Psyllid ID: psy3811


Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------9
MYSYSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMNFMDVPSDKLLEPPVSMMPGQHENNRK
ccccccHHHHHHHHHHHHHHHHHHHHcccEEEEccccccccccccccEEEEccccccccEEccccccccccccccccccccHHHHHccc
cccccHHHHHHHHHHHHHcHHHHHHccccEEEEccccccccccccccccccccccccccEEEEHccccHHHcccccEEEEccccccccc
mysysgadiSIVVRDALMQPVRLVQSAthfvrtsgpspvdpsktvddlltpcspstpgavemnfmdvpsdklleppvsmmpgqhennrk
mysysgadISIVVRDALMQPVRLVQSAThfvrtsgpspvdpsktvDDLLTPCSPSTPGAVEMNFMDVPSDKlleppvsmmpgqhennrk
MYSYSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMNFMDVPSDKLLEPPVSMMPGQHENNRK
******ADISIVVRDALMQPVRLVQSATHFV**********************************************************
**SYSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMNFMDVPSDKLLEPPVSMMPGQHENN**
MYSYSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMNFMDVPSDKLLEPPVSMM*********
MYSYSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMNFMDVPSDKLLEPPVSMMPG*******
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MYSYSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMNFMDVPSDKLLEPPVSMMPGQHENNRK
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query89 2.2.26 [Sep-21-2011]
Q5R658444 Vacuolar protein sorting- yes N/A 0.853 0.171 0.763 3e-27
O75351444 Vacuolar protein sorting- yes N/A 0.853 0.171 0.763 3e-27
Q793F9437 Vacuolar protein sorting- yes N/A 0.853 0.173 0.723 4e-27
Q8VEJ9437 Vacuolar protein sorting- yes N/A 0.853 0.173 0.723 4e-27
P46467444 Vacuolar protein sorting- no N/A 0.853 0.171 0.75 5e-27
Q0VD48444 Vacuolar protein sorting- yes N/A 0.853 0.171 0.75 6e-27
Q9UN37437 Vacuolar protein sorting- no N/A 0.853 0.173 0.723 7e-27
Q54PT2444 Vacuolar protein sorting- yes N/A 0.842 0.168 0.526 2e-15
P52917437 Vacuolar protein sorting- yes N/A 0.752 0.153 0.493 9e-14
Q09803432 Suppressor protein of bem yes N/A 0.786 0.162 0.447 2e-11
>sp|Q5R658|VPS4B_PONAB Vacuolar protein sorting-associated protein 4B OS=Pongo abelii GN=VPS4B PE=2 SV=1 Back     alignment and function desciption
 Score =  120 bits (300), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 58/76 (76%), Positives = 63/76 (82%)

Query: 4   YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMN 63
           YSGADISI+VRDALMQPVR VQSATHF +  GPS  DP+  VDDLLTPCSP  PGA+EM 
Sbjct: 336 YSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNHLVDDLLTPCSPGDPGAIEMT 395

