GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Shewanella loihica PV-4

Align fused aspartate kinase/homoserine dehydrogenase 2 (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 5208005 Shew_0521 bifunctional aspartate kinase II/homoserine dehydrogenase II (RefSeq)

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



>FitnessBrowser__PV4:5208005
          Length = 797

 Score =  572 bits (1473), Expect = e-167
 Identities = 342/804 (42%), Positives = 479/804 (59%), Gaps = 26/804 (3%)

Query: 14  LHKFGGSSLADVKCYLRVAGIMAEYSQPDDMMVVSAAGSTTNQLINWLKLSQTDRLSAHQ 73
           LHKFGGSSLAD  CY RVA I+  +   DD++VVSAAG +TN L   L+L  TD+L   +
Sbjct: 6   LHKFGGSSLADADCYRRVAHILLTHGHSDDLIVVSAAGKSTNFLYRLLELCDTDQLWQEE 65

Query: 74  VQQTLRRYQCDLISGLLPAEEADSLISAFVSDLERLAALLD-SGINDAVYAEVVGHGEVW 132
           +Q  L  YQ +LI  LL  E+A SL     +D  +L +LL    +ND    +VV  GE W
Sbjct: 66  LQ-VLVSYQQNLIEQLLSNEQARSLRERLATDKSQLTSLLSLDELNDYQRNQVVSFGERW 124

Query: 133 SARLMSAVLNQQGLPAAWLDAREFLRAERAAQPQVDEGLSYPLLQQLLVQHPGKRLVVTG 192
           S+ L++A+L + G+ A  +DAR  L A+  A PQ+  G S   +Q LL  HP +RLV+TG
Sbjct: 125 SSCLLAALLRESGVAATDVDARTLLVADEGAVPQIRLGESRQKVQALLEAHPQERLVITG 184

Query: 193 FISRNNAGETVLLGRNGSDYSATQIGALAGVSRVTIWSDVAGVYSADPRKVKDACLLPLL 252
           FI  N  G+T+LLGRNGSD+SAT + +LA + RVTIW+DV GV++ADP ++ DA LL  +
Sbjct: 185 FICANEQGDTLLLGRNGSDFSATLLASLADIERVTIWTDVEGVFNADPNRINDAKLLKSM 244

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

Query: 313 SHDDVCLIEFQVPASQDFKLAHKEIDQILK---RAQVRPLAV-GVHNDRQLLQFCYTSEV 368
           S   V L    +           E+ Q+L    +A + PLA   + + R  L F + ++ 
Sbjct: 304 SLSSVSLFSLTISV---------ELPQLLACFAQAGLTPLAYWSLAHGRAELAFTHENQK 354

Query: 369 ADSALKILDEAGLP-GELRLRQGLALVAMVGAGVTRNPLHCHRFWQQLKGQPVEFTWQSD 427
              A+     + L   EL+LR  L LVA+V A  +   L+   F + L  +        +
Sbjct: 355 QAQAIFEAKRSELGIDELQLRDDLGLVALVSADAS---LYRRGFSRLLSREAHPLC---N 408

Query: 428 DGISLVAVLRTGPTESLIQGLHQSVFRAEKRIGLVLFGKGNIGSRWLELFAREQSTLSAR 487
           DG+SLV ++       L Q +H+      KRIG++L G GNIG  W++LF R +  L+  
Sbjct: 409 DGLSLVTLVPKAQVNLLTQKVHRRCAGPRKRIGVLLLGIGNIGEAWIDLFKRARPVLNKE 468

Query: 488 TGFEFVLAGVVDSRRSLLSYDGLDASRALAFFNDEAVEQDEESLFLWMRAHPYDDLVVLD 547
                 L G++ S+++LLS   +D S     F +         LF  ++A   D+L+ LD
Sbjct: 469 LEVSVELVGLLSSKKALLSETDIDLSSWQQAFEERGTGWQYTHLFEQLQALNCDELIALD 528

Query: 548 VTASQQLADQYLDFASHGFHVISANKLAGASDSNKYRQIHDAFEKTGRHWLYNATVGAGL 607
           ++AS  L  QY +F + G H++SANKLAG+     Y+++          W YNA+ GAGL
Sbjct: 529 ISASADLTLQYPEFFARGIHIVSANKLAGSGPLAFYQELKQQLGNRRLFWRYNASCGAGL 588

Query: 608 PINHTVRDLIDSGDTILSISGIFSGTLSWLFLQFDGSVPFTELVDQAWQQGLTEPDPRDD 667
           P+ H + DL +SGD+I ++ GIFSGTL WLF  +D   PF+ELV +A   G+TEPDPRDD
Sbjct: 589 PVQHALNDLHNSGDSIEAVGGIFSGTLCWLFEHYDAKKPFSELVLEAKGLGITEPDPRDD 648

