Alignments for a candidate for asp-kinase in Ferroglobus placidus DSM 10642

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Ferroglobus placidus DSM 10642

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_012965315.1 FERP_RS04025 aspartate kinase, monofunctional class

Query= BRENDA::Q57991
         (473 letters)



>NCBI__GCF_000025505.1:WP_012965315.1
          Length = 463

 Score =  430 bits (1105), Expect = e-125
 Identities = 229/475 (48%), Positives = 328/475 (69%), Gaps = 19/475 (4%)

Query: 1   MTTVMKFGGTSVGSGERIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVR 60
           M  VMKFGG SV  GE I H A +V K  K D++VVVVVSAM  VT++L+  + +     
Sbjct: 1   MRIVMKFGGVSVKDGENILHCANLVKKYAK-DNEVVVVVSAMQGVTDSLLHAAHKCYKEA 59

Query: 61  DIAKVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGELTPK 120
               +  FI  + ++HY AIE A+K + IKE+V   ID+ ++ELEK+L+G++YLGELT +
Sbjct: 60  SHGFIKLFIAELAKRHYDAIETAVKDKRIKEKVINRIDNLLDELEKILLGISYLGELTKR 119

Query: 121 SRDYILSFGERLSSPILSGAIRDLGEKSIALEGGEAGIITDNNFGSAR----VKRLEVKE 176
           S DYILSFGERL +PI S ++  LG  S+AL GG+AGI+TD+N+G A+    V  L +K 
Sbjct: 120 SEDYILSFGERLLAPIFSASLISLGVDSVALTGGDAGIVTDSNYGRAKPLPEVYSL-IKS 178

Query: 177 RLLPLLK-EGIIPVVTGFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVSGV 235
           R+ PL+  + ++PVVTGFIG T++G ITTLGRGGSD +A LI   +DAD + +W +V GV
Sbjct: 179 RIEPLISIKKLVPVVTGFIGVTKDGNITTLGRGGSDLTATLIAAAIDADEVWLWKEVDGV 238

Query: 236 YTTDPRLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPESEG 295
            TTDP++VP A+ IP+LSY EAMEL++FGAK+LHPR IEP M++ IP+ +KNTF PE+EG
Sbjct: 239 MTTDPKIVPEAKLIPELSYQEAMELSHFGAKILHPRAIEPVMKRKIPVRIKNTFNPEAEG 298

Query: 296 TLITNDMEMSDSIVKAISTIKNVALINIFGAGMVGVSGTAARIFKALGEEEVNVILISQG 355
           T+I + +  +  +VKA+S I+ V+++NI GAG    +     +F+ L E +VNV++++Q 
Sbjct: 299 TVIRDGITSTKDVVKALSLIEKVSIVNISGAGF-DFAEIMTEVFRILAENKVNVVMVAQS 357

Query: 356 SSETNISLVVSEEDVDKALKALKREFGDFGKKSFLNNNLIRDVSVDKDVCVISVVGAGMR 415
           SSE N+S+V+ + D DKA+KALK+          + N  I+ V   +DV VIS VGAGM 
Sbjct: 358 SSELNLSIVIDDSDYDKAMKALKK----------IENGSIK-VEGIRDVAVISAVGAGMA 406

Query: 416 GAKGIAGKIFTAVSESGANIKMIAQGSSEVNISFVIDEKDLLNCVRKLHEKFIEK 470
           G  G+AG+IF+ +  +  N++MI+Q  SE NISF + + +    V+ LH++FI+K
Sbjct: 407 GTPGVAGRIFSTLGRNRINVRMISQSCSEYNISFAVSKNEGRKAVKVLHDEFIKK 461


Lambda     K      H
   0.316    0.135    0.364 

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: 603
Number of extensions: 31
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: 473
Length of database: 463
Length adjustment: 33
Effective length of query: 440
Effective length of database: 430
Effective search space:   189200
Effective search space used:   189200
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_012965315.1 FERP_RS04025 (aspartate kinase, monofunctional class)
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.22893.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-153  498.3   4.9   1.3e-153  498.1   4.9    1.0  1  lcl|NCBI__GCF_000025505.1:WP_012965315.1  FERP_RS04025 aspartate kinase, m


