RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3540
(202 letters)
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 126 bits (319), Expect = 2e-34
Identities = 58/171 (33%), Positives = 97/171 (56%), Gaps = 25/171 (14%)
Query: 19 IFIDEVDSLCSMRGSDSEHEASRRFKAELLIQMDGLNSSLYEDKIIMILAATNHPWDIDE 78
IFIDE+DSL S RG SE + RR +LL ++DG+ + + ++++AATN P D+D
Sbjct: 339 IFIDEIDSLASGRG-PSEDGSGRRVVGQLLTELDGIEKA----EGVLVIAATNRPDDLDP 393
Query: 79 AFRR--RFEKRVYIPLPNEWARYQLLTLCLEGVVIDV--NLDFHKISKMLEGYTGSDIAN 134
A R RF++ +Y+PLP+ R ++ + L + ++D +++++ EGY+G+DIA
Sbjct: 394 ALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAA 453
Query: 135 LARDAAMMSIRRKIMGQTPAQIKEIKQEDIDLPVTEKDFREAIARCRKSVT 185
L R+AA+ ++R E VT DF +A+ + + SVT
Sbjct: 454 LVREAALEALR----------------EARRREVTLDDFLDALKKIKPSVT 488
Score = 72.5 bits (178), Expect = 4e-15
Identities = 53/167 (31%), Positives = 83/167 (49%), Gaps = 19/167 (11%)
Query: 19 IFIDEVDSLCSMRGSDSEHEASRRFKAELLIQMDGLNSSLYEDKIIMILAATNHPWDIDE 78
IFIDE+D+L R SD E RR A+LL MDGL ++++ ATN P +D
Sbjct: 80 IFIDEIDALAPKRSSDQG-EVERRVVAQLLALMDGLKR-----GQVIVIGATNRPDGLDP 133
Query: 79 AFRR--RFEKRVYIPLPNEWARYQLLTLCLEGVVIDVNLDFHKISKMLEGYTGSDIANLA 136
A RR RF++ + + LP+E R ++L + + + ++ G +G+D+ LA
Sbjct: 134 AKRRPGRFDREIEVNLPDEAGRLEILQIHTRLMFLGPPGTGKTLAARTVGKSGADLGALA 193
Query: 137 RDAAMMSIRRKIMGQTPAQIKEIKQEDIDLPVTEKDFREAIARCRKS 183
++AA+ +RR I + VTE DF EA+ + S
Sbjct: 194 KEAALRELRRA-----------IDLVGEYIGVTEDDFEEALKKVLPS 229
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 116 bits (292), Expect = 3e-30
Identities = 56/185 (30%), Positives = 105/185 (56%), Gaps = 7/185 (3%)
Query: 19 IFIDEVDSLCSMRGSDSEHEASRRFKAELLIQMDGLNSSLYEDKIIMILAATNHPWDIDE 78
IF DE+D++ RG+ + + R +LL +MDG+ E ++++AATN P +D
Sbjct: 550 IFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQ----ELSNVVVIAATNRPDILDP 605
Query: 79 AFRR--RFEKRVYIPLPNEWARYQLLTLCLEGVVIDVNLDFHKISKMLEGYTGSDIANLA 136
A R RF++ + +P P+E AR ++ + + + ++D ++++M EGYTG+DI +
Sbjct: 606 ALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVC 665
Query: 137 RDAAMMSIRRKIMGQTPAQIKEIKQEDI-DLPVTEKDFREAIARCRKSVTAHDLSKYDSW 195
R+AAM ++R I +++ ++E + DL V + F EA+ + + SV+ D+ +Y+
Sbjct: 666 REAAMAALRESIGSPAKEKLEVGEEEFLKDLKVEMRHFLEALKKVKPSVSKEDMLRYERL 725
Query: 196 MNEFG 200
E
Sbjct: 726 AKELK 730
Score = 100 bits (251), Expect = 8e-25
Identities = 61/171 (35%), Positives = 100/171 (58%), Gaps = 9/171 (5%)
