Alignments for a candidate for asp-kinase in Pyrolobus fumarii 1A

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Pyrolobus fumarii 1A

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_014026853.1 PYRFU_RS06440 aspartate kinase

Query= BRENDA::Q57991
         (473 letters)



>NCBI__GCF_000223395.1:WP_014026853.1
          Length = 480

 Score =  279 bits (713), Expect = 2e-79
 Identities = 175/471 (37%), Positives = 268/471 (56%), Gaps = 24/471 (5%)

Query: 4   VMKFGGTSVGSGERIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVRDI- 62
           V KFGG+ + SGE     A+I T+  + +  V++VVSAM  VT+ L+ ++      RD  
Sbjct: 19  VAKFGGSVLKSGEDYARAAEI-TEELQREHSVILVVSAMKGVTDRLLRLA------RDFE 71

Query: 63  AKVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGELTPKSR 122
           A     I  + + H +A+  A  S  +  E    I   I+EL K++  +  LGE+TPK+ 
Sbjct: 72  ASPSVEIPELYQMHVEALRGAGVSGRLFGEAFSRIARLIDELTKIIWALRVLGEVTPKAL 131

Query: 123 DYILSFGERLSSPILSGAIRDLGEKSIALEGGEAGIITDNNFGSARVKRLE----VKERL 178
           DY++SFGERLS+ I+   +R  G ++ AL G EAGI+TD+ FG A     E    V+ RL
Sbjct: 132 DYVVSFGERLSAVIMEAVLRSRGIEAKALTGWEAGIVTDDRFGEANPIMEETVPRVRSRL 191

Query: 179 LPLLKEGIIPVVTGFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVSGVYTT 238
           LPL ++GI+P+VTGFI  T +G ITTLGRGGSDY+A+LI   L A  +  +TDV GV T 
Sbjct: 192 LPLTEKGIVPIVTGFIAATRKGDITTLGRGGSDYTASLIASILGATEVHFYTDVPGVMTA 251

Query: 239 DPRLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPESEGTLI 298
           DPRL+P AR IP+L  IEA+EL+  G K  HPRT EP +   I   + +  +P    T++
Sbjct: 252 DPRLIPEARTIPRLCVIEALELSRVGGKKFHPRTFEPLLYSKIRARILDAKDPHGPHTIV 311

Query: 299 TNDMEMSDSIVKAISTIKNVALINIFGAGMVGVSGTAARIFKALGEEEVNVILISQGSSE 358
             + E  D++ KA++ ++ +A++ + GA M G  GTA  +        VN++ ISQ  +E
Sbjct: 312 --EPECIDTL-KAVAVMRGLAVVRLEGAVMAGRIGTAMMVTSVSKRAGVNIVAISQPVTE 368

Query: 359 TNISLVVSEEDVDKALKALKREFGDFGKKSFLNNNLIRDVSVDKDVCVISVVGAGMRGAK 418
           T I +VV+EED ++  KAL  E          N  L  +V V+  +  +++VG G+R   
Sbjct: 369 TRIEIVVAEEDAERLAKALSEE--------IRNQELDVNVMVETGLSAVTIVGYGLRNPS 420

Query: 419 GIAGKIFTAVS-ESGANIKMIAQGSSEVNISFVIDEKDLLNCVRKLHEKFI 468
             A  +  A+S E    ++ I  G  + +++ V + +D +    ++H + +
Sbjct: 421 LRARVLSEALSLEPEPELRSITTGFHDASLTIVTNARDAVRIAERIHSRLL 471


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: 541
Number of extensions: 29
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: 473
Length of database: 480
Length adjustment: 33
Effective length of query: 440
Effective length of database: 447
Effective search space:   196680
Effective search space used:   196680
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_014026853.1 PYRFU_RS06440 (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.23756.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-107  345.6   0.0   2.9e-107  345.4   0.0    1.0  1  lcl|NCBI__GCF_000223395.1:WP_014026853.1  PYRFU_RS06440 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000223395.1:WP_014026853.1  PYRFU_RS06440 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.4   0.0  2.9e-107  2.9e-107       3     440 ..      17     470 ..      15     472 .. 0.92

