Align dihydroxyacid dehydratase (characterized)
to candidate 6939185 Sama_3279 dihydroxy-acid dehydratase (RefSeq)
Query= CharProtDB::CH_024768 (616 letters) >FitnessBrowser__SB2B:6939185 Length = 618 Score = 971 bits (2510), Expect = 0.0 Identities = 484/618 (78%), Positives = 543/618 (87%), Gaps = 2/618 (0%) Query: 1 MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60 M K RSAT+T GRNMAGARALWRATG+ D DFGKPIIA+ NSFTQFVPGHVHL+D+G LV Sbjct: 1 MAKLRSATSTEGRNMAGARALWRATGVKDTDFGKPIIAIANSFTQFVPGHVHLKDMGSLV 60 Query: 61 AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 A IE AGG+AKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADA+VCIS Sbjct: 61 ASAIEEAGGIAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADALVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDSQ 180 NCDKITPGMLMA+LRLNIPV+FVSGGPMEAGKTKLSD++IKLDLVDAM+ AD ++SD+ Sbjct: 121 NCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTKLSDKLIKLDLVDAMVAAADDRISDAD 180 Query: 181 SDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRIV 240 S+++ERSACPTCGSCSGMFTANSMNCLTEALGLS PGNGS+LATHADR++LFL AG+R++ Sbjct: 181 SEKIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSMLATHADRRELFLEAGRRVM 240 Query: 241 ELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD 300 +L KRYY +D S LPR+IAS AFENAM LD+AMGGS+NTVLHLLAAAQEAE+DFTM D Sbjct: 241 KLAKRYYGDDDASVLPRSIASFKAFENAMALDVAMGGSSNTVLHLLAAAQEAEVDFTMDD 300 Query: 301 IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGL--TLP 358 ID++SRKVP LCKVAPST KYHMEDVHRAGGV+ ILGELDRAGLL+ DV +V TL Sbjct: 301 IDRISRKVPHLCKVAPSTPKYHMEDVHRAGGVMAILGELDRAGLLHTDVNHVASEDGTLK 360 Query: 359 QTLEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYSK 418 LE++DV+LT+D+ V FRAGPAGI TT+AFSQ CRWDTLDDDR GCIRS E A+S+ Sbjct: 361 SVLERFDVVLTKDEKVHEFFRAGPAGIPTTRAFSQSCRWDTLDDDRREGCIRSREFAFSQ 420 Query: 419 DGGLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVVI 478 +GGLAVL GN AENGCIVKTAGVD+S LKF+G A+VYESQ+DAV ILGG+VVAGDVVVI Sbjct: 421 EGGLAVLSGNLAENGCIVKTAGVDESNLKFSGVARVYESQEDAVAGILGGEVVAGDVVVI 480 Query: 479 RYEGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSI 538 R+EGPKGGPGMQEMLYPTS+LKS GLG CALITDGRFSGGTSGLSIGHVSPEAASGG+I Sbjct: 481 RFEGPKGGPGMQEMLYPTSYLKSRGLGTQCALITDGRFSGGTSGLSIGHVSPEAASGGTI 540 Query: 539 GLIEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSFALRAYAS 598 GLIE+GD I IDIP R I+L VSDAEL +RR A +A+G AW P +R R VS AL+AYA Sbjct: 541 GLIENGDRIDIDIPGRSIKLLVSDAELESRRAAMNAKGPLAWKPLSRVRPVSMALKAYAM 600 Query: 599 LATSADKGAVRDKSKLGG 616 LATSADKGAVRD SKL G Sbjct: 601 LATSADKGAVRDVSKLEG 618 Lambda K H 0.317 0.134 0.386 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: 1274 Number of extensions: 51 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: 616 Length of database: 618 Length adjustment: 37 Effective length of query: 579 Effective length of database: 581 Effective search space: 336399 Effective search space used: 336399 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
Align candidate 6939185 Sama_3279 (dihydroxy-acid dehydratase (RefSeq))
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))
