GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Shewanella loihica PV-4

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 5208267 Shew_0779 aspartate kinase III (RefSeq)

Query= BRENDA::P08660
         (449 letters)



>FitnessBrowser__PV4:5208267
          Length = 452

 Score =  508 bits (1307), Expect = e-148
 Identities = 266/447 (59%), Positives = 340/447 (76%), Gaps = 1/447 (0%)

Query: 4   IVVSKFGGTSVADFDAMNRSADIVLSDANVRLVVLSASAGITNLLVALA-EGLEPGERFE 62
           IVV+KFGGTSVAD++AMNR ADIVL++   R+VV+SAS+G+TNLLV L  E ++   R +
Sbjct: 3   IVVAKFGGTSVADYEAMNRCADIVLANPETRVVVVSASSGVTNLLVELTQEHVDFERRQQ 62

Query: 63  KLDAIRNIQFAILERLRYPNVIREEIERLLENITVLAEAAALATSPALTDELVSHGELMS 122
            L AI +IQ+ IL+ L  P+ +   ++ +L  I  L+E+ +   + A TDEL++ GE  S
Sbjct: 63  LLKAIASIQYKILDELGQPHDVAARLDAILSKIASLSESLSQNRNKATTDELLAQGEQCS 122

Query: 123 TLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLPRLNEGLVITQ 182
           ++LF  +LRE+  +A  FDVR+VMRT+  FGRAEP I A+ +L    LLP L+E  ++TQ
Sbjct: 123 SVLFAAVLREKGERASAFDVRQVMRTDSHFGRAEPQIEAVKQLCTEHLLPLLSEQRIVTQ 182

Query: 183 GFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVVSAAKRIDE 242
           GFIG++ +G TTTLGRGGSDY+AALLAEAL AS V+IWTDVPGI+TTDPR+   A+ I E
Sbjct: 183 GFIGADEQGATTTLGRGGSDYSAALLAEALDASAVEIWTDVPGIFTTDPRLAPNARPIPE 242

Query: 243 IAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKTENPPLFRAL 302
           I+F EAAEMATFGAKVLHPAT+LPAVR  I VFVGSSK P  GGT + ++  + P++RA+
Sbjct: 243 ISFNEAAEMATFGAKVLHPATILPAVRHKIQVFVGSSKAPELGGTWIRHQVNDEPIYRAV 302

Query: 303 ALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSEVSVALTLDTTGSTSTG 362
           A+RR+QTLL LHSL MLH++GFLAE F  LARH ISVDLITTSEV+V+LTLD TGS S G
Sbjct: 303 AVRRDQTLLNLHSLQMLHAQGFLAETFATLARHKISVDLITTSEVNVSLTLDKTGSDSAG 362

Query: 363 DTLLTQSLLMELSALCRVEVEEGLALVALIGNDLSKACGVGKEVFGVLEPFNIRMICYGA 422
           ++LL+++LL ELS  CRV VE+GLALVA++GN ++   GV + VF VLEP N+RMIC GA
Sbjct: 363 NSLLSEALLQELSQHCRVRVEDGLALVAIVGNKIATTSGVCRRVFEVLEPHNVRMICQGA 422

Query: 423 SSHNLCFLVPGEDAEQVVQKLHSNLFE 449
           S HNLC LV   +A QVV  LH NLFE
Sbjct: 423 SPHNLCVLVAESEAAQVVSALHQNLFE 449


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: 497
Number of extensions: 12
Number of successful extensions: 3
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: 452
Length adjustment: 33
Effective length of query: 416
Effective length of database: 419
Effective search space:   174304
Effective search space used:   174304
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 5208267 Shew_0779 (aspartate kinase III (RefSeq))
to HMM TIGR00656 (aspartate kinase, monofunctional class (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/TIGR00656.hmm
# target sequence database:        /tmp/gapView.21824.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00656  [M=407]
Accession:   TIGR00656
Description: asp_kin_monofn: aspartate kinase, monofunctional class
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   6.3e-138  446.1   0.9   7.3e-138  445.9   0.9    1.0  1  lcl|FitnessBrowser__PV4:5208267  Shew_0779 aspartate kinase III (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208267  Shew_0779 aspartate kinase III (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  445.9   0.9  7.3e-138  7.3e-138       1     406 [.       1     449 [.       1     450 [. 0.94

  Alignments for each domain:
  == domain 1  score: 445.9 bits;  conditional E-value: 7.3e-138
                        TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelae....................... 55 
                                      ++++V+KFGGtsv++ e++++ a+ivl++    + +vVVvSA+s+vt+ lvel++                       
  lcl|FitnessBrowser__PV4:5208267   1 MSIVVAKFGGTSVADYEAMNRCADIVLAN---PETRVVVVSASSGVTNLLVELTQehvdferrqqllkaiasiqykil 75 
                                      679************************99...899********************9********98888666666666 PP

                        TIGR00656  56 ...................llklleaisdeisprerdelvsvGEllssallssalrelgvkaealdgkeagilTddef 114
                                                         + +l e+ s++ +++++del++ GE+ ss+l++ +lre+g++a a+d ++++++Td++f
  lcl|FitnessBrowser__PV4:5208267  76 delgqphdvaarldailskIASLSESLSQNRNKATTDELLAQGEQCSSVLFAAVLREKGERASAFD-VRQVMRTDSHF 152
                                      6666666666666665444444447777777***********************************.999******** PP

                        TIGR00656 115 gnAkikelate....erLlelLeegiivvvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvytt 188
                                      g+A+++++a++    e+Ll+lL e+ i v++GFiGa+e+G +TtLGRGGSD++Aalla+al+A+ vei+TDV+G++tt
  lcl|FitnessBrowser__PV4:5208267 153 GRAEPQIEAVKqlctEHLLPLLSEQRI-VTQGFIGADEQGATTTLGRGGSDYSAALLAEALDASAVEIWTDVPGIFTT 229
                                      ***********9*************65.79************************************************ PP

                        TIGR00656 189 DPrvveeakkidkisyeEalelAtlGakvlhpralelaveakvpilvrsskeke.egTlitnkkensslvkaialekn 265
                                      DPr+ ++a++i++is++Ea+e+At+Gakvlhp+++ +av+ k++++v ssk +e  gT i ++ + +++ +a+a++++
  lcl|FitnessBrowser__PV4:5208267 230 DPRLAPNARPIPEISFNEAAEMATFGAKVLHPATILPAVRHKIQVFVGSSKAPElGGTWIRHQVNDEPIYRAVAVRRD 307
                                      ***************************************************************99999********** PP

                        TIGR00656 266 varltvegegmlgkrgilaeifkaLaeeeinvdlisqtesetsislvvdeedvdeakkaLkeesgaae...lesleve 340
                                      +++l++++ +ml+ +g+lae f +La+++i+vdli+++e  +++sl++d++++d+a + L +e +++e    +++ ve
  lcl|FitnessBrowser__PV4:5208267 308 QTLLNLHSLQMLHAQGFLAETFATLARHKISVDLITTSE--VNVSLTLDKTGSDSAGNSLLSEALLQElsqHCRVRVE 383
                                      ************************************999..**********************9988887889***** PP

                        TIGR00656 341 edlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                       +la+v+ivg+ +  ++Gv  ++f++le++n+++++ ++s ++++vlv e +a ++v +lh++l+e
  lcl|FitnessBrowser__PV4:5208267 384 DGLALVAIVGNKIATTSGVCRRVFEVLEPHNVRMICQGASPHNLCVLVAESEAAQVVSALHQNLFE 449
                                      ***************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (452 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: 11.09
//
[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