GapMind for Amino acid biosynthesis

 

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

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_066327343.1 BLR17_RS04505 aspartate kinase

Query= BRENDA::P08660
         (449 letters)



>NCBI__GCF_900100165.1:WP_066327343.1
          Length = 418

 Score =  167 bits (422), Expect = 8e-46
 Identities = 119/365 (32%), Positives = 183/365 (50%), Gaps = 29/365 (7%)

Query: 6   VSKFGGTSVADFDAMNRSADIVLSDANVR--LVVLSASAGITNLLVALAEGLEPGERFEK 63
           V KFGG SV D   +    D VL  A  +  L+V+SA    TN L  + +          
Sbjct: 3   VFKFGGASVKDAAGIRNVYD-VLQKAGYQDVLLVVSAMGKTTNALEVVIKNY-------- 53

Query: 64  LDAIRNIQFAILERLRYPNVIREEI---------ERLLENITVLAEAAALATSPALT--- 111
            D    +  ++ E  +Y N I  ++           + E+ + L    A   SP      
Sbjct: 54  FDKSPELNASVQEIKKYHNQILLDLFEDENHAVFAAVNEHFSDLEYFLAHNKSPNYNFVY 113

Query: 112 DELVSHGELMSTLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLL 171
           D++VS GE++ST +    +    ++ QW DVR  ++TN+ +  AE D     EL    + 
Sbjct: 114 DQIVSMGEIISTTVLSYYMNFMGIETQWIDVRNYIKTNNNYRDAEVDW----ELTQSNIS 169

Query: 172 PRLN-EGLVITQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTD 230
             +  + L ITQGF+GS+    TTTLGR GSDYTAA+ A  L+A  V IW DVPG+   D
Sbjct: 170 KNIKTKSLNITQGFLGSDENNFTTTLGREGSDYTAAIFAYCLNAESVTIWKDVPGVMNAD 229

Query: 231 PRVVSAAKRIDEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVC 290
           PR    A  +++I++ EA E+A +GA V+HP TL P  + +IP+ V S  +P   GT+V 
Sbjct: 230 PRYFENASLLNQISYREAIELAFYGATVIHPKTLQPLQKKEIPLHVKSFINPLLKGTVVS 289

Query: 291 NKTENPPLFRALALRRNQTLLTLHSLNM-LHSRGFLAEVFGILARHNISVDLITTSEVSV 349
                 P      ++R Q L++L S++        ++E+FG+     I V+LI  S +S 
Sbjct: 290 KGATLEPFMPCFIVKREQLLISLSSIDFSFIMEENISEIFGLFHEFKIKVNLIQNSAISF 349

Query: 350 ALTLD 354
           ++ ++
Sbjct: 350 SVCVE 354


Lambda     K      H
   0.320    0.135    0.376 

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: 304
Number of extensions: 8
Number of successful extensions: 2
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: 449
Length of database: 418
Length adjustment: 32
Effective length of query: 417
Effective length of database: 386
Effective search space:   160962
Effective search space used:   160962
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: 51 (24.3 bits)

Align candidate WP_066327343.1 BLR17_RS04505 (aspartate kinase)
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.2692795.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.8e-81  260.4   0.0    2.1e-81  260.2   0.0    1.1  1  NCBI__GCF_900100165.1:WP_066327343.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066327343.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.2   0.0   2.1e-81   2.1e-81       5     351 ..       3     354 ..       1     385 [. 0.88

  Alignments for each domain:
  == domain 1  score: 260.2 bits;  conditional E-value: 2.1e-81
                             TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekirekhle 75 
                                           V KFGG Sv+++  i++v + ++k+  +  +v+ VvSAm+++T+aL  ++++  ++    ++ +++i++ h +
  NCBI__GCF_900100165.1:WP_066327343.1   3 VFKFGGASVKDAAGIRNVYDVLQKAGYQ--DVLLVVSAMGKTTNALEVVIKNYFDKSPelNASVQEIKKYHNQ 73 
                                           89*******************9999955..5***************999999877665587888999999988 PP

                             TIGR00657  76 aleelasqalkeklkallekeleevkk..........ereldlilsvGEklSaallaaaleelgvkavsllga 138
                                           +l  l +++ ++ + a++++++  ++           +  +d i+s+GE +S+++l+ +++  g  + ++++ 
  NCBI__GCF_900100165.1:WP_066327343.1  74 ILLDLFEDENHA-VFAAVNEHFSDLEYflahnkspnyNFVYDQIVSMGEIISTTVLSYYMNFMG-IETQWIDV 144
                                           887766543333.33444444444444567778999999*************************.78899*** PP

                             TIGR00657 139 eagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeve 211
                                           ++ i t++++++A+v  e +++++ k ++ + + +++GF+G++e++ +ttLGR GSD+tAa+ A +l+A+ v 
  NCBI__GCF_900100165.1:WP_066327343.1 145 RNYIKTNNNYRDAEVDWELTQSNISKNIKTKSLNITQGFLGSDENNFTTTLGREGSDYTAAIFAYCLNAESVT 217
                                           ************************************************************************* PP

                             TIGR00657 212 iytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTliva 284
                                           i++DV+G++ aDPr+ ++A +l++isy+Ea ELa +Ga v+hp+tl+p+ +++ip++vks  np  +GT++ +
  NCBI__GCF_900100165.1:WP_066327343.1 218 IWKDVPGVMNADPRYFENASLLNQISYREAIELAFYGATVIHPKTLQPLQKKEIPLHVKSFINPLLKGTVVSK 290
                                           ***********************************************************************99 PP

                             TIGR00657 285 kskseeepavkalsldknqalvsvsgttmk...pgilaevfgalaeakvnvdlilqsssetsisfvvdke 351
                                             +   ep +    ++++q l+s+s+        + ++e+fg  +e k++v+li   +s   isf v  e
  NCBI__GCF_900100165.1:WP_066327343.1 291 GAT--LEPFMPCFIVKREQLLISLSSIDFSfimEENISEIFGLFHEFKIKVNLIQ--NS--AISFSVCVE 354
                                           966..55899999999*******9999999888888999***************8..33..244444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (418 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 18.24
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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