Alignments for a candidate for asp-kinase in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Bacteroides thetaiotaomicron VPI-5482

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 350903 BT1375 aspartokinase (NCBI ptt file)

Query= BRENDA::Q9LYU8
         (569 letters)



>FitnessBrowser__Btheta:350903
          Length = 439

 Score =  238 bits (608), Expect = 3e-67
 Identities = 165/462 (35%), Positives = 252/462 (54%), Gaps = 32/462 (6%)

Query: 89  VMKFGGSSVASAERMKEVADLILTFPEESPVIVLSAMGKTTNNLLLAGEKAVSCGVSNAS 148
           V+KFGG+SV SA+RMKEVA LI     E  ++VLSAM  TTN L+   +         A+
Sbjct: 3   VLKFGGTSVGSAQRMKEVAKLITD--GEQKIVVLSAMSGTTNTLVEISDYLYKKNPEGAN 60

Query: 149 EIEELSIIKELHIRTVKELNIDPSVILTYLEELEQLLKGI-AMMKEL-TLRTRDYLVSFG 206
           EI  ++ ++  + + V EL          LE ++     I +  K+L TL     +++ G
Sbjct: 61  EI--INKLESKYKQHVDELFATQEYKQKGLEVIKSHFDYIRSYTKDLFTLFEEKVVLAQG 118

Query: 207 ECLSTRIFAAYLNTIGVKARQYDAFEIGFITTDDFTNGDILEATYPAVAKRLYDDWMH-- 264
           E +ST +   YL   GVK+    A E  F+ TD     D      P   K      +   
Sbjct: 119 ELISTAMVNFYLQECGVKSVLLPALE--FMRTDKNAEPD------PVYIKEKLQTQLELY 170

Query: 265 -DPAVPIVTGFLGKGWKTGAVTTLGRGGSDLTATTIGKALGLKEIQVWKDVDGVLTCDPT 323
            D  + I  GF+ +    G +  L RGGSD TA+ IG A+   EIQ+W D+DG+   DP 
Sbjct: 171 PDMEIYITQGFICRN-AYGEIDNLQRGGSDYTASLIGAAVKASEIQIWTDIDGMHNNDPR 229

Query: 324 IYKRATPVPYLTFDEAAELAYFGAQVLHPQSMRPAREGEIPVRVKNSYNPKAPGTIITKT 383
           I  +  PV  L F+EAAELAYFGA++LHP  ++PA+   IPVR+ N+ +P APGT+I  +
Sbjct: 230 IVDKTAPVRQLHFEEAAELAYFGAKILHPTCIQPAKYANIPVRLLNTMDPDAPGTLI--S 287

Query: 384 RDMTKSILTSIVLKRNVTMLDIASTRMLGQVGFLAKVFSIFEELGISVDVVATSEVSISL 443
            D  K  + ++  K N+T + I S+RML   GFL KVF IFE    S+D++ TSEV +S+
Sbjct: 288 NDTEKGKIKAVAAKNNITAIKIKSSRMLLAHGFLRKVFEIFESYQTSIDMICTSEVGVSV 347

Query: 444 TLDPSKLWSRELIQQELDHVVEELEKIAVVNLLKGRAIISLIGNVQHSSLILE-RAFHVL 502
           T+D +K          L+ ++++L+K   V + K   II ++G+++  ++  E +A   +
Sbjct: 348 TIDNTK---------HLNEILDDLKKYGTVTVDKDMCIICVVGDLEWENVGFEAKALDAM 398

Query: 503 YTKGVNVQMISQGASKVNISFIVNEAEAEGCVQALHKSFFES 544
             + + V+MIS G S  NISF++ + + +  +Q+L    F +
Sbjct: 399 --RDIPVRMISFGGSNYNISFLIRDCDKKTALQSLSDMLFNN 438


