GapMind for Amino acid biosynthesis

 

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

Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_010528243.1 GQW_RS0112430 bifunctional aspartate kinase/homoserine dehydrogenase I

Query= reanno::Btheta:351931
         (811 letters)



>NCBI__GCF_000220155.1:WP_010528243.1
          Length = 811

 Score =  825 bits (2132), Expect = 0.0
 Identities = 438/813 (53%), Positives = 572/813 (70%), Gaps = 4/813 (0%)

Query: 1   MKVMKFGGTSVGSVNSILSVKRIVESAGEPVIVVVSALGGITDKLINTSKMAAAGDSAYE 60
           MKV+KFGGTSVG+  +I  VK IVE     ++VVVSA GGITD+LI  +  AA G+  Y 
Sbjct: 1   MKVLKFGGTSVGTAENIKKVKEIVEGQKGQIVVVVSAFGGITDRLIRAAHKAAEGNPVYA 60

Query: 61  GEFREIVYRHVEMIKEVIPAGAGQVALQRQIGELLNELKDIFQGIYLIRDLSPKTSDTIV 120
            +   I+  H+++I  + P  A   A++  +  + +ELK I +G++LIR+LS K+  +I 
Sbjct: 61  TDIDNIIDDHLQIIDTLFPDIAANTAIRNGVEPIFDELKSINKGVFLIRELSEKSLASIS 120

Query: 121 SYGERLSSIIVAELIDEAKWFDSRTFIKTEKKHNKHTIDADLTNQLVKEAFHSIPKVSLV 180
             GERLSS I+A  +  A+WFDSR +IKT  ++ +   D   T + ++E    +  +SL 
Sbjct: 121 GIGERLSSKIIAAYLG-ARWFDSRLYIKTFVEYGRVHADLVYTYKHLREIQPQLADLSLF 179

Query: 181 PGFISSDKVSGDVTNLGRGGSDYTAAIIAAALDASSLEIWTDVDGFMTADPRVISTAYTI 240
           PGFISS+   G+ T LGRGGSDYTA+I+A+A DA  LEIWTDVDGFMTADP+VIS AY I
Sbjct: 180 PGFISSN-ARGENTTLGRGGSDYTASILASAFDAEMLEIWTDVDGFMTADPKVISRAYCI 238

Query: 241 SELSYVEATELCNFGAKVVYPPTIYPVCHKNIPIIIKNTFNPDGVGTVIKQETSNPQSKA 300
             LSY EA EL +FGAKV+YPPTI PV  KNIPI IKNTFNP   GT+I         + 
Sbjct: 239 EHLSYAEAMELSHFGAKVIYPPTILPVYQKNIPITIKNTFNPSAPGTLINGRQETAGQRQ 298

Query: 301 IKGISSINDTSLITVQGLGMVGVIGVNYRIFKALAKNGISVFLVSQASSENSTSIGVRNA 360
           IKGISSI   SL+T+QG+GMVGV G++ R+F +LA   I+V L+SQASSENS SI + ++
Sbjct: 299 IKGISSIKSVSLLTIQGIGMVGVSGISMRLFASLAAKNINVILISQASSENSISIVIDSS 358

Query: 361 DADLACEVLNEEFAKEIEMGEISPILAERNLATVAIVGENMKHTPGIAGKLFGTLGRNGI 420
             +LA   + +EF +E+    IS I+ +  +A VAIVGENMKHT GIAG LF ++G+NG+
Sbjct: 359 QTELAKMAIEQEFKRELSERHISNIIIDNEMAVVAIVGENMKHTTGIAGLLFNSVGKNGV 418

Query: 421 NVIACAQGASETNISFVVDSKSLRKSLNVIHDSFFLSEYQVLNLFICGIGTVGGSLVEQI 480
           NV A AQGASE NISFV+  K ++K+LNVIH++FFLS+Y  LNLF+ G GTVG  L+ +I
Sbjct: 419 NVYAIAQGASELNISFVIKEKDIKKALNVIHEAFFLSDYSRLNLFLVGKGTVGSRLIHKI 478

