RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3827
(581 letters)
>gnl|CDD|185400 PTZ00018, PTZ00018, histone H3; Provisional.
Length = 136
Score = 280 bits (718), Expect = 7e-93
Identities = 130/136 (95%), Positives = 135/136 (99%)
Query: 446 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE 505
MARTKQTARKSTGGKAPRKQLA+KAARKSAP TGG+KKPHRYRPGTVALREIRRYQKSTE
Sbjct: 1 MARTKQTARKSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTE 60
Query: 506 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI 565
LLIRKLPFQRLVREIAQDFKTDLRFQSSAV+ALQEA+EAYLVGLFEDTNLCAIHAKRVTI
Sbjct: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTI 120
Query: 566 MPKDIQLARRIRGERA 581
MPKDIQLARRIRGER+
Sbjct: 121 MPKDIQLARRIRGERS 136
>gnl|CDD|177733 PLN00121, PLN00121, histone H3; Provisional.
Length = 136
Score = 255 bits (653), Expect = 4e-83
Identities = 133/136 (97%), Positives = 136/136 (100%)
Query: 446 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE 505
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIR+YQKSTE
Sbjct: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTE 60
Query: 506 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI 565
LLIRKLPFQRLVREIAQDFKTDLRFQSSAV+ALQEA+EAYLVGLFEDTNLCAIHAKRVTI
Sbjct: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTI 120
Query: 566 MPKDIQLARRIRGERA 581
MPKDIQLARRIRGERA
Sbjct: 121 MPKDIQLARRIRGERA 136
>gnl|CDD|185399 PTZ00017, PTZ00017, histone H2A; Provisional.
Length = 134
Score = 203 bits (518), Expect = 4e-63
Identities = 87/116 (75%), Positives = 98/116 (84%), Gaps = 3/116 (2%)
Query: 1 MSGRGKGGKAKAKSK---TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEY 57
G+GK G KA K +RS++AGLQFPVGR+HR L+KG YA+RVGAGAPVYLAAV+EY
Sbjct: 1 KGGKGKTGGGKAGKKKPVSRSAKAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEY 60
Query: 58 LAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 113
L AEVLELAGNAA+DNKK RI PRH+QLAIRNDEELNKLL+GVTIA GGVLPNI
Sbjct: 61 LTAEVLELAGNAAKDNKKKRITPRHIQLAIRNDEELNKLLAGVTIASGGVLPNIHK 116
>gnl|CDD|128705 smart00428, H3, Histone H3.
Length = 105
Score = 199 bits (507), Expect = 6e-62
Identities = 89/105 (84%), Positives = 93/105 (88%), Gaps = 2/105 (1%)
Query: 479 GGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVM 536
GG K RYRPG VALREIR+YQKST+LLIRK PFQRLVREIAQ F T DLRFQSSA+M
Sbjct: 1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIM 60
Query: 537 ALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 581
ALQEA+EAYLVGLFEDTNL AIHAKRVTIMPKDIQLARRIRGER
Sbjct: 61 ALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIRGERL 105
>gnl|CDD|238029 cd00074, H2A, Histone 2A; H2A is a subunit of the nucleosome. The
nucleosome is an octamer containing two H2A, H2B, H3,
and H4 subunits. The H2A subunit performs essential
roles in maintaining structural integrity of the
nucleosome, chromatin condensation, and binding of
specific chromatin-associated proteins.
Length = 115
Score = 199 bits (508), Expect = 7e-62
Identities = 89/106 (83%), Positives = 96/106 (90%)
Query: 7 GGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELA 66
GGK K+K ++RS+RAGLQFPVGRIHR L+KG YAERVGAGAPVYLAAV+EYL AEVLELA
Sbjct: 3 GGKKKSKKRSRSARAGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELA 62
Query: 67 GNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQ 112
GNAARDNKK RI PRHLQLA+RNDEELNKLL GVTIA GGVLPNI
Sbjct: 63 GNAARDNKKKRITPRHLQLAVRNDEELNKLLKGVTIASGGVLPNIH 108
>gnl|CDD|177758 PLN00157, PLN00157, histone H2A; Provisional.
