RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1676
(343 letters)
>gnl|CDD|149439 pfam08375, Rpn3_C, Proteasome regulatory subunit C-terminal. This
eukaryotic domain is found at the C-terminus of 26S
proteasome regulatory subunits such as the non-ATPase
Rpn3 subunit which is essential for proteasomal
function. It occurs together with the PCI/PINT domain
(pfam01399).
Length = 68
Score = 111 bits (279), Expect = 5e-31
Identities = 42/67 (62%), Positives = 50/67 (74%)
Query: 274 DIYCTVEPQLAFHQRIAFCLDLHNQSVKAMRYPPKSYGKDLESAEERREREQQDLELAKE 333
D+Y T EPQ AF +RI FCL LHN +VKAMRYPP K+ E AEE RER+Q +LELAKE
Sbjct: 1 DVYSTKEPQQAFDERIQFCLQLHNDAVKAMRYPPDKEKKEEEKAEEARERDQLELELAKE 60
Query: 334 MAEEDDD 340
++E D D
Sbjct: 61 LSEGDLD 67
>gnl|CDD|216479 pfam01399, PCI, PCI domain. This domain has also been called the
PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).
Length = 100
Score = 83.0 bits (206), Expect = 6e-20
Identities = 31/99 (31%), Positives = 53/99 (53%), Gaps = 1/99 (1%)
Query: 169 YFQLTQAVRMGELQKFNEVLTTYGNQFRTDYTFKLILRLRHNVIKTAIRSIGASYSRITP 228
Y L +A G+L F E+L ++ D +L+ LR + + +R + YS I+
Sbjct: 1 YRDLLRAFYSGDLSDFEEILADNEDELLDDGLAELLEDLRRKIRELNLRRLAKPYSSISL 60
Query: 229 TKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYM 267
+ +A+ LGL S ++ E I++K IRDG I +D+ G +
Sbjct: 61 SDLAKLLGL-SVDEVEKILSKLIRDGRIRGKIDQVNGIV 98
>gnl|CDD|214803 smart00753, PAM, PCI/PINT associated module.
Length = 88
Score = 75.4 bits (186), Expect = 3e-17
Identities = 28/91 (30%), Positives = 48/91 (52%), Gaps = 3/91 (3%)
Query: 202 KLILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLD 261
+L+ RL+ + T + + YS I+ + +A+ LGL PE E +++KAIRDG I A +D
Sbjct: 1 QLVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPE-VEKLVSKAIRDGEISAKID 59
Query: 262 REKGYMQSKESADIYCTVEPQLAFHQRIAFC 292
+ G ++ +E EP F + +
Sbjct: 60 QVNGIVEFEEVDPRRS--EPLAQFAETLKKL 88
>gnl|CDD|214509 smart00088, PINT, motif in proteasome subunits, Int-6, Nip-1 and
TRIP-15. Also called the PCI (Proteasome, COP9,
Initiation factor 3) domain. Unknown function.
Length = 88
Score = 75.4 bits (186), Expect = 3e-17
Identities = 28/91 (30%), Positives = 48/91 (52%), Gaps = 3/91 (3%)
Query: 202 KLILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLD 261
+L+ RL+ + T + + YS I+ + +A+ LGL PE E +++KAIRDG I A +D
Sbjct: 1 QLVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPE-VEKLVSKAIRDGEISAKID 59
Query: 262 REKGYMQSKESADIYCTVEPQLAFHQRIAFC 292
+ G ++ +E EP F + +
Sbjct: 60 QVNGIVEFEEVDPRRS--EPLAQFAETLKKL 88
>gnl|CDD|220553 pfam10075, PCI_Csn8, COP9 signalosome, subunit CSN8. This PCI_Csn8
domain is conserved from plants to humans. It is a
signature protein motif found in components of CSN (COP9
signalosome). It functions as a structural scaffold for
subunit-subunit interactions within the complex and is a
key regulator of photomorphogenic development.
