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

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.3124559.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  FitnessBrowser__MR1:203139  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__MR1:203139  
   #    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.sqalk 86 
                                  KFGG+S+++++  ++va+i++ + ++  + +VVvSA +++T+ L +l +  +s++  +e+++++ + +   +e+l  +++ +
  FitnessBrowser__MR1:203139   7 HKFGGSSLADADCYRRVAHILLTHGHS--DDLVVVSAAGKTTNFLYKLLSLRDSNQLwQEELQVLISYQQGLIEQLLsNEQAR 87 
                                 6*******************9999855..589************************997777777777766777766444444 PP

                   TIGR00657  87 eklkallekeleevkk.......ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterl 162
                                    ++l+  + +++         + +   ++s+GE+ Sa+l+aa+l+e g  a+s ++a + +++d++       ++++++++
  FitnessBrowser__MR1:203139  88 DLRERLTTDKAQLISLlsldvrnDYQISHVVSFGERWSARLMAALLRESG-VAASHVDACSILVADEAAVPQI-RVQESRAKV 168
                                 4444444444444433777887799999**********************.7788888888888877655544.788888888 PP

                   TIGR00657 163 eklleeg..iivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalE 243
                                 ++ll +      v++GFi a+e g++ +LGR+GSD++A+l+A++ + ++v i+tDV+G++ aDP+++++A++l+++s +Ea  
  FitnessBrowser__MR1:203139 169 QALLAAHpnERLVITGFICANERGDTLLLGRNGSDFSASLIASLADIERVTIWTDVEGVFNADPNKINDAKLLKSMSLAEADR 251
                                 888888776899*********************************************************************** PP

                   TIGR00657 244 LaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmkpgilaevfgala 326
                                 La+lG+ vLh rtl+p+ + ++ + v+s++  +++ Tli ++s+s ++p v+   + +  +l+  +++    g +a ++ +l 
  FitnessBrowser__MR1:203139 252 LARLGSPVLHSRTLQPLFNTEVSLAVRSSYASHTDFTLIAPHSSSASAPVVT---NLNAVVLFGFKIA----GDVASLLDQLV 327
                                 ******************************************8866655554...4444455544444....55688888888 PP

                   TIGR00657 327 eakvnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeenin 409
                                 ea+    +   s+ ++ ++++   e+ ++ ++ll ++  e+  +++++++++l lv+lv+a+ +++    a++++  a+    
  FitnessBrowser__MR1:203139 328 EAGLTPLAHWVSA-HQRLELAYTAENQKQVQKLL-DAQAEALGIRDLQINTELGLVALVSADAEHYRRSFARLLSRDAK---- 404
                                 9998887777444.4679**************98.5678888999*******************988877777766555.... PP

                   TIGR00657 410 iemissseikisvvvdekdaekavealhe 438
                                    + s + +++++v++++++ +++++h+
  FitnessBrowser__MR1:203139 405 --PLFSGDLSLVTLVPQSQVNLLTQKVHR 431
                                 ..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: 0.00u 0.02s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 24.67
//
[ok]

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