Query: 64  FMDVPSDKLLEPPVSM 79
           +MDVP DKLLEP VSM
Sbjct: 396 WMDVPGDKLLEPVVSM 411




Involved in late steps of the endosomal multivesicular bodies (MVB) pathway. Recognizes membrane-associated ESCRT-III assemblies and catalyzes their disassembly, possibly in combination with membrane fission. Redistributes the ESCRT-III components to the cytoplasm for further rounds of MVB sorting. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. In conjunction with the ESCRT machinery also appears to function in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and enveloped virus budding (lentiviruses).
Pongo abelii (taxid: 9601)
>sp|O75351|VPS4B_HUMAN Vacuolar protein sorting-associated protein 4B OS=Homo sapiens GN=VPS4B PE=1 SV=2 Back     alignment and function description
>sp|Q793F9|VPS4A_RAT Vacuolar protein sorting-associated protein 4A OS=Rattus norvegicus GN=Vps4a PE=2 SV=1 Back     alignment and function description
>sp|Q8VEJ9|VPS4A_MOUSE Vacuolar protein sorting-associated protein 4A OS=Mus musculus GN=Vps4a PE=1 SV=1 Back     alignment and function description
>sp|P46467|VPS4B_MOUSE Vacuolar protein sorting-associated protein 4B OS=Mus musculus GN=Vps4b PE=1 SV=2 Back     alignment and function description
>sp|Q0VD48|VPS4B_BOVIN Vacuolar protein sorting-associated protein 4B OS=Bos taurus GN=VPS4B PE=2 SV=1 Back     alignment and function description
>sp|Q9UN37|VPS4A_HUMAN Vacuolar protein sorting-associated protein 4A OS=Homo sapiens GN=VPS4A PE=1 SV=1 Back     alignment and function description
>sp|Q54PT2|VPS4_DICDI Vacuolar protein sorting-associated protein 4 OS=Dictyostelium discoideum GN=vps4 PE=3 SV=1 Back     alignment and function description
>sp|P52917|VPS4_YEAST Vacuolar protein sorting-associated protein 4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=VPS4 PE=1 SV=1 Back     alignment and function description
>sp|Q09803|VPS4_SCHPO Suppressor protein of bem1/bed5 double mutants OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=vps4 PE=3 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query89
242022394 439 vacuolar sorting protein 4A, putative [P 0.853 0.173 0.802 3e-28
193704544 441 PREDICTED: vacuolar protein sorting-asso 0.853 0.172 0.802 8e-28
195396781 442 GJ16581 [Drosophila virilis] gi|19414677 0.853 0.171 0.789 1e-27
344268942 444 PREDICTED: vacuolar protein sorting-asso 0.865 0.173 0.766 3e-27
351705642 436 Vacuolar protein sorting-associated prot 0.853 0.174 0.776 4e-27
267844871 438 vacuolar protein sorting 4 [Bombyx mori] 0.853 0.173 0.776 5e-27
350422808 441 PREDICTED: vacuolar protein sorting-asso 0.853 0.172 0.763 6e-27
340715547 441 PREDICTED: vacuolar protein sorting-asso 0.853 0.172 0.763 6e-27
195132049 442 GI14672 [Drosophila mojavensis] gi|19390 0.853 0.171 0.763 9e-27
357621249 440 vacuolar protein sorting 4 [Danaus plexi 0.853 0.172 0.763 9e-27
>gi|242022394|ref|XP_002431625.1| vacuolar sorting protein 4A, putative [Pediculus humanus corporis] gi|212516933|gb|EEB18887.1| vacuolar sorting protein 4A, putative [Pediculus humanus corporis] Back     alignment and taxonomy information
 Score =  129 bits (323), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 61/76 (80%), Positives = 65/76 (85%)

Query: 4   YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMN 63
           YSGADISIVVRDALMQPVR VQ+ATHFVR  GPSP DPS  VDDLLTPCSP   GA+EMN
Sbjct: 331 YSGADISIVVRDALMQPVRKVQTATHFVRVRGPSPTDPSVIVDDLLTPCSPGHKGAIEMN 390

