RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2129
(498 letters)
>gnl|CDD|215740 pfam00134, Cyclin_N, Cyclin, N-terminal domain. Cyclins regulate
cyclin dependent kinases (CDKs). Human cyclin-O is a
Uracil-DNA glycosylase that is related to other cyclins.
Cyclins contain two domains of similar all-alpha fold,
of which this family corresponds with the N-terminal
domain.
Length = 127
Score = 175 bits (445), Expect = 3e-53
Identities = 74/175 (42%), Positives = 100/175 (57%), Gaps = 48/175 (27%)
Query: 202 DIYQYLLKCERRIRPKANYMRKQNDINSEMRSVLVDWLIEVAEEYKMHNETLHLAINYVD 261
DIY YL + E RP +Y+ +Q DIN +MR++L+DWL+EV EE+K+ ETL+LA+NY+
Sbjct: 1 DIYAYLRELEEEDRPPPDYLDQQPDINPKMRAILIDWLVEVHEEFKLLPETLYLAVNYL- 59
Query: 262 RFLSLMSVVRSKLQLLGTTALFVASIIEVAEEYKMHNETLHLAINYVDRFLSLMSVVRSK 321
DRFLS V R+K
Sbjct: 60 -----------------------------------------------DRFLSKQPVPRTK 72
Query: 322 LQLLGTTALFVASKYEEIYPPEVNEFVYITDDTYTKKQLLKMETLILKVLNFDLN 376
LQL+G T L +A+KYEEIYPP V +FVYITD+ YTK+++L+ME LIL LN+DL+
Sbjct: 73 LQLVGVTCLLIAAKYEEIYPPSVEDFVYITDNAYTKEEILRMELLILSTLNWDLS 127
>gnl|CDD|227357 COG5024, COG5024, Cyclin [Cell division and chromosome
partitioning].
Length = 440
Score = 130 bits (329), Expect = 3e-33
Identities = 113/479 (23%), Positives = 194/479 (40%), Gaps = 90/479 (18%)
Query: 10 ENRIDHIETTRLKTQNNVSKPQRAVLGVINQNTSKADLSRK----AKTVANQKIGLKVQN 65
+++ + + N+ + + A++ +NQ ++ LS + +G +
Sbjct: 21 SKNKPNVKLILQQPEMNILETRSAIVDFLNQLSTVTRLSNGINFHSSKSTKLVVGTCLWL 80
Query: 66 SNTNQCSKAIEKPIQQQKPQQYSSSIFPRHVQKPTNAFPFKIHEDDSTDEVTDKEEKHHD 125
+ + + ++ + + S + +DS + + D K +
Sbjct: 81 AKKTWGIISSGESNERARIPRLSECNLDSILFIQMT------LNEDSYEPMIDYILKKDE 134
Query: 126 DKEYGNEENEVFDEVAMLPQAFCKAKVWKDEEEPMSLEKSILSPMSVDLSQTEKGTPTRN 185
+ E +E + DE++ S +S DL T++ P
Sbjct: 135 NSLSPYELDENQLAL--------------DEKQAESKRESQSWQ---DLDATDQEDPLMV 177
Query: 186 VEDMVCMLINADDYRDDIYQYLLKCERRIRPKANYMRKQNDINSEMRSVLVDWLIEVAEE 245
E Y DI++YLLK E P NY+ KQ+ MRS+LVDWL+EV
Sbjct: 178 PE-----------YASDIFEYLLKLELIDLPNPNYLIKQSLYEWSMRSILVDWLVEV--- 223
Query: 246 YKMHNETLHLAINYVDRFLSLMSVVRSKLQLLGTTALFVASIIEVAEEYKMHNETLHLAI 305
H K LL ETL LAI
Sbjct: 224 ---HG----------------------KFGLL--------------------PETLFLAI 238
Query: 306 NYVDRFLSLMSVVRSKLQLLGTTALFVASKYEEIYPPEVNEFVYITDDTYTKKQLLKMET 365
N +DRFLS V K QL+G +ALF+ASKYEE+ P + + VY TD +T+ +++ E
Sbjct: 239 NIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRAER 298
