GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Shewanella oneidensis MR-1

Align fused aspartate kinase/homoserine dehydrogenase 2 (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 203139 SO4055 aspartokinase II/homoserine dehydrogenase, methionine-sensitive (NCBI ptt file)

Query= ecocyc::ASPKINIIHOMOSERDEHYDROGII-MONOMER
         (810 letters)



>FitnessBrowser__MR1:203139
          Length = 797

 Score =  571 bits (1472), Expect = e-167
 Identities = 342/802 (42%), Positives = 480/802 (59%), Gaps = 22/802 (2%)

Query: 14  LHKFGGSSLADVKCYLRVAGIMAEYSQPDDMMVVSAAGSTTNQLINWLKLSQTDRLSAHQ 73
           LHKFGGSSLAD  CY RVA I+  +   DD++VVSAAG TTN L   L L  +++L   +
Sbjct: 6   LHKFGGSSLADADCYRRVAHILLTHGHSDDLVVVSAAGKTTNFLYKLLSLRDSNQLWQEE 65

Query: 74  VQQTLRRYQCDLISGLLPAEEADSLISAFVSDLERLAALLDSGI-NDAVYAEVVGHGEVW 132
           +Q  L  YQ  LI  LL  E+A  L     +D  +L +LL   + ND   + VV  GE W
Sbjct: 66  LQ-VLISYQQGLIEQLLSNEQARDLRERLTTDKAQLISLLSLDVRNDYQISHVVSFGERW 124

Query: 133 SARLMSAVLNQQGLPAAWLDAREFLRAERAAQPQVDEGLSYPLLQQLLVQHPGKRLVVTG 192
           SARLM+A+L + G+ A+ +DA   L A+ AA PQ+    S   +Q LL  HP +RLV+TG
Sbjct: 125 SARLMAALLRESGVAASHVDACSILVADEAAVPQIRVQESRAKVQALLAAHPNERLVITG 184

Query: 193 FISRNNAGETVLLGRNGSDYSATQIGALAGVSRVTIWSDVAGVYSADPRKVKDACLLPLL 252
           FI  N  G+T+LLGRNGSD+SA+ I +LA + RVTIW+DV GV++ADP K+ DA LL  +
Sbjct: 185 FICANERGDTLLLGRNGSDFSASLIASLADIERVTIWTDVEGVFNADPNKINDAKLLKSM 244

Query: 253 RLDEASELARLAAPVLHARTLQPVSGSEIDLQLRCSYTPDQGSTRIERVLASGTGARIVT 312
            L EA  LARL +PVLH+RTLQP+  +E+ L +R SY      T I    +S   A +VT
Sbjct: 245 SLAEADRLARLGSPVLHSRTLQPLFNTEVSLAVRSSYASHTDFTLIAPH-SSSASAPVVT 303

Query: 313 SHDDVCLIEFQVPASQDFKLAHKEIDQILKRAQVRPLAVGVHNDRQLLQFCYTSEVADSA 372
           + + V L  F++            +DQ+++ A + PLA  V +  Q L+  YT+E     
Sbjct: 304 NLNAVVLFGFKIAGD-----VASLLDQLVE-AGLTPLAHWV-SAHQRLELAYTAENQKQV 356

Query: 373 LKILD---EAGLPGELRLRQGLALVAMVGAGVTRNPLHCHRFWQQLKGQPVEFTWQSDDG 429
            K+LD   EA    +L++   L LVA+V A       H  R + +L  +  +  +  D  
Sbjct: 357 QKLLDAQAEALGIRDLQINTELGLVALVSADAE----HYRRSFARLLSRDAKPLFSGD-- 410

Query: 430 ISLVAVLRTGPTESLIQGLHQSVFRAEKRIGLVLFGKGNIGSRWLELFAREQSTLSARTG 489
           +SLV ++       L Q +H+      KRIG++L G GNIG  W++LF     +L+    
Sbjct: 411 LSLVTLVPQSQVNLLTQKVHRRCAGPRKRIGVLLLGVGNIGEAWVKLFKSVSPSLNQELE 470

Query: 490 FEFVLAGVVDSRRSLLSYDGLDASRALAFFNDEAVEQDEESLFLWMRAHPYDDLVVLDVT 549
            +  L G+V S ++L+   G+D       F++EA     E LF  +     D+L+ LD++
Sbjct: 471 AQVELVGLVTSSKALIKSKGVDLQSWQQEFDNEATPWQYEHLFEQLEQLNCDELIALDIS 530

Query: 550 ASQQLADQYLDFASHGFHVISANKLAGASDSNKYRQIHDAFEKTGRHWLYNATVGAGLPI 609
           AS  L  QY +F   G H++SANKLAG+     YR++ +        W YNA+ GAGLPI
Sbjct: 531 ASASLTLQYPEFFERGIHMVSANKLAGSGPLPFYRELKEQLGYRRLFWRYNASCGAGLPI 590

Query: 610 NHTVRDLIDSGDTILSISGIFSGTLSWLFLQFDGSVPFTELVDQAWQQGLTEPDPRDDLS 669
            H + DL +SGD++ ++ GIFSGTL WLF ++D S PF+ELV +A   G+TEPDPRDDLS
Sbjct: 591 QHALNDLRNSGDSVEAVGGIFSGTLCWLFEKYDTSKPFSELVIEARGLGITEPDPRDDLS 650

Query: 670 GKDVMRKLVILAREAGYNIEPDQVRVESLVPAHCEGGSIDHFFENGDELNEQMVQRLEAA 729
           G+D+ RKL+ILARE G  IE + + + SLVPAH     ++ F     EL+++++Q+  AA
Sbjct: 651 GRDMQRKLLILAREIGLEIELEDIELRSLVPAHLADIPLEQFLARIGELDDELLQQYGAA 710

Query: 730 REMGLVLRYVARFDANG---KARVGVEAVREDHPLASLLPCDNVFAIESRWYRDNPLVIR 786
            E   VLRYVA  D +G   KA VG++ +   HP A+L P DNVF I S +Y+ NPL+IR
Sbjct: 711 AEQNKVLRYVASLDNSGAVLKAEVGLQWIDASHPYANLTPGDNVFVIRSAFYQGNPLIIR 770

Query: 787 GPGAGRDVTAGAIQSDINRLAQ 808
           GPGAGR+VTA A+QSD+ ++ +
Sbjct: 771 GPGAGREVTAAAVQSDLTQICR 792


Lambda     K      H
   0.320    0.135    0.397 

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: 1491
Number of extensions: 60
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: 810
Length of database: 797
Length adjustment: 41
Effective length of query: 769
Effective length of database: 756
Effective search space:   581364
Effective search space used:   581364
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)

Align candidate 203139 SO4055 (aspartokinase II/homoserine dehydrogenase, methionine-sensitive (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.23794.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    2.3e-67  213.9   0.0    3.7e-67  213.2   0.0    1.2  1  lcl|FitnessBrowser__MR1:203139  SO4055 aspartokinase II/homoseri


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:203139  SO4055 aspartokinase II/homoserine dehydrogenase, methionine-sensitive (NCBI ptt file
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.2   0.0   3.7e-67   3.7e-67       6     438 ..       7     431 ..       4     434 .. 0.83

  Alignments for each domain:
  == domain 1  score: 213.2 bits;  conditional E-value: 3.7e-67
                       TIGR00657   6 qKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee.keliekirekhlealeela.s 82 
                                      KFGG+S+++++  ++va+i++ + ++  + +VVvSA +++T+ L +l +  +s++  +e+++++ + +   +e+l  +
  lcl|FitnessBrowser__MR1:203139   7 HKFGGSSLADADCYRRVAHILLTHGHS--DDLVVVSAAGKTTNFLYKLLSLRDSNQLwQEELQVLISYQQGLIEQLLsN 83 
                                     6*******************9999855..589************************99777777777776677776644 PP

                       TIGR00657  83 qalkeklkallekeleevkk.......ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvl 154
                                     ++ +   ++l+  + +++         + +   ++s+GE+ Sa+l+aa+l+e g  a+s ++a + +++d++       
  lcl|FitnessBrowser__MR1:203139  84 EQARDLRERLTTDKAQLISLlsldvrnDYQISHVVSFGERWSARLMAALLRESG-VAASHVDACSILVADEAAVPQI-R 160
                                     44444444444444444433777887799999**********************.7788888888888877655544.7 PP

                       TIGR00657 155 eeikterleklleeg..iivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeAr 231
                                     ++++++++++ll +      v++GFi a+e g++ +LGR+GSD++A+l+A++ + ++v i+tDV+G++ aDP+++++A+
  lcl|FitnessBrowser__MR1:203139 161 VQESRAKVQALLAAHpnERLVITGFICANERGDTLLLGRNGSDFSASLIASLADIERVTIWTDVEGVFNADPNKINDAK 239
                                     88888888888888776899*********************************************************** PP

                       TIGR00657 232 rldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsg 310
                                     +l+++s +Ea  La+lG+ vLh rtl+p+ + ++ + v+s++  +++ Tli ++s+s ++p v+   + +  +l+  ++
  lcl|FitnessBrowser__MR1:203139 240 LLKSMSLAEADRLARLGSPVLHSRTLQPLFNTEVSLAVRSSYASHTDFTLIAPHSSSASAPVVT---NLNAVVLFGFKI 315
                                     ******************************************************8866655554...444445554444 PP

                       TIGR00657 311 ttmkpgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagm 389
                                     +    g +a ++ +l ea+    +   s+ ++ ++++   e+ ++ ++ll ++  e+  +++++++++l lv+lv+a+ 
  lcl|FitnessBrowser__MR1:203139 316 A----GDVASLLDQLVEAGLTPLAHWVSA-HQRLELAYTAENQKQVQKLL-DAQAEALGIRDLQINTELGLVALVSADA 388
                                     4....556888888889998887777444.4679**************98.5678888999****************** PP

                       TIGR00657 390 ksapgvaakifeaLaeeniniemissseikisvvvdekdaekavealhe 438
                                     +++    a++++  a+       + s + +++++v++++++ +++++h+
  lcl|FitnessBrowser__MR1:203139 389 EHYRRSFARLLSRDAK------PLFSGDLSLVTLVPQSQVNLLTQKVHR 431
                                     *988877777766555......344577888888888888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (797 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: 13.17
//
[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:

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