Align dihydroxyacid dehydratase (characterized)
to candidate BPHYT_RS10100 BPHYT_RS10100 dihydroxy-acid dehydratase
Query= CharProtDB::CH_024768 (616 letters) >FitnessBrowser__BFirm:BPHYT_RS10100 Length = 620 Score = 919 bits (2374), Expect = 0.0 Identities = 463/617 (75%), Positives = 524/617 (84%), Gaps = 3/617 (0%) Query: 1 MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60 MP YRS T+THGRNMAGARALWRATGM D DFGKPIIAVVNSFTQFVPGHVHLRDLG LV Sbjct: 1 MPDYRSKTSTHGRNMAGARALWRATGMKDGDFGKPIIAVVNSFTQFVPGHVHLRDLGALV 60 Query: 61 AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 A++IEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS Sbjct: 61 AKEIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQ---IIKLDLVDAMIQGADPKVS 177 NCDKITPGMLMA++RLNIPV+FVSGGPMEAGK K I K+DL+DAMI+ D +VS Sbjct: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVKSPTDGQVIAKIDLIDAMIKAGDSRVS 180 Query: 178 DSQSDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGK 237 D++ ++ERSACPTCGSCSGMFTANSMNCLTEA+GL+ PGNG+++ATHA RK LF AG+ Sbjct: 181 DAEVAEIERSACPTCGSCSGMFTANSMNCLTEAIGLALPGNGTIVATHAWRKGLFEQAGR 240 Query: 238 RIVELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFT 297 +V+L +RYY+++D S LPR+IASK AFENAM LD+AMGGSTNTVLHLLAAAQE +DFT Sbjct: 241 LVVDLCRRYYQEDDASVLPRSIASKQAFENAMALDVAMGGSTNTVLHLLAAAQEGGVDFT 300 Query: 298 MSDIDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTL 357 MSDID++SRKVP LCKVAP+T K+H+EDVHRAGG+ GILGEL RA LL+ NV TL Sbjct: 301 MSDIDRISRKVPCLCKVAPATDKFHIEDVHRAGGIPGILGELARAELLDLSCGNVHSGTL 360 Query: 358 PQTLEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYS 417 + ++DV + + FRA P GI TT AFSQ+ + LD DR GCIRS + AYS Sbjct: 361 GNAIAKWDVAGGAGEEAQKFFRAAPGGIPTTVAFSQEATFAALDTDRNTGCIRSKQSAYS 420 Query: 418 KDGGLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVV 477 KDGGLAVLYGN AE GCIVKTAGVD+S F+G A+V+ESQDDAVEAILG KVVAGDVVV Sbjct: 421 KDGGLAVLYGNLAEKGCIVKTAGVDESQWIFSGRARVFESQDDAVEAILGDKVVAGDVVV 480 Query: 478 IRYEGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGS 537 IRYEGPKGGPGMQEMLYPTS+LKS GLGK+CAL TDGRFSGG+SGL IGH SPEAA GG+ Sbjct: 481 IRYEGPKGGPGMQEMLYPTSYLKSKGLGKSCALFTDGRFSGGSSGLVIGHASPEAAEGGT 540 Query: 538 IGLIEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSFALRAYA 597 IGL+E+GD+I IDIPNR + L VSDAELA RREA +ARGDKAW P NRER VS AL+AYA Sbjct: 541 IGLVEEGDVIEIDIPNRKMHLVVSDAELARRREAMEARGDKAWQPANRERVVSQALQAYA 600 Query: 598 SLATSADKGAVRDKSKL 614 +LATSAD+GAVRD S+L Sbjct: 601 ALATSADRGAVRDLSQL 617 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: 1280 Number of extensions: 52 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: 620 Length adjustment: 37 Effective length of query: 579 Effective length of database: 583 Effective search space: 337557 Effective search space used: 337557 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 BPHYT_RS10100 BPHYT_RS10100 (dihydroxy-acid dehydratase)