Length = 132
Score = 194 bits (495), Expect = 9e-60
Identities = 88/115 (76%), Positives = 100/115 (86%), Gaps = 2/115 (1%)
Query: 1 MSGRGK--GGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYL 58
MSGRGK GG K+ +RS++AGLQFPVGRI R L+ G YA RVGAGAPVYLAAV+EYL
Sbjct: 1 MSGRGKRKGGGGGKKATSRSAKAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYL 60
Query: 59 AAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 113
AAEVLELAGNAARDNKK+RI+PRH+QLA+RNDEEL+KLL GVTIA GGVLPNI +
Sbjct: 61 AAEVLELAGNAARDNKKSRIVPRHIQLAVRNDEELSKLLGGVTIAAGGVLPNIHS 115
>gnl|CDD|197711 smart00414, H2A, Histone 2A.
Length = 106
Score = 189 bits (483), Expect = 2e-58
Identities = 87/98 (88%), Positives = 91/98 (92%)
Query: 16 TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK 75
+RS+RAGLQFPVGRIHRLLRKG YA+RVGAGAPVYLAAV+EYL AEVLELAGNAARDNKK
Sbjct: 1 SRSARAGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKK 60
Query: 76 TRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 113
RI PRHLQLAIRNDEELNKLL GVTIAQGGVLPNI
Sbjct: 61 RRITPRHLQLAIRNDEELNKLLKGVTIAQGGVLPNIHK 98
>gnl|CDD|197718 smart00427, H2B, Histone H2B.
Length = 97
Score = 183 bits (465), Expect = 7e-56
Identities = 81/97 (83%), Positives = 93/97 (95%)
Query: 232 KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 291
KK+ +RKE+YAIYIYKVLKQVHPDTG+SS+AMSIMNSFVNDIFERIAAE+S+LA YNK+
Sbjct: 1 KKRVKKRKETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKK 60
Query: 292 STITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 328
ST++SREIQTAVRL+LPGELAKHAVSEGTKAVTK +S
Sbjct: 61 STLSSREIQTAVRLILPGELAKHAVSEGTKAVTKASS 97
>gnl|CDD|215081 PLN00158, PLN00158, histone H2B; Provisional.
Length = 116
Score = 171 bits (433), Expect = 4e-51
Identities = 84/121 (69%), Positives = 96/121 (79%), Gaps = 6/121 (4%)
Query: 209 AGKSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMN 268
A S K KKA K K KK + E+Y IYIYKVLKQVHPDTG+SSKAMSIMN
Sbjct: 2 AKTPSKKPAKKAAKGAK------KKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMN 55
Query: 269 SFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 328
SF+NDIFE+IA E+ +LA YNK+ T+TSREIQTAVRL+LPGELAKHAVSEGTKAVTK+TS
Sbjct: 56 SFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTS 115
Query: 329 S 329
+
Sbjct: 116 A 116
>gnl|CDD|215080 PLN00156, PLN00156, histone H2AX; Provisional.
Length = 139
Score = 172 bits (436), Expect = 4e-51
Identities = 86/113 (76%), Positives = 97/113 (85%), Gaps = 1/113 (0%)
Query: 1 MSGRGKGGKAKA-KSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLA 59
+ +G GK KA KS +RSS+AGLQFPVGRI R L+ G YAERVGAGAPVYL+AV+EYLA
Sbjct: 5 GTTKGGRGKPKATKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLA 64
Query: 60 AEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQ 112
AEVLELAGNAARDNKK RI+PRH+QLA+RNDEEL+KLL VTIA GGVLPNI
Sbjct: 65 AEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGSVTIAAGGVLPNIH 117
>gnl|CDD|227587 COG5262, HTA1, Histone H2A [Chromatin structure and dynamics].
Length = 132
Score = 167 bits (424), Expect = 2e-49
Identities = 89/114 (78%), Positives = 98/114 (85%), Gaps = 2/114 (1%)
Query: 3 GRGKGGKAKA--KSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 60
GKGGKA S++RS++AGL FPVGR+ RLL+KGNY R+GAGAPVYLAAV+EYLAA
Sbjct: 3 SGGKGGKAADARVSQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAA 62
Query: 61 EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAG 114
E+LELAGNAARDNKK RIIPRHLQLAIRNDEELNKLL VTIAQGGVLPNI G
Sbjct: 63 EILELAGNAARDNKKKRIIPRHLQLAIRNDEELNKLLGDVTIAQGGVLPNINPG 116
>gnl|CDD|215082 PLN00161, PLN00161, histone H3; Provisional.