# 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/TIGR00110.hmm # target sequence database: /tmp/gapView.30216.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00110 [M=543] Accession: TIGR00110 Description: ilvD: dihydroxy-acid dehydratase 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-257 840.5 2.2 3.3e-257 840.3 2.2 1.0 1 lcl|FitnessBrowser__SB2B:6939185 Sama_3279 dihydroxy-acid dehydra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6939185 Sama_3279 dihydroxy-acid dehydratase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 840.3 2.2 3.3e-257 3.3e-257 2 542 .. 18 612 .. 17 613 .. 0.98 Alignments for each domain: == domain 1 score: 840.3 bits; conditional E-value: 3.3e-257 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmkysL 78 aral++atG+kd d++kPiia++ns+t++vPghvhlkd+++lv+ +ie+aGg+akefntiav+DGiamgh+Gm+ysL lcl|FitnessBrowser__SB2B:6939185 18 ARALWRATGVKDTDFGKPIIAIANSFTQFVPGHVHLKDMGSLVASAIEEAGGIAKEFNTIAVDDGIAMGHGGMLYSL 94 79*************************************************************************** PP TIGR00110 79 psreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfeavgey 155 psre+iaDsve++v+ah++Dalv+is+CDki+PGmlmaalrlniP+++vsGGpmeagktkls+k++++d+++a++++ lcl|FitnessBrowser__SB2B:6939185 95 PSRELIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTKLSDKLIKLDLVDAMVAA 171 ***************************************************************************** PP TIGR00110 156 aagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivelvkknik 232 a++++s++++e+iersacPt+gsCsG+ftansm+cltealGlslPg++++lat+a+++el+ ++g+r+++l k+++ lcl|FitnessBrowser__SB2B:6939185 172 ADDRISDADSEKIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSMLATHADRRELFLEAGRRVMKLAKRYYG 248 ****************************************************************************9 PP TIGR00110 233 .......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv.ied 301 Pr+i++ +afena++ld+a+GGs+ntvLhlla+a+ea+v++++dd+dr+srkvP+l+k++Ps+ k+ +ed lcl|FitnessBrowser__SB2B:6939185 249 dddasvlPRSIASFKAFENAMALDVAMGGSSNTVLHLLAAAQEAEVDFTMDDIDRISRKVPHLCKVAPSTPKYhMED 325 9999******************************************************************9999*** PP TIGR00110 302 lhraGGvsavlkeldkegllhkdaltvtGk..tlaetlekvkvlr...............................v 345 +hraGGv+a+l+eld++gllh+d+ v+ + tl+ +le+ +v + lcl|FitnessBrowser__SB2B:6939185 326 VHRAGGVMAILGELDRAGLLHTDVNHVASEdgTLKSVLERFDVVLtkdekvheffragpagipttrafsqscrwdtL 402 *************************99875559*********99999****************************94 PP TIGR00110 346 dqd....virsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvv 418 d+d +irs + ++++egglavL Gnlae+G++vk+agv+e+ lkf G a+v+es+e+a+++ilgg+v +Gdvvv lcl|FitnessBrowser__SB2B:6939185 403 DDDrregCIRSREFAFSQEGGLAVLSGNLAENGCIVKTAGVDESNLKFSGVARVYESQEDAVAGILGGEVVAGDVVV 479 4444566********************************************************************** PP TIGR00110 419 iryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienr 495 ir+eGPkGgPGm+emL+Pts+l++ GLg ++aLitDGrfsGgt+GlsiGhvsPeaa+gG+i+l+e+GD+i iDi+ r lcl|FitnessBrowser__SB2B:6939185 480 IRFEGPKGGPGMQEMLYPTSYLKSRGLGTQCALITDGRFSGGTSGLSIGHVSPEAASGGTIGLIENGDRIDIDIPGR 556 ***************************************************************************** PP TIGR00110 496 kldlevseeelaerrakakkkea.........revkgaLakyaklvssadkGavld 542 ++l vs++el++rra++++k++ r v+ aL++ya l++sadkGav+d lcl|FitnessBrowser__SB2B:6939185 557 SIKLLVSDAELESRRAAMNAKGPlawkplsrvRPVSMALKAYAMLATSADKGAVRD 612 ******************************9999********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (618 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 0.02s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 7.09 // [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