Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate Pf1N1B4_2303 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= SwissProt::Q1MIB2
(612 letters)
>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303
Length = 613
Score = 940 bits (2430), Expect = 0.0
Identities = 464/608 (76%), Positives = 522/608 (85%), Gaps = 2/608 (0%)
Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60
MP YRS+T+THGRNMAGAR LWRATGMKD DF KPIIA+ NSFTQFVPGHVHLKDLGQLV
Sbjct: 1 MPDYRSKTSTHGRNMAGARALWRATGMKDDDFKKPIIAIANSFTQFVPGHVHLKDLGQLV 60
Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
AREIE AGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRE+IADSVEYMVNAHCADA+VCIS
Sbjct: 61 AREIERAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCIS 120
Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180
NCDKITPGMLMASLRLNIP +FVSGGPMEAGK + +H LDLVDAMV AAD SDE
Sbjct: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKL--ASHGLDLVDAMVIAADSSASDEK 178
Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240
V ERSACPTCGSCSGMFTANSMNCL EALGL+LPGNGSTLATH DR++LF++AG IV
Sbjct: 179 VAEYERSACPTCGSCSGMFTANSMNCLVEALGLALPGNGSTLATHSDREQLFLQAGRTIV 238
Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300
+L +RYY ++D LPR IA+ +AFENAMTLDIAMGGSTNT+LH+LAAA E EIDF + D
Sbjct: 239 ELCKRYYGENDESVLPRNIANFKAFENAMTLDIAMGGSTNTILHLLAAAQEAEIDFDLRD 298
Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360
ID LSR VP L KVAP HMEDVHRAGGI SILG L +GGLL+ D PTVH++++ +
Sbjct: 299 IDRLSRHVPQLCKVAPNIQKYHMEDVHRAGGIFSILGSLARGGLLHTDLPTVHSKSMAEG 358
Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420
I +WDIT+T E V F++A P GIPTQ AFSQ RW+ LD DRENG IRSVEH +SK+G
Sbjct: 359 IAKWDITQTTDEAVHHFFKAGPAGIPTQTAFSQSTRWETLDDDRENGCIRSVEHAYSKEG 418
Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480
GLAVL GN+A+DGC+VKTAGVDESI F G A++FESQD++V+ ILA+EVKAGD+V+IRY
Sbjct: 419 GLAVLYGNIALDGCVVKTAGVDESIHVFEGNAKIFESQDSAVRGILADEVKAGDIVIIRY 478
Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540
EGPKGGPGMQEMLYPTSYLKSKGLGKACAL+TDGRFSGGTSGLSIGHASPEAA GG IGL
Sbjct: 479 EGPKGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAAGGAIGL 538
Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFATS 600
V++GD + IDIPNR+I+L +S+ E+AARRAEQD KGW P EVR R VTTALKAYA ATS
Sbjct: 539 VQDGDKVLIDIPNRSINLLISDEEMAARRAEQDKKGWKPVEVRPRKVTTALKAYALLATS 598
Query: 601 ADRGAVRD 608
AD+GAVR+
Sbjct: 599 ADKGAVRN 606
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: 1215
Number of extensions: 33
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: 612
Length of database: 613
Length adjustment: 37
Effective length of query: 575
Effective length of database: 576
Effective search space: 331200
Effective search space used: 331200
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 Pf1N1B4_2303 (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.23265.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
2.5e-255 834.0 1.8 3e-255 833.8 1.8 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 Dihydroxy-acid dehydratase (EC 4
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 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 ! 833.8 1.8 3e-255 3e-255 2 542 .. 18 606 .. 17 607 .. 0.98
Alignments for each domain:
== domain 1 score: 833.8 bits; conditional E-value: 3e-255
TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsD 65
aral++atG+kd+d++kPiia++ns+t++vPghvhlkdl++lv++eie+aGgvakefntiav+D
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 18 ARALWRATGMKDDDFKKPIIAIANSFTQFVPGHVHLKDLGQLVAREIERAGGVAKEFNTIAVDD 81
79************************************************************** PP
TIGR00110 66 GiamgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsG 129
Giamgh+Gm+ysLpsreiiaDsve++v+ah++Da+v+is+CDki+PGmlma+lrlniP+i+vsG
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 82 GIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCISNCDKITPGMLMASLRLNIPVIFVSG 145
**************************************************************** PP
TIGR00110 130 GpmeagktklsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmaclte 193
Gpmeagktkl + +d+++a++ +a++ s+e++ e+ersacPt+gsCsG+ftansm+cl e
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 146 GPMEAGKTKL--ASHGLDLVDAMVIAADSSASDEKVAEYERSACPTCGSCSGMFTANSMNCLVE 207
*********8..557899********************************************** PP
TIGR00110 194 alGlslPgsstllatsaekkelakksgkrivelvkknik.......Prdiltkeafenaitldl 250
alGl+lPg++++lat++++++l+ ++g++ivel+k+++ Pr+i++ +afena+tld+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 208 ALGLALPGNGSTLATHSDREQLFLQAGRTIVELCKRYYGendesvlPRNIANFKAFENAMTLDI 271
**************************************99999********************* PP
TIGR00110 251 alGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlk 313
a+GGstnt+Lhlla+a+ea+++++l d+drlsr+vP+l+k++P+ +k+ +ed+hraGG+ ++l+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 272 AMGGSTNTILHLLAAAQEAEIDFDLRDIDRLSRHVPQLCKVAPNIQKYhMEDVHRAGGIFSILG 335
*********************************************9999*************** PP
TIGR00110 314 eldkegllhkdaltvtGktlaetlekvkvlr................................. 344
+l + gllh+d tv k++ae ++k ++++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 336 SLARGGLLHTDLPTVHSKSMAEGIAKWDITQttdeavhhffkagpagiptqtafsqstrwetld 399
*****************************999******************************77 PP
TIGR00110 345 ..vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeai 406
++ +irs++++++kegglavL+Gn+a +G+vvk+agv+e+i +feG+ak+fes++ a+ +i
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 400 ddRENGCIRSVEHAYSKEGGLAVLYGNIALDGCVVKTAGVDESIHVFEGNAKIFESQDSAVRGI 463
555555********************************************************** PP
TIGR00110 407 lggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvs 470
l+ +vk+Gd+v+iryeGPkGgPGm+emL+Pts+l++ GLgk++aL+tDGrfsGgt+GlsiGh s
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 464 LADEVKAGDIVIIRYEGPKGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHAS 527
**************************************************************** PP
TIGR00110 471 PeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea.......revkgaLak 527
Peaa+gGai+lv+dGDk+ iDi+nr ++l +s+ee+a+rra+++kk++ r+v aL++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 528 PEAAAGGAIGLVQDGDKVLIDIPNRSINLLISDEEMAARRAEQDKKGWkpvevrpRKVTTALKA 591
************************************************9*****999******* PP
TIGR00110 528 yaklvssadkGavld 542
ya l++sadkGav++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 592 YALLATSADKGAVRN 606
*************87 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (543 nodes)
Target sequences: 1 (613 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: 11.54
//
[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