Query: 17 STIFIDEVDSLCSMRGSDSEHEASRRFKAELLIQMDGLNSSLYEDKIIMILAATNHPWDI 76
S IFIDE+D++ R + E +R A+LL MDGL ++I+I ATN P +
Sbjct: 273 SIIFIDEIDAIAPKR-EEVTGEVEKRVVAQLLTLMDGLKG---RGRVIVI-GATNRPDAL 327
Query: 77 DEAFRR--RFEKRVYIPLPNEWARYQLLTLCLEGVVIDVNLDFHKISKMLEGYTGSDIAN 134
D A RR RF++ + I +P++ AR ++L + + + ++D K++++ G+ G+D+A
Sbjct: 328 DPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAA 387
Query: 135 LARDAAMMSIRRKI-MGQTPAQIKEIKQEDID-LPVTEKDFREAIARCRKS 183
LA++AAM ++RR I G+ + +EI E + L VT KDF EA+ S
Sbjct: 388 LAKEAAMAALRRFIREGKINFEAEEIPAEVLKELKVTMKDFMEALKMVEPS 438
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 90.0 bits (224), Expect = 2e-21
Identities = 48/170 (28%), Positives = 85/170 (50%), Gaps = 31/170 (18%)
Query: 17 STIFIDEVDSLCSMRGSDSEHEASR---RFKAELLIQMDGLNSSLYEDKIIMILAATNHP 73
S IFIDE+D++ + R DS R R ELL Q+DG + + ++ ATN P
Sbjct: 246 SIIFIDEIDAIGAKR-FDSGTSGDREVQRTMLELLNQLDGFDPR----GNVKVIMATNRP 300
Query: 74 WDIDEAFRR--RFEKRVYIPLPNEWARYQLLTLCLEGVVIDVNLDFHKISKMLEGYTGSD 131
+D A R RF++++ PLP+E R ++L + + + ++D ++++ EG++G+D
Sbjct: 301 DILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLARLTEGFSGAD 360
Query: 132 IANLARDAAMMSIR--RKIMGQTPAQIKEIKQEDIDLPVTEKDFREAIAR 179
+ + +A M +IR R VT +DF +A+ +
Sbjct: 361 LKAICTEAGMFAIRERRDE-------------------VTMEDFLKAVEK 391
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 89.5 bits (223), Expect = 3e-21
Identities = 51/167 (30%), Positives = 86/167 (51%), Gaps = 29/167 (17%)
Query: 17 STIFIDEVDSLCSMR---GSDSEHEASRRFKAELLIQMDGLNSSLYEDKIIMILAATNHP 73
S IFIDE+D++ + R G+ + E R +LL +MDG + KII AATN
Sbjct: 226 SIIFIDEIDAIAAKRTDSGTSGDREVQRTL-MQLLAEMDGFDP-RGNVKII---AATNRI 280
Query: 74 WDI-DEAFRR--RFEKRVYIPLPNEWARYQLLTLCLEGVVIDVNLDFHKISKMLEGYTGS 130
DI D A R RF++ + +PLP+E R ++L + + + ++D +++++ EG +G+
Sbjct: 281 -DILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELTEGASGA 339
Query: 131 DIANLARDAAMMSIRRKIMGQTPAQIKEIKQEDIDLPVTEKDFREAI 177
D+ + +A M +IR + VT +DF +AI
Sbjct: 340 DLKAICTEAGMFAIRDD---------RTE--------VTMEDFLKAI 369
>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 79.6 bits (197), Expect = 2e-19
Identities = 31/75 (41%), Positives = 44/75 (58%), Gaps = 5/75 (6%)
Query: 19 IFIDEVDSLCSMRGSDSEHEASRRFKAELLIQMDGLNSSLYEDKIIMILAATNHPWDIDE 78
IFIDE+D+L RGS SRR +LL ++DG SS ++++AATN P +D
Sbjct: 61 IFIDEIDALAGSRGS-GGDSESRRVVNQLLTELDGFTSS---LSKVIVIAATNRPDKLDP 116
Query: 79 AFRR-RFEKRVYIPL 92
A R RF++ + PL
Sbjct: 117 ALLRGRFDRIIEFPL 131
