Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 6936415 Sama_0603 aspartate kinase III (RefSeq)
Query= BRENDA::P08660 (449 letters) >FitnessBrowser__SB2B:6936415 Length = 452 Score = 507 bits (1306), Expect = e-148 Identities = 269/447 (60%), Positives = 338/447 (75%), Gaps = 1/447 (0%) Query: 4 IVVSKFGGTSVADFDAMNRSADIVLSDANVRLVVLSASAGITNLLVALAEGLEPGER-FE 62 +VV+KFGGTSVADF+AM+R A IVL+++ RLVV+SAS+G+TNLLV L + ER + Sbjct: 3 LVVAKFGGTSVADFNAMSRCAAIVLANSATRLVVVSASSGVTNLLVELTQATVTDERRLQ 62 Query: 63 KLDAIRNIQFAILERLRYPNVIREEIERLLENITVLAEAAALATSPALTDELVSHGELMS 122 L I IQ+AIL++L P + ++ LL I+VL+E+ L S A+ DEL+S GE S Sbjct: 63 LLKQIAQIQYAILDKLERPQDVAAALDALLSRISVLSESLILNRSKAIMDELLSMGEQCS 122 Query: 123 TLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLPRLNEGLVITQ 182 LLF +LR++ ++ FDVR+VMRT+ FGRAEP I +A LA L P L +V+TQ Sbjct: 123 ALLFSAVLRQQGAKSSSFDVRQVMRTDSHFGRAEPQIEDIAALARDFLQPLLERDIVVTQ 182 Query: 183 GFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVVSAAKRIDE 242 GFIG++ +GRTTTLGRGGSDY+AALLAEAL A V+IWTDV GIYTTDPR+ A+ I E Sbjct: 183 GFIGADAEGRTTTLGRGGSDYSAALLAEALRADAVEIWTDVAGIYTTDPRLAPNARPIAE 242 Query: 243 IAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKTENPPLFRAL 302 I+F EAAEMATFGAKVLHPAT+LPAVR I VFVGSS++P GGT + ++ +NPP++RA+ Sbjct: 243 ISFNEAAEMATFGAKVLHPATILPAVRQQIQVFVGSSREPEKGGTWIRHQVDNPPIYRAV 302 Query: 303 ALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSEVSVALTLDTTGSTSTG 362 A+RR+QTLL LHSL MLH+RGFLAE F LARH ISVDLITTSEV+V+LTLD TGS STG Sbjct: 303 AVRRDQTLLNLHSLQMLHARGFLAETFATLARHKISVDLITTSEVNVSLTLDKTGSDSTG 362 Query: 363 DTLLTQSLLMELSALCRVEVEEGLALVALIGNDLSKACGVGKEVFGVLEPFNIRMICYGA 422 LL+++LL ELS CRV VE+ LALVA+IGN ++ G+ ++VF VLE N+RMIC GA Sbjct: 363 SGLLSEALLQELSQHCRVRVEDNLALVAIIGNRIASTPGICRQVFTVLENHNVRMICQGA 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: 471 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 6936415 Sama_0603 (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.25936.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-138 447.6 1.6 2.4e-138 447.5 1.6 1.0 1 lcl|FitnessBrowser__SB2B:6936415 Sama_0603 aspartate kinase III ( Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6936415 Sama_0603 aspartate kinase III (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 447.5 1.6 2.4e-138 2.4e-138 1 406 [. 1 449 [. 1 450 [. 0.94 Alignments for each domain: == domain 1 score: 447.5 bits; conditional E-value: 2.4e-138 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelae..............llklleai 63 ++l+V+KFGGtsv++++++ + a ivl++ ++VVvSA+s+vt+ lvel++ + ++++ai lcl|FitnessBrowser__SB2B:6936415 1 MSLVVAKFGGTSVADFNAMSRCAAIVLAN---SATRLVVVSASSGVTNLLVELTQatvtderrlqllkqIAQIQYAI 74 679************************99...8899*******************9999999888655544444444 PP TIGR00656 64 sdei............................sprerdelvsvGEllssallssalrelgvkaealdgkeagilTdd 112 d+ s++ +del+s+GE+ s+ l+s +lr++g k+ ++d ++++++Td+ lcl|FitnessBrowser__SB2B:6936415 75 LDKLerpqdvaaaldallsrisvlseslilnrSKAIMDELLSMGEQCSALLFSAVLRQQGAKSSSFD-VRQVMRTDS 150 44448888888899999999999999999*99***********************************.999****** PP TIGR00656 113 efgnAkikelate....erLlelLeegiivvvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGv 185 +fg+A++++++++ L +lLe++ ivv++GFiGa+ eG++TtLGRGGSD++Aalla+al Ad vei+TDV G+ lcl|FitnessBrowser__SB2B:6936415 151 HFGRAEPQIEDIAalarDFLQPLLERD-IVVTQGFIGADAEGRTTTLGRGGSDYSAALLAEALRADAVEIWTDVAGI 226 **********99999855566666666.************************************************* PP TIGR00656 186 yttDPrvveeakkidkisyeEalelAtlGakvlhpralelaveakvpilvrsskeke.egTlitnkkensslvkaia 261 yttDPr+ ++a++i++is++Ea+e+At+Gakvlhp+++ +av+++++++v ss e+e gT i ++ +n+++ +a+a lcl|FitnessBrowser__SB2B:6936415 227 YTTDPRLAPNARPIAEISFNEAAEMATFGAKVLHPATILPAVRQQIQVFVGSSREPEkGGTWIRHQVDNPPIYRAVA 303 *********************************************************999***************** PP TIGR00656 262 leknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtesetsislvvdeedvdeakkaLkeesgaae...le 335 +++++++l++++ +ml+ rg+lae f +La+++i+vdli+++e +++sl++d++++d++ + L +e +++e + lcl|FitnessBrowser__SB2B:6936415 304 VRRDQTLLNLHSLQMLHARGFLAETFATLARHKISVDLITTSE--VNVSLTLDKTGSDSTGSGLLSEALLQElsqHC 378 ****************************************999..*********************99888877789 PP TIGR00656 336 sleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 ++ ve +la+v+i+g+ + ++pG+ ++f++le++n+++++ ++s ++++vlv e +a ++v++lhe+l+e lcl|FitnessBrowser__SB2B:6936415 379 RVRVEDNLALVAIIGNRIASTPGICRQVFTVLENHNVRMICQGASPHNLCVLVAESEAAQVVKALHENLFE 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.47 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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