Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate H281DRAFT_05312 H281DRAFT_05312 dihydroxyacid dehydratase
Query= SwissProt::Q1MIB2
(612 letters)
>FitnessBrowser__Burk376:H281DRAFT_05312
Length = 619
Score = 922 bits (2384), Expect = 0.0
Identities = 464/617 (75%), Positives = 516/617 (83%), Gaps = 7/617 (1%)
Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60
MP YRS+T+T GRNMAGAR LWRATGMKD DF KPIIAVVNSFTQFVPGHVHLKDLGQLV
Sbjct: 1 MPAYRSKTSTAGRNMAGARSLWRATGMKDEDFSKPIIAVVNSFTQFVPGHVHLKDLGQLV 60
Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSR++IADSVEYMVNAHCADAMVCIS
Sbjct: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRDIIADSVEYMVNAHCADAMVCIS 120
Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKV-VMHGKTHA-----LDLVDAMVAAADD 174
NCDKITPGMLMA++RLNIP +FVSGGPMEAGK + + KT LDLVDAMV AAD
Sbjct: 121 NCDKITPGMLMAAMRLNIPVIFVSGGPMEAGKTRLANPKTGTIEFKKLDLVDAMVIAADK 180
Query: 175 KISDEDVQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVE 234
SD DV +ERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNG+ +ATH DR++LF
Sbjct: 181 AYSDADVAEVERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTVVATHADREQLFKR 240
Query: 235 AGHLIVDLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEI 294
AG IV+LAR+YYEQ++ LPR + K AFENAMTLDIAMGGSTNT+LH+LA A E EI
Sbjct: 241 AGRRIVELARQYYEQEEASVLPRAVGFK-AFENAMTLDIAMGGSTNTILHLLAIAREAEI 299
Query: 295 DFTMADIDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHA 354
DFTM DID LSR VP L KVAP + H+EDVHRAGGIM+ILGELD+ G L D PTVHA
Sbjct: 300 DFTMTDIDRLSRIVPQLCKVAPNTNKYHIEDVHRAGGIMAILGELDRAGKLQTDVPTVHA 359
Query: 355 ETLGDAIDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEH 414
TL DA+D+WDI RT E VR FY A P G+PTQVAFSQ RW LD DR G IRS EH
Sbjct: 360 PTLKDALDQWDIVRTGDEAVRTFYMAGPAGVPTQVAFSQNTRWPSLDLDRAEGCIRSYEH 419
Query: 415 PFSKDGGLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGD 474
FSK+GGLAVL GN+A+DGC+VKTAGVDESIL F G A V ESQD +V+ ILA +VKAGD
Sbjct: 420 AFSKEGGLAVLTGNIALDGCVVKTAGVDESILVFEGTAHVTESQDEAVENILAGKVKAGD 479
Query: 475 VVVIRYEGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAAN 534
VV++RYEGPKGGPGMQEMLYPTSY+KS+GLGKACAL+TDGRFSGGTSGLSIGH SPEAA
Sbjct: 480 VVIVRYEGPKGGPGMQEMLYPTSYIKSQGLGKACALLTDGRFSGGTSGLSIGHCSPEAAA 539
Query: 535 GGTIGLVREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAY 594
GG IGLVR+GD I IDIPNRTI++ +S+ ELA+RR EQ+AKGW P + R R V+ ALKAY
Sbjct: 540 GGAIGLVRDGDKIRIDIPNRTINVLLSDAELASRRDEQNAKGWKPAKPRPRKVSAALKAY 599
Query: 595 AAFATSADRGAVRDLNV 611
A SAD+GAVRDL++
Sbjct: 600 AKLVMSADKGAVRDLSL 616
Lambda K H
0.318 0.134 0.391
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: 1200
Number of extensions: 33
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: 612
Length of database: 619
Length adjustment: 37
Effective length of query: 575
Effective length of database: 582
Effective search space: 334650
Effective search space used: 334650
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 H281DRAFT_05312 H281DRAFT_05312 (dihydroxyacid 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.16434.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.1e-257 841.9 2.8 1.3e-257 841.6 2.8 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_05312 H281DRAFT_05312 dihydroxyacid de
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05312 H281DRAFT_05312 dihydroxyacid dehydratase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 841.6 2.8 1.3e-257 1.3e-257 2 542 .. 18 613 .. 17 614 .. 0.98
