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

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.1318766.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  FitnessBrowser__Cola:Echvi_1827  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Cola:Echvi_1827  
   #    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.keliekirekhleale 78 
                                      + iV+KFGG Sv+++  ik++ +i+ ++   + ++v+VvSA++++T+aL e+ +   ++ +  + i+ +r++hl++ +
  FitnessBrowser__Cola:Echvi_1827   3 KAIVYKFGGASVKDAAAIKNLSNILFNRL--RSPMVIVVSAIGKTTNALEEILRLKYDGVDfYSNITILRKNHLAICQ 78 
                                      579***********************999..668********************999999978899999*******99 PP

                        TIGR00657  79 ela.sqalkeklkallekeleevkk...........ereldlilsvGEklSaallaaaleelgvkavsllgaeagilt 144
                                      el  +      +  ++e+ + ++ +           ++ +d+++ +GE lS++++ a+l++++ ++  + +a+  ilt
  FitnessBrowser__Cola:Echvi_1827  79 ELFeEG---DLVFGMVENIFLQLARvlevpltkenyDEYYDRVVGFGELLSTKIIHAYLCHRQ-QYCIWQDARDFILT 152
                                      998553...444455555555555556689999999***************************.9************* PP

                        TIGR00657 145 dsefgrAk....vleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdG 218
                                      d++f+ Ak    +++   +++l ++l++   vv++GF+G+t++g+ ttLGR GSD++Aa+ A+ l+A+ v i++DV+G
  FitnessBrowser__Cola:Echvi_1827 153 DDNFRFAKvdweQTARQCQQKLVPVLKQL-PVVTQGFVGSTKDGQPTTLGREGSDFSAAIFAKSLGAESVTIWKDVPG 229
                                      ********544333333344444444443.56779******************************************* PP

                        TIGR00657 219 iytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseeepavka 296
                                      ++ aDP+  +e+ + d ++y+Ea+E++ +Ga v+hprt++p+++akip++v+s  +pe++GT+i+   +   + +v +
  FitnessBrowser__Cola:Echvi_1827 230 VLNADPKRFEETVKFDRLDYKEAAEMTFYGASVIHPRTIKPLANAKIPLFVRSFLQPEEQGTVIGDFGE--GSINVPT 305
                                      *****************************************************************9966..5578999 PP

                        TIGR00657 297 lsldknqalvsvsgttmk...pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellkkkvkeekale 371
                                      + +++ q+lv+ + t         + +v   l + k   +li   ss  +is++ d+e   k ++ll    +e k + 
  FitnessBrowser__Cola:Echvi_1827 306 IVVKDRQVLVTFEVTDFTfinESHMHQVYAELDRLKLRANLIQ--SSAITISICTDRELF-KLEQLL----EEMKGIF 376
                                      999999999999988888778999999**************98..555689999988764.455553....4666777 PP

                        TIGR00657 372 evevekklalvslv 385
                                      +v+++++l lv++ 
  FitnessBrowser__Cola:Echvi_1827 377 KVKYNEGLQLVTVK 390
                                      79999999988875 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 24.07
//
[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:

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