Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate Ac3H11_955 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= SwissProt::Q1MIB2
(612 letters)
>FitnessBrowser__acidovorax_3H11:Ac3H11_955
Length = 619
Score = 918 bits (2373), Expect = 0.0
Identities = 463/619 (74%), Positives = 515/619 (83%), Gaps = 11/619 (1%)
Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60
MP+YRS+T+T GRNMAGAR LWRATGMKD DF KPIIAVVNSFTQFVPGHVHLKDLGQLV
Sbjct: 1 MPIYRSKTSTAGRNMAGARSLWRATGMKDDDFSKPIIAVVNSFTQFVPGHVHLKDLGQLV 60
Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSR++IADSVEYMVNAHCADAMVCIS
Sbjct: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRDIIADSVEYMVNAHCADAMVCIS 120
Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKV--------VMHGKTHALDLVDAMVAAA 172
NCDKITPGMLMA++RLNIP +FVSGGPMEAGK VM K LDLVDAMV AA
Sbjct: 121 NCDKITPGMLMAAMRLNIPVIFVSGGPMEAGKTRLANPVTKVMEFKK--LDLVDAMVIAA 178
Query: 173 DDKISDEDVQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLF 232
D SD DV +ERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNG+ +ATH DR++LF
Sbjct: 179 DSNYSDADVAEVERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTVVATHADREQLF 238
Query: 233 VEAGHLIVDLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEG 292
AG IVDLA++YYEQDD + LPR++ K AFENAMTLDIAMGGSTNT+LH+LA A E
Sbjct: 239 KRAGRRIVDLAKQYYEQDDERVLPRSVGFK-AFENAMTLDIAMGGSTNTILHLLAIASEA 297
Query: 293 EIDFTMADIDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTV 352
EI FTMADID LSR VP L KVAP + H+EDVHRAGGIM+ILGELD+ G L+ D PTV
Sbjct: 298 EIPFTMADIDRLSRVVPQLCKVAPNTNKYHIEDVHRAGGIMAILGELDRAGKLHTDVPTV 357
Query: 353 HAETLGDAIDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSV 412
H TL DA+D+WDI RT E VR FY A P G+PTQVAFSQ RW LD DR G IRS
Sbjct: 358 HTATLKDALDQWDIVRTQDEAVRTFYMAGPAGVPTQVAFSQATRWPSLDLDRAEGCIRSY 417
Query: 413 EHPFSKDGGLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKA 472
+H FSK+GGLAVL GN+A+DGC+VK+AGVDESIL F G A V ESQD +V ILA++V+A
Sbjct: 418 DHAFSKEGGLAVLTGNIAVDGCVVKSAGVDESILVFEGTAHVTESQDEAVANILADKVQA 477
Query: 473 GDVVVIRYEGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEA 532
GDVV++RYEGPKGGPGMQEMLYPTSY+KSKGLGKACAL+TDGRFSGGTSGLSIGH SPEA
Sbjct: 478 GDVVIVRYEGPKGGPGMQEMLYPTSYIKSKGLGKACALLTDGRFSGGTSGLSIGHCSPEA 537
Query: 533 ANGGTIGLVREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALK 592
A GG IGLV+ GD I IDIPNRTI++ VS+ ELA RR Q+AKGW P + R R V+ ALK
Sbjct: 538 AAGGAIGLVQNGDRIRIDIPNRTINVLVSDEELAKRREAQNAKGWKPAQPRPRKVSAALK 597
Query: 593 AYAAFATSADRGAVRDLNV 611
AYA SAD+GAVRDL++
Sbjct: 598 AYAKLVMSADKGAVRDLSL 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: 1164
Number of extensions: 26
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 Ac3H11_955 (Dihydroxy-acid dehydratase (EC 4.2.1.9))
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.16099.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
2.4e-257 840.7 3.5 2.8e-257 840.5 3.5 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 Dihydroxy-acid dehydratase (EC 4
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 Dihydroxy-acid dehydratase (EC 4.2.1.9)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 840.5 3.5 2.8e-257 2.8e-257 2 542 .. 18 613 .. 17 614 .. 0.97
Alignments for each domain:
== domain 1 score: 840.5 bits; conditional E-value: 2.8e-257
TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavs 64
ar+l++atG+kd+d++kPiiavvns+t++vPghvhlkdl++lv++eieaaGgvakefntiav+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 18 ARSLWRATGMKDDDFSKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTIAVD 80
69************************************************************* PP
TIGR00110 65 DGiamgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivv 127
DGiamgh+Gm+ysLpsr+iiaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniP+i+v
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 81 DGIAMGHDGMLYSLPSRDIIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPVIFV 143
*************************************************************** PP
TIGR00110 128 sGGpmeagktkl......sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlft 184
sGGpmeagkt+l +++++d+++a++ +a+++ s++++ e+ersacPt+gsCsG+ft
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 144 SGGPMEAGKTRLanpvtkVMEFKKLDLVDAMVIAADSNYSDADVAEVERSACPTCGSCSGMFT 206
***********955554444567889************************************* PP
TIGR00110 185 ansmacltealGlslPgsstllatsaekkelakksgkrivelvkknik.......Prdiltke 240
ansm+cltealGlslPg++t+ at+a++++l+k++g+riv+l k++++ Pr++ +
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 207 ANSMNCLTEALGLSLPGNGTVVATHADREQLFKRAGRRIVDLAKQYYEqddervlPRSV-GFK 268
************************************************99999999986.589 PP
TIGR00110 241 afenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv.iedl 302
afena+tld+a+GGstnt+Lhllaia+ea++ +++ d+drlsr vP+l+k++P+++k+ ied+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 269 AFENAMTLDIAMGGSTNTILHLLAIASEAEIPFTMADIDRLSRVVPQLCKVAPNTNKYhIEDV 331
*********************************************************99**** PP
TIGR00110 303 hraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr..................... 344
hraGG++a+l+eld++g+lh+d+ tv tl++ l++ ++ r
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 332 HRAGGIMAILGELDRAGKLHTDVPTVHTATLKDALDQWDIVRtqdeavrtfymagpagvptqv 394
****************************************999******************** PP
TIGR00110 345 ..............vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpa 393
+ +irs d++++kegglavL+Gn+a +G+vvk agv+e+il+feG+a
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 395 afsqatrwpsldldRAEGCIRSYDHAFSKEGGLAVLTGNIAVDGCVVKSAGVDESILVFEGTA 457
**********88655555********************************************* PP
TIGR00110 394 kvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGr 456
+v es++ea++ il+ kv++Gdvv++ryeGPkGgPGm+emL+Pts++++ GLgk++aL+tDGr
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 458 HVTESQDEAVANILADKVQAGDVVIVRYEGPKGGPGMQEMLYPTSYIKSKGLGKACALLTDGR 520
*************************************************************** PP
TIGR00110 457 fsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea. 518
fsGgt+GlsiGh sPeaa+gGai+lv++GD+i+iDi+nr++++ vs+eela+rr+++++k++
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 521 FSGGTSGLSIGHCSPEAAAGGAIGLVQNGDRIRIDIPNRTINVLVSDEELAKRREAQNAKGWk 583
*************************************************************99 PP
TIGR00110 519 ......revkgaLakyaklvssadkGavld 542
r+v+ aL++yaklv sadkGav+d
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 584 paqprpRKVSAALKAYAKLVMSADKGAVRD 613
99**99**********************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 12.70
//
[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