Length = 135
Score = 164 bits (417), Expect = 2e-48
Identities = 83/134 (61%), Positives = 101/134 (75%), Gaps = 8/134 (5%)
Query: 446 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE 505
MAR Q ++ GK P+K+ + ++ KKPHRYRPGTVALREIR+YQKSTE
Sbjct: 1 MARRLQ-GKRFRKGKKPQKEASGVTRQELD------KKPHRYRPGTVALREIRKYQKSTE 53
Query: 506 LLIRKLPFQRLVREIAQDFKTD-LRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVT 564
LLIRKLPF RLVREI+ + + R+ + A++ALQEA+E +LV LFED NLCAIHAKRVT
Sbjct: 54 LLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVT 113
Query: 565 IMPKDIQLARRIRG 578
IMPKD+QLARRIRG
Sbjct: 114 IMPKDMQLARRIRG 127
>gnl|CDD|165721 PLN00153, PLN00153, histone H2A; Provisional.
Length = 129
Score = 161 bits (409), Expect = 2e-47
Identities = 87/113 (76%), Positives = 98/113 (86%)
Query: 1 MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 60
M+GRGKG + K+ +RS++AGLQFPVGRI R L+KG YAER+GAGAPVYLAAV+EYL A
Sbjct: 1 MAGRGKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTA 60
Query: 61 EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 113
EVLELAGNAARDNKK RI+PRH+QLAIRNDEEL KLL VTIA GGVLPNI A
Sbjct: 61 EVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHA 113
>gnl|CDD|185642 PTZ00463, PTZ00463, histone H2B; Provisional.
Length = 117
Score = 142 bits (358), Expect = 3e-40
Identities = 75/113 (66%), Positives = 92/113 (81%), Gaps = 2/113 (1%)
Query: 218 KKAGKAQKNIAKSD--KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIF 275
KK KA+K D KK+K R +SY +YI+KVLKQVHPDTG+S K+M+IMNSF+ D F
Sbjct: 4 KKPAKAKKAATGPDGKKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTF 63
Query: 276 ERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 328
E+IA E+SRL Y +R T++SREIQTA+RL+LPGELAKHAVSEGTKAVTK+TS
Sbjct: 64 EKIATEASRLCKYTRRDTLSSREIQTAIRLVLPGELAKHAVSEGTKAVTKFTS 116
>gnl|CDD|165727 PLN00160, PLN00160, histone H3; Provisional.
Length = 97
Score = 138 bits (349), Expect = 3e-39
Identities = 66/93 (70%), Positives = 80/93 (86%), Gaps = 1/93 (1%)
Query: 488 RPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF-KTDLRFQSSAVMALQEASEAYL 546
RPG AL+EI+ YQKST+LLIR+LPF RLVREI + + R+Q SA++ALQEA+EA+L
Sbjct: 2 RPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHL 61
Query: 547 VGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 579
VGLFED+NLCAIH KRVTIMPKD+QLARRIRG+
Sbjct: 62 VGLFEDSNLCAIHGKRVTIMPKDMQLARRIRGQ 94
>gnl|CDD|177756 PLN00154, PLN00154, histone H2A; Provisional.
Length = 136
Score = 129 bits (326), Expect = 1e-35
Identities = 71/113 (62%), Positives = 83/113 (73%), Gaps = 2/113 (1%)
Query: 1 MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVMEYLA 59
+ K K K K +RSSRAGLQFPVGRIHR L++ A RVGA A VY AA++EYL
Sbjct: 15 TAAAAKKDKDKKKPTSRSSRAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLT 74
Query: 60 AEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQ 112
AEVLELAGNA++D K RI PRHLQLAIR DEEL+ L+ G TIA GGV+P+I
Sbjct: 75 AEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIKG-TIAGGGVIPHIH 126
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4.
Length = 75
Score = 116 bits (294), Expect = 1e-31
Identities = 41/75 (54%), Positives = 50/75 (66%)
Query: 503 STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR 562
S+ LLI KLPF R+VRE+ + F +LR S A +ALQEA E L + ED L A HAKR
Sbjct: 1 SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60
Query: 563 VTIMPKDIQLARRIR 577
TI P+DIQLA R+
Sbjct: 61 KTITPRDIQLAVRLD 75
Score = 92.6 bits (231), Expect = 4e-23
Identities = 33/75 (44%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 17 RSSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK 75
S L+ P R+ R L++G YAE R+ + APV L +E L E+LE AG AR K+
Sbjct: 1 SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60
Query: 76 TRIIPRHLQLAIRND 90
I PR +QLA+R D
Sbjct: 61 KTITPRDIQLAVRLD 75
Score = 90.7 bits (226), Expect = 2e-22
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 236 HRRKESYAIYIYKVLKQVHPD----TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 291
R + +V++++ +SSKA + + D+ E I ++ LA + KR
Sbjct: 1 SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60
Query: 292 STITSREIQTAVRLL 306
TIT R+IQ AVRL
Sbjct: 61 KTITPRDIQLAVRLD 75
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and
dynamics].
