GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Klebsiella variicola At-22

Align fused aspartate kinase/homoserine dehydrogenase 2 (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_008807866.1 KVAR_RS25005 bifunctional aspartate kinase/homoserine dehydrogenase II

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



>NCBI__GCF_000025465.1:WP_008807866.1
          Length = 810

 Score = 1475 bits (3818), Expect = 0.0
 Identities = 737/810 (90%), Positives = 779/810 (96%)

Query: 1   MSVIAQAGAKGRQLHKFGGSSLADVKCYLRVAGIMAEYSQPDDMMVVSAAGSTTNQLINW 60
           MSVIAQAGAKGRQLHKFGGSSLAD KCYLRVAGIM EYSQ  DMMVVSAAGSTTNQLI+W
Sbjct: 1   MSVIAQAGAKGRQLHKFGGSSLADAKCYLRVAGIMKEYSQAGDMMVVSAAGSTTNQLISW 60

Query: 61  LKLSQTDRLSAHQVQQTLRRYQCDLISGLLPAEEADSLISAFVSDLERLAALLDSGINDA 120
           LKLSQ+DRL+AHQVQQ+LRRYQ +LI GL+    AD+LI+AF+ DLERLA LLD G+ +A
Sbjct: 61  LKLSQSDRLAAHQVQQSLRRYQTELIGGLVEPAAADTLIAAFIHDLERLAGLLDGGVTEA 120

Query: 121 VYAEVVGHGEVWSARLMSAVLNQQGLPAAWLDAREFLRAERAAQPQVDEGLSYPLLQQLL 180
           VYAEVVGHGEVWSARLM+AVLNQ G+ AAWLDAR FLRAERAAQPQVDEGLSYPLLQQL+
Sbjct: 121 VYAEVVGHGEVWSARLMAAVLNQLGMEAAWLDARAFLRAERAAQPQVDEGLSYPLLQQLM 180

Query: 181 VQHPGKRLVVTGFISRNNAGETVLLGRNGSDYSATQIGALAGVSRVTIWSDVAGVYSADP 240
            QHP KRLVVTGFISRN AGETVLLGRNGSDYSATQIGALAG SRVTIWSDVAGVYSADP
Sbjct: 181 AQHPNKRLVVTGFISRNQAGETVLLGRNGSDYSATQIGALAGASRVTIWSDVAGVYSADP 240

Query: 241 RKVKDACLLPLLRLDEASELARLAAPVLHARTLQPVSGSEIDLQLRCSYTPDQGSTRIER 300
           RKVKDACLLPLLRLDEASELARLAAPVLHARTLQPVS S+IDLQLRCSYTP+QGSTRIER
Sbjct: 241 RKVKDACLLPLLRLDEASELARLAAPVLHARTLQPVSASDIDLQLRCSYTPEQGSTRIER 300

Query: 301 VLASGTGARIVTSHDDVCLIEFQVPASQDFKLAHKEIDQILKRAQVRPLAVGVHNDRQLL 360
           VLASGTGARIVTSHDDVCL+EFQVPAS DFKLAHKE+D +LKRAQ+RPLAVGVH DR+LL
Sbjct: 301 VLASGTGARIVTSHDDVCLVEFQVPASHDFKLAHKELDALLKRAQLRPLAVGVHADRKLL 360

Query: 361 QFCYTSEVADSALKILDEAGLPGELRLRQGLALVAMVGAGVTRNPLHCHRFWQQLKGQPV 420
           QFCYTSEVADSALK+LDEAGLPGELRLRQ LALVAMVGAGVTRNPLHCHRFWQQLKGQPV
Sbjct: 361 QFCYTSEVADSALKLLDEAGLPGELRLRQKLALVAMVGAGVTRNPLHCHRFWQQLKGQPV 420

Query: 421 EFTWQSDDGISLVAVLRTGPTESLIQGLHQSVFRAEKRIGLVLFGKGNIGSRWLELFARE 480
           EFTWQS++GISLVAVLR GPTESLIQGLHQ++FRAEKRIGL+LFGKGNIGSRWLELFARE
Sbjct: 421 EFTWQSEEGISLVAVLRAGPTESLIQGLHQTLFRAEKRIGLMLFGKGNIGSRWLELFARE 480

Query: 481 QSTLSARTGFEFVLAGVVDSRRSLLSYDGLDASRALAFFNDEAVEQDEESLFLWMRAHPY 540
           Q+TLSARTGFEFVLAGVVDS+RSLL+YDGLDASRALAFFNDEAVEQDEESLFLWMRAHPY
Sbjct: 481 QTTLSARTGFEFVLAGVVDSKRSLLNYDGLDASRALAFFNDEAVEQDEESLFLWMRAHPY 540

Query: 541 DDLVVLDVTASQQLADQYLDFASHGFHVISANKLAGASDSNKYRQIHDAFEKTGRHWLYN 600
           DDLVVLDVTAS+QLADQYLDFASHGFHVISANKLAGAS S+KYRQIHDAFEKTGRHWLYN
Sbjct: 541 DDLVVLDVTASEQLADQYLDFASHGFHVISANKLAGASSSDKYRQIHDAFEKTGRHWLYN 600

Query: 601 ATVGAGLPINHTVRDLIDSGDTILSISGIFSGTLSWLFLQFDGSVPFTELVDQAWQQGLT 660
           ATVGAGLP+NHTVRDLIDSGDTIL +SGIFSGTLSWLFLQFDG+VPFT+LVDQAWQQGLT
Sbjct: 601 ATVGAGLPVNHTVRDLIDSGDTILGLSGIFSGTLSWLFLQFDGTVPFTDLVDQAWQQGLT 660

