GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Desulforamulus 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.373300.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  NCBI__GCF_000215085.1:WP_013842892.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000215085.1:WP_013842892.1  
   #    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 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerde 74 
                                           +l+V+KFGG+svg+ erik++a++v++e ++g++vvV vSAm+ +td l++l+      +++ +++ +re+d+
  NCBI__GCF_000215085.1:WP_013842892.1   1 MLVVKKFGGSSVGDPERIKRVARRVVEEHQKGNQVVVAVSAMGDTTDDLISLM------KQVTNNPPEREMDM 67 
                                           79**************************************************9......8************* PP

                             TIGR00656  75 lvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGat 147
                                           l+s+GE++s+all++a+r+lg + ++l+g++ gi Tdd +++Aki +++t  r+ e L++g +vvvaGF+G +
  NCBI__GCF_000215085.1:WP_013842892.1  68 LLSTGEQISIALLAMAIRDLGSDVVSLTGGQVGIYTDDVHTKAKILRIET-GRVREELNQGRVVVVAGFQGVN 139
                                           **************************************************.********************** PP

                             TIGR00656 148 eeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhp 220
                                            +G+iTtLGRGGSD+tA++laaal Ad +ei+TDV+GvyttDPrvv+ea+k+ +isy+E+lelA+lGa+vlhp
  NCBI__GCF_000215085.1:WP_013842892.1 140 PDGDITTLGRGGSDTTAVALAAALRADVCEIFTDVDGVYTTDPRVVPEARKLSHISYDEMLELASLGAQVLHP 212
                                           ************************************************************************* PP

                             TIGR00656 221 ralelaveakvpilvrsskekeegTlitn..kkensslvkaialeknvarltvegegmlgkrgilaeifkaLa 291
                                           r++ela+++++p+ vr s+++ egT +++  ++en ++v+++a++ nva++ ++  ++ +k+g++ +ifkaL+
  NCBI__GCF_000215085.1:WP_013842892.1 213 RSVELAKQYGIPLHVRTSFNHMEGTIVEEapDMENAPVVSGVAHDYNVAKIGLF--DVPDKPGVAKTIFKALS 283
                                           ****************************99999*99******************..***************** PP

                             TIGR00656 292 eeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvas 361
                                           +++invd+i+q+  +   ++i ++    d+ +a +++++ +++++++    +ed+a+vsivgag++++pGva+
  NCBI__GCF_000215085.1:WP_013842892.1 284 KQSINVDMIIQSAMRnnmNDIGFTTTIDDLRKALQIIEAIQDEVGFKGYTHDEDVAKVSIVGAGMISHPGVAA 356
                                           ************99888899***************************************************** PP

                             TIGR00656 362 eifkaleekninilmisssetkisvlvdekdaekavrklhekle 405
                                            +f+al++++in+ mi++se+k+s +++ +d+ekav++lh+k++
  NCBI__GCF_000215085.1:WP_013842892.1 357 DMFEALADEGINLEMITTSEIKVSCVIKRADTEKAVKALHKKFV 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 17.73
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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