Length = 91
Score = 114 bits (288), Expect = 9e-31
Identities = 43/92 (46%), Positives = 58/92 (63%), Gaps = 5/92 (5%)
Query: 489 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVG 548
PG V L+EIRRYQ+ST+LL+ K P +R++R+ + R SSA+ LQEA E YL
Sbjct: 1 PGAVGLKEIRRYQRSTDLLLPKAPVRRILRKAGAE-----RVSSSAIEELQEALEEYLEE 55
Query: 549 LFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 580
+ ED A HAKR T+ +DI+LA + G R
Sbjct: 56 IAEDAVELAEHAKRKTVKAEDIKLALKRLGRR 87
Score = 30.8 bits (70), Expect = 0.42
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 259 VSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPG 309
VSS A+ + + + E IA ++ LA + KR T+ + +I+ A++ L
Sbjct: 37 VSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRR 87
>gnl|CDD|240330 PTZ00252, PTZ00252, histone H2A; Provisional.
Length = 134
Score = 104 bits (261), Expect = 1e-26
Identities = 54/110 (49%), Positives = 75/110 (68%), Gaps = 2/110 (1%)
Query: 9 KAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGN 68
KA RS++AGL FPVGR+ LLR+G YA R+GA VY+AAV+EYL AE+LEL+
Sbjct: 10 KASKSGSGRSAKAGLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVK 69
Query: 69 AARDN--KKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAA 116
AA K R+ PR + LA+R+D++L LL VT+++GGV+P++ A
Sbjct: 70 AAAQQAKKPKRLTPRTVTLAVRHDDDLGSLLKNVTLSRGGVMPSLNKALA 119
>gnl|CDD|165723 PLN00155, PLN00155, histone H2A; Provisional.
Length = 58
Score = 79.0 bits (194), Expect = 2e-18
Identities = 41/58 (70%), Positives = 50/58 (86%)
Query: 1 MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYL 58
M+GRGKG + K+ +RS++AGLQFPVGRI R L+KG YAER+GAGAPVYLAAV+EYL
Sbjct: 1 MAGRGKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYL 58
>gnl|CDD|227572 COG5247, BUR6, Class 2 transcription repressor NC2, alpha subunit
(DRAP1 homolog) [Transcription].
Length = 113
Score = 42.3 bits (99), Expect = 6e-05
Identities = 18/82 (21%), Positives = 37/82 (45%)
Query: 24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHL 83
+FP+ R+ ++++ +VG PV + +E E++ L+ AR R+ L
Sbjct: 23 RFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFL 82
Query: 84 QLAIRNDEELNKLLSGVTIAQG 105
+ A +DE+ + L +
Sbjct: 83 KRATESDEKFDFLKNMEQFKNR 104
>gnl|CDD|201453 pfam00808, CBFD_NFYB_HMF, Histone-like transcription factor
(CBF/NF-Y) and archaeal histone. This family includes
archaebacterial histones and histone like transcription
factors from eukaryotes.
Length = 65
Score = 35.7 bits (83), Expect = 0.005
Identities = 14/63 (22%), Positives = 28/63 (44%)
Query: 25 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQ 84
P+ R+ R+++ A R+ A +A +E + A + K+ I H++
Sbjct: 3 LPIARVKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAEHIK 62
Query: 85 LAI 87
LA+
Sbjct: 63 LAV 65
Score = 31.0 bits (71), Expect = 0.20
Identities = 15/58 (25%), Positives = 29/58 (50%)
Query: 246 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAV 303
+ +++K +S A ++ V + E IA+E++ + KR TI + I+ AV
Sbjct: 8 VKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAEHIKLAV 65
Score = 27.2 bits (61), Expect = 4.7
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 1/65 (1%)
Query: 509 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPK 568
+LP R V+ I + R A + E E ++ + + KR TI +
Sbjct: 1 AELPIAR-VKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAE 59
Query: 569 DIQLA 573
I+LA
Sbjct: 60 HIKLA 64
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 30.1 bits (68), Expect = 0.66
Identities = 8/23 (34%), Positives = 17/23 (73%)
Query: 504 TELLIRKLPFQRLVREIAQDFKT 526
+++L+R +PF+ V+E+ + F T
Sbjct: 1 SKILVRNIPFEATVKELRELFST 23
>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional.