>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for correct
cell division in bacteria. It has ATP-dependent zinc
metalloprotease activity. It was formerly designated
cell division protein FtsH [Cellular processes, Cell
division, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 495
Score = 76.6 bits (189), Expect = 2e-16
Identities = 46/165 (27%), Positives = 88/165 (53%), Gaps = 25/165 (15%)
Query: 19 IFIDEVDSLCSMRGSD--SEHEASRRFKAELLIQMDGLNSSLYEDKIIMILAATNHPWDI 76
IFIDE+D++ RG+ ++ + +LL++MDG ++ +I ++AATN P +
Sbjct: 151 IFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTN---TGVI-VIAATNRPDVL 206
Query: 77 DEAFRR--RFEKRVYIPLPNEWARYQLLTLCLEGVVIDVNLDFHKISKMLEGYTGSDIAN 134
D A R RF+++V + LP+ R ++L + + + ++D +++ G++G+D+AN
Sbjct: 207 DPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPGFSGADLAN 266
Query: 135 LARDAAMMSIRRKIMGQTPAQIKEIKQEDIDLPVTEKDFREAIAR 179
L +AA+++ R+ +T +T D EAI R
Sbjct: 267 LLNEAALLAARK---NKT--------------EITMNDIEEAIDR 294
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 75.8 bits (186), Expect = 3e-16
Identities = 42/131 (32%), Positives = 78/131 (59%), Gaps = 8/131 (6%)
Query: 19 IFIDEVDSLCSMRGSD--SEHEASRRFKAELLIQMDGLNSSLYEDKIIMILAATNHPWDI 76
IFIDE+D++ RG+ H+ + ++L++MDG ++ I+++AATN P +
Sbjct: 248 IFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEG----NEGIIVIAATNRPDVL 303
Query: 77 DEAFRR--RFEKRVYIPLPNEWARYQLLTLCLEGVVIDVNLDFHKISKMLEGYTGSDIAN 134
D A R RF+++V + LP+ R Q+L + + V + ++D I++ G++G+D+AN
Sbjct: 304 DPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLAN 363
Query: 135 LARDAAMMSIR 145
L +AA+ + R
Sbjct: 364 LVNEAALFAAR 374
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 73.3 bits (180), Expect = 1e-15
Identities = 42/135 (31%), Positives = 75/135 (55%), Gaps = 10/135 (7%)
Query: 17 STIFIDEVDSLCSMR---GSDSEHEASRRFKAELLIQMDGLNSSLYEDKIIMILAATNHP 73
S IFIDE+D++ + R G+ + E R +LL ++DG + + ++AATN P
Sbjct: 217 SIIFIDEIDAIAAKRTDSGTSGDREVQRTL-MQLLAELDGFDPR----GNVKVIAATNRP 271
Query: 74 WDIDEAFRR--RFEKRVYIPLPNEWARYQLLTLCLEGVVIDVNLDFHKISKMLEGYTGSD 131
+D A R RF++ + +PLP+ R ++L + + + ++D I+KM EG +G+D
Sbjct: 272 DILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAKMTEGASGAD 331
Query: 132 IANLARDAAMMSIRR 146
+ + +A M +IR
Sbjct: 332 LKAICTEAGMFAIRE 346
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 70.4 bits (173), Expect = 2e-14
Identities = 50/168 (29%), Positives = 91/168 (54%), Gaps = 31/168 (18%)