Query: 366 LILKVLNFDLNIPTVHSFICHITVSGHLDQSVLYLAQYLSELALVSGDPFLQFLPSLIAC 425
+L+VL+F+++ P+ SF+ I+ + D A++ SE++ V F+Q PS A
Sbjct: 299 YMLEVLDFNISWPSPMSFLRRISKASDYDIFSRTPAKFSSEISPVD-YKFIQISPSWCAA 357
Query: 426 SAIALARYCLDYKEAWPSSLADITG-HSLDSLTECVKCLHEVHRKGEAASQKAAYNKYK 483
+A+ L+R L + W +L +G ++ L + E + + A + KY
Sbjct: 358 AAMYLSRKILS-QNQWDRTLIHYSGNYTNPDLKPLNESNKENLQN-PSVHHDAIFPKYP 414
>gnl|CDD|217307 pfam02984, Cyclin_C, Cyclin, C-terminal domain. Cyclins regulate
cyclin dependent kinases (CDKs). Human CCNO is a
Uracil-DNA glycosylase that is related to other cyclins.
Cyclins contain two domains of similar all-alpha fold,
of which this family corresponds with the C-terminal
domain.
Length = 117
Score = 105 bits (263), Expect = 4e-27
Identities = 42/118 (35%), Positives = 63/118 (53%), Gaps = 2/118 (1%)
Query: 378 PTVHSFICHITVSGHLDQSVLYLAQYLSELALVSGDPFLQFLPSLIACSAIALARYCLDY 437
PT SF+ + + D LA+YL EL+L+ D FL++ PSLIA +A+ LAR L
Sbjct: 1 PTPLSFLRRFSKAADYDLETRTLAKYLLELSLLDYD-FLKYPPSLIAAAAVYLARKTLG- 58
Query: 438 KEAWPSSLADITGHSLDSLTECVKCLHEVHRKGEAASQKAAYNKYKLNLWKNVSTVEA 495
W +L TG+S + L CVK L E+ + + +A KY + + +VST+
Sbjct: 59 SPPWTETLEHYTGYSEEDLKPCVKLLLELLLRAPNSKLQAVRKKYSSSKFGSVSTLPP 116
>gnl|CDD|214641 smart00385, CYCLIN, domain present in cyclins, TFIIB and
Retinoblastoma. A helical domain present in cyclins and
TFIIB (twice) and Retinoblastoma (once). A protein
recognition domain functioning in cell-cycle and
transcription control.
Length = 83
Score = 83.4 bits (207), Expect = 7e-20
Identities = 28/83 (33%), Positives = 47/83 (56%), Gaps = 2/83 (2%)
Query: 287 IIEVAEEYKMHNETLHLAINYVDRFLSLMSVVRSKLQLLGTTALFVASKYEEIYPPEVNE 346
+ V + + ETL+LA+N +DRFLS ++ L+ AL++ASK EE P
Sbjct: 3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKEL 62
Query: 347 FVYITDDTYTKKQLLKMETLILK 369
Y +T++++L+ME L+L+
Sbjct: 63 VHYTGY--FTEEEILRMERLLLE 83
Score = 51.8 bits (125), Expect = 1e-08
Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 3/84 (3%)
Query: 383 FICHITVSGHLDQSVLYLAQYLSELALVSGDPFLQFLPSLIACSAIALARYCLDYKEAWP 442
F+ + + +LD L LA L + L FL++ PSLIA +A+ LA + W
Sbjct: 2 FLRRVCKALNLDPETLNLAVNLLDRFLSD-YKFLKYSPSLIAAAALYLASKTEE-TPPWT 59
Query: 443 SSLADITG-HSLDSLTECVKCLHE 465
L TG + + + + L E
Sbjct: 60 KELVHYTGYFTEEEILRMERLLLE 83
>gnl|CDD|238003 cd00043, CYCLIN, Cyclin box fold. Protein binding domain
functioning in cell-cycle and transcription control.