Query: 64  FMDVPSDKLLEPPVSM 79
           +MDVP DKL EPPV+M
Sbjct: 391 WMDVPGDKLYEPPVTM 406




Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193704544|ref|XP_001949643.1| PREDICTED: vacuolar protein sorting-associated protein 4B isoform 1 [Acyrthosiphon pisum] Back     alignment and taxonomy information
>gi|195396781|ref|XP_002057007.1| GJ16581 [Drosophila virilis] gi|194146774|gb|EDW62493.1| GJ16581 [Drosophila virilis] Back     alignment and taxonomy information
>gi|344268942|ref|XP_003406315.1| PREDICTED: vacuolar protein sorting-associated protein 4B-like [Loxodonta africana] Back     alignment and taxonomy information
>gi|351705642|gb|EHB08561.1| Vacuolar protein sorting-associated protein 4B [Heterocephalus glaber] Back     alignment and taxonomy information
>gi|267844871|ref|NP_001161188.1| vacuolar protein sorting 4 [Bombyx mori] gi|261291948|gb|ACX69978.1| vacuolar protein sorting 4 [Bombyx mori] Back     alignment and taxonomy information
>gi|350422808|ref|XP_003493289.1| PREDICTED: vacuolar protein sorting-associated protein 4B-like [Bombus impatiens] Back     alignment and taxonomy information
>gi|340715547|ref|XP_003396273.1| PREDICTED: vacuolar protein sorting-associated protein 4B-like [Bombus terrestris] Back     alignment and taxonomy information
>gi|195132049|ref|XP_002010456.1| GI14672 [Drosophila mojavensis] gi|193908906|gb|EDW07773.1| GI14672 [Drosophila mojavensis] Back     alignment and taxonomy information
>gi|357621249|gb|EHJ73146.1| vacuolar protein sorting 4 [Danaus plexippus] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query89
UNIPROTKB|F1PVE5444 VPS4B "Uncharacterized protein 0.853 0.171 0.763 7.5e-27
UNIPROTKB|O75351444 VPS4B "Vacuolar protein sortin 0.853 0.171 0.763 9.8e-27
UNIPROTKB|Q0VD48444 VPS4B "Vacuolar protein sortin 0.853 0.171 0.75 3.1e-26
FB|FBgn0027605442 Vps4 "Vacuolar protein sorting 0.853 0.171 0.75 5.1e-26
MGI|MGI:1100499444 Vps4b "vacuolar protein sortin 0.853 0.171 0.75 7e-26
RGD|1305969444 Vps4b "vacuolar protein sortin 0.853 0.171 0.75 7e-26
MGI|MGI:1890520437 Vps4a "vacuolar protein sortin 0.853 0.173 0.723 2.4e-25
RGD|628810437 Vps4a "vacuolar protein sortin 0.853 0.173 0.723 2.4e-25
UNIPROTKB|Q793F9437 Vps4a "Vacuolar protein sortin 0.853 0.173 0.723 2.4e-25
UNIPROTKB|Q9UN37437 VPS4A "Vacuolar protein sortin 0.853 0.173 0.723 3.1e-25
UNIPROTKB|F1PVE5 VPS4B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
 Score = 302 (111.4 bits), Expect = 7.5e-27, P = 7.5e-27
 Identities = 58/76 (76%), Positives = 63/76 (82%)

Query:     4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMN 63
             YSGADISI+VRDALMQPVR VQSATHF +  GPS  DP+K VDDLLTPCSP  PGA+EM 
Sbjct:   336 YSGADISIIVRDALMQPVRKVQSATHFKKVCGPSRADPNKIVDDLLTPCSPGDPGAIEMT 395

Query:    64 FMDVPSDKLLEPPVSM 79
             +MDVP DKLLEP V M
Sbjct:   396 WMDVPGDKLLEPVVCM 411




GO:0005524 "ATP binding" evidence=IEA
GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA
UNIPROTKB|O75351 VPS4B "Vacuolar protein sorting-associated protein 4B" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q0VD48 VPS4B "Vacuolar protein sorting-associated protein 4B" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
FB|FBgn0027605 Vps4 "Vacuolar protein sorting 4" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
MGI|MGI:1100499 Vps4b "vacuolar protein sorting 4b (yeast)" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1305969 Vps4b "vacuolar protein sorting 4 homolog B (S. cerevisiae)" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
MGI|MGI:1890520 Vps4a "vacuolar protein sorting 4a (yeast)" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|628810 Vps4a "vacuolar protein sorting 4 homolog A (S. cerevisiae)" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|Q793F9 Vps4a "Vacuolar protein sorting-associated protein 4A" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|Q9UN37 VPS4A "Vacuolar protein sorting-associated protein 4A" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q8VEJ9VPS4A_MOUSENo assigned EC number0.72360.85390.1739yesN/A
Q54PT2VPS4_DICDINo assigned EC number0.52630.84260.1689yesN/A
Q0VD48VPS4B_BOVINNo assigned EC number0.750.85390.1711yesN/A
O75351VPS4B_HUMANNo assigned EC number0.76310.85390.1711yesN/A
Q793F9VPS4A_RATNo assigned EC number0.72360.85390.1739yesN/A
Q5R658VPS4B_PONABNo assigned EC number0.76310.85390.1711yesN/A

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!


Prediction of Functionally Associated Proteins


Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query89
pfam0933662 pfam09336, Vps4_C, Vps4 C terminal oligomerisation 2e-12
>gnl|CDD|204202 pfam09336, Vps4_C, Vps4 C terminal oligomerisation domain Back     alignment and domain information
 Score = 56.5 bits (137), Expect = 2e-12
 Identities = 21/32 (65%), Positives = 26/32 (81%)

Query: 48 LLTPCSPSTPGAVEMNFMDVPSDKLLEPPVSM 79
           LTPCSP  PGA+EM +MD+  DKLLEPP++M
Sbjct: 1  KLTPCSPGDPGAIEMTWMDIEEDKLLEPPLTM 32


This domain is found at the C terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation. Length = 62

Conserved Domains Detected by HHsearch ?

