GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Flavobacterium glycines Gm-149

Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_066328676.1 BLR17_RS00255 bifunctional aspartate kinase/homoserine dehydrogenase I

Query= reanno::Cola:Echvi_2000
         (815 letters)



>NCBI__GCF_900100165.1:WP_066328676.1
          Length = 803

 Score =  482 bits (1240), Expect = e-140
 Identities = 289/822 (35%), Positives = 480/822 (58%), Gaps = 31/822 (3%)

Query: 1   MKIIKFGGSSIANYENIQKVFSIIEQK-SEKEAFALVFSAFGGVTEQLLQCANIAQQSEE 59
           MKI+KFGG S++N E I KV SII  K ++ E  A+V SA G  T++L +   +A ++ +
Sbjct: 1   MKILKFGGKSLSNGEGINKVVSIITDKVNQGEKIAIVVSARGNATDELEEILAVASKNAD 60

Query: 60  SYHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDY 119
            Y ++L++ +K            QQ   A   +   F  L  LF G+ LI + S++  D 
Sbjct: 61  -YKSLLEQFKK-----------YQQDVYANVDLSEEFAVLDKLFEGVSLIGDYSSKIKDQ 108

Query: 120 VLSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSH 179
           +LS GE LS  +L A L  KG+   + D+R  +KTD +FG A+   + + K +  +FK +
Sbjct: 109 ILSIGELLSAKLLTAILVEKGVNARFADSRTFLKTDSKFGDAQPLEQVSKKNVIKYFKDN 168

Query: 180 DD-IKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLV 238
           DD + V+TGFIGS     TTT+GR+GS+YTAS+ A  L A++++ +T V G+ TA+P LV
Sbjct: 169 DDAVNVVTGFIGSNINNVTTTLGRNGSNYTASLLANYLDAKELQNYTHVDGIYTANPDLV 228

Query: 239 YTAFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDSG 298
             A  I  L++NEA EL++FGA ++   T+ P ++++IP+ I NTF  +  GT I+  S 
Sbjct: 229 ADAKKIDHLTFNEANELANFGATILHAKTIIPLLEKNIPLRILNTFNHENEGTLITATSK 288

Query: 299 EGKIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSICVA 358
            G  IK +S +++++++N++G GL+   GV  R F  + +N I++ +ISQ SSE  I + 
Sbjct: 289 SGG-IKTLSVLEDLALVNLEGRGLLGKTGVDARIFKVMGDNNISVSIISQGSSERGIGLV 347

Query: 359 IASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQALG 418
           +A   A++A   +E+EF  +  S ++++I +  D++VI+++G+++        R + AL 
Sbjct: 348 VAESQATKAMIELEKEFENDFYSKDVNKISVTDDVSVISIIGQDL----STFYRPYTALI 403

Query: 419 RNNVNVAAIAQGSSELNISAVITQADLQKALNALH-EAFFLSDYKVLHLFLVGVGLIGKA 477
           +N +         +  N+S V+ +++L KALN +H E F +S  K +++ + G GL+G  
Sbjct: 404 KNKIIPILFNNTVTGKNVSLVVKKSELNKALNVIHGEIFGVS--KKINIAVFGHGLVGGT 461

Query: 478 LTKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEPMDMDKFIG 537
           L   I +  K +++   + + I  +ANS+ +  ++DG     V     N     +   I 
Sbjct: 462 LINQILESAKAIEKRKDIKLNIFAIANSKNVLLNKDGVSPNWVNEIQTNGFAYTIKDVIA 521

Query: 538 TMTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLAGQR 597
              E +  N + VD TAS    + Y  ++++   +++ NK AN+     YK+L+K+  + 
Sbjct: 522 YANENHLENLIAVDNTASAAFVENYIPLVENGFDLISSNKVANTLSYGFYKELRKVLAEN 581

Query: 598 GVRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELE-KGMPFSEVVA 656
              + YETNV AGLP+I+T++ L LSG+++ +I+ V SG+++Y+F+    K  PFS+++ 
Sbjct: 582 QKNYLYETNVGAGLPLIDTIKLLHLSGENITKIKGVFSGTLSYLFNNFSAKDAPFSDILK 641

Query: 657 QAKEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAASVPEF 716
           +A + GYTEPDPR+DL G DV RK+LIL RE      FE++ IQ+++PE   +  S  +F
Sbjct: 642 EAIDNGYTEPDPREDLCGNDVGRKLLILARELDLQNEFEEIAIQNLIPEHLRE-GSAADF 700

Query: 717 FKKLQKHDGHFQQLLDEANAKGEKLRFMATL------ENGKAKVGLNSLDSEHPFFTLKG 770
             KL++ D  + ++ +E       LR++  L      + G  +V L S+ S+     LKG
Sbjct: 701 LTKLKEFDPIYTKIKEE-QKPNHVLRYIGELSGDLQNDKGILEVKLVSVPSDTALGGLKG 759

