RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3926
(512 letters)
>gnl|CDD|215804 pfam00226, DnaJ, DnaJ domain. DnaJ domains (J-domains) are
associated with hsp70 heat-shock system and it is
thought that this domain mediates the interaction.
DnaJ-domain is therefore part of a chaperone (protein
folding) system. The T-antigens, although not in Prosite
are confirmed as DnaJ containing domains from
literature.
Length = 63
Score = 83.3 bits (207), Expect = 5e-20
Identities = 32/63 (50%), Positives = 41/63 (65%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L + D S+++I+ AYRK ALK HPDKNP D A E F +++A EVL D RA
Sbjct: 1 DYYEILGVPRDASDEEIKKAYRKLALKYHPDKNPGDPAAEEKFKEINEAYEVLSDPEKRA 60
Query: 313 AYD 315
YD
Sbjct: 61 IYD 63
>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog
subfamily C member 17. The CD corresponds to the RRM
of some eukaryotic DnaJ homolog subfamily C member 17
and similar proteins. DnaJ/Hsp40 (heat shock protein
40) proteins are highly conserved and play crucial
roles in protein translation, folding, unfolding,
translocation, and degradation. They act primarily by
stimulating the ATPase activity of Hsp70s, an important
chaperonine family. Members in this family contains an
N-terminal DnaJ domain or J-domain, which mediates the
interaction with Hsp70. They also contains a RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
C-terminus, which may play an essential role in RNA
binding. .
Length = 74
Score = 83.1 bits (206), Expect = 9e-20
Identities = 32/74 (43%), Positives = 50/74 (67%), Gaps = 1/74 (1%)
Query: 24 RLRIRWKSSSTDTDVYTRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAKLY 83
RL+++WK + D Y+ + L KIFSKYG ++ +V+S KK+GSA++EF +A A
Sbjct: 2 RLKVKWKRKKGNGD-YSEDELRKIFSKYGDVSDVVVSSKKKGSAIVEFASKKAAEAAVEN 60
Query: 84 ELGLPNCPLTLNYL 97
E GLP+ PL +++L
Sbjct: 61 ECGLPSNPLLVSWL 74
Score = 83.1 bits (206), Expect = 9e-20
Identities = 32/74 (43%), Positives = 50/74 (67%), Gaps = 1/74 (1%)
Query: 412 RLRIRWKSSSTDTDVYTRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAKLY 471
RL+++WK + D Y+ + L KIFSKYG ++ +V+S KK+GSA++EF +A A
Sbjct: 2 RLKVKWKRKKGNGD-YSEDELRKIFSKYGDVSDVVVSSKKKGSAIVEFASKKAAEAAVEN 60
Query: 472 ELGLPNCPLTLNYL 485
E GLP+ PL +++L
Sbjct: 61 ECGLPSNPLLVSWL 74
>gnl|CDD|236757 PRK10767, PRK10767, chaperone protein DnaJ; Provisional.
Length = 371
Score = 86.4 bits (215), Expect = 2e-18
Identities = 32/63 (50%), Positives = 43/63 (68%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L ++ + SE +I+ AYRK A+K HPD+NP DK+A E F + +A EVL D RA
Sbjct: 5 DYYEVLGVSRNASEDEIKKAYRKLAMKYHPDRNPGDKEAEEKFKEIKEAYEVLSDPQKRA 64
Query: 313 AYD 315
AYD
Sbjct: 65 AYD 67
>gnl|CDD|99751 cd06257, DnaJ, DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock
protein 40) proteins are highly conserved and play
crucial roles in protein translation, folding,
unfolding, translocation, and degradation. They act
primarily by stimulating the ATPase activity of Hsp70s,
an important chaperonine family. Hsp40 proteins are
characterized by the presence of a J domain, which
mediates the interaction with Hsp70. They may contain
other domains as well, and the architectures provide a
means of classification.
Length = 55
Score = 74.1 bits (183), Expect = 7e-17
Identities = 29/55 (52%), Positives = 39/55 (70%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLD 307
D Y +L + D S+++I+ AYRK ALK HPDKNPDD +A E F +++A EVL D
Sbjct: 1 DYYDILGVPPDASDEEIKKAYRKLALKYHPDKNPDDPEAEEKFKEINEAYEVLSD 55
>gnl|CDD|223560 COG0484, DnaJ, DnaJ-class molecular chaperone with C-terminal Zn
finger domain [Posttranslational modification, protein
turnover, chaperones].
Length = 371
Score = 77.7 bits (192), Expect = 2e-15
Identities = 33/63 (52%), Positives = 44/63 (69%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L ++ D SE++I+ AYRK A K HPD+NP DK+A E F +++A EVL D RA
Sbjct: 5 DYYEILGVSKDASEEEIKKAYRKLAKKYHPDRNPGDKEAEEKFKEINEAYEVLSDPEKRA 64
Query: 313 AYD 315
AYD
Sbjct: 65 AYD 67
>gnl|CDD|197617 smart00271, DnaJ, DnaJ molecular chaperone homology domain.