Length = 1052
Score = 31.5 bits (71), Expect = 1.4
Identities = 14/37 (37%), Positives = 17/37 (45%)
Query: 450 KQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHR 486
K A+K KAP K++A K A K A K R
Sbjct: 1014 KAAAKKKVAKKAPAKKVARKPAAKKAAKKPARKAAGR 1050
Score = 30.0 bits (67), Expect = 4.2
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 447 ARTKQTARKSTGGKAP------RKQLATKAARKSAPATGGVKKPHR 486
A K+ A+K+ KA +K A K K APA +KP
Sbjct: 991 AMKKKVAKKAPAKKAAAKKAAAKKAAAKKKVAKKAPAKKVARKPAA 1036
>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein.
Mitofilin controls mitochondrial cristae morphology.
Mitofilin is enriched in the narrow space between the
inner boundary and the outer membranes, where it forms a
homotypic interaction and assembles into a large
multimeric protein complex. The first 78 amino acids
contain a typical amino-terminal-cleavable mitochondrial
presequence rich in positive-charged and hydroxylated
residues and a membrane anchor domain. In addition, it
has three centrally located coiled coil domains.
Length = 493
Score = 30.8 bits (70), Expect = 2.2
Identities = 13/88 (14%), Positives = 29/88 (32%), Gaps = 7/88 (7%)
Query: 211 KSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIY----IYKVLKQVHPDTGVSSKAMSI 266
++ +V K+I + + + +E + + L + D S K ++
Sbjct: 98 EAKATSVAAEATTPKSIQELVEALEELLEELLKETASDPVVQELVSIFNDLIDSIKEDNL 157
Query: 267 M---NSFVNDIFERIAAESSRLAHYNKR 291
S + E + S +LA
Sbjct: 158 KDDLESLIASAKEELDQLSKKLAELKAE 185
>gnl|CDD|173968 cd08050, TAF6, TATA Binding Protein (TBP) Associated Factor 6
(TAF6) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 6 (TAF6) is one of several TAFs that bind TBP and
are involved in forming Transcription Factor IID (TFIID)
complex. TFIID is one of seven General Transcription
Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and
TFIID) that are involved in accurate initiation of
transcription by RNA polymerase II in eukaryotes. TFIID
plays an important role in the recognition of promoter
DNA and assembly of the pre-initiation complex. TFIID
complex is composed of the TBP and at least 13 TAFs.
TAFs are named after their electrophoretic mobility in
polyacrylamide gels in different species. A new, unified
nomenclature has been suggested for the pol II TAFs to
show the relationship between TAF orthologs and
paralogs. Several hypotheses are proposed for TAFs
functions such as serving as activator-binding sites,
core-promoter recognition or a role in essential
catalytic activity. These TAFs, with the help of
specific activators, are required only for expression of
a subset of genes and are not universally involved for
transcription as are GTFs. In yeast and human cells,
TAFs have been found as components of other complexes
besides TFIID. Several TAFs interact via histone-fold
(HFD) motifs; the HFD is the interaction motif involved
in heterodimerization of the core histones and their
assembly into nucleosome octamers. The minimal HFD
contains three alpha-helices linked by two loops and is
found in core histones, TAFs and many other
transcription factors. TFIID has a histone octamer-like
substructure. TAF6 is a shared subunit of histone
acetyltransferase complex SAGA and TFIID complexes. TAF6
domain interacts with TAF9 and makes a novel
histone-like heterodimer that is structurally related to
histones H4 and H3. TAF6 may also interact with the
downstream core promoter element (DPE).
Length = 343
Score = 30.8 bits (70), Expect = 2.3
Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 19/73 (26%)
Query: 506 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI 565
L I L + + +A+D + LR +QEA++ H+KR +
Sbjct: 12 LGIDSLS-DEVAQLLAEDVEYRLR------EIIQEAAK------------FMRHSKRRKL 52
Query: 566 MPKDIQLARRIRG 578
D+ A R+R
Sbjct: 53 TTSDVNHALRLRN 65
>gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF;
Reviewed.