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 89
KOG0739|consensus439 99.95
PF0933662 Vps4_C: Vps4 C terminal oligomerisation domain; In 99.47
KOG0737|consensus386 98.76
KOG0738|consensus491 98.27
KOG0730|consensus693 97.64
KOG0740|consensus428 97.59
PTZ00454398 26S protease regulatory subunit 6B-like protein; P 97.07
KOG0733|consensus 802 96.88
COG1222406 RPT1 ATP-dependent 26S proteasome regulatory subun 96.63
TIGR01243733 CDC48 AAA family ATPase, CDC48 subfamily. This sub 96.61
COG0464494 SpoVK ATPases of the AAA+ class [Posttranslational 96.52
PRK03992389 proteasome-activating nucleotidase; Provisional 96.38
PTZ00361438 26 proteosome regulatory subunit 4-like protein; P 96.37
TIGR01242364 26Sp45 26S proteasome subunit P45 family. Many pro 96.2
CHL00206 2281 ycf2 Ycf2; Provisional 96.17
KOG0733|consensus802 96.08
CHL00195489 ycf46 Ycf46; Provisional 95.71
PRK10733 644 hflB ATP-dependent metalloprotease; Reviewed 95.09
TIGR01243 733 CDC48 AAA family ATPase, CDC48 subfamily. This sub 94.92
TIGR01241 495 FtsH_fam ATP-dependent metalloprotease FtsH. HflB( 94.43
KOG0731|consensus 774 94.09
KOG0730|consensus 693 93.49
KOG0735|consensus952 93.42
CHL00176 638 ftsH cell division protein; Validated 92.04
KOG0726|consensus440 91.76
KOG0734|consensus 752 87.97
KOG0727|consensus408 87.43
COG0465 596 HflB ATP-dependent Zn proteases [Posttranslational 85.1
KOG0732|consensus 1080 82.42
KOG0728|consensus404 80.77
>KOG0739|consensus Back     alignment and domain information
Probab=99.95  E-value=3.9e-30  Score=202.35  Aligned_cols=85  Identities=69%  Similarity=1.077  Sum_probs=77.7

Q ss_pred             CCCCchhhHHHHHHHHhhhHHHhhhhhhhhhhhcCCCCCCCCCCCCCccccCCCCCCCccccccccCCCCcccCCCcccC
Q psy3811           1 MYSYSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMNFMDVPSDKLLEPPVSMM   80 (89)
Q Consensus         1 teGySGsDi~~l~reA~m~pvr~~~~a~~f~~~~~~~~~~~~~~~~~~~tPCsp~dpga~ems~~di~~~~l~~P~vt~~   80 (89)
                      |||||||||+++||+|+|+|||++|.|+||+++.+++  +.+. +.+.++||||+||||++|+|+|+++++|.+|+|||.
T Consensus       331 TeGySGsDisivVrDalmePvRkvqsAthFk~v~~~s--~~~~-~~~lltpcspgd~ga~em~w~dv~~dkl~eP~vt~~  407 (439)
T KOG0739|consen  331 TEGYSGSDISIVVRDALMEPVRKVQSATHFKKVSGPS--NPSE-VDDLLTPCSPGDPGAIEMSWMDVPADKLLEPPVTMR  407 (439)
T ss_pred             cCCCCcCceEEEehhhhhhhHHHhhhhhhhhccCCCC--Chhh-hccccCCCCCCCcchhhhhhccCCHhhccCCCccHH
Confidence            8999999999999999999999999999999998876  2222 567899999999999999999999999999999999


Q ss_pred             cccccccC
Q psy3811          81 PGQHENNR   88 (89)
Q Consensus        81 Df~~a~~~   88 (89)
                      ||..+..|
T Consensus       408 D~~k~l~~  415 (439)
T KOG0739|consen  408 DFLKSLSR  415 (439)
T ss_pred             HHHHHHhh
Confidence            99988654