Query: 771 SDNMILFTTERYNDFPMIVRGPGAGADVTAAGVFADIIRLGN 812
           SD+     TE Y D P++++G GAG+ VTA GVF DI+RL +
Sbjct: 760 SDSFFEIYTESYGDRPIVIQGAGAGSAVTARGVFGDILRLSD 801


Lambda     K      H
   0.317    0.134    0.375 

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: 1471
Number of extensions: 84
Number of successful extensions: 9
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: 815
Length of database: 803
Length adjustment: 41
Effective length of query: 774
Effective length of database: 762
Effective search space:   589788
Effective search space used:   589788
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)

Align candidate WP_066328676.1 BLR17_RS00255 (bifunctional aspartate kinase/homoserine dehydrogenase I)
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.2438427.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.9e-99  318.3   7.1    4.9e-99  318.3   7.1    1.4  2  NCBI__GCF_900100165.1:WP_066328676.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066328676.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.3   7.1   4.9e-99   4.9e-99       5     440 ..       3     441 ..       1     443 [. 0.91
   2 ?   -4.1   0.1      0.32      0.32     384     417 ..     457     490 ..     456     493 .. 0.82

  Alignments for each domain:
  == domain 1  score: 318.3 bits;  conditional E-value: 4.9e-99
                             TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee.keliekirekhlea 76 
                                           ++KFGG S+ n+e i+kv+ i++ + ++g++ ++VvSA+++ Td+L e+   +s++++ k+l+e+ ++ + + 
  NCBI__GCF_900100165.1:WP_066328676.1   3 ILKFGGKSLSNGEGINKVVSIITDKVNQGEKIAIVVSARGNATDELEEILAVASKNADyKSLLEQFKKYQQDV 75 
                                           79**************************************************999998777777777777776 PP

                             TIGR00657  77 leela.sqalkeklkallekeleevkk.....ereldlilsvGEklSaallaaaleelgvkavsllgaeagil 143
                                            ++++ s+       a+l+k +e v       ++ +d ils+GE lSa+ll+a+l e+g  ++ + +++  + 
  NCBI__GCF_900100165.1:WP_066328676.1  76 YANVDlSE-----EFAVLDKLFEGVSLigdysSKIKDQILSIGELLSAKLLTAILVEKG-VNARFADSRTFLK 142
                                           66666553.....3344444444444445566***************************.8899********* PP

                             TIGR00657 144 tdsefgrAkvleeikterleklleeg..iivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiyt 214
                                           tds+fg+A+ le+++++++ k+ + +   + vv+GFiG++ ++ +ttLGR+GS +tA+llA+ l+A+e++ yt
  NCBI__GCF_900100165.1:WP_066328676.1 143 TDSKFGDAQPLEQVSKKNVIKYFKDNddAVNVVTGFIGSNINNVTTTLGRNGSNYTASLLANYLDAKELQNYT 215
                                           *******************999999889********************************************* PP

                             TIGR00657 215 DVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivaksk 287
                                            VdGiyta P +v +A+++d+++++Ea ELa++Ga +Lh +t+ p+ +++ip+++ +tfn+e+eGTli+a+sk
  NCBI__GCF_900100165.1:WP_066328676.1 216 HVDGIYTANPDLVADAKKIDHLTFNEANELANFGATILHAKTIIPLLEKNIPLRILNTFNHENEGTLITATSK 288
                                           ***********************************************************************77 PP

                             TIGR00657 288 seeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkake 358
                                           s     +k+ls+ ++ alv+++g +     g+ a++f+ + +++++v +i+q sse +i +vv +++a ka  
  NCBI__GCF_900100165.1:WP_066328676.1 289 S---GGIKTLSVLEDLALVNLEGRGLLgkTGVDARIFKVMGDNNISVSIISQGSSERGIGLVVAESQATKAMI 358
                                           4...46*******************9999****************************************9999 PP

                             TIGR00657 359 llkkkvkee...kaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis.sseikisvvvdek 427
                                           +l+k+++++   k++++++v+++++++s++G+++++        ++ ++++ i+i      +  ++s+vv+++
  NCBI__GCF_900100165.1:WP_066328676.1 359 ELEKEFENDfysKDVNKISVTDDVSVISIIGQDLST---FYRPYTALIKNKIIPILFNNtVTGKNVSLVVKKS 428
                                           999888875333788899*****************9...555555666667788888778899********** PP

                             TIGR00657 428 daekavealhekl 440
                                           + +ka++++h ++
  NCBI__GCF_900100165.1:WP_066328676.1 429 ELNKALNVIHGEI 441
                                           **********876 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 0.32
                             TIGR00657 384 lvGagmksapgvaakifeaLaeeniniemissse 417
                                           lvG  +++++   ak++e+ ++ ++ni +i+ s 
  NCBI__GCF_900100165.1:WP_066328676.1 457 LVGGTLINQILESAKAIEKRKDIKLNIFAIANSK 490
                                           6888888888999999999999999999998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (803 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: 46.60
//
[ok]

This GapMind analysis is from Jul 26 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