Present in cyclins, TFIIB and Retinoblastoma (RB).The
cyclins consist of 8 classes of cell cycle regulators
that regulate cyclin dependent kinases (CDKs). TFIIB is
a transcription factor that binds the TATA box. Cyclins,
TFIIB and RB contain 2 copies of the domain.
Length = 88
Score = 83.1 bits (206), Expect = 1e-19
Identities = 32/82 (39%), Positives = 52/82 (63%), Gaps = 2/82 (2%)
Query: 287 IIEVAEEYKMHNETLHLAINYVDRFLSLMSVVRSKLQLLGTTALFVASKYEEIYPPEVNE 346
+ VA+ + ETL LA+N +DRFL SV+ L+ AL++A+K EEI PP + +
Sbjct: 9 LRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEI-PPWLKD 67
Query: 347 FVYITDDTYTKKQLLKMETLIL 368
V++T T++++L+ME L+L
Sbjct: 68 LVHVTGY-ATEEEILRMEKLLL 88
Score = 54.6 bits (132), Expect = 1e-09
Identities = 23/90 (25%), Positives = 36/90 (40%), Gaps = 3/90 (3%)
Query: 376 NIPTVHSFICHITVSGHLDQSVLYLAQYLSELALVSGDPFLQFLPSLIACSAIALARYCL 435
PT F+ + + L L LA L + L+ L PSL+A +A+ LA
Sbjct: 1 MRPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDY-SVLGRSPSLVAAAALYLAAKVE 59
Query: 436 DYKEAWPSSLADITG-HSLDSLTECVKCLH 464
+ W L +TG + + + K L
Sbjct: 60 E-IPPWLKDLVHVTGYATEEEILRMEKLLL 88
>gnl|CDD|227640 COG5333, CCL1, Cdk activating kinase (CAK)/RNA polymerase II
transcription initiation/nucleotide excision repair
factor TFIIH/TFIIK, cyclin H subunit [Cell division and
chromosome partitioning / Transcription / DNA
replication, recombination, and repair].
Length = 297
Score = 44.0 bits (104), Expect = 1e-04
Identities = 34/166 (20%), Positives = 73/166 (43%), Gaps = 11/166 (6%)
Query: 287 IIEVAEEYKMHNETLHLAINYVDRFLSLMSVVRSKLQLLGTTALFVASKYEEIYPPEVNE 346
I+++ + L AI + RF SV L + TT +++A K E+ P +++
Sbjct: 52 IMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDT-PRDISI 110
Query: 347 FVYITDDTYT------KKQLLKMETLILKVLNFDLNIPTVHSFICHITVSGHLDQS--VL 398
+ D ++ ++++L+ E +L+ L+FDL++ + ++ +L
Sbjct: 111 ESFEARDLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKYKLL 170
Query: 399 YLAQYLSELALVSGDPFLQFLPSLIACSAIALARYCLDYKEAWPSS 444
+A + AL + D L + P +IA +A+ +A +
Sbjct: 171 QIAWKIINDALRT-DLCLLYPPHIIALAALLIA-CEVLGMPIIKLL 214
>gnl|CDD|240377 PTZ00352, PTZ00352, 60S ribosomal protein L13; Provisional.
