GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Shewanella sp. ANA-3

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 7023909 Shewana3_1129 aspartate kinase (RefSeq)

Query= BRENDA::O69077
         (412 letters)



>FitnessBrowser__ANA3:7023909
          Length = 418

 Score =  343 bits (881), Expect = 4e-99
 Identities = 197/408 (48%), Positives = 275/408 (67%), Gaps = 8/408 (1%)

Query: 3   LIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQPV 62
           L V+KFGGTSVG++ERIE VAE++ K    G+  V+V+SAM+GETNRL  LA QI  +  
Sbjct: 12  LFVKKFGGTSVGSIERIEVVAEQIAKSAHNGELQVLVLSAMAGETNRLFALAAQIDPRAS 71

Query: 63  PRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTHIR 122
            RELD++VSTGEQ++IAL++MAL +RG+ A S TG+QV+I T+S   +A I  +D  ++ 
Sbjct: 72  ARELDMLVSTGEQISIALMAMALQRRGINARSLTGDQVQIHTNSQFGRASIERVDTAYLT 131

Query: 123 ADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTD 182
           + L  G V +VAGFQG+D NG++TTLGRGGSDTT VALAAALKADECQI+TDV GV+TTD
Sbjct: 132 SLLNDGIVPIVAGFQGIDPNGDVTTLGRGGSDTTAVALAAALKADECQIFTDVPGVFTTD 191

Query: 183 PRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLITI 242
           P +   ARRLD I F+ MLEMA LG+KVL   +VE+A ++ VPLRVL SF+ G GTLI  
Sbjct: 192 PNIDSSARRLDVIGFDVMLEMAKLGAKVLHPDSVEYAQRFKVPLRVLSSFEAGHGTLIQF 251

Query: 243 DDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMI----VQN 298
            DE E      + GIA N+  A LTI+G+  +      +L  ++   ++V+ I    +  
Sbjct: 252 GDESELAMAASVQGIAINKALATLTIKGLFTSSEHYQALLACLARLEIDVEFITPLKLNE 311

Query: 299 VAHDNTTDFTFTVHRND-YLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGV 357
            +      F     + D  L+ LE+L +   ++   + I +   AKVS+VG G+++  G+
Sbjct: 312 TSAAECVSFMLAEAKVDILLHELELLSE---SLDLGQLIVERQRAKVSLVGKGLQAKVGL 368

Query: 358 ASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 405
            ++M + L  E+I+ +++STSE K+S VI+E+ L  AVRALH AFEL+
Sbjct: 369 LTKMLDVLGNETIHAKLLSTSESKLSTVIDERDLHKAVRALHHAFELN 416


Lambda     K      H
   0.317    0.133    0.362 

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: 421
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: 412
Length of database: 418
Length adjustment: 31
Effective length of query: 381
Effective length of database: 387
Effective search space:   147447
Effective search space used:   147447
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 7023909 Shewana3_1129 (aspartate kinase (RefSeq))
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.4598.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.4e-121  391.8   3.8   6.2e-106  341.0   0.8    2.0  2  lcl|FitnessBrowser__ANA3:7023909  Shewana3_1129 aspartate kinase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7023909  Shewana3_1129 aspartate kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.1   1.9e-18   1.9e-18       2      61 ..      11      70 ..      10      74 .. 0.94
   2 !  341.0   0.8  6.2e-106  6.2e-106     103     441 ..      72     414 ..      69     415 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 1.9e-18
                         TIGR00657  2 aliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvssee 61
                                      +l V KFGGtSvg++eri+ va+ + k++++g+  v V+SAmag T++L +la ++++++
  lcl|FitnessBrowser__ANA3:7023909 11 KLFVKKFGGTSVGSIERIEVVAEQIAKSAHNGELQVLVLSAMAGETNRLFALAAQIDPRA 70
                                      6789***************************************************99876 PP

  == domain 2  score: 341.0 bits;  conditional E-value: 6.2e-106
                         TIGR00657 103 ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterleklleegiivvvaGFiG 179
                                        reld+++s+GE++S+al+a+al+++g++a+sl+g++ +i t+s+fgrA+ +e ++t+ l++ll+ gi+++vaGF+G
  lcl|FitnessBrowser__ANA3:7023909  72 ARELDMLVSTGEQISIALMAMALQRRGINARSLTGDQVQIHTNSQFGRAS-IERVDTAYLTSLLNDGIVPIVAGFQG 147
                                       689***********************************************.************************** PP

                         TIGR00657 180 atekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprt 256
                                       ++++g++ttLGRGGSD+tA++lAaalkAde++i+tDV+G++t+DP+i ++Arrld i ++ +lE+a+lGakvLhp++
  lcl|FitnessBrowser__ANA3:7023909 148 IDPNGDVTTLGRGGSDTTAVALAAALKADECQIFTDVPGVFTTDPNIDSSARRLDVIGFDVMLEMAKLGAKVLHPDS 224
                                       ***************************************************************************** PP

                         TIGR00657 257 lepamrakipivvkstfnpeaeGTlivaksk..seeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvn 331
                                       +e+a r+k+p++v s+f+    GTli   ++     +  v++++ +k  a ++++g    ++  + ++ +la+ +++
  lcl|FitnessBrowser__ANA3:7023909 225 VEYAQRFKVPLRVLSSFEAG-HGTLIQFGDEseLAMAASVQGIAINKALATLTIKGLFTSSEHYQALLACLARLEID 300
                                       ******************99.*****9888877444589************************************** PP

                         TIGR00657 332 vdlil.qsssets....isfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaL 403
                                       v+ i+ ++ +ets    +sf++ + ++d   ++l + + e  +l+++ ve++ a+vslvG+g++ + g+++k++++L
  lcl|FitnessBrowser__ANA3:7023909 301 VEFITpLKLNETSaaecVSFMLAEAKVDILLHEL-ELLSESLDLGQLIVERQRAKVSLVGKGLQAKVGLLTKMLDVL 376
                                       *****966666666678**************998.67999999********************************** PP

                         TIGR00657 404 aeeniniemissseikisvvvdekdaekavealheklv 441
                                        +e i  + +s+se k+s+v+de+d +kav+alh++++
  lcl|FitnessBrowser__ANA3:7023909 377 GNETIHAKLLSTSESKLSTVIDERDLHKAVRALHHAFE 414
                                       ***********************************996 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: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 2.61
//
[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