Length = 144
Score = 33.4 bits (77), Expect = 0.056
Identities = 26/100 (26%), Positives = 40/100 (40%), Gaps = 9/100 (9%)
Query: 146 LLLGDIPDRQIFRQAVLRRALSPYFQLTQAVRMGELQKFNEVLTTY-GNQFRTDYTFKLI 204
LLL IP +++ L+ L + + + T N + DYT I
Sbjct: 25 LLLKRIPQAIKESNPEIQQLLTLGQLLWEN-------DYAKFWQTLRSNDWSEDYTPF-I 76
Query: 205 LRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAE 244
L + +G +YS I+ +AE LGL S E+ E
Sbjct: 77 AGLEDTIRDEIAALVGKAYSSISIDDLAELLGLSSDEELE 116
>gnl|CDD|227403 COG5071, RPN5, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 439
Score = 32.6 bits (74), Expect = 0.30
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 207 LRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGY 266
LR VI+ IR I YSRI +++ L + SP + E I+ + G A ++R
Sbjct: 335 LRKRVIEHNIRVIANYYSRIHCSRLGVLLDM-SPSETEQFISDLVNKGHFYAKINRPAQI 393
Query: 267 MQSKESADI 275
+ ++S ++
Sbjct: 394 ISFEKSQNV 402
>gnl|CDD|129821 TIGR00738, rrf2_super, Rrf2 family protein. This model represents
a superfamily of probable transcriptional regulators.
One member, RRF2 of Desulfovibrio vulgaris is an
apparent regulatory protein experimentally
(MEDLINE:97293189). The N-terminal region appears
related to the DNA-binding biotin repressor region of
the BirA bifunctional according to results after three
rounds of PSI-BLAST with a fairly high stringency
[Unknown function, General].
Length = 132
Score = 29.9 bits (68), Expect = 0.75
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 231 IAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKESADI 275
IAE+ G+ S E I+ R G++E+ GY ++ +I
Sbjct: 31 IAERQGI-SRSYLEKILRTLRRAGLVESVRGPGGGYRLARPPEEI 74
>gnl|CDD|234315 TIGR03695, menH_SHCHC,
2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate
synthase. This protein catalyzes the formation of
SHCHC, or (1 R,6
R)-2-succinyl-6-hydroxy-2,
4-cyclohexadiene-1-carboxylate, by elmination of
pyruvate from
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-
carboxylate (SEPHCHC). Note that SHCHC synthase activity
previously was attributed to MenD, which in fact is
SEPHCHC synthase [Biosynthesis of cofactors, prosthetic
groups, and carriers, Menaquinone and ubiquinone].
Length = 252
Score = 29.9 bits (68), Expect = 1.6
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 314 LESAEERREREQQDLELAKEMAEEDDDGF 342
L + EER R Q D +LA+ +E + F
Sbjct: 108 LATEEERAARRQNDEQLAQRFEQEGIEAF 136
>gnl|CDD|224990 COG2079, PrpD, Uncharacterized protein involved in propionate
catabolism [General function prediction only].
Length = 453
Score = 30.4 bits (69), Expect = 1.7
Identities = 29/150 (19%), Positives = 52/150 (34%), Gaps = 16/150 (10%)
Query: 203 LILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDA----EFIIAKAIRDGVI-E 257
L LR R + I SI I +K +PEDA +I+A A+ DG+
Sbjct: 282 LALREREGLQADDIESIVIRTHEAAIRIIGKKGPPANPEDADHSLPYILAVALLDGLTAL 341
Query: 258 ATLDREKGYMQSKESAD----IYCTVEPQL--AFHQRIAFCLDLHNQSVK---AMRYPPK 308
D E ++ I +P+ + + + +++ + + YP
Sbjct: 342 DYYDPE--RLRDPRIDALRKKIELREDPEFTALYPAKRPIRVTVYDGTGVLEVEVDYPLG 399
Query: 309 SYGKDLESAEERREREQQDLELAKEMAEED 338
LE + + +L E +D
Sbjct: 400 HPRNPLEWDPLLEKFRRLNLFRHFEPERQD 429
>gnl|CDD|221862 pfam12930, DUF3836, Family of unknown function (DUF3836). Family
of uncharacterized proteins found in Bacteroidales
species. Test.