>PF09336 Vps4_C: Vps4 C terminal oligomerisation domain; InterPro: IPR015415 This domain is found at the C-terminal of ATPase proteins involved in vacuolar sorting Back     alignment and domain information
>KOG0737|consensus Back     alignment and domain information
>KOG0738|consensus Back     alignment and domain information
>KOG0730|consensus Back     alignment and domain information
>KOG0740|consensus Back     alignment and domain information
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional Back     alignment and domain information
>KOG0733|consensus Back     alignment and domain information
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily Back     alignment and domain information
>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>PRK03992 proteasome-activating nucleotidase; Provisional Back     alignment and domain information
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional Back     alignment and domain information
>TIGR01242 26Sp45 26S proteasome subunit P45 family Back     alignment and domain information
>CHL00206 ycf2 Ycf2; Provisional Back     alignment and domain information
>KOG0733|consensus Back     alignment and domain information
>CHL00195 ycf46 Ycf46; Provisional Back     alignment and domain information
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed Back     alignment and domain information
>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily Back     alignment and domain information
>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH Back     alignment and domain information
>KOG0731|consensus Back     alignment and domain information
>KOG0730|consensus Back     alignment and domain information
>KOG0735|consensus Back     alignment and domain information
>CHL00176 ftsH cell division protein; Validated Back     alignment and domain information
>KOG0726|consensus Back     alignment and domain information
>KOG0734|consensus Back     alignment and domain information
>KOG0727|consensus Back     alignment and domain information
>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>KOG0732|consensus Back     alignment and domain information
>KOG0728|consensus Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query89
1xwi_A322 Crystal Structure Of Vps4b Length = 322 2e-29
2zam_A444 Crystal Structure Of Mouse Skd1VPS4B APO-Form Lengt 4e-28
3mhv_C117 Crystal Structure Of Vps4 And Vta1 Length = 117 1e-15
3eih_A340 Crystal Structure Of S.Cerevisiae Vps4 In The Prese 2e-14
3eie_A322 Crystal Structure Of S.Cerevisiae Vps4 In The So4-B 3e-14
2rko_A331 Crystal Structure Of The Vps4p-Dimer Length = 331 4e-14
2qp9_X355 Crystal Structure Of S.Cerevisiae Vps4 Length = 355 4e-13
>pdb|1XWI|A Chain A, Crystal Structure Of Vps4b Length = 322 Back     alignment and structure

Iteration: 1

Score = 123 bits (309), Expect = 2e-29, Method: Compositional matrix adjust. Identities = 58/77 (75%), Positives = 63/77 (81%) Query: 3 SYSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEM 62 YSGADISI+VRDALMQPVR VQSATHF + GPS DP+ VDDLLTPCSP PGA+EM Sbjct: 213 GYSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNHLVDDLLTPCSPGDPGAIEM 272 Query: 63 NFMDVPSDKLLEPPVSM 79 +MDVP DKLLEP VSM Sbjct: 273 TWMDVPGDKLLEPVVSM 289
>pdb|2ZAM|A Chain A, Crystal Structure Of Mouse Skd1VPS4B APO-Form Length = 444 Back     alignment and structure
>pdb|3MHV|C Chain C, Crystal Structure Of Vps4 And Vta1 Length = 117 Back     alignment and structure
>pdb|3EIH|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The Presence Of Atpgammas Length = 340 Back     alignment and structure
>pdb|3EIE|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The So4-Bound State Length = 322 Back     alignment and structure
>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer Length = 331 Back     alignment and structure
>pdb|2QP9|X Chain X, Crystal Structure Of S.Cerevisiae Vps4 Length = 355 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query89
1xwi_A322 SKD1 protein; VPS4B, AAA ATPase, protein transport 1e-24
2zan_A444 Vacuolar protein sorting-associating protein 4B; S 4e-24
3eie_A322 Vacuolar protein sorting-associated protein 4; AAA 3e-20
2qp9_X355 Vacuolar protein sorting-associated protein 4; ATP 3e-19
3d8b_A357 Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s 4e-06
3b9p_A297 CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc 8e-06
3vfd_A389 Spastin; ATPase, microtubule severing, hydrolase; 4e-05
>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens} Length = 322 Back     alignment and structure
 Score = 93.2 bits (232), Expect = 1e-24
 Identities = 58/76 (76%), Positives = 63/76 (82%)

