Alignments for a candidate for asp-kinase in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Shewanella oneidensis MR-1

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 203070 SO3986 aspartokinase III, lysine-sensitive (NCBI ptt file)

Query= BRENDA::P08660
         (449 letters)



>FitnessBrowser__MR1:203070
          Length = 451

 Score =  514 bits (1324), Expect = e-150
 Identities = 270/447 (60%), Positives = 339/447 (75%), Gaps = 1/447 (0%)

Query: 4   IVVSKFGGTSVADFDAMNRSADIVLSDANVRLVVLSASAGITNLLVALA-EGLEPGERFE 62
           +VV+KFGGTSVAD+ AMNR A+IVL + + RLVV+SAS+G+TNLLV L  E +    R +
Sbjct: 3   LVVAKFGGTSVADYGAMNRCAEIVLGNPDCRLVVVSASSGVTNLLVELTQESINDDGRLQ 62

Query: 63  KLDAIRNIQFAILERLRYPNVIREEIERLLENITVLAEAAALATSPALTDELVSHGELMS 122
           +L  I  IQ+AIL++L  PN +   +++LL  + VL+EA   A S A  DEL+S GE  S
Sbjct: 63  RLKQIAQIQYAILDKLGRPNDVAAALDKLLSRMAVLSEALVSARSKATMDELLSLGEQCS 122

Query: 123 TLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLPRLNEGLVITQ 182
           + LF  +LRE+   +  FDVR+V+RT+  FGRAEP +  +A L+   LLP L+E +++TQ
Sbjct: 123 SALFAAVLREKGANSSAFDVRRVLRTDSHFGRAEPQVEQIALLSREHLLPLLSEQVIVTQ 182

Query: 183 GFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVVSAAKRIDE 242
           GFIG++  G+TTTLGRGGSDY+AALLAEAL AS V+IWTDV GIYTTDPR+   A  I E
Sbjct: 183 GFIGADEAGQTTTLGRGGSDYSAALLAEALTASAVEIWTDVAGIYTTDPRLAPNAHPIAE 242

Query: 243 IAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKTENPPLFRAL 302
           I+F EAAEMATFGAKVLHPAT+LPAVR  I VFVGSSK+P  GGT + ++ E+ P+FRA+
Sbjct: 243 ISFNEAAEMATFGAKVLHPATILPAVRQQIQVFVGSSKEPEKGGTWIRHQVEDAPVFRAV 302

Query: 303 ALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSEVSVALTLDTTGSTSTG 362
           ALRR+QTLL LHSL MLH++GFLAE F  LARH ISVDLITTSEV+V+LTLD TGS S+G
Sbjct: 303 ALRRDQTLLNLHSLQMLHAQGFLAETFATLARHKISVDLITTSEVNVSLTLDKTGSDSSG 362

Query: 363 DTLLTQSLLMELSALCRVEVEEGLALVALIGNDLSKACGVGKEVFGVLEPFNIRMICYGA 422
             LL+++LL ELS  CRV VE+GLALVA+IGN ++   G+ + VF VLEP N+RMIC GA
Sbjct: 363 QGLLSEALLQELSQHCRVRVEDGLALVAIIGNRIATTAGICRRVFEVLEPHNVRMICQGA 422

Query: 423 SSHNLCFLVPGEDAEQVVQKLHSNLFE 449
           S HNLC LV   +A QVV+ LH NLFE
Sbjct: 423 SPHNLCVLVAESEAAQVVKALHENLFE 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: 502
Number of extensions: 9
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: 449
Length of database: 451
Length adjustment: 33
Effective length of query: 416
Effective length of database: 418
Effective search space:   173888
Effective search space used:   173888
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 203070 SO3986 (aspartokinase III, lysine-sensitive (NCBI ptt file))
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.7739.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.1e-134  435.4   1.0   1.2e-134  435.2   1.0    1.0  1  lcl|FitnessBrowser__MR1:203070  SO3986 aspartokinase III, lysine


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:203070  SO3986 aspartokinase III, lysine-sensitive (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.2   1.0  1.2e-134  1.2e-134       1     406 [.       1     449 [.       1     450 [. 0.94

  Alignments for each domain:
  == domain 1  score: 435.2 bits;  conditional E-value: 1.2e-134
                       TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelae..............llklleaisd 65 
                                     ++l+V+KFGGtsv++  ++++ a+ivl +    + ++VVvSA+s+vt+ lvel++              + ++++ai d
  lcl|FitnessBrowser__MR1:203070   1 MSLVVAKFGGTSVADYGAMNRCAEIVLGN---PDCRLVVVSASSGVTNLLVELTQesinddgrlqrlkqIAQIQYAILD 76 
                                     679*************************9...899*******************9999999998887774444444444 PP

                       TIGR00656  66 ei............................sprerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgn 116
                                     +                             s++++del+s+GE+ ssal++ +lre+g ++ a+d ++ +++Td++fg+
  lcl|FitnessBrowser__MR1:203070  77 KLgrpndvaaaldkllsrmavlsealvsarSKATMDELLSLGEQCSSALFAAVLREKGANSSAFD-VRRVLRTDSHFGR 154
                                     446666666666666666677777777777***********************************.999********** PP

                       TIGR00656 117 Akikelate....erLlelLeegiivvvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPr 191
                                     A+++ ++++    e+Ll+lL e+ ++v++GFiGa+e G++TtLGRGGSD++Aalla+al A+ vei+TDV G+yttDPr
  lcl|FitnessBrowser__MR1:203070 155 AEPQVEQIAllsrEHLLPLLSEQ-VIVTQGFIGADEAGQTTTLGRGGSDYSAALLAEALTASAVEIWTDVAGIYTTDPR 232
                                     ******9999999*********9.889**************************************************** PP

                       TIGR00656 192 vveeakkidkisyeEalelAtlGakvlhpralelaveakvpilvrsskeke.egTlitnkkensslvkaialeknvarl 269
                                     + ++a++i++is++Ea+e+At+Gakvlhp+++ +av+++++++v sske+e  gT i ++ e  ++++a+al++++++l
  lcl|FitnessBrowser__MR1:203070 233 LAPNAHPIAEISFNEAAEMATFGAKVLHPATILPAVRQQIQVFVGSSKEPEkGGTWIRHQVEDAPVFRAVALRRDQTLL 311
                                     ***************************************************999************************* PP

                       TIGR00656 270 tvegegmlgkrgilaeifkaLaeeeinvdlisqtesetsislvvdeedvdeakkaLkeesgaae...lesleveedlav 345
                                     ++++ +ml+ +g+lae f +La+++i+vdli+++e  +++sl++d++++d++ + L +e +++e    +++ ve +la+
  lcl|FitnessBrowser__MR1:203070 312 NLHSLQMLHAQGFLAETFATLARHKISVDLITTSE--VNVSLTLDKTGSDSSGQGLLSEALLQElsqHCRVRVEDGLAL 388
                                     ********************************999..********************999888877789********** PP

                       TIGR00656 346 vsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                     v+i+g+ +  + G+  ++f++le++n+++++ ++s ++++vlv e +a ++v++lhe+l+e
  lcl|FitnessBrowser__MR1:203070 389 VAIIGNRIATTAGICRRVFEVLEPHNVRMICQGASPHNLCVLVAESEAAQVVKALHENLFE 449
                                     **********************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (451 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: 00:00:00.02
# Mc/sec: 7.74
//
[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