Length = 132
Score = 28.8 bits (65), Expect = 1.7
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 63 LLRNYLHYNL-YDQADKLVKKSAFPENASNNEWARFH 98
L N++ YN YD ++ +K A+ N+ N W ++
Sbjct: 57 TLTNHMKYNYKYDDQGRVTEKEAYKWNSVKNTWEPYY 93
>gnl|CDD|132810 cd07277, PX_RUN, The phosphoinositide binding Phox Homology domain
of uncharacterized proteins containing PX and RUN
domains. The PX domain is a phosphoinositide (PI)
binding module involved in targeting proteins to
PI-enriched membranes. Members in this subfamily are
uncharacterized proteins containing an N-terminal RUN
domain and a C-terminal PX domain. PX domain harboring
proteins have been implicated in highly diverse
functions such as cell signaling, vesicular trafficking,
protein sorting, lipid modification, cell polarity and
division, activation of T and B cells, and cell
survival. In addition to protein-lipid interaction, the
PX domain may also be involved in protein-protein
interaction. The RUN domain is found in GTPases in the
Rap and Rab families and may play a role in Ras-like
signaling pathways.
Length = 118
Score = 28.5 bits (64), Expect = 2.0
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 296 HNQSVKAMRYPPK-SYG-KDLESAEERREREQQDL 328
V++ +PPK + G KD + EERR+R Q L
Sbjct: 51 KFPVVRSFDFPPKKAIGNKDAKFVEERRKRLQVYL 85
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional.
Length = 393
Score = 29.6 bits (67), Expect = 2.2
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 306 PPKSYGKDLESAEERREREQQDLELAKEMAEEDDD 340
PP+ +LE ERRE +++LE A EE DD
Sbjct: 91 PPELKSGELEKRRERREEAEEELEKAI---EEGDD 122
>gnl|CDD|224439 COG1522, Lrp, Transcriptional regulators [Transcription].
Length = 154
Score = 27.7 bits (62), Expect = 5.2
Identities = 17/44 (38%), Positives = 26/44 (59%), Gaps = 4/44 (9%)
Query: 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE---ATLDREK 264
+RI+ ++AE++GL SP I + +GVI+ A LD EK
Sbjct: 21 ARISNAELAERVGL-SPSTVLRRIKRLEEEGVIKGYTAVLDPEK 63
>gnl|CDD|143440 cd07122, ALDH_F20_ACDH, Coenzyme A acylating aldehyde dehydrogenase
(ACDH), ALDH family 20-like. Coenzyme A acylating
aldehyde dehydrogenase (ACDH, EC=1.2.1.10), an NAD+ and
CoA-dependent acetaldehyde dehydrogenase, functions as a
single enzyme (such as the Ethanolamine utilization
protein, EutE, in Salmonella typhimurium) or as part of
a multifunctional enzyme to convert acetaldehyde into
acetyl-CoA . The E. coli aldehyde-alcohol dehydrogenase
includes the functional domains, alcohol dehydrogenase
(ADH), ACDH, and pyruvate-formate-lyase deactivase; and
the Entamoeba histolytica aldehyde-alcohol dehydrogenase
2 (ALDH20A1) includes the functional domains ADH and
ACDH and may be critical enzymes in the fermentative
pathway.