Length = 212
Score = 35.5 bits (82), Expect = 0.032
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 55 ANQKIGLKVQNSNTNQCSKAIEKPIQQQKPQQYSSSIFPRHVQKPTNAFPFKIHEDDSTD 114
A + IG+ V + N+ +++ +++ K +FPR +KP F I D S +
Sbjct: 87 AARSIGIAVDHRRRNRSQESLNLNVKRLKAYLSKLVLFPRKGKKPKKGFA-GIPADTSKE 145
Query: 115 EVTDKEEKHHDDKE 128
EV K + + E
Sbjct: 146 EVVALPVKQNKNSE 159
>gnl|CDD|129660 TIGR00569, ccl1, cyclin ccl1. All proteins in this family for
which functions are known are cyclins that are
components of TFIIH, a complex that is involved in
nucleotide excision repair and transcription initiation.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, StanfordUniversity) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 305
Score = 34.4 bits (79), Expect = 0.11
Identities = 39/144 (27%), Positives = 65/144 (45%), Gaps = 9/144 (6%)
Query: 293 EYKMHNETLHLAINYVDRFLSLMSVVRSKLQLLGTTALFVASKYEEIYPPEVNEFVYITD 352
+ M + AI Y RF SV+ +++ T +F+A K EE +++FV
Sbjct: 71 KPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFN-VSIDQFVGNLK 129
Query: 353 DTYTK--KQLLKMETLILKVLNFDLNI----PTVHSFICHI-TVSGHLDQSVLYLAQYLS 405
+T K +Q+L+ E L+++ LNF L + + F+ I T L+
Sbjct: 130 ETPLKALEQVLEYELLLIQQLNFHLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADK 189
Query: 406 EL-ALVSGDPFLQFLPSLIACSAI 428
L + D +L + PS IA +AI
Sbjct: 190 FLNRTLLTDAYLLYTPSQIALAAI 213
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 33.2 bits (76), Expect = 0.27
Identities = 31/124 (25%), Positives = 45/124 (36%), Gaps = 19/124 (15%)
Query: 239 LIEVAEEYKM----HNETLHLAINYVDRFLSLMSVVRSKLQLLGTTALFVASIIEVAEEY 294
L+E A + + E LAI +D FLS +V + + I E+ E+
Sbjct: 66 LLENARSFGWDLEVYIEKGKLAI--LDAFLSEKGLVSIVVGDPLDLEELLDRIREIVEKE 123
Query: 295 KMHN------ETLHLAIN---YVDRFLSLMSVVRSKLQLLGTTALFVASK-YEEIYPPEV 344
L L +N V R L L+ K LG T+L EE V
Sbjct: 124 GADRVVIDSITELTLYLNDPALVRRILLLLKRFLKK---LGVTSLLTTEAPVEERGESGV 180
Query: 345 NEFV 348
E++
Sbjct: 181 EEYI 184
>gnl|CDD|165268 PHA02962, PHA02962, hypothetical protein; Provisional.
Length = 722
Score = 32.2 bits (73), Expect = 0.83
Identities = 35/153 (22%), Positives = 67/153 (43%), Gaps = 35/153 (22%)
Query: 181 TPTRNVEDMVCMLINA---DDYRDDIYQYLLKCERRI----RPKANYMRK----QN-DIN 228
T + ED +C I+A D DD +L+C +I K +RK +N D+
Sbjct: 182 TFIK--EDDICFFIDALEDADDDDDTLYLILECNDKILDSDEVKDAIIRKICKGENIDV- 238
Query: 229 SEMRSVLVDWLIE----------------VAEEYKMHNETLHLAINYVDRFLSLMSVVRS 272
+ + + I+ + EY + +++L + Y+D++ + + +
Sbjct: 239 --LGYYVKHYFIDHAKLGIYYNIFFAERDIISEYGLKDDSLAIICKYIDKYSKSIPSI-A 295
Query: 273 KLQLLGTTALFVASIIEVAEEYKMHNETLHLAI 305
KL + + +ASII+ + MHNE L++ I
Sbjct: 296 KLLIDNSNYSLLASIIDRIPD-DMHNENLYMNI 327
>gnl|CDD|203922 pfam08377, MAP2_projctn, MAP2/Tau projection domain. This domain
is found in the MAP2/Tau family of proteins which
includes MAP2, MAP4, Tau, and their homologs. All
isoforms contain a conserved C-terminal domain
containing tubulin-binding repeats (pfam00418), and a
N-terminal projection domain of varying size. This
domain has a net negative charge and exerts a long-range
repulsive force. This provides a mechanism that can
regulate microtubule spacing which might facilitate
efficient organelle transport.
