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

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.6164.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 17.44
//
[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