Query: 19 IFIDEVDSL-----CSMRGSDSEHEASRRFKAELLIQMDGLNSSLYEDKIIMILAATNHP 73
IFIDE+D++ + G + E E + +LL++MDG + + ++++AATN P
Sbjct: 246 IFIDEIDAVGRQRGAGLGGGNDEREQT---LNQLLVEMDGFGGN----EGVIVIAATNRP 298
Query: 74 WDIDEAFRR--RFEKRVYIPLPNEWARYQLLTLCLEGVVIDVNLDFHKISKMLEGYTGSD 131
+D A R RF++++ + LP+ R Q+L + + + ++D KI++ G++G+D
Sbjct: 299 DVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAEDVDLKKIARGTPGFSGAD 358
Query: 132 IANLARDAAMMSIRRKIMGQTPAQIKEIKQEDIDLPVTEKDFREAIAR 179
+ANL +AA+++ RR K+E +T +D EAI R
Sbjct: 359 LANLLNEAALLAARRN------------KKE-----ITMRDIEEAIDR 389
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 65.1 bits (159), Expect = 1e-12
Identities = 40/144 (27%), Positives = 78/144 (54%), Gaps = 8/144 (5%)
Query: 19 IFIDEVDSLCSMRGS--DSEHEASRRFKAELLIQMDGLNSSLYEDKIIMILAATNHPWDI 76
+FIDE+D++ RG+ ++ + +LL +MDG +K ++++AATN +
Sbjct: 279 VFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFK----GNKGVIVIAATNRVDIL 334
Query: 77 DEAFRR--RFEKRVYIPLPNEWARYQLLTLCLEGVVIDVNLDFHKISKMLEGYTGSDIAN 134
D A R RF++++ + LP+ R +L + + ++ I++ G++G+D+AN
Sbjct: 335 DAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKLSPDVSLELIARRTPGFSGADLAN 394
Query: 135 LARDAAMMSIRRKIMGQTPAQIKE 158
L +AA+++ RRK T +I
Sbjct: 395 LLNEAAILTARRKKATITMKEIDT 418
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 61.0 bits (148), Expect = 3e-11
Identities = 38/162 (23%), Positives = 74/162 (45%), Gaps = 24/162 (14%)
Query: 17 STIFIDEVDSLC------SMRGSDSEHEASRRFKAELLIQMDGLNSSLYEDKIIMILAAT 70
+FIDE+D++ +RG SE + LL ++DG+ E++ ++ +AAT
Sbjct: 212 CIVFIDELDAIALDRRYQELRGDVSEIVNA------LLTELDGIK----ENEGVVTIAAT 261
Query: 71 NHPWDIDEAFRRRFEKRVYIPLPNEWARYQLLTLCLEGVVIDVNLDFHKISKMLEGYTGS 130
N P +D A R RFE+ + LPN+ R ++L + + V+ D ++ +G +G
Sbjct: 262 NRPELLDPAIRSRFEEEIEFKLPNDEERLEILEYYAKKFPLPVDADLRYLAAKTKGMSGR 321
Query: 131 DIANLARDAAMM--------SIRRKIMGQTPAQIKEIKQEDI 164
DI A+ + R+ + + + ++ +
Sbjct: 322 DIKEKVLKTALHRAIAEDREKVEREDIEKALKKERKRRAPRP 363
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 59.4 bits (144), Expect = 1e-10
Identities = 45/148 (30%), Positives = 71/148 (47%), Gaps = 20/148 (13%)
Query: 6 RTNVPSNSYRVSTIFIDEVDSLCSMR-----GSDSEHEASRRFKAELLIQMDGLNSSLYE 60
R N PS IFIDEVDS+ + R G+D E +R ELL QMDG + +
Sbjct: 235 RENAPS------IIFIDEVDSIATKRFDAQTGADRE---VQRILLELLNQMDGFDQTT-N 284
Query: 61 DKIIMILAATNHPWDIDEAFRR--RFEKRVYIPLPNEWARYQLLTLCLEGVVIDVNLDFH 118
K+IM ATN +D A R R ++++ PLP+ + + + + +D