Length = 1134
Score = 31.3 bits (70), Expect = 1.5
Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 7/77 (9%)
Query: 110 DDSTDEVTDKEEKHHDDKEYGNEENEVFDEVAML------PQAFCKAKVWKDEEEPMSLE 163
+D D V +K E+H D KE+ E EV D+V + Q K + E P E
Sbjct: 583 NDKLDTVLEKSEEHVDSKEHAKESEEVGDKVELFGLGVTYEQTSAKELITTKETAPERAE 642
Query: 164 KSILS-PMSVDLSQTEK 179
K + S P ++ T K
Sbjct: 643 KGLSSVPEVAEVETTTK 659
>gnl|CDD|233187 TIGR00921, 2A067, The (Largely Archaeal Putative)
Hydrophobe/Amphiphile Efflux-3 (HAE3) Family.
Characterized members of the RND superfamily all
probably catalyze substrate efflux via an H+ antiport
mechanism. These proteins are found ubiquitously in
bacteria, archaea and eukaryotes. They fall into seven
phylogenetic families, this family (2.A.6.7) consists of
uncharacterised putative transporters, largely in the
Archaea [Transport and binding proteins, Unknown
substrate].
Length = 719
Score = 30.6 bits (69), Expect = 2.1
Identities = 16/64 (25%), Positives = 27/64 (42%), Gaps = 6/64 (9%)
Query: 173 DLSQTEKGTPTRNVEDMVCMLINADDYRD-DIYQYLLKCERRIRPKANYMRKQNDINSEM 231
+ Q E GT T + ++I DD + Y+ + E+R+R K Y+ M
Sbjct: 46 HVLQREFGTST----KTLLVVIEGDDVTRKPVLDYMRRLEQRLREKP-YVTNVRSAADIM 100
Query: 232 RSVL 235
R +
Sbjct: 101 RQIP 104
>gnl|CDD|180437 PRK06169, PRK06169, putative amidase; Provisional.
Length = 466
Score = 30.4 bits (69), Expect = 2.5
Identities = 13/36 (36%), Positives = 15/36 (41%), Gaps = 5/36 (13%)
Query: 168 SPMSVDLSQTEKGTPTRNVEDMVCML--INADDYRD 201
SP L+ G TR V D +L I D RD
Sbjct: 206 SPFGT-LAHV--GPMTRTVADAALLLDVIARPDARD 238
>gnl|CDD|233618 TIGR01887, dipeptidaselike, dipeptidase, putative. This model
represents a clade of probable zinc dipeptidases,
closely related to the characterized non-specific
dipeptidase, PepV. Many enzymes in this clade have been
given names including the terms "Xaa-His" and
"carnosinase" due to the early mis-characterization of
the Lactobacillus delbrueckii PepV enzyme. These names
are likely too specific.
Length = 447
Score = 29.3 bits (66), Expect = 5.2
Identities = 23/77 (29%), Positives = 31/77 (40%), Gaps = 7/77 (9%)
Query: 350 ITDDTYTKKQLLKMETLILKVLNFDLNIPTVHSFICHITVSGHLD------QSVLYLAQY 403
I+ T+ + LK I K L D + I S H + YLA +
Sbjct: 213 ISGKKLTEVEQLKFVFFIAKELEGDFEVNDGTLTITLEGKSAHGSAPEKGINAATYLALF 272
Query: 404 LSELALVSGD-PFLQFL 419
L++L L G FLQFL
Sbjct: 273 LAQLNLAGGAKAFLQFL 289
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
0.317 0.131 0.374
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,378,446
Number of extensions: 2328953
Number of successful extensions: 1976
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1968
Number of HSP's successfully gapped: 33
Length of query: 498
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 397
Effective length of database: 6,457,848
Effective search space: 2563765656
Effective search space used: 2563765656
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: 61 (27.2 bits)