Query: 661 EPDPRDDLSGKDVMRKLVILAREAGYNIEPDQVRVESLVPAHCEGGSIDHFFENGDELNE 720
           EPDPR DLSGKDVMRKLVILAREAGY+IEPDQVRVESLVPAHCE GS+DHFFENG+ELNE
Sbjct: 661 EPDPRVDLSGKDVMRKLVILAREAGYDIEPDQVRVESLVPAHCEEGSVDHFFENGEELNE 720

Query: 721 QMVQRLEAAREMGLVLRYVARFDANGKARVGVEAVREDHPLASLLPCDNVFAIESRWYRD 780
           QM+QRLEAAREMGLVLRYVARFDANGKARVGVEAVRE+HPLA+LLPCDNVFAIESRWYRD
Sbjct: 721 QMLQRLEAAREMGLVLRYVARFDANGKARVGVEAVREEHPLAALLPCDNVFAIESRWYRD 780

Query: 781 NPLVIRGPGAGRDVTAGAIQSDINRLAQLL 810
           NPLVIRGPGAGRDVTAGAIQSDINRLAQLL
Sbjct: 781 NPLVIRGPGAGRDVTAGAIQSDINRLAQLL 810


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: 2058
Number of extensions: 47
Number of successful extensions: 1
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: 810
Length adjustment: 41
Effective length of query: 769
Effective length of database: 769
Effective search space:   591361
Effective search space used:   591361
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: 56 (26.2 bits)

Align candidate WP_008807866.1 KVAR_RS25005 (bifunctional aspartate kinase/homoserine dehydrogenase II)
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.1510783.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.4e-69  220.4   0.0    3.1e-69  220.1   0.0    1.1  1  NCBI__GCF_000025465.1:WP_008807866.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025465.1:WP_008807866.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.1   0.0   3.1e-69   3.1e-69       6     441 ..      15     453 ..      12     454 .. 0.86

  Alignments for each domain:
  == domain 1  score: 220.1 bits;  conditional E-value: 3.1e-69
                             TIGR00657   6 qKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekirekhlea 76 
                                            KFGG+S+++++   +va i+k+ ++ g   + VvSA +++T++L++  +  +s++   +++ + +r+ + e 
  NCBI__GCF_000025465.1:WP_008807866.1  15 HKFGGSSLADAKCYLRVAGIMKEYSQAG--DMMVVSAAGSTTNQLISWLKLSQSDRLaaHQVQQSLRRYQTEL 85 
                                           6**********************99998..67899****************9999976555555666666666 PP

                             TIGR00657  77 leela.sqalkeklkallekeleevkk..........ereldlilsvGEklSaallaaaleelgvkavsllga 138
                                           +  l  +    +   +l+++ ++ +++          e+ +++++ +GE  Sa+l+aa+l++lg  ++++l+a
  NCBI__GCF_000025465.1:WP_008807866.1  86 IGGLVeP----AAADTLIAAFIHDLERlaglldggvtEAVYAEVVGHGEVWSARLMAAVLNQLG-MEAAWLDA 153
                                           6666634....44444455555554445557889******************************.778899** PP

                             TIGR00657 139 eagiltdsefgrAkvleeikterleklleeg..iivvvaGFiGatekgeittLGRGGSDltAallAaalkAde 209
                                           +a ++++++ +  +  e  +   l++l+ +   +  vv+GFi  ++ ge+++LGR+GSD++A+ ++a+ +A++
  NCBI__GCF_000025465.1:WP_008807866.1 154 RAFLRAERAAQPQV-DEGLSYPLLQQLMAQHpnKRLVVTGFISRNQAGETVLLGRNGSDYSATQIGALAGASR 225
                                           ******99887777.88888888888877767799************************************** PP

                             TIGR00657 210 veiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTli 282
                                           v i+ DV G+y+aDPr+v++A +l+ +  +Ea+ELa+l a vLh rtl+p+ +++i++  + ++ pe++ T i
  NCBI__GCF_000025465.1:WP_008807866.1 226 VTIWSDVAGVYSADPRKVKDACLLPLLRLDEASELARLAAPVLHARTLQPVSASDIDLQLRCSYTPEQGSTRI 298
                                           *******************************************************************999*** PP

                             TIGR00657 283 vakskseeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlilqsssetsisfvvdkedadk 355
                                                s    ++ +++ d   + ++v  + + +   +e+   l++a+    ++   ++++ ++f+   e ad+
  NCBI__GCF_000025465.1:WP_008807866.1 299 ERVLASGTGARIVTSHDDVCLVEFQVPASHDFKLAHKELDALLKRAQLRPLAVGVHADRKLLQFCYTSEVADS 371
                                           9998877766666666666666667776666699999*****************8888888************ PP

                             TIGR00657 356 akellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemissseikisvvvdekd 428
                                           a +ll    +e+   +e+++ +klalv++vGag+  +p    ++ ++L+ + +     s   i+++ v +   
  NCBI__GCF_000025465.1:WP_008807866.1 372 ALKLL----DEAGLPGELRLRQKLALVAMVGAGVTRNPLHCHRFWQQLKGQPVEFTWQSEEGISLVAVLRAGP 440
                                           ***96....6899999*********************************965555555555555556677888 PP

                             TIGR00657 429 aekavealheklv 441
                                            e +++ lh+ l+
  NCBI__GCF_000025465.1:WP_008807866.1 441 TESLIQGLHQTLF 453
                                           8999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (810 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 48.13
//
[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:

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