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.10590.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 17.24
//
[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