Length = 436
Score = 28.6 bits (65), Expect = 5.3
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 227 TPTKIAEKLGLESPEDAEFIIAKAIRDGVIEAT-LDREK 264
+ KIAE G+E PED + ++A+ GV L REK
Sbjct: 293 SAQKIAELAGIEVPEDTKVLVAE--ETGVGPEEPLSREK 329
>gnl|CDD|233061 TIGR00629, uvde, UV damage endonuclease UvdE. All proteins in this
family for which functions are known are UV dimer
endonucleases that function in an alternative nucleotide
excision repair process. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 312
Score = 28.4 bits (63), Expect = 5.4
Identities = 39/145 (26%), Positives = 60/145 (41%), Gaps = 24/145 (16%)
Query: 166 LSPYFQLTQAVRMGEL-QKFNEVLTTYGNQFRTDYTFKLILRLRHNVIKTAIRSIGASYS 224
L + Q + +GEL + LT + QF R +V+K+AIR +
Sbjct: 88 LVTFAQ-KELREIGELAKTHQHRLTFHPGQF------TQFTSPRESVVKSAIRDLAYHDE 140
Query: 225 RITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDR-EKGYMQ---------SKESAD 274
++ K+AE+L +DA II G + TL R + Y + E+ D
Sbjct: 141 MLSAMKLAEQLN----KDAVIIIHIGGAFGNKDTTLARFHQNYKRLSQSIKERLVLENDD 196
Query: 275 IYCTVEPQLAFHQR--IAFCLDLHN 297
+ TVE L + I F LD H+
Sbjct: 197 VTWTVEDLLPVCEELNIPFVLDFHH 221
>gnl|CDD|205590 pfam13412, HTH_24, Winged helix-turn-helix DNA-binding.
Length = 48
Score = 25.5 bits (57), Expect = 6.4
Identities = 10/34 (29%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257
RI+ ++AE+LGL S + + +G+I+
Sbjct: 16 PRISQRELAERLGL-SLGTVNRRLKRLEEEGLIK 48
>gnl|CDD|227624 COG5308, NUP170, Nuclear pore complex subunit [Intracellular
trafficking and secretion].
Length = 1263
Score = 28.4 bits (63), Expect = 7.3
Identities = 29/150 (19%), Positives = 56/150 (37%), Gaps = 6/150 (4%)
Query: 190 TYGNQFRTDYTFKLILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAK 249
T+ F + T KLI + +++ I+S G S + T ++E+ G + + + +
Sbjct: 739 TFSELFTPNKTKKLIKEILKSLVNRNIQS-GGSIEYLIKT-LSERCGSFCSAE-DVLYFR 795
Query: 250 AIRDGVIEATLDREKGYMQSKESADIYCTVEPQLAFHQRIAFCLDLHNQSVKAMRYPPKS 309
A+ + RE + L + L ++ ++ Y PK+
Sbjct: 796 ALE--HLNKAKSREVDLESLNNHLKNAVQLNESLV-AKYNEEGLRYAVTTMISLNYYPKA 852
Query: 310 YGKDLESAEERREREQQDLELAKEMAEEDD 339
LE A E + Q + +AE D
Sbjct: 853 VNFLLEYAVEIDKGNQACAYVLNGLAENDP 882
>gnl|CDD|233603 TIGR01862, N2-ase-Ialpha, nitrogenase component I, alpha chain.
This model represents the alpha chain of all three
varieties (Mo-Fe, V-Fe, and Fe-Fe) of component I of
nitrogenase [Central intermediary metabolism, Nitrogen
fixation].
Length = 443
Score = 27.8 bits (62), Expect = 9.0
Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 4/66 (6%)
Query: 205 LRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREK 264
L R+ + I G +Y+ + IA G+E + AE +IA+ + LD K
Sbjct: 257 LEERYGIPWMKIDFFGFTYTAESLRAIAAFFGIE--KRAEEVIAEEKAK--WKPELDYYK 312
Query: 265 GYMQSK 270
+Q K
Sbjct: 313 ERLQGK 318
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
0.321 0.134 0.380
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,508,427
Number of extensions: 1714680
Number of successful extensions: 2153
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2145
Number of HSP's successfully gapped: 42
Length of query: 343
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 245
Effective length of database: 6,590,910
Effective search space: 1614772950
Effective search space used: 1614772950
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 (21.9 bits)
S2: 59 (26.4 bits)