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.370618.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: 00:00:00.01
# Mc/sec: 13.00
//
[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