Length = 470
Score = 30.6 bits (70), Expect = 2.5
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 505 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEA 544
E LI K+ F R+ ++A+ K R+Q AV+AL A
Sbjct: 368 EPLIGKVRFSRIGIKLAETHKKGYRWQHEAVIALASPDNA 407
>gnl|CDD|153337 cd07653, F-BAR_CIP4-like, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Cdc42-Interacting Protein
4 and similar proteins. F-BAR domains are dimerization
modules that bind and bend membranes and are found in
proteins involved in membrane dynamics and actin
reorganization. This subfamily is composed of
Cdc42-Interacting Protein 4 (CIP4), Formin Binding
Protein 17 (FBP17), FormiN Binding Protein 1-Like
(FNBP1L), and similar proteins. CIP4 and FNBP1L are
Cdc42 effectors that bind Wiskott-Aldrich syndrome
protein (WASP) and function in endocytosis. CIP4 and
FBP17 bind to the Fas ligand and may be implicated in
the inflammatory response. CIP4 may also play a role in
phagocytosis. Members of this subfamily typically
contain an N-terminal F-BAR domain and a C-terminal SH3
domain. In addition, some members such as FNBP1L contain
a central Cdc42-binding HR1 domain. F-BAR domains form
banana-shaped dimers with a positively-charged concave
surface that binds to negatively-charged lipid
membranes. They can induce membrane deformation in the
form of long tubules.
Length = 251
Score = 29.9 bits (68), Expect = 3.3
Identities = 9/54 (16%), Positives = 17/54 (31%), Gaps = 3/54 (5%)
Query: 518 REIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQ 571
++ Q F + Q + E L + + I AK + + K
Sbjct: 201 TDLPQIFD---KLQELDEKRINRTVELLLQAAEIERKVIPIIAKCLDGIKKAGD 251
>gnl|CDD|185507 PTZ00191, PTZ00191, 60S ribosomal protein L23a; Provisional.
Length = 145
Score = 28.9 bits (65), Expect = 4.3
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 8/67 (11%)
Query: 460 KAPRKQLATKAARKSAPATGGVKK--------PHRYRPGTVALREIRRYQKSTELLIRKL 511
KAP K+ KA + + A GVK +RP T+ L + +Y + + +KL
Sbjct: 1 KAPAKKAKKKAKKAAKAAKKGVKVKKRKVRTSVRFFRPKTLRLPKKPKYPRRVKPASKKL 60
Query: 512 PFQRLVR 518
+++
Sbjct: 61 DKYSIIK 67
>gnl|CDD|173964 cd07981, TAF12, TATA Binding Protein (TBP) Associated Factor 12
(TAF12) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 12 (TAF12) is one of several TAFs that bind TBP
and are involved in forming the TFIID complex. TFIID is
one of the seven General Transcription Factors (GTFs)
(TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are
involved in accurate initiation of transcription by RNA
polymerase II in eukaryotes. TFIID plays an important
role in the recognition of promoter DNA and assembly of
the pre-initiation complex. TFIID complex is composed of
the TBP and at least 13 TAFs. TAFs are named after their
electrophoretic mobility in polyacrylamide gels in
different species. A new, unified nomenclature has been
suggested for the pol II TAFs to show the relationship
between TAF orthologs and paralogs. Several hypotheses
are proposed for TAFs function such as serving as
activator-binding sites, core-promoter recognition or a
role in essential catalytic activity. These TAFs, with
the help of specific activators, are required only for
expression of a subset of genes and are not universally
involved for transcription as are GTFs. In yeast and
human cells, TAFs have been found as components of other
complexes besides TFIID. Several TAFs interact via
histone-fold (HFD) motifs; the HFD is the interaction
motif involved in heterodimerization of the core
histones and their assembly into nucleosome octamers.
The minimal HFD contains three alpha-helices linked by
two loops and is found in core histones, TAFs and many
other transcription factors. TFIID has a histone
octamer-like substructure. TAF12 domain interacts with
TAF4 and makes a novel histone-like heterodimer that
binds DNA and has a core promoter function of a subset
of genes.
Length = 72
Score = 27.2 bits (61), Expect = 4.6
Identities = 10/51 (19%), Positives = 25/51 (49%)
Query: 250 LKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ 300
LK++ P + ++ +D + + ++ RLA + K T+ +++Q
Sbjct: 11 LKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQ 61
>gnl|CDD|112650 pfam03847, TFIID_20kDa, Transcription initiation factor TFIID
subunit A.