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025505.1:WP_012965315.1  FERP_RS04025 aspartate kinase, monofunctional class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  498.1   4.9  1.3e-153  1.3e-153       2     441 ..       1     459 [.       1     460 [. 0.97

  Alignments for each domain:
  == domain 1  score: 498.1 bits;  conditional E-value: 1.3e-153
                                 TIGR00657   2 aliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee....keli 66 
                                               ++iV+KFGG Sv+++e+i ++a++vkk + k+n+vvVVvSAm+gvTd+L++ a+k+ +e++    k +i
  lcl|NCBI__GCF_000025505.1:WP_012965315.1   1 MRIVMKFGGVSVKDGENILHCANLVKKYA-KDNEVVVVVSAMQGVTDSLLHAAHKCYKEAShgfiKLFI 68 
                                               68***********************9999.777***************************99999999* PP

                                 TIGR00657  67 ekirekhlealeela.sqalkeklkallekeleevkk............ereldlilsvGEklSaalla 122
                                               +++ ++h++a+e++   + +kek+ + +++ l+e++k            +r++d+ils+GE+l a++++
  lcl|NCBI__GCF_000025505.1:WP_012965315.1  69 AELAKRHYDAIETAVkDKRIKEKVINRIDNLLDELEKillgisylgeltKRSEDYILSFGERLLAPIFS 137
                                               ***************999*************************************************** PP

                                 TIGR00657 123 aaleelgvkavsllgaeagiltdsefgrAk...vleeikterleklleeg.iivvvaGFiGatekgeit 187
                                               a l +lgv++v+l+g++agi+tds++grAk   ++++ +++r+e+l++ +  ++vv+GFiG+t++g+it
  lcl|NCBI__GCF_000025505.1:WP_012965315.1 138 ASLISLGVDSVALTGGDAGIVTDSNYGRAKplpEVYSLIKSRIEPLISIKkLVPVVTGFIGVTKDGNIT 206
                                               *********************************9**************9989***************** PP

                                 TIGR00657 188 tLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprt 256
                                               tLGRGGSDltA+l+Aaa++Adev+++++VdG++t+DP+ivpeA++++e+sy+Ea+EL+++Gak+Lhpr+
  lcl|NCBI__GCF_000025505.1:WP_012965315.1 207 TLGRGGSDLTATLIAAAIDADEVWLWKEVDGVMTTDPKIVPEAKLIPELSYQEAMELSHFGAKILHPRA 275
                                               ********************************************************************* PP

                                 TIGR00657 257 lepamrakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk.pgilaevfga 324
                                               +ep+m+ kip+++k+tfnpeaeGT+i    +s++   vkalsl ++ ++v++sg++ + ++i+ evf++
  lcl|NCBI__GCF_000025505.1:WP_012965315.1 276 IEPVMKRKIPVRIKNTFNPEAEGTVIRDGITSTK-DVVKALSLIEKVSIVNISGAGFDfAEIMTEVFRI 343
                                               *****************************99665.9********************************* PP

                                 TIGR00657 325 laeakvnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksap 393
                                               lae+kvnv++++qssse ++s+v+d++d+dka ++lkk   e+  + +ve  +++a++s vGagm+++p
  lcl|NCBI__GCF_000025505.1:WP_012965315.1 344 LAENKVNVVMVAQSSSELNLSIVIDDSDYDKAMKALKK--IENGSI-KVEGIRDVAVISAVGAGMAGTP 409
                                               ***********************************954..445555.59******************** PP

                                 TIGR00657 394 gvaakifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441
                                               gva++if++L ++ in++mis  +se++is+ v+++++ kav++lh++++
  lcl|NCBI__GCF_000025505.1:WP_012965315.1 410 GVAGRIFSTLGRNRINVRMISqsCSEYNISFAVSKNEGRKAVKVLHDEFI 459
                                               *********************999************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (463 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: 7.56
//
[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