Lambda     K      H
   0.318    0.134    0.377 

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: 461
Number of extensions: 19
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: 569
Length of database: 439
Length adjustment: 34
Effective length of query: 535
Effective length of database: 405
Effective search space:   216675
Effective search space used:   216675
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: 52 (24.6 bits)

Align candidate 350903 BT1375 (aspartokinase (NCBI ptt file))
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.31931.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    1.6e-96  310.0   0.1    1.8e-96  309.8   0.1    1.0  1  lcl|FitnessBrowser__Btheta:350903  BT1375 aspartokinase (NCBI ptt f


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350903  BT1375 aspartokinase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.8   0.1   1.8e-96   1.8e-96       5     441 ..       3     436 ..       1     437 [. 0.90

  Alignments for each domain:
  == domain 1  score: 309.8 bits;  conditional E-value: 1.8e-96
                          TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee...keliekirekhleal 77 
                                        V+KFGGtSvg+++r+k+vak+++  +    q +VV+SAm+g+T+ Lve+++ + +++    +e+i+k+++k  + +
  lcl|FitnessBrowser__Btheta:350903   3 VLKFGGTSVGSAQRMKEVAKLITDGE----QKIVVLSAMSGTTNTLVEISDYLYKKNPegaNEIINKLESKYKQHV 74 
                                        89********************9877....889*****************99877776688889999999999999 PP

                          TIGR00657  78 eela.sqalkeklkallekeleevkk.......ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltd 145
                                        +el   q+ k+k  ++++++++ +++         e+ ++l+ GE +S+a++  +l+e gvk+v ll a + ++td
  lcl|FitnessBrowser__Btheta:350903  75 DELFaTQEYKQKGLEVIKSHFDYIRSytkdlftLFEEKVVLAQGELISTAMVNFYLQECGVKSV-LLPALEFMRTD 149
                                        998889999999999999999999889999998778889*********************8777.56667789999 PP

                          TIGR00657 146 sefgrAk.vleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiy 220
                                        ++ +    +++e  + +le + +   i++++GFi  +  gei  L RGGSD+tA+l++aa+kA+e++i+tD+dG +
  lcl|FitnessBrowser__Btheta:350903 150 KNAEPDPvYIKEKLQTQLELYPD-MEIYITQGFICRNAYGEIDNLQRGGSDYTASLIGAAVKASEIQIWTDIDGMH 224
                                        88766553444444444444443.47************************************************** PP

                          TIGR00657 221 taDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseeepavka 296
                                          DPriv ++  + ++ +eEa+ELa++Gak+Lhp +++pa+ a+ip++  +t++p+a+GTli ++++   + ++ka
  lcl|FitnessBrowser__Btheta:350903 225 NNDPRIVDKTAPVRQLHFEEAAELAYFGAKILHPTCIQPAKYANIPVRLLNTMDPDAPGTLISNDTE---KGKIKA 297
                                        *****************************************************************55...578*** PP

                          TIGR00657 297 lsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellkkkvkeekal 370
                                        ++ ++n + ++++++ m    g+l +vf++ ++ + ++d+i   +se ++s ++d  ++++ +e+l    +++k+ 
  lcl|FitnessBrowser__Btheta:350903 298 VAAKNNITAIKIKSSRMLlaHGFLRKVFEIFESYQTSIDMIC--TSEVGVSVTID--NTKHLNEIL----DDLKKY 365
                                        *****************999**********************..77767666665..555666664....678999 PP

                          TIGR00657 371 eevevekklalvslvGagmksapgvaakifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441
                                        ++v+v+k+++++ +vG+   ++ g  ak+++a+++  i+++mis   s+++is+++++ d ++a++ l ++l+
  lcl|FitnessBrowser__Btheta:350903 366 GTVTVDKDMCIICVVGDLEWENVGFEAKALDAMRD--IPVRMISfgGSNYNISFLIRDCDKKTALQSLSDMLF 436
                                        *********************************99..********9***********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (439 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: 7.79
//
[ok]

This GapMind analysis is from Apr 09 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