Sbjct: 285 VKVIM---ATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVDLE 341
Query: 119 KISKMLEGYTGSDIANLARDAAMMSIRR 146
E + +DIA + ++A M ++R+
Sbjct: 342 DFVSRPEKISAADIAAICQEAGMQAVRK 369
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 49.8 bits (119), Expect = 2e-07
Identities = 44/152 (28%), Positives = 82/152 (53%), Gaps = 14/152 (9%)
Query: 17 STIFIDEVDSLCSMR---GSDSEHEASRRFKAELLIQMDGLNSSLYEDKIIMILAATNHP 73
S +FIDE+D++ + R S E E R ELL Q+DG +S + K+IM ATN
Sbjct: 278 SIVFIDEIDAIGTKRYDATSGGEKEIQRTM-LELLNQLDGFDSR-GDVKVIM---ATNRI 332
Query: 74 WDIDEAFRR--RFEKRVYIPLPNEWARYQLLTLCLEGVVI--DVNLDFHKISKMLEGYTG 129
+D A R R ++++ P P+E + ++ + + + DV+L+ ++K + +G
Sbjct: 333 ESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIMAK--DELSG 390
Query: 130 SDIANLARDAAMMSIRRKIMGQTPAQIKEIKQ 161
+DI + +A ++++R + M T A ++ K+
Sbjct: 391 ADIKAICTEAGLLALRERRMKVTQADFRKAKE 422
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 45.6 bits (108), Expect = 2e-06
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 14/78 (17%)
Query: 17 STIFIDEVDSLCSMRGSDSEHEASRRFKAELLIQMDGLNSSLYEDKIIMILAATNHPW-- 74
+FIDE+DSL SR + LL ++ LN + + + ++ ATN P
Sbjct: 86 GVLFIDEIDSL------------SRGAQNALLRVLETLNDLRIDRENVRVIGATNRPLLG 133
Query: 75 DIDEAFRRRFEKRVYIPL 92
D+D A R + R+ IPL
Sbjct: 134 DLDRALYDRLDIRIVIPL 151
>gnl|CDD|204202 pfam09336, Vps4_C, Vps4 C terminal oligomerisation domain. 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
Score = 42.2 bits (100), Expect = 5e-06
Identities = 15/34 (44%), Positives = 24/34 (70%)
Query: 167 PVTEKDFREAIARCRKSVTAHDLSKYDSWMNEFG 200
P+T KDF +A+A + +V+ DL K++ + NEFG
Sbjct: 29 PLTMKDFIKALATTKPTVSKDDLEKHEEFTNEFG 62
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 37.7 bits (87), Expect = 0.001
Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 9/83 (10%)
Query: 12 NSYRVSTIFIDEVDSLCSMRGSDSEHEASRRFKAELLIQMDGLNSSLYEDKIIMILAATN 71
+ + +DE+ SL D+E EA EL + L E + +IL +
Sbjct: 75 RKLKPDVLILDEITSLL-----DAEQEALLLLLEELRL----LLLLKSEKNLTVILTTND 125
Query: 72 HPWDIDEAFRRRFEKRVYIPLPN 94
RRRF++R+ + L
Sbjct: 126 EKDLGPALLRRRFDRRIVLLLIL 148
>gnl|CDD|130763 TIGR01702, CO_DH_cata, carbon-monoxide dehydrogenase, catalytic
subunit. This model represents the carbon-monoxide
dehydrogenase catalytic subunit. This protein is related
to prismane (also called hybrid cluster protein), a
complex whose activity is not yet fully described; the
two share similar sets of ligands to unusual
metal-containing clusters.
