tusciae DSM 2912

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Kyrpidia tusciae DSM 2912

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013074687.1 BTUS_RS03195 aspartate kinase

Query= BRENDA::P08495
         (408 letters)



>NCBI__GCF_000092905.1:WP_013074687.1
          Length = 415

 Score =  418 bits (1074), Expect = e-121
 Identities = 226/403 (56%), Positives = 291/403 (72%), Gaps = 1/403 (0%)

Query: 1   MGLIVQKFGGTSVGSVEKIQNAANRAIAEKQKGHQVVVVVSAMGKSTDELVSLAKAISDQ 60
           M  IV KFGG+SV + E++   A R    K +GHQV VVVSAMG +TD+L++LAK ++++
Sbjct: 1   MARIVMKFGGSSVATAERMVKVAQRVAKTKAEGHQVAVVVSAMGDTTDDLIALAKQVNER 60

Query: 61  PSKREMDMLLATGEQVTISLLSMALQEKGYDAVSYTGWQAGIRTEAIHGNARITDIDTSV 120
           P  RE+DMLL+TGEQV+I++L+MALQ  G  A S TG QAG R E + G ARI ++    
Sbjct: 61  PPARELDMLLSTGEQVSIAVLTMALQGLGVPATSLTGGQAGFRVEQVFGKARILEVRPDR 120

Query: 121 LADQLEKGKIVIVAGFQGMTEDCEITTLGRGGSDTTAVALAAALKADKCDIYTDVPGVFT 180
           +   L  G + +VAGFQG+T+D EI TLGRGGSDTTAVALAAALKAD C+IYTDV GV+T
Sbjct: 121 VDALLRDGHVAVVAGFQGVTDDGEIATLGRGGSDTTAVALAAALKADVCEIYTDVDGVYT 180

Query: 181 TDPRYVKSARKLEGISYDEMLELANLGAGVLHPRAVEFAKNYQVPLEVRSSTETEAGTLI 240
           TDPR VK A K+  ISYDEMLELANLGA VLHPRAVE+AK Y+VPL VRSS     GT +
Sbjct: 181 TDPRIVKEAAKIPEISYDEMLELANLGAVVLHPRAVEYAKLYRVPLVVRSSFHDGPGTWV 240

Query: 241 EEESSMEQNLIVRGIAFEDQITRVTIYGLTSGLTTLSTIFTTLAKRNINVDIIIQTQA-E 299
           +EE+++EQ  +VRGIA +  + +V++ G+ +   +L  +F  LA+ N+NVDII+Q+    
Sbjct: 241 KEEANVEQGQVVRGIAHDLNVAKVSLVGVPNRQDSLGKVFHALAEENVNVDIIVQSIVHN 300

Query: 300 DKTGISFSVKTEDADQTVAVLEEYKDALEFEKIETESKLAKVSIVGSGMVSNPGVAAEMF 359
           D   ISF+V  +D   T+ VLE+ + AL   +I TE  LAKVSIVG+GM+SNPGVAA MF
Sbjct: 301 DVHDISFTVCRDDLPVTLRVLEDLRVALGAGEIVTEEDLAKVSIVGAGMISNPGVAARMF 360

Query: 360 AVLAQKNILIKMVSTSEIKVSTVVSENDMVKAVESLHDAFELS 402
             L +  + I+MVSTSEIKVS VV   D+ +AV+ LH AFELS
Sbjct: 361 DALIEAGMSIRMVSTSEIKVSCVVDARDVKRAVQVLHQAFELS 403


Lambda     K      H
   0.313    0.128    0.337 

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: 357
Number of extensions: 13
Number of successful extensions: 2
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: 408
Length of database: 415
Length adjustment: 31
Effective length of query: 377
Effective length of database: 384
Effective search space:   144768
Effective search space used:   144768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_013074687.1 BTUS_RS03195 (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.27842.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-138  447.9  11.6     2e-138  447.7  11.6    1.0  1  lcl|NCBI__GCF_000092905.1:WP_013074687.1  BTUS_RS03195 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092905.1:WP_013074687.1  BTUS_RS03195 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.7  11.6    2e-138    2e-138       3     406 ..       3     402 ..       1     403 [. 0.98

  Alignments for each domain:
  == domain 1  score: 447.7 bits;  conditional E-value: 2e-138
                                 TIGR00656   3 liVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispre 71 
                                                iV+KFGG+sv+  er+ k+a++v k++ eg++v VVvSAm+ +td l++la      +++++ +  re
  lcl|NCBI__GCF_000092905.1:WP_013074687.1   3 RIVMKFGGSSVATAERMVKVAQRVAKTKAEGHQVAVVVSAMGDTTDDLIALA------KQVNERPPARE 65 
                                               59**************************************************......9********** PP

                                 TIGR00656  72 rdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvv 140
                                                d+l+s+GE++s+a+l++al+ lgv a++l+g++ag++ ++ fg+A+i e+ +  r+  lL +g + vv
  lcl|NCBI__GCF_000092905.1:WP_013074687.1  66 LDMLLSTGEQVSIAVLTMALQGLGVPATSLTGGQAGFRVEQVFGKARILEVRP-DRVDALLRDGHVAVV 133
                                               *****************************************************.*************** PP

                                 TIGR00656 141 aGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEale 209
                                               aGF+G t +Gei tLGRGGSD+tA++laaalkAd +eiyTDV+GvyttDPr+v+ea ki++isy+E+le
  lcl|NCBI__GCF_000092905.1:WP_013074687.1 134 AGFQGVTDDGEIATLGRGGSDTTAVALAAALKADVCEIYTDVDGVYTTDPRIVKEAAKIPEISYDEMLE 202
                                               ********************************************************************* PP

                                 TIGR00656 210 lAtlGakvlhpralelaveakvpilvrsskekeegTlitn..kkensslvkaialeknvarltvegegm 276
                                               lA+lGa vlhpra+e+a+ + vp++vrss++   gT + +  + e+ ++v++ia++ nva+++++  g+
  lcl|NCBI__GCF_000092905.1:WP_013074687.1 203 LANLGAVVLHPRAVEYAKLYRVPLVVRSSFHDGPGTWVKEeaNVEQGQVVRGIAHDLNVAKVSLV--GV 269
                                               ***************************************965555669*****************..9* PP

                                 TIGR00656 277 lgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveed 342
                                                +++  l ++f aLaee++nvd+i+q+  +    +is++v + d++ + ++L++   a++  ++ +eed
  lcl|NCBI__GCF_000092905.1:WP_013074687.1 270 PNRQDSLGKVFHALAEENVNVDIIVQSIVHndvHDISFTVCRDDLPVTLRVLEDLRVALGAGEIVTEED 338
                                               ***************************988777899********************************* PP

                                 TIGR00656 343 lavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                               la+vsivgag++++pGva+++f al e ++ i m+s+se+k+s +vd +d+++av+ lh+++e+
  lcl|NCBI__GCF_000092905.1:WP_013074687.1 339 LAKVSIVGAGMISNPGVAARMFDALIEAGMSIRMVSTSEIKVSCVVDARDVKRAVQVLHQAFEL 402
                                               **************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (415 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: 10.59
//
[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