Query: 668 LSGKDVMRKLVILAREAGYNIEPDQVRVESLVPAHCEGGSIDHFFENGDELNEQMVQRLE 727
           LSG+D+ RKL+ILARE GY+IE D + +ESLVP       +D F +   EL+ +M+Q+ +
Sbjct: 649 LSGRDMQRKLLILAREIGYDIELDDIELESLVPTKLAEIPLDDFIKRMAELDGEMLQQYQ 708

Query: 728 AAREMGLVLRYVARFDANG---KARVGVEAVREDHPLASLLPCDNVFAIESRWYRDNPLV 784
           AA E   VLRYVA  D+     KA+VG++ V   HP A+L P DNVF I S +Y+DNPL+
Sbjct: 709 AAAEQNKVLRYVASLDSEQGQLKAKVGIQWVDRSHPYANLTPGDNVFVIRSDFYQDNPLI 768

Query: 785 IRGPGAGRDVTAGAIQSDINRLAQ 808
           IRGPGAGR+VTA A+QSD+ ++ +
Sbjct: 769 IRGPGAGREVTAAAVQSDLAQICR 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: 1467
Number of extensions: 76
Number of successful extensions: 5
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 5208005 Shew_0521 (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.10755.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
    2.6e-66  210.4   0.0    4.3e-66  209.7   0.0    1.2  1  lcl|FitnessBrowser__PV4:5208005  Shew_0521 bifunctional aspartate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208005  Shew_0521 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 !  209.7   0.0   4.3e-66   4.3e-66       6     394 ..       7     393 ..       4     433 .. 0.78

  Alignments for each domain:
  == domain 1  score: 209.7 bits;  conditional E-value: 4.3e-66
                        TIGR00657   6 qKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee.keliekirekhlealeelas 82 
                                       KFGG+S+++++  ++va+i++ + +++   ++VvSA +++T+ L  l e ++ ++  +e+++++ + + + +e+l s
  lcl|FitnessBrowser__PV4:5208005   7 HKFGGSSLADADCYRRVAHILLTHGHSD--DLIVVSAAGKSTNFLYRLLELCDTDQLwQEELQVLVSYQQNLIEQLLS 82 
                                      6*******************99998555..78999*******************999988888888888888888885 PP

                        TIGR00657  83 qalkeklkallekeleevkk........ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAk 152
                                      ++ +  l++ l++   ++ +        + ++  ++s+GE+ S+ llaa+l+e gv a + ++a+  +++d+      
  lcl|FitnessBrowser__PV4:5208005  83 NEQARSLRERLATDKSQLTSllsldelnDYQRNQVVSFGERWSSCLLAALLRESGVAA-TDVDARTLLVADEGAVPQI 159
                                      556666655555555555556788899899*************************633.3445555555554433333 PP

                        TIGR00657 153 vleeikterleklleeg..iivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivp 228
                                          ++++++++lle+      v++GFi a+e+g++ +LGR+GSD++A+llA++ + ++v i+tDV+G++ aDP+ ++
  lcl|FitnessBrowser__PV4:5208005 160 -RLGESRQKVQALLEAHpqERLVITGFICANEQGDTLLLGRNGSDFSATLLASLADIERVTIWTDVEGVFNADPNRIN 236
                                      .4555666666666666556699******************************************************* PP

                        TIGR00657 229 eArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseeepavkalsldknqalv 306
                                      +A++l+++s  Ea  La+lG+ vLh+rtl+p+   ++ + v+s++ p+++ Tli +ks+s ++p v++ls+    +l+
  lcl|FitnessBrowser__PV4:5208005 237 DAKLLKSMSLTEANRLAHLGSPVLHNRTLQPLFDTEVSLAVRSSYAPHTDFTLIAPKSSSASAPVVTSLSS---VSLF 311
                                      *********************************************************99888888887765...4556 PP

                        TIGR00657 307 svsgttmkpgilaevfgalaeakvnvdlil.qsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvs 383
                                      s+ ++        +++ + a+a+    +   +  ++  ++f+ ++   ++a+++  ++ ++e  + e+++ ++l lv+
  lcl|FitnessBrowser__PV4:5208005 312 SLTISVEL----PQLLACFAQAGLTPLAYWsLAHGRAELAFTHEN--QKQAQAIF-EAKRSELGIDELQLRDDLGLVA 382
                                      55555554....566778888887776666133344445555555..55555554.346788999999********** PP

                        TIGR00657 384 lvGagmksapg 394
                                      lv+a+ + +  
  lcl|FitnessBrowser__PV4:5208005 383 LVSADASLYRR 393
                                      **999876544 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: 11.86
//
[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