Length = 621
Score = 30.1 bits (68), Expect = 0.75
Identities = 19/91 (20%), Positives = 34/91 (37%), Gaps = 15/91 (16%)
Query: 83 RFEKRVYIPLPNEWA--RYQLLTLCLEGVVIDVNLDFHKISKMLEGYTGSDIANLARDAA 140
R V++ L + T ++ +V+DVN I + E Y + I + +A
Sbjct: 297 RQGHYVFVGLAGNNLSQELLIATGAIDAMVVDVNCTMPSIPAIAECY-HTKIITVDDNA- 354
Query: 141 MMSIRRKIMGQT-----PAQIKEIKQEDIDL 166
KI G P + +E + I +
Sbjct: 355 ------KIPGADHIPYDPEKAEETAKTIIRM 379
>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 512
Score = 30.1 bits (68), Expect = 0.92
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 19 IFIDEVDSLCSMRGSDSEHEASRRFKAELLIQMDGLNSSLYEDKIIMILAATNHPWDIDE 78
+F DE+DSL RGS + +LL ++DG+ S D +I+I A+N ID
Sbjct: 293 VFFDEMDSLFRTRGSGVSSDVETTVVPQLLAEIDGVESL---DNVIVI-GASNREDMIDP 348
Query: 79 AFRR--RFEKRVYIPLPN 94
A R R + ++ I P+
Sbjct: 349 AILRPGRLDVKIRIERPD 366
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 29.7 bits (67), Expect = 0.99
Identities = 14/88 (15%), Positives = 30/88 (34%), Gaps = 23/88 (26%)
Query: 19 IFIDEVDSLCSMRGSDSEHEASRRFKAELLIQMD------GLNSSLYEDKIIMILAATNH 72
+ +DE++ A + LL ++ +++ +++A N
Sbjct: 116 LLLDEIN------------RAPPEVQNALLEALEERQVTVPGLTTIRLPPPFIVIATQNP 163
Query: 73 PWDID-----EAFRRRFEKRVYIPLPNE 95
EA RF R+Y+ P+
Sbjct: 164 GEYEGTYPLPEALLDRFLLRIYVDYPDS 191
>gnl|CDD|216206 pfam00939, Na_sulph_symp, Sodium:sulfate symporter transmembrane
region. There are also some members in this family that
do not match the Prosite motif, and belong to the
subfamily SODIT1.
Length = 471
Score = 29.6 bits (67), Expect = 1.1
Identities = 17/64 (26%), Positives = 24/64 (37%), Gaps = 8/64 (12%)
Query: 9 VPSNSYRVSTIFIDEVDSLCSMRGSDSEHEASRRFKAELLIQMDGLNSSLYEDKI--IMI 66
+PSN+ R I + SL GS E + R+ A L+ + I M
Sbjct: 137 IPSNTARAGGIVFPIIMSLPPAFGSTPEKGSPRKIGAYLMWTV------YQSTSITSAMF 190
Query: 67 LAAT 70
L A
Sbjct: 191 LTAM 194
>gnl|CDD|225080 COG2169, Ada, Adenosine deaminase [Nucleotide transport and
metabolism].
Length = 187
Score = 28.9 bits (65), Expect = 1.5
Identities = 18/85 (21%), Positives = 30/85 (35%), Gaps = 24/85 (28%)
Query: 80 FRRRFEKRVYIPLPNEWARYQLLTLCLEGVVIDVNLDFHKISKMLEGYTGSDIANLARDA 139
R F+ + P E+AR + + + K L G+ + + DA
Sbjct: 114 LHRLFKAITGMT-PKEYARARRM---------------GRARKQLR--MGASVTDAQIDA 155
Query: 140 AMMSIRR------KIMGQTPAQIKE 158
S R KI+G TP + +
Sbjct: 156 GFESSSRFYDAFSKILGMTPTKFRH 180
>gnl|CDD|192778 pfam11582, DUF3240, Protein of unknown function (DUF3240). This
family of proteins with unknown function appears to be
restricted to Proteobacteria.