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.12968.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.6e-254 829.2 5.3 8.8e-254 828.9 5.3 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS10100 BPHYT_RS10100 dihydroxy-acid deh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS10100 BPHYT_RS10100 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 828.9 5.3 8.8e-254 8.8e-254 2 542 .. 18 613 .. 17 614 .. 0.98 Alignments for each domain: == domain 1 score: 828.9 bits; conditional E-value: 8.8e-254 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgh 71 aral++atG+kd d++kPiiavvns+t++vPghvhl+dl+ lv++eieaaGgvakefntiav+DGiamgh lcl|FitnessBrowser__BFirm:BPHYT_RS10100 18 ARALWRATGMKDGDFGKPIIAVVNSFTQFVPGHVHLRDLGALVAKEIEAAGGVAKEFNTIAVDDGIAMGH 87 79******************************************************************** PP TIGR00110 72 eGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl.. 139 +Gm+ysLpsre+iaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniP+++vsGGpmeagk+k lcl|FitnessBrowser__BFirm:BPHYT_RS10100 88 GGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVKSpt 157 ******************************************************************9888 PP TIGR00110 140 .sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 ++ i ++d+++a++++ ++++s++e+ eiersacPt+gsCsG+ftansm+cltea+Gl+lPg++t+ at lcl|FitnessBrowser__BFirm:BPHYT_RS10100 158 dGQVIAKIDLIDAMIKAGDSRVSDAEVAEIERSACPTCGSCSGMFTANSMNCLTEAIGLALPGNGTIVAT 227 78999***************************************************************** PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagv 271 +a +k l++++g+ +v+l++++++ Pr+i++k+afena++ld+a+GGstntvLhlla+a+e gv lcl|FitnessBrowser__BFirm:BPHYT_RS10100 228 HAWRKGLFEQAGRLVVDLCRRYYQeddasvlPRSIASKQAFENAMALDVAMGGSTNTVLHLLAAAQEGGV 297 ********************************************************************** PP TIGR00110 272 klslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekv 340 +++++d+dr+srkvP+l+k++P+++k+ ied+hraGG++++l+el +++ll+ + +v tl++ ++k lcl|FitnessBrowser__BFirm:BPHYT_RS10100 298 DFTMSDIDRISRKVPCLCKVAPATDKFhIEDVHRAGGIPGILGELARAELLDLSCGNVHSGTLGNAIAKW 367 ***************************9****************************************** PP TIGR00110 341 kvlr...................................vdqd..virsldnpvkkegglavLkGnlaee 373 +v + +irs++++++k+gglavL+Gnlae+ lcl|FitnessBrowser__BFirm:BPHYT_RS10100 368 DVAGgageeaqkffraapggipttvafsqeatfaaldtdR--NtgCIRSKQSAYSKDGGLAVLYGNLAEK 435 **999******************************77444..256************************* PP TIGR00110 374 GavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvgl 443 G++vk+agv+e+ + f G+a+vfes+++a+eailg kv +GdvvviryeGPkGgPGm+emL+Pts+l++ lcl|FitnessBrowser__BFirm:BPHYT_RS10100 436 GCIVKTAGVDESQWIFSGRARVFESQDDAVEAILGDKVVAGDVVVIRYEGPKGGPGMQEMLYPTSYLKSK 505 ********************************************************************** PP TIGR00110 444 GLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerraka 513 GLgk++aL tDGrfsGg++Gl+iGh sPeaaegG+i+lve+GD i+iDi+nrk++l vs++ela+rr+++ lcl|FitnessBrowser__BFirm:BPHYT_RS10100 506 GLGKSCALFTDGRFSGGSSGLVIGHASPEAAEGGTIGLVEEGDVIEIDIPNRKMHLVVSDAELARRREAM 575 ********************************************************************** PP TIGR00110 514 kkkea.........revkgaLakyaklvssadkGavld 542 +++++ r v+ aL++ya l++sad+Gav+d lcl|FitnessBrowser__BFirm:BPHYT_RS10100 576 EARGDkawqpanreRVVSQALQAYAALATSADRGAVRD 613 **999999****9999********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (620 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 7.48 // [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