Length = 67
Score = 26.9 bits (60), Expect = 4.8
Identities = 10/55 (18%), Positives = 26/55 (47%)
Query: 246 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ 300
+ +++Q+ +T + ++ +D E + + +LA + K + R+IQ
Sbjct: 5 LQDLVQQIDSNTKLDEDVEDLLLEIADDFVESVTTFACKLAKHRKSDKLEVRDIQ 59
>gnl|CDD|217552 pfam03429, MSP1b, Major surface protein 1B. The major surface
protein (MSP1) of the cattle pathogen Anaplasma is a
heterodimer comprised of MSP1a and MSP1b. This family is
the MSP1b chain. There MSP1 proteins are putative
adhesins for bovine erythrocytes.
Length = 726
Score = 29.7 bits (66), Expect = 5.4
Identities = 30/107 (28%), Positives = 45/107 (42%), Gaps = 15/107 (14%)
Query: 271 VNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL--LPGELA-KHAVSEGTKAVTKYT 327
++ +F+R +AE RL + K + T + + ++ L L +L+ K A KA KY
Sbjct: 19 ISAVFQRKSAELQRLNDFIKGADGTLKNVHPHMKSLEALSKQLSEKIAAEAAAKADAKYE 78
Query: 328 SSKCRAKTKQEEGALGFLFGLLGQEHGLDVGQNSSLGDGDAGQELVQ 374
S RAK G LG L L DA ++L Q
Sbjct: 79 SVGLRAKAAAALGNLGRLV------------ARGKLKSSDAPKDLDQ 113
>gnl|CDD|146273 pfam03546, Treacle, Treacher Collins syndrome protein Treacle.
Length = 519
Score = 29.1 bits (64), Expect = 7.0
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 1/66 (1%)
Query: 419 GSAGSDALGVVALAQETVDSSDGELDTMARTKQTARKSTGGKAPRKQLATKAARKSAPAT 478
G G V A QE +SS+ E D+ A+ T K P+ + A A ++ PA
Sbjct: 357 GKTGPAVAQVKAEVQEDSESSEEESDSEEAAATPAQVKTSVKTPQAK-ANPAPTRAPPAK 415
Query: 479 GGVKKP 484
G P
Sbjct: 416 GAASAP 421
>gnl|CDD|220258 pfam09481, CRISPR_Cse1, CRISPR-associated protein Cse1
(CRISPR_cse1). Clusters of short DNA repeats with
non-homologous spacers, which are found at regular
intervals in the genomes of phylogenetically distinct
prokaryotic species, comprise a family with recognisable
features. This family is known as CRISPR (short for
Clustered, Regularly Interspaced Short Palindromic
Repeats). A number of protein families appear only in
association with these repeats and are designated Cas
(CRISPR-Associated) proteins. This entry, represented by
CT1972 from Chlorobaculum tepidum, is found in the
CRISPR/Cas subtype Ecoli regions of many bacteria (most
of which are mesophiles), and not in Archaea. It is
designated Cse1.
Length = 475
Score = 28.9 bits (65), Expect = 8.8
Identities = 17/99 (17%), Positives = 31/99 (31%), Gaps = 16/99 (16%)
Query: 175 TDGGLGDSLDVVTEYFPVP--------LGASFSESLSSLTTAAGKSSGKAVKKAGKAQKN 226
D + + P+P L A E++ A ++ A+K+A A
Sbjct: 356 MDNMQAKWYEWRMDLLPLPAALLSDEDLRAQIKEAVD-AAEEAARALRSALKEAWFALGK 414
Query: 227 IAKSDKKKKHRRKESYAIY-------IYKVLKQVHPDTG 258
AK DK + + ++L + D
Sbjct: 415 DAKGDKSFVDLAGRAEERFWQRLESAFRRLLADLEEDDD 453
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
0.314 0.131 0.360
Gapped
Lambda K H
0.267 0.0663 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 29,150,546
Number of extensions: 2914839
Number of successful extensions: 2177
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2158
Number of HSP's successfully gapped: 62
Length of query: 581
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 479
Effective length of database: 6,413,494
Effective search space: 3072063626
Effective search space used: 3072063626
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: 42 (22.0 bits)
S2: 62 (27.8 bits)