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_1218 Echvi_1218 aspartate kinase

Query= BRENDA::P08660
         (449 letters)



>FitnessBrowser__Cola:Echvi_1218
          Length = 439

 Score =  249 bits (637), Expect = 1e-70
 Identities = 148/448 (33%), Positives = 255/448 (56%), Gaps = 16/448 (3%)

Query: 6   VSKFGGTSVADFDAMNRSADIVLSDANVRLVVLSASAGITNLLVALAEGLEPGERF---E 62
           + KFGGTSV   + M++  D++  D   +++VLSA +G TN LV + E L  G++    E
Sbjct: 3   IMKFGGTSVGKPERMHQVKDLITRDNERKIIVLSALSGTTNALVGIGEALAEGKKDLAKE 62

Query: 63  KLDAIRNIQFAILERLRYPNVIREEIERLL-ENITVLAEAAALATSPALTDELVSHGELM 121
           ++D +        + L      R++ E+++ E+   L     ++ + A+  ++++ GEL+
Sbjct: 63  RIDTLHAHYQEFYKALLESEAGRKKAEKIIKEHFEFLNIILKISFNEAINRDILAQGELL 122

Query: 122 STLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLPRLNEGLVIT 181
           ST LF  +L+E+D+ A +    + M  ++    +EP++A +++     L     + L IT
Sbjct: 123 STKLFYTLLQEKDIPAIFLPALEYMSIDEN---SEPEVAKISDRLKAILKNYDKDALFIT 179

Query: 182 QGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVVSAAKRID 241
           QG+I   ++     L RGGSDYTA+L+  A+ AS V+IWTD+ G++  DPRVV   + I 
Sbjct: 180 QGYICKNHRNEVDNLKRGGSDYTASLIGAAIKASVVEIWTDIDGMHNNDPRVVDKTRPIA 239

Query: 242 EIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKTENPPLFRA 301
           +++F EAAE+A FGAK+LHPA++ PA   +IPV + ++  P A GT +    E     +A
Sbjct: 240 QLSFDEAAELAYFGAKILHPASIWPAQTYNIPVKLLNTMQPEAPGTTI-TAEETGKGVKA 298

Query: 302 LALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSEVSVALTLDTTGSTST 361
           +A +     + + S  ML + GFL +VF I  ++   +D+ITTSEV+V++T+D       
Sbjct: 299 IAAKDGIIAVKIKSSRMLLAYGFLRKVFEIFEKYKTPIDMITTSEVAVSVTID------- 351

Query: 362 GDTLLTQSLLMELSALCRVEVEEGLALVALIGNDLSKACGVGKEVFGVLEPFNIRMICYG 421
            D    + ++MEL      E++    +V + GN +++  G+ KEV   L+ F +RM+ YG
Sbjct: 352 -DDTHLKEIIMELEKFGNTEIDYKQTIVCVAGNMIAENTGMIKEVVVALQDFPVRMVSYG 410

Query: 422 ASSHNLCFLVPGEDAEQVVQKLHSNLFE 449
            S +N+  LV  +   + +Q+L+  LF+
Sbjct: 411 GSRNNVSILVDTKYKNEALQRLNDELFQ 438


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: 378
Number of extensions: 14
Number of successful extensions: 5
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: 439
Length adjustment: 32
Effective length of query: 417
Effective length of database: 407
Effective search space:   169719
Effective search space used:   169719
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_1218 Echvi_1218 (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.11825.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
    4.6e-89  285.4   1.0    5.2e-89  285.2   1.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_1218  Echvi_1218 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_1218  Echvi_1218 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.2   1.0   5.2e-89   5.2e-89       5     441 ..       3     437 ..       1     438 [. 0.90

  Alignments for each domain:
  == domain 1  score: 285.2 bits;  conditional E-value: 5.2e-89
                            TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee...keliekirekhle 75 
                                          ++KFGGtSvg+ er+++v +++++++e +   ++V+SA +g+T+aLv + e + ++++   ke i+++ ++  e
  lcl|FitnessBrowser__Cola:Echvi_1218   3 IMKFGGTSVGKPERMHQVKDLITRDNERK---IIVLSALSGTTNALVGIGEALAEGKKdlaKERIDTLHAHYQE 73 
                                          79**********************99555...***********************9987776666666666666 PP

                            TIGR00657  76 aleela.sqalkeklkallekeleevkk.......ereldlilsvGEklSaallaaaleelgvkavsllgaeag 141
                                            ++l  s+a ++k ++++++++e ++        e+ +  il+ GE lS++l+  +l+e+++ a+ l + e  
  lcl|FitnessBrowser__Cola:Echvi_1218  74 FYKALLeSEAGRKKAEKIIKEHFEFLNIilkisfnEAINRDILAQGELLSTKLFYTLLQEKDIPAIFLPALEYM 147
                                          66666667777777777777777666558899999999999**********************99999888877 PP

                            TIGR00657 142 iltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytD 215
                                           + +++  +   +++ + + ++k  +++ + +++G+i  ++ +e+  L RGGSD+tA+l++aa+kA++vei+tD
  lcl|FitnessBrowser__Cola:Echvi_1218 148 SIDENSEPEVA-KISDRLKAILKNYDKDALFITQGYICKNHRNEVDNLKRGGSDYTASLIGAAIKASVVEIWTD 220
                                          66655544444.5788888888999999********************************************** PP

                            TIGR00657 216 VdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskse 289
                                          +dG +  DPr+v ++r ++++s++Ea+ELa++Gak+Lhp+++ pa  ++ip+   +t++pea+GT i+a+++  
  lcl|FitnessBrowser__Cola:Echvi_1218 221 IDGMHNNDPRVVDKTRPIAQLSFDEAAELAYFGAKILHPASIWPAQTYNIPVKLLNTMQPEAPGTTITAEET-- 292
                                          **********************************************************************55.. PP

                            TIGR00657 290 eepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellk 361
                                            + vka++ ++  + v+++++ m   +g+l +vf++ ++ k  +d+i+  +se  +s ++d++   + ke+  
  lcl|FitnessBrowser__Cola:Echvi_1218 293 -GKGVKAIAAKDGIIAVKIKSSRMLlaYGFLRKVFEIFEKYKTPIDMIT--TSEVAVSVTIDDD--THLKEI-- 359
                                          .688********************999**********************..7765666666654..444444.. PP

                            TIGR00657 362 kkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..sseikisvvvdekdaekav 433
                                            ++e+++++++e++ k  +v + G+ ++++ g++++++ aL++  ++++m+s   s  ++s++vd k+ ++a+
  lcl|FitnessBrowser__Cola:Echvi_1218 360 --IMELEKFGNTEIDYKQTIVCVAGNMIAENTGMIKEVVVALQD--FPVRMVSygGSRNNVSILVDTKYKNEAL 429
                                          ..688999**********************************99..9******999****************** PP

                            TIGR00657 434 ealheklv 441
                                          + l ++l+
  lcl|FitnessBrowser__Cola:Echvi_1218 430 QRLNDELF 437
                                          ****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (439 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: 10.68
//
[ok]

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