Query: 4   YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMN 63
           YSGADISI+VRDALMQPVR VQSATHF +  GPS  DP+  VDDLLTPCSP  PGA+EM 
Sbjct: 214 YSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNHLVDDLLTPCSPGDPGAIEMT 273

Query: 64  FMDVPSDKLLEPPVSM 79
           +MDVP DKLLEP VSM
Sbjct: 274 WMDVPGDKLLEPVVSM 289


>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A Length = 444 Back     alignment and structure
>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C Length = 322 Back     alignment and structure
>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A* Length = 355 Back     alignment and structure
>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens} Length = 357 Back     alignment and structure
>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster} Length = 297 Back     alignment and structure
>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens} Length = 389 Back     alignment and structure

Structure Templates Detected by HHsearch ?

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query89
2zan_A444 Vacuolar protein sorting-associating protein 4B; S 99.69
1xwi_A322 SKD1 protein; VPS4B, AAA ATPase, protein transport 99.63
3eie_A322 Vacuolar protein sorting-associated protein 4; AAA 99.46
2qp9_X355 Vacuolar protein sorting-associated protein 4; ATP 99.45
2krk_A86 26S protease regulatory subunit 8; structural geno 98.71
3vlf_B88 26S protease regulatory subunit 7 homolog; heat re 98.7
3aji_B83 S6C, proteasome (prosome, macropain) 26S subunit, 98.69
2dzn_B82 26S protease regulatory subunit 6B homolog; ankyri 98.64
3kw6_A78 26S protease regulatory subunit 8; structural geno 98.62
3cf2_A806 TER ATPase, transitional endoplasmic reticulum ATP 98.56
2x8a_A274 Nuclear valosin-containing protein-like; nuclear p 97.77
4b4t_J405 26S protease regulatory subunit 8 homolog; hydrola 97.68
4b4t_K428 26S protease regulatory subunit 6B homolog; hydrol 97.59
4b4t_I437 26S protease regulatory subunit 4 homolog; hydrola 97.56
4b4t_L437 26S protease subunit RPT4; hydrolase, AAA-atpases, 97.53
4b4t_M434 26S protease regulatory subunit 6A; hydrolase, AAA 97.52
4b4t_H467 26S protease regulatory subunit 7 homolog; hydrola 97.49
3cf2_A 806 TER ATPase, transitional endoplasmic reticulum ATP 96.82
1ypw_A806 Transitional endoplasmic reticulum ATPase; AAA, P9 96.68
3cf0_A301 Transitional endoplasmic reticulum ATPase; AAA, P9 96.28
3d8b_A357 Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s 95.8
3b9p_A297 CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc 95.48
1ixz_A254 ATP-dependent metalloprotease FTSH; AAA domain fol 95.05
1lv7_A257 FTSH; alpha/beta domain, four helix bundle, hydrol 93.54
2qz4_A262 Paraplegin; AAA+, SPG7, protease, ADP, structural 93.4
1iy2_A278 ATP-dependent metalloprotease FTSH; AAA domain fol 93.34
3hu3_A489 Transitional endoplasmic reticulum ATPase; VCP, tr 92.91
3vfd_A389 Spastin; ATPase, microtubule severing, hydrolase; 92.55
2r62_A268 Cell division protease FTSH homolog; ATPase domain 92.08
3h4m_A285 Proteasome-activating nucleotidase; ATPase, PAN, A 92.03
2ce7_A 476 Cell division protein FTSH; metalloprotease; HET: 90.88
2dhr_A 499 FTSH; AAA+ protein, hexameric Zn metalloprotease, 89.34
>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A Back     alignment and structure
Probab=99.69  E-value=1.2e-17  Score=129.92  Aligned_cols=87  Identities=66%  Similarity=0.978  Sum_probs=77.3