Query: 481 RCQQQKLMMENGLKLHVVGIIDAAKAMFSREGFDLANFREELQKKGKDSNLQTIRDEIVG 540
             Q+ KL+  N LK+ +VG+      +F +EG D     E+L+K+G   ++   RD+I+ 
Sbjct: 479 ATQRDKLIKNNSLKIRLVGLAGRNSMIFDKEGLDPNTAIEKLEKEGTPGDVSQFRDKIIE 538

Query: 541 MNIFNSVFVDCTASPDIASLYKDLLQHNVSVVAANKIAASSAYENYRELKTIARQRGVKY 600
           MN+ NSVFVDC+AS ++ASLY  LL+ NVSVV ANKIA+SS+YE YR+LK  AR++GVK+
Sbjct: 539 MNMANSVFVDCSASDEVASLYLSLLEANVSVVTANKIASSSSYETYRKLKETARKKGVKF 598

Query: 601 LFETNVGAGLPIINTINDLIHSGDKILKIEAVLSGTLNYIFNKISADIPFSRTIKMAQEE 660
            +ETNVGAGLPII  INDL+ SG+KILK+EAVLSGTLNYI N +S   P S+ I  A+E+
Sbjct: 599 FYETNVGAGLPIIAPINDLVRSGEKILKMEAVLSGTLNYIVNSVSEKKPLSQVIIEAKEK 658

Query: 661 RYSEPDPRIDLSGKDVIRKLVILAREAGYHIEQEDVEKNLFVPNDFFE-GSLDDFWKRVP 719
            YSEPDPRIDLSG DV+RK +ILAREAGY +E   VE   FVP  + +  SLD F +++ 
Sbjct: 659 GYSEPDPRIDLSGTDVVRKALILAREAGYPLESSGVEVEPFVPQQYLDLPSLDLFLEKIA 718

Query: 720 SLDADFEARRQVLEKEHKHWRFVAKL-EDGKASVGLQEVGANHPFYGLEGSNNIILLTTE 778
            LD  FE RRQ    E+K  R+ A +  +GKA VGL EV   HPF+ LEGSNNI+L+ +E
Sbjct: 719 ELDITFEKRRQKALAENKKLRYAAHMTANGKAKVGLIEVDHKHPFFDLEGSNNIVLIWSE 778

Query: 779 RYKEYPMMIQGYGAGAGVTAAGVFADIMSIANV 811
            Y E+PM I+GYGAGA VTAAGV ADI+ +ANV
Sbjct: 779 HYFEHPMQIKGYGAGADVTAAGVLADIIKVANV 811


Lambda     K      H
   0.317    0.135    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: 1454
Number of extensions: 59
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: 811
Length of database: 811
Length adjustment: 41
Effective length of query: 770
Effective length of database: 770
Effective search space:   592900
Effective search space used:   592900
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: 56 (26.2 bits)

Align candidate WP_010528243.1 GQW_RS0112430 (bifunctional aspartate kinase/homoserine dehydrogenase I)
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.1532308.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     3e-116  375.0   3.2     3e-116  375.0   3.2    1.6  2  NCBI__GCF_000220155.1:WP_010528243.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000220155.1:WP_010528243.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  375.0   3.2    3e-116    3e-116       5     441 ..       3     453 ..       1     454 [. 0.94
   2 ?   -1.8   0.0     0.064     0.064      33     148 ..     542     575 ..     524     607 .. 0.55

  Alignments for each domain:
  == domain 1  score: 375.0 bits;  conditional E-value: 3e-116
                             TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekirekhle 75 
                                           V+KFGGtSvg++e+ikkv +iv+ +k  g q vVVvSA +g+Td+L+  a+k+ +++   ++ i++i ++hl+
  NCBI__GCF_000220155.1:WP_010528243.1   3 VLKFGGTSVGTAENIKKVKEIVEGQK--G-QIVVVVSAFGGITDRLIRAAHKAAEGNPvyATDIDNIIDDHLQ 72 
                                           89*********************999..5.99*********************999988999*********** PP

