Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 7023422 Shewana3_0652 aspartate kinase III (RefSeq)
Query= BRENDA::P08660 (449 letters) >FitnessBrowser__ANA3:7023422 Length = 451 Score = 517 bits (1331), Expect = e-151 Identities = 272/447 (60%), Positives = 339/447 (75%), Gaps = 1/447 (0%) Query: 4 IVVSKFGGTSVADFDAMNRSADIVLSDANVRLVVLSASAGITNLLVALA-EGLEPGERFE 62 +VV+KFGGTSVAD+ AMNR ADIVL + + RLVV+SAS+G+TNLLV L E + R + Sbjct: 3 LVVAKFGGTSVADYGAMNRCADIVLGNPDCRLVVVSASSGVTNLLVELTQESMNDDGRLQ 62 Query: 63 KLDAIRNIQFAILERLRYPNVIREEIERLLENITVLAEAAALATSPALTDELVSHGELMS 122 +L I IQ+AIL++L PN + +++LL + VL+EA A S A DEL+S GE S Sbjct: 63 RLKQIAQIQYAILDKLGRPNDVAAALDKLLSRMAVLSEALASQRSKATMDELLSLGEQCS 122 Query: 123 TLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLPRLNEGLVITQ 182 + LF +LRE+ + FDVR+V+RT+ FGRAEP + +A L+ LLP L+E +++TQ Sbjct: 123 SALFAAVLREKGANSSAFDVRRVLRTDSHFGRAEPQVEQIAILSREHLLPLLSEQVIVTQ 182 Query: 183 GFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVVSAAKRIDE 242 GFIGS+ G+TTTLGRGGSDY+AALLAEAL AS V+IWTDV GIYTTDPR+ A I E Sbjct: 183 GFIGSDEAGQTTTLGRGGSDYSAALLAEALKASAVEIWTDVAGIYTTDPRLAPNAHPIAE 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: 506 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 7023422 Shewana3_0652 (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.2983.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-135 437.4 0.8 3.2e-135 437.2 0.8 1.0 1 lcl|FitnessBrowser__ANA3:7023422 Shewana3_0652 aspartate kinase I Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7023422 Shewana3_0652 aspartate kinase III (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 437.2 0.8 3.2e-135 3.2e-135 1 406 [. 1 449 [. 1 450 [. 0.93 Alignments for each domain: == domain 1 score: 437.2 bits; conditional E-value: 3.2e-135 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelae...................... 55 ++l+V+KFGGtsv++ ++++ a+ivl + + ++VVvSA+s+vt+ lvel++ lcl|FitnessBrowser__ANA3:7023422 1 MSLVVAKFGGTSVADYGAMNRCADIVLGN---PDCRLVVVSASSGVTNLLVELTQesmnddgrlqrlkqiaqiqyai 74 679*************************9...899*******************99999999999887744444443 PP TIGR00656 56 ..llklleaisdei............................sprerdelvsvGEllssallssalrelgvkaeald 102 s++++del+s+GE+ ssal++ +lre+g ++ a+d lcl|FitnessBrowser__ANA3:7023422 75 ldK----------LgrpndvaaaldkllsrmavlsealasqrSKATMDELLSLGEQCSSALFAAVLREKGANSSAFD 141 330..........34444444445555555555555555555*********************************** PP TIGR00656 103 gkeagilTddefgnAkikelate....erLlelLeegiivvvaGFiGateeGeiTtLGRGGSDltAallaaalkAdr 175 ++ +++Td++fg+A+++ ++++ e+Ll+lL e+ ++v++GFiG++e G++TtLGRGGSD++Aalla+alkA+ lcl|FitnessBrowser__ANA3:7023422 142 -VRRVLRTDSHFGRAEPQVEQIAilsrEHLLPLLSEQ-VIVTQGFIGSDEAGQTTTLGRGGSDYSAALLAEALKASA 216 .999***************99999999*********9.889************************************ PP TIGR00656 176 veiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpralelaveakvpilvrsskeke.egTlitnkk 251 vei+TDV G+yttDPr+ ++a++i++is++Ea+e+At+Gakvlhp+++ +av+++++++v sske+e gT i ++ lcl|FitnessBrowser__ANA3:7023422 217 VEIWTDVAGIYTTDPRLAPNAHPIAEISFNEAAEMATFGAKVLHPATILPAVRQQIQVFVGSSKEPEkGGTWIRHQV 293 *******************************************************************999******* PP TIGR00656 252 ensslvkaialeknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtesetsislvvdeedvdeakkaLkee 328 e ++++a+al++++++l++++ +ml+ +g+lae f +La+++i+vdli+++e +++sl++d++++d++ + L +e lcl|FitnessBrowser__ANA3:7023422 294 EDAPVFRAVALRRDQTLLNLHSLQMLHAQGFLAETFATLARHKISVDLITTSE--VNVSLTLDKTGSDSSGQGLLSE 368 **************************************************999..********************99 PP TIGR00656 329 sgaae...lesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhe 402 +++e +++ ve +la+v+i+g+ + + G+ ++f++le++n+++++ ++s ++++vlv e +a ++v++lhe lcl|FitnessBrowser__ANA3:7023422 369 ALLQElsqHCRVRVEDGLALVAIIGNRIATTAGICRRVFEVLEPHNVRMICQGASPHNLCVLVAESEAAQVVKALHE 445 9888877789******************************************************************* PP TIGR00656 403 klee 406 +l+e lcl|FitnessBrowser__ANA3:7023422 446 NLFE 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: 10.91 // [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