Alignments for a candidate for asp-kinase in Desulfobulbus mediterraneus DSM 13871

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Desulfobulbus mediterraneus DSM 13871

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_028585318.1 G494_RS0115930 hypothetical protein

Query= BRENDA::Q57991
         (473 letters)



>NCBI__GCF_000429965.1:WP_028585318.1
          Length = 460

 Score =  258 bits (660), Expect = 2e-73
 Identities = 157/469 (33%), Positives = 262/469 (55%), Gaps = 23/469 (4%)

Query: 4   VMKFGGTSVGSGERIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVRDIA 63
           V+K GG  +   + IRH+++++    K     ++VVSA+  VT+ L+    +AL  +D  
Sbjct: 3   VIKIGGGCLKGIKTIRHISRLIPSYGKGH---ILVVSALYGVTDILINGIDKAL--KDEE 57

Query: 64  KVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGELTPKSRD 123
            +   ++ I + H       ++S E  +  K+ +   ++ LE+   G+ + GELTPK  D
Sbjct: 58  LILPHLEIILKLHLSVATHLMESAECVQGYKRELADTVKLLERYYYGLNFTGELTPKMAD 117

Query: 124 YILSFGERLSSPILSGAIRDLGEKSIALEGGEAGIITDNNFGSARVKRLE-----VKERL 178
            I   GER S+ +L+  +R  G     +   E  + TD  FG A V  LE     +++ L
Sbjct: 118 AISCLGERFSAQLLAWTLRSYGLNCGYMFPQEMPLYTDGKFGDATVD-LEATGKALQDSL 176

Query: 179 LPLLKEGIIPVVTGFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVSGVYTT 238
           LP L    +  V GF G +++G ITT GRGGSDYSAA I    DA+++EIW DV G  T 
Sbjct: 177 LPYLAAHDMVFVPGFYGVSQKGEITTFGRGGSDYSAAAIAAAADAEVLEIWKDVDGFMTA 236

Query: 239 DPRLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPESEGTLI 298
           DP+ VP A  I  LSY E  EL+YFGA +LHPRT+EP  ++GI I++KNT  PE+ GT+I
Sbjct: 237 DPKFVPQAEFIHCLSYEECAELSYFGATILHPRTVEPVRQRGIEIVIKNTMRPEARGTVI 296

Query: 299 TNDMEMSDSIVKAISTIKNVALINIFGAGMVGVSGTAARIFKALGEEEVNVILISQGSSE 358
           T+    S  I+K+I+  +++A++ +  +G+    G  + +  A+ +  +N+   S  +++
Sbjct: 297 TDSSGQSAKIIKSITYTEDIAILKVHASGVGYRPGILSIVSGAITDAALNI--KSVVATQ 354

Query: 359 TNISLVVSEEDVDKALKALKREFGDFGKKSFLNNNLIRDVSVDKDVCVISVVGAGMRGAK 418
           T IS ++S++D+D A  AL+R          +     R +  + ++ ++++VG G+  + 
Sbjct: 355 TCISFLLSKKDLDPAFAALER----------IQPRPYRLLEREDELVLLAIVGEGLSSSM 404

Query: 419 GIAGKIFTAVSESGANIKMIAQGSSEVNISFVIDEKDLLNCVRKLHEKF 467
           G+A + F+A+S    N++MI+ G S+  + F++    L   V  LH+ F
Sbjct: 405 GVAARCFSAISGEDINVEMISFGPSKAALYFLLHRDKLYQGVHALHQTF 453


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: 489
Number of extensions: 23
Number of successful extensions: 6
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: 460
Length adjustment: 33
Effective length of query: 440
Effective length of database: 427
Effective search space:   187880
Effective search space used:   187880
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_028585318.1 G494_RS0115930 (hypothetical protein)
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.6135.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.9e-100  320.7   0.0      1e-99  320.6   0.0    1.0  1  lcl|NCBI__GCF_000429965.1:WP_028585318.1  G494_RS0115930 hypothetical prot


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429965.1:WP_028585318.1  G494_RS0115930 hypothetical protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.6   0.0     1e-99     1e-99       5     441 ..       3     454 ..       1     455 [. 0.95

  Alignments for each domain:
  == domain 1  score: 320.6 bits;  conditional E-value: 1e-99
                                 TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekire 71 
                                               V K GG  ++ ++ i+++ +++ +   kg   + VvSA  gvTd L++ ++k+ ++ee     +e i +
  lcl|NCBI__GCF_000429965.1:WP_028585318.1   3 VIKIGGGCLKGIKTIRHISRLIPSYG-KG--HILVVSALYGVTDILINGIDKALKDEEliLPHLEIILK 68 
                                               89******************999877.44..699*******************99999888899***** PP

                                 TIGR00657  72 khlealeela.sqalkeklkallekeleevkk............ereldlilsvGEklSaallaaalee 127
                                                hl+ + +l  s +  +  k+ l+  ++++++            ++  d+i ++GE+ Sa+lla +l++
  lcl|NCBI__GCF_000429965.1:WP_028585318.1  69 LHLSVATHLMeSAECVQGYKRELADTVKLLERyyyglnftgeltPKMADAISCLGERFSAQLLAWTLRS 137
                                               *******99989999999999999999999989************************************ PP

                                 TIGR00657 128 lgvkavsllgaeagiltdsefgrAk....vleeikterleklleegiivvvaGFiGatekgeittLGRG 192
                                               +g +   ++ +e ++ td++fg+A+    ++ ++ ++ l+++l +  +v v GF G+++kgeitt GRG
  lcl|NCBI__GCF_000429965.1:WP_028585318.1 138 YGLNCGYMFPQEMPLYTDGKFGDATvdleATGKALQDSLLPYLAAHDMVFVPGFYGVSQKGEITTFGRG 206
                                               **99999******************887777788899999***************************** PP

                                 TIGR00657 193 GSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepam 261
                                               GSD++Aa++Aaa +A+++ei++DVdG +taDP+ vp+A  +  +syeE +EL+++Ga +Lhprt+ep++
  lcl|NCBI__GCF_000429965.1:WP_028585318.1 207 GSDYSAAAIAAAADAEVLEIWKDVDGFMTADPKFVPQAEFIHCLSYEECAELSYFGATILHPRTVEPVR 275
                                               ********************************************************************* PP

                                 TIGR00657 262 rakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaea 328
                                               + +i+iv+k+t+ pea GT+i+ +s  ++++++k+++++++ a+++v+ ++    pgil+ v ga+++a
  lcl|NCBI__GCF_000429965.1:WP_028585318.1 276 QRGIEIVIKNTMRPEARGTVITDSSG-QSAKIIKSITYTEDIAILKVHASGVGyrPGILSIVSGAITDA 343
                                               ************************88.556*************999987666666************** PP

                                 TIGR00657 329 kvnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaa 397
                                                 n+ +++  + +t isf ++k+d+d a ++l++   + +  + +e e++l l ++vG+g++s +gvaa
  lcl|NCBI__GCF_000429965.1:WP_028585318.1 344 ALNIKSVV--ATQTCISFLLSKKDLDPAFAALER--IQPRPYRLLEREDELVLLAIVGEGLSSSMGVAA 408
                                               *******9..55668****************964..78888889************************* PP

                                 TIGR00657 398 kifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441
                                               + f+a++ e+in+emis   s  ++ ++ + ++  + v+alh+ ++
  lcl|NCBI__GCF_000429965.1:WP_028585318.1 409 RCFSAISGEDINVEMISfgPSKAALYFLLHRDKLYQGVHALHQTFF 454
                                               ******************99***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (460 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: 9.92
//
[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