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.11297.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: 9.92
//
[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:

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