  Alignments for each domain:
  == domain 1  score: 345.4 bits;  conditional E-value: 2.9e-107
                                 TIGR00657   3 liVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekeliekire 71 
                                               l+V+KFGG++++++e   ++a+i ++ +  +++v+ VvSAm+gvTd+L+ la+ ++  ++  +i ++ +
  lcl|NCBI__GCF_000223395.1:WP_014026853.1  17 LLVAKFGGSVLKSGEDYARAAEITEELQ-REHSVILVVSAMKGVTDRLLRLARDFEASPS-VEIPELYQ 83 
                                               68*******************9877766.777***************************5.67888888 PP

                                 TIGR00657  72 khlealeela.sqalkeklkallekeleevkk............ereldlilsvGEklSaallaaalee 127
                                                h+eal  +  s  l  +  + +++ ++e+ k            ++ ld+++s+GE+lSa ++ a+l++
  lcl|NCBI__GCF_000223395.1:WP_014026853.1  84 MHVEALRGAGvSGRLFGEAFSRIARLIDELTKiiwalrvlgevtPKALDYVVSFGERLSAVIMEAVLRS 152
                                               88888888888877777777777777777777788899999999************************* PP

                                 TIGR00657 128 lgvkavsllgaeagiltdsefgrAk....vleeikterleklleegiivvvaGFiGatekgeittLGRG 192
                                               +g++a +l+g+eagi+td++fg+A+    +++   ++rl++l e+gi+++v+GFi+at+kg+ittLGRG
  lcl|NCBI__GCF_000223395.1:WP_014026853.1 153 RGIEAKALTGWEAGIVTDDRFGEANpimeETVPRVRSRLLPLTEKGIVPIVTGFIAATRKGDITTLGRG 221
                                               *************************876666667899******************************** PP

                                 TIGR00657 193 GSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepam 261
                                               GSD+tA+l+A+ l+A+ev+ ytDV+G++taDPr++peAr ++ + + EalEL+++G k +hprt+ep+ 
  lcl|NCBI__GCF_000223395.1:WP_014026853.1 222 GSDYTASLIASILGATEVHFYTDVPGVMTADPRLIPEARTIPRLCVIEALELSRVGGKKFHPRTFEPLL 290
                                               ********************************************************************* PP

                                 TIGR00657 262 rakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaea 328
                                                +ki+ ++ + ++p+++ T++ ++        +ka+++ +  a+v ++g+ m+   g++  v++  ++a
  lcl|NCBI__GCF_000223395.1:WP_014026853.1 291 YSKIRARILDAKDPHGPHTIVEPECI----DTLKAVAVMRGLAVVRLEGAVMAgrIGTAMMVTSVSKRA 355
                                               **********************9944....579********************9999************ PP

                                 TIGR00657 329 kvnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaa 397
                                               +vn+++i+q + et i++vv +eda++ +++l++++++++   +v ve++l+ v++vG+g+++    a 
  lcl|NCBI__GCF_000223395.1:WP_014026853.1 356 GVNIVAISQPVTETRIEIVVAEEDAERLAKALSEEIRNQELDVNVMVETGLSAVTIVGYGLRNPSLRAR 424
                                               ***************************************************************666566 PP

                                 TIGR00657 398 kifeaLaee.niniemis..sseikisvvvdekdaekavealhekl 440
                                                + eaL+ e +   + i     + ++++v + +da++++e +h++l
  lcl|NCBI__GCF_000223395.1:WP_014026853.1 425 VLSEALSLEpEPELRSITtgFHDASLTIVTNARDAVRIAERIHSRL 470
                                               66677764315667777767899********************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (480 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: 11.10
//
[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