                             TIGR00657  76 aleela.sqalkeklkallekeleevkk............ereldlilsvGEklSaallaaaleelgvkavsl 135
                                           ++++l    a ++ +++ +e  ++e+k+            e++l+ i  +GE+lS++++aa+l ++       
  NCBI__GCF_000220155.1:WP_010528243.1  73 IIDTLFpDIAANTAIRNGVEPIFDELKSinkgvflirelsEKSLASISGIGERLSSKIIAAYLGARW------ 139
                                           *****96667777888899999999999999*******************************97765...... PP

                             TIGR00657 136 lgaeagiltdsefgrAkvleeikterleklleeg..iivvvaGFiGatekgeittLGRGGSDltAallAaalk 206
                                           ++++  i t  e+gr   +  + t +++  ++ +   + ++ GFi ++  ge ttLGRGGSD+tA++lA+a +
  NCBI__GCF_000220155.1:WP_010528243.1 140 FDSRLYIKTFVEYGRVH-ADLVYTYKHLREIQPQlaDLSLFPGFISSNARGENTTLGRGGSDYTASILASAFD 211
                                           9**************99.55555555544444444589*********************************** PP

                             TIGR00657 207 AdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeG 279
                                           A+ +ei+tDVdG +taDP++++ A  ++++sy+Ea+EL+++Gakv++p t+ p+ +++ipi +k+tfnp+a+G
  NCBI__GCF_000220155.1:WP_010528243.1 212 AEMLEIWTDVDGFMTADPKVISRAYCIEHLSYAEAMELSHFGAKVIYPPTILPVYQKNIPITIKNTFNPSAPG 284
                                           ************************************************************************* PP

                             TIGR00657 280 Tlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdk 350
                                           Tli + ++   + ++k++s+ k+ +l++++g +m   +gi  ++f  la +++nv+li+q sse+sis+v+d 
  NCBI__GCF_000220155.1:WP_010528243.1 285 TLINGRQETAGQRQIKGISSIKSVSLLTIQGIGMVgvSGISMRLFASLAAKNINVILISQASSENSISIVIDS 357
                                           ********9999************************************************************* PP

                             TIGR00657 351 edadkakellk...kkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..ssei 418
                                           ++++ ak + +   k +++e+ ++++ +++++a+v++vG++mk++ g+a+ +f+ + ++++n+ +i+  +se 
  NCBI__GCF_000220155.1:WP_010528243.1 358 SQTELAKMAIEqefKRELSERHISNIIIDNEMAVVAIVGENMKHTTGIAGLLFNSVGKNGVNVYAIAqgASEL 430
                                           **999999988777788999***********************************************9***** PP

                             TIGR00657 419 kisvvvdekdaekavealheklv 441
                                           +is+v++ekd +ka++++he+++
  NCBI__GCF_000220155.1:WP_010528243.1 431 NISFVIKEKDIKKALNVIHEAFF 453
                                           *********************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.064
                             TIGR00657  33 gnqvvVVvSAmagvTdaLvelaekvsseeekeliekirekhlealeelasqalkeklkallekeleevkkere 105
                                            n+v+V +SA  +v    ++l e   s  +                                           
  NCBI__GCF_000220155.1:WP_010528243.1 542 ANSVFVDCSASDEVASLYLSLLEANVSVVT------------------------------------------- 571
                                           347777777777777777766666555553........................................... PP

                             TIGR00657 106 ldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsef 148
                                                                                  +++ 
  NCBI__GCF_000220155.1:WP_010528243.1 572 ---------------------------------------ANKI 575
                                           .......................................2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (811 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 22.54
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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:

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:

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:

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:

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