Alignments for a candidate for asp-kinase in Desulfotomaculum ruminis DSM 2154

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Desulfotomaculum ruminis DSM 2154

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013842892.1 DESRU_RS14810 aspartate kinase

Query= BRENDA::P9WPX3
         (421 letters)



>NCBI__GCF_000215085.1:WP_013842892.1
          Length = 404

 Score =  400 bits (1029), Expect = e-116
 Identities = 208/405 (51%), Positives = 297/405 (73%), Gaps = 9/405 (2%)

Query: 3   LVVQKYGGSSVADAERIRRVAERIVATKKQGNDVVVVVSAMGDTTDDLLDLAQQVCPAPP 62
           LVV+K+GGSSV D ERI+RVA R+V   ++GN VVV VSAMGDTTDDL+ L +QV   PP
Sbjct: 2   LVVKKFGGSSVGDPERIKRVARRVVEEHQKGNQVVVAVSAMGDTTDDLISLMKQVTNNPP 61

Query: 63  PRELDMLLTAGERISNALVAMAIESLGAHARSFTGSQAGVITTGTHGNAKIIDVTPGRLQ 122
            RE+DMLL+ GE+IS AL+AMAI  LG+   S TG Q G+ T   H  AKI+ +  GR++
Sbjct: 62  EREMDMLLSTGEQISIALLAMAIRDLGSDVVSLTGGQVGIYTDDVHTKAKILRIETGRVR 121

Query: 123 TALEEGRVVLVAGFQGVSQDTKDVTTLGRGGSDTTAVAMAAALGADVCEIYTDVDGIFSA 182
             L +GRVV+VAGFQGV+ D  D+TTLGRGGSDTTAVA+AAAL ADVCEI+TDVDG+++ 
Sbjct: 122 EELNQGRVVVVAGFQGVNPD-GDITTLGRGGSDTTAVALAAALRADVCEIFTDVDGVYTT 180

Query: 183 DPRIVRNARKLDTVTFEEMLEMAACGAKVLMLRCVEYARRHNIPVHVRSSYSDRPGTVVV 242
           DPR+V  ARKL  ++++EMLE+A+ GA+VL  R VE A+++ IP+HVR+S++   GT+V 
Sbjct: 181 DPRVVPEARKLSHISYDEMLELASLGAQVLHPRSVELAKQYGIPLHVRTSFNHMEGTIV- 239

Query: 243 GSIKDVP-MED-PILTGVAHDRSEAKVTIVGLPDIPGYAAKVFRAVADADVNIDMVLQNV 300
              ++ P ME+ P+++GVAHD + AK+ +  +PD PG A  +F+A++   +N+DM++Q  
Sbjct: 240 ---EEAPDMENAPVVSGVAHDYNVAKIGLFDVPDKPGVAKTIFKALSKQSINVDMIIQ-- 294

Query: 301 SKVEDGKTDITFTCSRDVGPAAVEKLDSLRNEIGFSQLLYDDHIGKVSLIGAGMRSHPGV 360
           S + +   DI FT + D    A++ ++++++E+GF    +D+ + KVS++GAGM SHPGV
Sbjct: 295 SAMRNNMNDIGFTTTIDDLRKALQIIEAIQDEVGFKGYTHDEDVAKVSIVGAGMISHPGV 354

Query: 361 TATFCEALAAVGVNIELISTSEIRISVLCRDTELDKAVVALHEAF 405
            A   EALA  G+N+E+I+TSEI++S + +  + +KAV ALH+ F
Sbjct: 355 AADMFEALADEGINLEMITTSEIKVSCVIKRADTEKAVKALHKKF 399


Lambda     K      H
   0.318    0.134    0.376 

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: 448
Number of extensions: 24
Number of successful extensions: 7
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: 421
Length of database: 404
Length adjustment: 31
Effective length of query: 390
Effective length of database: 373
Effective search space:   145470
Effective search space used:   145470
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_013842892.1 DESRU_RS14810 (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.6298.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-145  470.7   9.9   2.4e-145  470.5   9.9    1.0  1  lcl|NCBI__GCF_000215085.1:WP_013842892.1  DESRU_RS14810 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000215085.1:WP_013842892.1  DESRU_RS14810 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  470.5   9.9  2.4e-145  2.4e-145       2     405 ..       1     400 [.       1     402 [. 0.99

  Alignments for each domain:
  == domain 1  score: 470.5 bits;  conditional E-value: 2.4e-145
                                 TIGR00656   2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 
                                               +l+V+KFGG+svg+ erik++a++v++e ++g++vvV vSAm+ +td l++l+      +++ +++ +r
  lcl|NCBI__GCF_000215085.1:WP_013842892.1   1 MLVVKKFGGSSVGDPERIKRVARRVVEEHQKGNQVVVAVSAMGDTTDDLISLM------KQVTNNPPER 63 
                                               79**************************************************9......8********* PP

                                 TIGR00656  71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139
                                               e+d+l+s+GE++s+all++a+r+lg + ++l+g++ gi Tdd +++Aki +++t  r+ e L++g +vv
  lcl|NCBI__GCF_000215085.1:WP_013842892.1  64 EMDMLLSTGEQISIALLAMAIRDLGSDVVSLTGGQVGIYTDDVHTKAKILRIET-GRVREELNQGRVVV 131
                                               ******************************************************.************** PP

                                 TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208
                                               vaGF+G + +G+iTtLGRGGSD+tA++laaal Ad +ei+TDV+GvyttDPrvv+ea+k+ +isy+E+l
  lcl|NCBI__GCF_000215085.1:WP_013842892.1 132 VAGFQGVNPDGDITTLGRGGSDTTAVALAAALRADVCEIFTDVDGVYTTDPRVVPEARKLSHISYDEML 200
                                               ********************************************************************* PP

                                 TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitn..kkensslvkaialeknvarltvegeg 275
                                               elA+lGa+vlhpr++ela+++++p+ vr s+++ egT +++  ++en ++v+++a++ nva++ ++  +
  lcl|NCBI__GCF_000215085.1:WP_013842892.1 201 ELASLGAQVLHPRSVELAKQYGIPLHVRTSFNHMEGTIVEEapDMENAPVVSGVAHDYNVAKIGLF--D 267
                                               ****************************************99999*99******************..* PP

                                 TIGR00656 276 mlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaeleslevee 341
                                               + +k+g++ +ifkaL++++invd+i+q+  +   ++i ++    d+ +a +++++ +++++++    +e
  lcl|NCBI__GCF_000215085.1:WP_013842892.1 268 VPDKPGVAKTIFKALSKQSINVDMIIQSAMRnnmNDIGFTTTIDDLRKALQIIEAIQDEVGFKGYTHDE 336
                                               ****************************99888899********************************* PP

                                 TIGR00656 342 dlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405
                                               d+a+vsivgag++++pGva+ +f+al++++in+ mi++se+k+s +++ +d+ekav++lh+k++
  lcl|NCBI__GCF_000215085.1:WP_013842892.1 337 DVAKVSIVGAGMISHPGVAADMFEALADEGINLEMITTSEIKVSCVIKRADTEKAVKALHKKFV 400
                                               **************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (404 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: 00:00:00.01
# Mc/sec: 8.54
//
[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