Length = 101
Score = 27.6 bits (62), Expect = 1.8
Identities = 20/87 (22%), Positives = 35/87 (40%), Gaps = 7/87 (8%)
Query: 99 YQLLTLC----LEGVVIDVNLDFHKISKMLEGYTGSDIANLARDAAMMSIRRKIMGQTPA 154
LLTL L+ ++D ++ + + G+T + A R+ A+ +I ++ G
Sbjct: 3 SVLLTLIAPRELKDDLVDCLIEL---TDAVSGFTLLEAAGHGREHALFTIAEQVRGYRDM 59
Query: 155 QIKEIKQEDIDLPVTEKDFREAIARCR 181
EI + DL R A A
Sbjct: 60 VKVEIVLPEADLERLLAALRAANAHTP 86
>gnl|CDD|223936 COG1004, Ugd, Predicted UDP-glucose 6-dehydrogenase [Cell envelope
biogenesis, outer membrane].
Length = 414
Score = 28.7 bits (65), Expect = 2.3
Identities = 8/29 (27%), Positives = 19/29 (65%), Gaps = 5/29 (17%)
Query: 11 SNSY---RVSTIFIDEVDSLCSMRGSDSE 36
+N++ ++S FI+E+ ++C G+D +
Sbjct: 209 ANAFLATKIS--FINEIANICEKVGADVK 235
>gnl|CDD|235809 PRK06464, PRK06464, phosphoenolpyruvate synthase; Validated.
Length = 795
Score = 28.6 bits (65), Expect = 2.3
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 7/73 (9%)
Query: 119 KISKMLEGYTGSDIANLARDAAMMSIRRKIMGQT-PAQI-KEIKQEDIDLPVTEKDFREA 176
KI ++L+G D+ LA+ A IR+ I+ P + +EI++ L + A
Sbjct: 65 KIYELLDGLDVDDVDALAKAGA--QIRQLIIDTPFPPDLEQEIREAYAKLSAGYGEASVA 122
Query: 177 IARCRKSVTAHDL 189
+ R S TA DL
Sbjct: 123 V---RSSATAEDL 132
>gnl|CDD|218027 pfam04324, Fer2_BFD, BFD-like [2Fe-2S] binding domain. The two Fe
ions are each coordinated by two conserved cysteine
residues. This domain occurs alone in small proteins
such as Bacterioferritin-associated ferredoxin (BFD).
The function of BFD is not known, but it may may be a
general redox and/or regulatory component involved in
the iron storage or mobilisation functions of
bacterioferritin in bacteria. This domain is also found
in nitrate reductase proteins in association with
Nitrite and sulphite reductase 4Fe-4S domain
(pfam01077), Nitrite/Sulfite reductase ferredoxin-like
half domain (pfam03460) and Pyridine
nucleotide-disulphide oxidoreductase (pfam00070). It is
also found in NifU nitrogen fixation proteins, in
association with NifU-like N terminal domain (pfam01592)
and NifU-like domain (pfam01106).
Length = 55
Score = 25.3 bits (56), Expect = 4.8
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 168 VTEKDFREAIARCRKSVTAHDLSKY 192
VTE + R+AIA + T ++ +
Sbjct: 9 VTEGEIRDAIAEATGAKTLEEVKRR 33
>gnl|CDD|148296 pfam06603, UpxZ, UpxZ family of transcription anti-terminator
antagonists. The UpxZ family of proteins acts to
inhibit transcription of heterologous capsular
polysaccharide loci in Bacteroides species by
interfering with the action of the UpxY family of
transcription anti-terminators. As antagonists of
polysaccharide locus-specific UpxY transcription
anti-terminators, the UpxZ proteins exert a hierarchical
level of regulation, insuring that only one of the
multiple phase-variable capsular polysaccharide loci per
cell characteristic of this genus is transcribed at a
time.
