GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Echinicola vietnamensis KMM 6221, DSM 17526

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate Echvi_1827 Echvi_1827 aspartate kinase

Query= BRENDA::P08660
         (449 letters)



>FitnessBrowser__Cola:Echvi_1827
          Length = 423

 Score =  172 bits (435), Expect = 2e-47
 Identities = 123/404 (30%), Positives = 201/404 (49%), Gaps = 20/404 (4%)

Query: 1   MSEIVVSKFGGTSVADFDAMNRSADIVLSDANVRLVVLSASAGITNLLVALAEGLEPGER 60
           M++ +V KFGG SV D  A+   ++I+ +     +V++ ++ G T    AL E L    +
Sbjct: 1   MTKAIVYKFGGASVKDAAAIKNLSNILFNRLRSPMVIVVSAIGKTTN--ALEEILRL--K 56

Query: 61  FEKLDAIRNIQFAILERLRYPNVIREE---IERLLENITV-LAEAAALATSPALTDE--- 113
           ++ +D   NI       L     + EE   +  ++ENI + LA    +  +    DE   
Sbjct: 57  YDGVDFYSNITILRKNHLAICQELFEEGDLVFGMVENIFLQLARVLEVPLTKENYDEYYD 116

Query: 114 -LVSHGELMSTLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLP 172
            +V  GEL+ST +    L  R     W D R  + T+D F  A+ D    A     +L+P
Sbjct: 117 RVVGFGELLSTKIIHAYLCHRQQYCIWQDARDFILTDDNFRFAKVDWEQTARQCQQKLVP 176

Query: 173 RLNEGLVITQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPR 232
            L +  V+TQGF+GS   G+ TTLGR GSD++AA+ A++L A  V IW DVPG+   DP+
Sbjct: 177 VLKQLPVVTQGFVGSTKDGQPTTLGREGSDFSAAIFAKSLGAESVTIWKDVPGVLNADPK 236

Query: 233 VVSAAKRIDEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNK 292
                 + D + + EAAEM  +GA V+HP T+ P   + IP+FV S   P   GT++ + 
Sbjct: 237 RFEETVKFDRLDYKEAAEMTFYGASVIHPRTIKPLANAKIPLFVRSFLQPEEQGTVIGDF 296

Query: 293 TENPPLFRALALRRNQTLLTLHSLNMLH-SRGFLAEVFGILARHNISVDLITTSEVSVAL 351
            E       + ++  Q L+T    +    +   + +V+  L R  +  +LI +S +++++
Sbjct: 297 GEGSINVPTIVVKDRQVLVTFEVTDFTFINESHMHQVYAELDRLKLRANLIQSSAITISI 356

Query: 352 TLDTTGSTSTGDTLLTQSLLMELSALCRVEVEEGLALVALIGND 395
             D        +    + LL E+  + +V+  EGL LV +   D
Sbjct: 357 CTDR-------ELFKLEQLLEEMKGIFKVKYNEGLQLVTVKNYD 393


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: 322
Number of extensions: 10
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: 423
Length adjustment: 32
Effective length of query: 417
Effective length of database: 391
Effective search space:   163047
Effective search space used:   163047
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 Echvi_1827 Echvi_1827 (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.28601.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
    2.9e-77  246.5   0.0    3.5e-77  246.3   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_1827  Echvi_1827 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_1827  Echvi_1827 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.3   0.0   3.5e-77   3.5e-77       2     385 ..       3     390 ..       2     419 .. 0.86

  Alignments for each domain:
  == domain 1  score: 246.3 bits;  conditional E-value: 3.5e-77
                            TIGR00657   2 aliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee.keliekirekhl 74 
                                          + iV+KFGG Sv+++  ik++ +i+ ++   + ++v+VvSA++++T+aL e+ +   ++ +  + i+ +r++hl
  lcl|FitnessBrowser__Cola:Echvi_1827   3 KAIVYKFGGASVKDAAAIKNLSNILFNRL--RSPMVIVVSAIGKTTNALEEILRLKYDGVDfYSNITILRKNHL 74 
                                          579***********************999..668********************999999978899999***** PP

                            TIGR00657  75 ealeela.sqalkeklkallekeleevkk...........ereldlilsvGEklSaallaaaleelgvkavsll 136
                                          ++ +el  +      +  ++e+ + ++ +           ++ +d+++ +GE lS++++ a+l++++ ++  + 
  lcl|FitnessBrowser__Cola:Echvi_1827  75 AICQELFeEG---DLVFGMVENIFLQLARvlevpltkenyDEYYDRVVGFGELLSTKIIHAYLCHRQ-QYCIWQ 144
                                          **99998553...444455555555555556689999999***************************.9***** PP

                            TIGR00657 137 gaeagiltdsefgrAk....vleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalk 206
                                          +a+  iltd++f+ Ak    +++   +++l ++l++   vv++GF+G+t++g+ ttLGR GSD++Aa+ A+ l+
  lcl|FitnessBrowser__Cola:Echvi_1827 145 DARDFILTDDNFRFAKvdweQTARQCQQKLVPVLKQL-PVVTQGFVGSTKDGQPTTLGREGSDFSAAIFAKSLG 217
                                          ****************544333333344444444443.56779******************************* PP

                            TIGR00657 207 AdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGT 280
                                          A+ v i++DV+G++ aDP+  +e+ + d ++y+Ea+E++ +Ga v+hprt++p+++akip++v+s  +pe++GT
  lcl|FitnessBrowser__Cola:Echvi_1827 218 AESVTIWKDVPGVLNADPKRFEETVKFDRLDYKEAAEMTFYGASVIHPRTIKPLANAKIPLFVRSFLQPEEQGT 291
                                          ************************************************************************** PP

                            TIGR00657 281 livakskseeepavkalsldknqalvsvsgttmk...pgilaevfgalaeakvnvdlilqsssetsisfvvdke 351
                                          +i+   +   + +v ++ +++ q+lv+ + t         + +v   l + k   +li   ss  +is++ d+e
  lcl|FitnessBrowser__Cola:Echvi_1827 292 VIGDFGE--GSINVPTIVVKDRQVLVTFEVTDFTfinESHMHQVYAELDRLKLRANLIQ--SSAITISICTDRE 361
                                          ***9966..5578999999999999999988888778999999**************98..5556899999887 PP

                            TIGR00657 352 dadkakellkkkvkeekaleevevekklalvslv 385
                                             k ++ll    +e k + +v+++++l lv++ 
  lcl|FitnessBrowser__Cola:Echvi_1827 362 LF-KLEQLL----EEMKGIFKVKYNEGLQLVTVK 390
                                          64.455553....466677779999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (423 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: 00:00:00.01
# Mc/sec: 12.07
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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