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

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.4366.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 9.37
//
[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