Q ss_pred             CCCCchhhHHHHHHHHhhhHHHhhhhhhhhhhhcCCCCCCCCCCCCCccccCCCCCCCccccccccCCCCcccCCCcccC
Q psy3811           1 MYSYSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMNFMDVPSDKLLEPPVSMM   80 (89)
Q Consensus         1 teGySGsDi~~l~reA~m~pvr~~~~a~~f~~~~~~~~~~~~~~~~~~~tPCsp~dpga~ems~~di~~~~l~~P~vt~~   80 (89)
                      |+||||+||..||++|+|.+||+++.++||+.+.+....+.....++.|+||+++++++++|+|.+++.+++..|+|+|+
T Consensus       333 t~G~sgadl~~l~~~a~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~  412 (444)
T 2zan_A          333 TDGYSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNCIVNDLLTPCSPGDPGAIEMTWMDVPGDKLLEPVVSMW  412 (444)
T ss_dssp             TTTCCHHHHHHHHHHHHTHHHHHHHHCSEEEEECCBCSSCTTSBCSCEEEEECTTSTTEEECCTTTSCTTCBCCCCEEHH
T ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccccccccccccccccCCCCcccchhcccccCchhhccCCccCHH
Confidence            68999999999999999999999999999998876554344444567899999999999999999999999999999999


Q ss_pred             ccccccc
Q psy3811          81 PGQHENN   87 (89)
Q Consensus        81 Df~~a~~   87 (89)
                      ||+.|..
T Consensus       413 df~~a~~  419 (444)
T 2zan_A          413 DMLRSLS  419 (444)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999864



>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens} Back     alignment and structure
>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C Back     alignment and structure
>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A* Back     alignment and structure
>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens} Back     alignment and structure
>3vlf_B 26S protease regulatory subunit 7 homolog; heat repeat, chaperone, chaperone-protein binding complex; HET: DNA; 3.80A {Saccharomyces cerevisiae} PDB: 4a3v_B* Back     alignment and structure
>3aji_B S6C, proteasome (prosome, macropain) 26S subunit, ATPA; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dwz_B* 2dvw_B* Back     alignment and structure
>2dzn_B 26S protease regulatory subunit 6B homolog; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} PDB: 2dzo_B Back     alignment and structure
>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens} Back     alignment and structure
>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A* Back     alignment and structure
>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens} Back     alignment and structure
>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae} Back     alignment and structure
>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae} Back     alignment and structure
>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae} Back     alignment and structure
>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae} Back     alignment and structure
>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae} Back     alignment and structure
>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae} Back     alignment and structure
>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A* Back     alignment and structure
>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus} Back     alignment and structure
>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens} Back     alignment and structure
>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster} Back     alignment and structure
>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A* Back     alignment and structure
>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20 Back     alignment and structure
>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens} Back     alignment and structure
>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20 Back     alignment and structure
>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A* Back     alignment and structure
>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens} Back     alignment and structure
>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A* Back     alignment and structure
>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii} Back     alignment and structure
>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E* Back     alignment and structure
>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 89
d1d2na_246 c.37.1.20 (A:) Hexamerization domain of N-ethylmal 0.002
d1r7ra3265 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p 0.003
>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]} Length = 246 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]
 Score = 33.0 bits (74), Expect = 0.002
 Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 8/45 (17%)

Query: 4   YSGADISIVVRDALM--------QPVRLVQSATHFVRTSGPSPVD 40
             G  + I ++  LM         P   V+     +R  G SP+D
Sbjct: 202 VKGKKVWIGIKKLLMLIEMSLQMDPEYRVRKFLALLREEGASPLD 246


>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Length = 265 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query89
d1e32a2258 Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu 98.23
d1lv7a_256 AAA domain of cell division protein FtsH {Escheric 96.8
d1ixza_247 AAA domain of cell division protein FtsH {Thermus 96.78
d1r7ra3265 Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu 96.75
>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]
Probab=98.23  E-value=7.4e-08  Score=68.27  Aligned_cols=25  Identities=24%  Similarity=0.341  Sum_probs=23.2

Q ss_pred             CCCCchhhHHHHHHHHhhhHHHhhh
Q psy3811           1 MYSYSGADISIVVRDALMQPVRLVQ   25 (89)
Q Consensus         1 teGySGsDi~~l~reA~m~pvr~~~   25 (89)
                      |+||||+||.+||++|++.++|+..
T Consensus       203 t~G~s~adl~~lv~~A~~~a~~~~~  227 (258)
T d1e32a2         203 THGHVGADLAALCSEAALQAIRKKM  227 (258)
T ss_dssp             CTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCHHHHHHHHHHHHHHHHHhhc
Confidence            7999999999999999999998754



>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure