GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Shewanella sp. ANA-3

Align fused aspartate kinase/homoserine dehydrogenase 2 (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 7026471 Shewana3_3613 bifunctional aspartate kinase II/homoserine dehydrogenase II (RefSeq)

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



>FitnessBrowser__ANA3:7026471
          Length = 797

 Score =  563 bits (1451), Expect = e-164
 Identities = 340/802 (42%), Positives = 472/802 (58%), 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  VQQTLRRYQCDLISGLLPAEEADSLISAFVSDLERLAALLD-SGINDAVYAEVVGHGEVW 132
           +Q  L  YQ  LI  LL  E+A  L     +D  +L +LL     ND   + VV  GE W
Sbjct: 66  LQ-VLISYQQGLIEQLLSNEQARDLRERLTTDKAQLISLLSLDSRNDYQISHVVSFGERW 124

Query: 133 SARLMSAVLNQQGLPAAWLDAREFLRAERAAQPQVDEGLSYPLLQQLLVQHPGKRLVVTG 192
           SARLM+A+L + G+ A+ +DA   L A+ AA PQ+    S   +Q LL  HP +RLV+TG
Sbjct: 125 SARLMAALLRESGVAASHVDACSILVADEAAVPQIRVQESRTKVQTLLAAHPNERLVITG 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++       L        L  A + PLA  + +  Q L+  YT+E     
Sbjct: 304 NLNAVVLFGFKIAGDVASLLEQ------LVEAGLTPLAHWL-SAHQRLELAYTAENQKQV 356

Query: 373 LKILD---EAGLPGELRLRQGLALVAMVGAGVTRNPLHCHRFWQQLKGQPVEFTWQSDDG 429
            K+LD   EA    +L++   L LVA+V A       H  R + +L  +  +  +  D  
Sbjct: 357 QKLLDAQAEALGIKDLQINTELGLVALVSADAE----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+    +D       F+ EA     E LF  +     D+L+ LD++
Sbjct: 471 ARVELVGLVSSSKALIKSTAVDLENWQQEFDAEATPWQYEHLFEQLEQLNCDELIALDIS 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 GRDMQRKLLILAREIGLEIELEDIELRSLVPAHLADIPLEQFLARIGELDDELQQQYGAA 710

Query: 730 REMGLVLRYVARFDANG---KARVGVEAVREDHPLASLLPCDNVFAIESRWYRDNPLVIR 786
            E   VLRYVA  D +G   KA VG++ +  +HP A+L P DNVF I S +Y+ NPL+IR
Sbjct: 711 AEQNKVLRYVASLDNSGATLKAEVGLQWIDANHPYANLTPGDNVFVIRSAFYQGNPLIIR 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: 63
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 7026471 Shewana3_3613 (bifunctional aspartate kinase II/homoserine dehydrogenase II (RefSeq))
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.5203.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
      1e-67  215.1   0.0    1.6e-67  214.5   0.0    1.2  1  lcl|FitnessBrowser__ANA3:7026471  Shewana3_3613 bifunctional aspar


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026471  Shewana3_3613 bifunctional aspartate kinase II/homoserine dehydrogenase II (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.5   0.0   1.6e-67   1.6e-67       6     438 ..       7     431 ..       4     434 .. 0.83

  Alignments for each domain:
  == domain 1  score: 214.5 bits;  conditional E-value: 1.6e-67
                         TIGR00657   6 qKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee.keliekirekhlealeela 81 
                                        KFGG+S+++++  ++va+i++ + ++  + +VVvSA +++T+ L +l +  +s++  +e+++++ + +   +e+l 
  lcl|FitnessBrowser__ANA3:7026471   7 HKFGGSSLADADCYRRVAHILLTHGHS--DDLVVVSAAGKTTNFLYKLLSLRDSNQLwQEELQVLISYQQGLIEQLL 81 
                                       6*******************9999855..589************************998888888777777777777 PP

                         TIGR00657  82 .sqalkeklkallekeleevkk.......ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgr 150
                                        +++ +   ++l+  + +++         + +   ++s+GE+ Sa+l+aa+l+e g  a+s ++a + +++d++   
  lcl|FitnessBrowser__ANA3:7026471  82 sNEQARDLRERLTTDKAQLISLlsldsrnDYQISHVVSFGERWSARLMAALLRESG-VAASHVDACSILVADEAAVP 157
                                       45444444444444444444448888888888999*********************.77888888888888776555 PP

                         TIGR00657 151 Akvleeikterleklleeg..iivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPr 225
                                           +++++ ++++ll +      v++GFi a+e g++ +LGR+GSD++A+l+A++ + ++v i+tDV+G++ aDP+
  lcl|FitnessBrowser__ANA3:7026471 158 QI-RVQESRTKVQTLLAAHpnERLVITGFICANERGDTLLLGRNGSDFSASLIASLADIERVTIWTDVEGVFNADPN 233
                                       44.677777777777777666899***************************************************** PP

                         TIGR00657 226 ivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseeepavkalsldkn 302
                                       ++++A++l+++s +Ea  La+lG+ vLh rtl+p+ + ++ + v+s++  +++ Tli ++s+s ++p v+   + + 
  lcl|FitnessBrowser__ANA3:7026471 234 KINDAKLLKSMSLAEADRLARLGSPVLHSRTLQPLFNTEVSLAVRSSYASHTDFTLIAPHSSSASAPVVT---NLNA 307
                                       ************************************************************8866655554...4444 PP

                         TIGR00657 303 qalvsvsgttmkpgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekkl 379
                                        +l+  +++    g +a ++++l ea+    +  +s++ + ++++   e+ ++ ++ll ++  e+  +++++++++l
  lcl|FitnessBrowser__ANA3:7026471 308 VVLFGFKIA----GDVASLLEQLVEAGLTPLAHWLSAH-QRLELAYTAENQKQVQKLL-DAQAEALGIKDLQINTEL 378
                                       455544444....5568888889999999988887777.478*************998.5688888999******** PP

                         TIGR00657 380 alvslvGagmksapgvaakifeaLaeeniniemissseikisvvvdekdaekavealhe 438
                                        lv+lv+a+ +++    a++++  a+       + s + +++++v++++++ +++++h+
  lcl|FitnessBrowser__ANA3:7026471 379 GLVALVSADAEHYRRSFARLLSRDAK------PLFSGDLSLVTLVPQSQVNLLTQKVHR 431
                                       ***********988887777766555......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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 18.71
//
[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