Length = 106
Score = 26.5 bits (59), Expect = 5.1
Identities = 22/86 (25%), Positives = 36/86 (41%), Gaps = 25/86 (29%)
Query: 25 DSLCSMRGSDSEHEASRRFKAELLIQMDGLNSSLY-----EDKIIMILAATNHPWDIDEA 79
+ L S +G E EA+ L + G N+++Y E+K ++L + WD+ +
Sbjct: 39 NDLYSQKGETPEEEANL-----CLALLMGYNATIYNNGEKEEKKQVVL---DRSWDVLDK 90
Query: 80 FRRRFEKRVYIPLPNEWARYQLLTLC 105
LP + QLLT C
Sbjct: 91 ------------LPASLLKCQLLTYC 104
>gnl|CDD|236199 PRK08244, PRK08244, hypothetical protein; Provisional.
Length = 493
Score = 27.4 bits (61), Expect = 5.2
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 5/37 (13%)
Query: 165 DLPVTEKDFREAIARCRKSVTAHDLSKYD-SWMNEFG 200
D PVT ++ + ++ R + D D WM+ FG
Sbjct: 228 DEPVTLEELKTSLIR----ICGTDFGLNDPVWMSRFG 260
>gnl|CDD|216072 pfam00708, Acylphosphatase, Acylphosphatase.
Length = 90
Score = 26.0 bits (58), Expect = 5.4
Identities = 7/26 (26%), Positives = 14/26 (53%)
Query: 149 MGQTPAQIKEIKQEDIDLPVTEKDFR 174
G A+++E++ E++D DF
Sbjct: 63 SGPPLARVEEVEVEELDADGDFDDFE 88
>gnl|CDD|216665 pfam01725, Ham1p_like, Ham1 family. This family consists of the
HAM1 protein and hypothetical archaeal bacterial and C.
elegans proteins. HAM1 controls 6-N-hydroxylaminopurine
(HAP) sensitivity and mutagenesis in S. cerevisiae
inosine triphosphate pyrophosphatase. The HAM1 protein
protects the cell from HAP, either on the level of
deoxynucleoside triphosphate or the DNA level by a yet
unidentified set of reactions.
Length = 181
Score = 26.7 bits (60), Expect = 6.2
Identities = 8/34 (23%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 146 RKIMGQTPAQIKEIKQEDIDLPVTEKDFREAIAR 179
+ I+G ++ ++K I++ T F E A
Sbjct: 15 KAILGDLGIEVIDLKHFPIEVEETGDTFEE-NAL 47
>gnl|CDD|235038 PRK02436, xerD, site-specific tyrosine recombinase XerD-like
protein; Reviewed.
Length = 245
Score = 26.9 bits (60), Expect = 7.0
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 149 MGQTPAQIKEIKQEDIDL 166
+G TP++I +K DIDL
Sbjct: 124 LGLTPSEIAGLKVADIDL 141
>gnl|CDD|222742 pfam14415, DUF4424, Domain of unknown function (DUF4424). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 310 and 361 amino
acids in length.
Length = 248
Score = 26.6 bits (59), Expect = 8.3
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 76 IDEAFRRRFEKRVYIPLPNEWARYQLLT 103
ID AF++ +KR L Y L T
Sbjct: 169 IDAAFKKALQKRGAGGLGERDLDYVLTT 196
>gnl|CDD|132313 TIGR03269, met_CoM_red_A2, methyl coenzyme M reductase system,
component A2. The enzyme that catalyzes the final step
in methanogenesis, methyl coenzyme M reductase, contains
alpha, beta, and gamma chains. In older literature, the
complex of alpha, beta, and gamma chains was termed
component C, while this single chain protein was termed
methyl coenzyme M reductase system component A2 [Energy
metabolism, Methanogenesis].
Length = 520
Score = 27.1 bits (60), Expect = 8.3
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 74 WDIDEAFRRRFEKRVYIPLPNEWARY 99
W++ + RRR KR+ I L +A Y
Sbjct: 97 WNLSDKLRRRIRKRIAIMLQRTFALY 122
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.134 0.391
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,516,631
Number of extensions: 994529
Number of successful extensions: 1143
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1102
Number of HSP's successfully gapped: 47
Length of query: 202
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 110
Effective length of database: 6,857,034
Effective search space: 754273740
Effective search space used: 754273740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.8 bits)