Alignments for a candidate for asp-kinase in Thermophagus xiamenensis HS1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Thermophagus xiamenensis HS1

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_010528330.1 GQW_RS0112980 aspartate kinase

Query= BRENDA::Q9RUL9
         (473 letters)



>NCBI__GCF_000220155.1:WP_010528330.1
          Length = 418

 Score =  159 bits (401), Expect = 2e-43
 Identities = 122/398 (30%), Positives = 198/398 (49%), Gaps = 18/398 (4%)

Query: 12  VMKFGGTNMQSAHAIRHSASLAGRSVREGVK--VVVVVSAMAGVTNGLLHLADAAQSGDI 69
           V KFGG +++ A+A+R+   +      EG++  +VVV+SAM   TN +  L ++  SG+ 
Sbjct: 3   VSKFGGASVKDANAVRNLVRIV-----EGLEKPLVVVISAMGKTTNAMEALVESYFSGND 57

Query: 70  ARANDEIAALRTRHFTAAQELGAAPDSETVRELRELHETLRQAVYGVYLLRELTPRSRDL 129
           A   +    +   H   A++L    D   +R   +  E+L Q +     L        D 
Sbjct: 58  AELKERFRNIIAYHEKIAKDLFGEVDIPELRPFYDCVESLSQRLEQQPSLH--FDYEYDQ 115

Query: 130 IVAFGERLSAPLMSLALEQSGLRARHLTGGEAGILTDTNFGNARPLPGTYERVGDRLSGF 189
           IV++GE  S  L++  L+ SG+R + +   +  + TD  + NA        ++      F
Sbjct: 116 IVSYGELFSTLLVNAYLKYSGIRTQWIDVRQI-LKTDDLYRNANVDWSLTNKLMAEAFTF 174

Query: 190 LSAGVTPVIAGFMGETEQGAITTLGRGGTDFSATIVGKALGADEVWAWKDVDGVMSADPR 249
               V  V  GF+G T     TTLGR G+D++A I+G  + A+ V  WKDV GV++ADPR
Sbjct: 175 EEVDVY-VTQGFIGGTISNITTTLGREGSDYTAAIIGHVMDAERVTVWKDVPGVLNADPR 233

Query: 250 VVGDASNIGVLSYGEVMELAYFGAKVLHPLAVTPLQDSGIPLRVKSAADPDFAGTLVRSQ 309
           +  +A  +  LSY E +EL+Y+GA+V+HP  + PLQ+  IPL VKS  +PD  GT+++ +
Sbjct: 234 IFPNAQKMDTLSYAETIELSYYGAQVIHPKTLKPLQNKQIPLYVKSFLNPDLPGTIIQQE 293

Query: 310 AEEIPGRPVKAVTAIKNVSLLTVTGAGVLGVPEVIASVFTAIARENITLLMVSQSSSMSN 369
                  P+  +   KN   LT++      + E   S   A+  E    + + Q+S+++ 
Sbjct: 294 GGN-NNMPIYILR--KNQVFLTLSPRDFSFITEGNLSEILAVFNEFHVRINLLQTSALNF 350

Query: 370 VSLAVPSADAARALQALRAGLSSELNVEETNGVAVLAI 407
            +      D  R L  L   L  +L V   + V +L I
Sbjct: 351 TA----CVDNGRELMPLLEKLKEQLVVRYNDNVELLTI 384


Lambda     K      H
   0.316    0.131    0.358 

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: 338
Number of extensions: 15
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 473
Length of database: 418
Length adjustment: 32
Effective length of query: 441
Effective length of database: 386
Effective search space:   170226
Effective search space used:   170226
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_010528330.1 GQW_RS0112980 (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.979362.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.1e-81  259.2   0.0    4.8e-81  259.0   0.0    1.0  1  NCBI__GCF_000220155.1:WP_010528330.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000220155.1:WP_010528330.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.0   0.0   4.8e-81   4.8e-81       5     352 ..       3     358 ..       1     415 [. 0.83

  Alignments for each domain:
  == domain 1  score: 259.0 bits;  conditional E-value: 4.8e-81
                             TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee...keliekirekhl 74 
                                           V KFGG Sv++++ ++++++iv+  +   ++ vVV+SAm+++T+a+ +l+e+  s+++   ke  ++i + h+
  NCBI__GCF_000220155.1:WP_010528330.1   3 VSKFGGASVKDANAVRNLVRIVEGLE---KPLVVVISAMGKTTNAMEALVESYFSGNDaelKERFRNIIAYHE 72 
                                           89*********************998...689*********************99999888888889999999 PP

                             TIGR00657  75 ealeela.sqalke..klkallekeleevkk......ereldlilsvGEklSaallaaaleelgvkavsllga 138
                                           ++++ l  +  + e   + + +e+  + +++      + e+d i+s+GE  S+ l+ a+l+  g    ++++ 
  NCBI__GCF_000220155.1:WP_010528330.1  73 KIAKDLFgEVDIPElrPFYDCVESLSQRLEQqpslhfDYEYDQIVSYGELFSTLLVNAYLKYSG-IRTQWIDV 144
                                           9999887544332211344555555555555899999***************************.78899*** PP

                             TIGR00657 139 eagiltdsefgrAkvleeikterleklleeg..iivvvaGFiGatekgeittLGRGGSDltAallAaalkAde 209
                                           ++ + td+ +++A+v  + +++ ++++ + +   ++v++GFiG t ++ +ttLGR GSD+tAa++++ ++A++
  NCBI__GCF_000220155.1:WP_010528330.1 145 RQILKTDDLYRNANVDWSLTNKLMAEAFTFEevDVYVTQGFIGGTISNITTTLGREGSDYTAAIIGHVMDAER 217
                                           **************77777777776665544369*************************************** PP

                             TIGR00657 210 veiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTli 282
                                           v +++DV+G++ aDPri p+A+++d++sy+E  EL+++Ga+v+hp+tl+p+ +++ip+ vks  np+ +GT+i
  NCBI__GCF_000220155.1:WP_010528330.1 218 VTVWKDVPGVLNADPRIFPNAQKMDTLSYAETIELSYYGAQVIHPKTLKPLQNKQIPLYVKSFLNPDLPGTII 290
                                           ************************************************************************* PP

                             TIGR00657 283 vakskseeepavkalsldknqalvsvsgttmk...pgilaevfgalaeakvnvdlilqsssetsisfvvdked 352
                                            ++  +++   +    l+knq+++++s         g l+e++   +e +v ++l+   +s  + + +vd+  
  NCBI__GCF_000220155.1:WP_010528330.1 291 QQEGGNNN---MPIYILRKNQVFLTLSPRDFSfitEGNLSEILAVFNEFHVRINLLQ--TSALNFTACVDNGR 358
                                           **977555...5556799999999999999989999*****************9987..44344444554433 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (418 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.36
//
[ok]

This GapMind analysis is from Jul 26 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:

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 2024 update 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 original 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