Alignments for each domain:
== domain 1 score: 841.6 bits; conditional E-value: 1.3e-257
TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGi 67
ar+l++atG+kded++kPiiavvns+t++vPghvhlkdl++lv++eieaaGgvakefntiav+DGi
lcl|FitnessBrowser__Burk376:H281DRAFT_05312 18 ARSLWRATGMKDEDFSKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTIAVDDGI 83
69**************************************************************** PP
TIGR00110 68 amgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpme 133
amgh+Gm+ysLpsr+iiaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniP+i+vsGGpme
lcl|FitnessBrowser__Burk376:H281DRAFT_05312 84 AMGHDGMLYSLPSRDIIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPVIFVSGGPME 149
****************************************************************** PP
TIGR00110 134 agktkl......sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmaclte 193
agkt+l + +++++d+++a++ +a++ s++++ e+ersacPt+gsCsG+ftansm+clte
lcl|FitnessBrowser__Burk376:H281DRAFT_05312 150 AGKTRLanpktgTIEFKKLDLVDAMVIAADKAYSDADVAEVERSACPTCGSCSGMFTANSMNCLTE 215
****99777765568899************************************************ PP
TIGR00110 194 alGlslPgsstllatsaekkelakksgkrivelvkknik.......Prdiltkeafenaitldlal 252
alGlslPg++t+ at+a++++l+k++g+rivel +++++ Pr + +afena+tld+a+
lcl|FitnessBrowser__Burk376:H281DRAFT_05312 216 ALGLSLPGNGTVVATHADREQLFKRAGRRIVELARQYYEqeeasvlPRAV-GFKAFENAMTLDIAM 280
***************************************99999988875.689************ PP
TIGR00110 253 GGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldk 317
GGstnt+Lhllaia+ea++++++ d+drlsr vP+l+k++P+++k+ ied+hraGG++a+l+eld+
lcl|FitnessBrowser__Burk376:H281DRAFT_05312 281 GGSTNTILHLLAIAREAEIDFTMTDIDRLSRIVPQLCKVAPNTNKYhIEDVHRAGGIMAILGELDR 346
*********************************************99******************* PP
TIGR00110 318 egllhkdaltvtGktlaetlekvkvlr...................................vdqd 348
+g+l++d+ tv tl++ l++ ++ r +
lcl|FitnessBrowser__Burk376:H281DRAFT_05312 347 AGKLQTDVPTVHAPTLKDALDQWDIVRtgdeavrtfymagpagvptqvafsqntrwpsldldRAEG 412
**************************9*******************************88655555 PP
TIGR00110 349 virsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
+irs +++++kegglavL+Gn+a +G+vvk+agv+e+il+feG+a+v es++ea+e il+gkvk+G
lcl|FitnessBrowser__Burk376:H281DRAFT_05312 413 CIRSYEHAFSKEGGLAVLTGNIALDGCVVKTAGVDESILVFEGTAHVTESQDEAVENILAGKVKAG 478
****************************************************************** PP
TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaia 480
dvv++ryeGPkGgPGm+emL+Pts++++ GLgk++aL+tDGrfsGgt+GlsiGh sPeaa+gGai+
lcl|FitnessBrowser__Burk376:H281DRAFT_05312 479 DVVIVRYEGPKGGPGMQEMLYPTSYIKSQGLGKACALLTDGRFSGGTSGLSIGHCSPEAAAGGAIG 544
****************************************************************** PP
TIGR00110 481 lvedGDkikiDienrkldlevseeelaerrakakkkea.......revkgaLakyaklvssadkGa 539
lv+dGDki+iDi+nr++++ +s++ela+rr+++++k++ r+v+ aL++yaklv sadkGa
lcl|FitnessBrowser__Burk376:H281DRAFT_05312 545 LVRDGDKIRIDIPNRTINVLLSDAELASRRDEQNAKGWkpakprpRKVSAALKAYAKLVMSADKGA 610
*************************************9999**999******************** PP
TIGR00110 540 vld 542
v+d
lcl|FitnessBrowser__Burk376:H281DRAFT_05312 611 VRD 613
*97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (543 nodes)
Target sequences: 1 (619 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 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 8.03
//
[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