Length = 60
Score = 66.5 bits (163), Expect = 4e-14
Identities = 29/57 (50%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKK-AIETFHLLSKAIEVLLDK 308
D Y +L + D S +I+ AYRK ALK HPDKNP DK+ A E F +++A EVL D
Sbjct: 2 DYYEILGVPRDASLDEIKKAYRKLALKYHPDKNPGDKEEAEEKFKEINEAYEVLSDP 58
>gnl|CDD|233829 TIGR02349, DnaJ_bact, chaperone protein DnaJ. This model
represents bacterial forms of DnaJ, part of the
DnaK-DnaJ-GrpE chaperone system. The three components
typically are encoded by consecutive genes. DnaJ
homologs occur in many genomes, typically not near DnaK
and GrpE-like genes; most such genes are not included by
this family. Eukaryotic (mitochondrial and chloroplast)
forms are not included in the scope of this family.
Length = 354
Score = 71.1 bits (175), Expect = 2e-13
Identities = 31/63 (49%), Positives = 42/63 (66%), Gaps = 1/63 (1%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L ++ D SE++I+ AYRK A K HPD+N DK+A E F +++A EVL D RA
Sbjct: 1 DYYEILGVSKDASEEEIKKAYRKLAKKYHPDRNK-DKEAEEKFKEINEAYEVLSDPEKRA 59
Query: 313 AYD 315
YD
Sbjct: 60 QYD 62
>gnl|CDD|237664 PRK14294, PRK14294, chaperone protein DnaJ; Provisional.
Length = 366
Score = 70.6 bits (173), Expect = 4e-13
Identities = 31/63 (49%), Positives = 42/63 (66%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L +T D SE++I+ +YRK A+K HPD+NP DK+A E F ++A EVL D R
Sbjct: 5 DYYEILGVTRDASEEEIKKSYRKLAMKYHPDRNPGDKEAEELFKEAAEAYEVLSDPKKRG 64
Query: 313 AYD 315
YD
Sbjct: 65 IYD 67
>gnl|CDD|237668 PRK14301, PRK14301, chaperone protein DnaJ; Provisional.
Length = 373
Score = 69.0 bits (169), Expect = 1e-12
Identities = 30/63 (47%), Positives = 42/63 (66%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L ++ D SE +I+ AYRK AL+ HPD+NPD+ +A + F ++A EVL D RA
Sbjct: 5 DYYEVLGVSRDASEDEIKKAYRKLALQYHPDRNPDNPEAEQKFKEAAEAYEVLRDAEKRA 64
Query: 313 AYD 315
YD
Sbjct: 65 RYD 67
>gnl|CDD|184611 PRK14297, PRK14297, chaperone protein DnaJ; Provisional.
Length = 380
Score = 67.1 bits (164), Expect = 5e-12
Identities = 27/63 (42%), Positives = 40/63 (63%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L L S+ +I+ A+RK A+K HPDKN +K+A E F +++A +VL D +A
Sbjct: 5 DYYEVLGLEKGASDDEIKKAFRKLAIKYHPDKNKGNKEAEEKFKEINEAYQVLSDPQKKA 64
Query: 313 AYD 315
YD
Sbjct: 65 QYD 67
>gnl|CDD|237660 PRK14289, PRK14289, chaperone protein DnaJ; Provisional.
Length = 386
Score = 66.4 bits (162), Expect = 8e-12
Identities = 28/63 (44%), Positives = 41/63 (65%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L ++ + +I+ AYRKKA++ HPDKNP DK+A E F ++A +VL D R+
Sbjct: 6 DYYEVLGVSKTATVDEIKKAYRKKAIQYHPDKNPGDKEAEEKFKEAAEAYDVLSDPDKRS 65
Query: 313 AYD 315
YD
Sbjct: 66 RYD 68
>gnl|CDD|237655 PRK14279, PRK14279, chaperone protein DnaJ; Provisional.
Length = 392
Score = 65.5 bits (160), Expect = 2e-11
Identities = 28/63 (44%), Positives = 38/63 (60%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y L ++ D S ++I+ AYRK A + HPD NP D A E F +S+A +VL D + R
Sbjct: 10 DFYKELGVSSDASAEEIKKAYRKLARELHPDANPGDPAAEERFKAVSEAHDVLSDPAKRK 69
Query: 313 AYD 315
YD
Sbjct: 70 EYD 72
>gnl|CDD|237658 PRK14284, PRK14284, chaperone protein DnaJ; Provisional.
Length = 391
Score = 65.2 bits (159), Expect = 2e-11
Identities = 29/64 (45%), Positives = 42/64 (65%)
Query: 252 LDLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSAR 311
+D Y +L ++ S ++I+ AYRK A+K HPDKNP D +A + F +S+A EVL D R
Sbjct: 1 MDYYTILGVSKTASPEEIKKAYRKLAVKYHPDKNPGDAEAEKRFKEVSEAYEVLSDAQKR 60
Query: 312 AAYD 315
+YD
Sbjct: 61 ESYD 64
>gnl|CDD|237654 PRK14278, PRK14278, chaperone protein DnaJ; Provisional.
Length = 378
Score = 64.7 bits (158), Expect = 3e-11
Identities = 29/63 (46%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D YGLL ++ + S+ +I+ AYRK A + HPD NPD+ +A E F +S A EVL D R
Sbjct: 4 DYYGLLGVSRNASDAEIKRAYRKLARELHPDVNPDE-EAQEKFKEISVAYEVLSDPEKRR 62
Query: 313 AYD 315
D
Sbjct: 63 IVD 65
>gnl|CDD|237657 PRK14281, PRK14281, chaperone protein DnaJ; Provisional.
Length = 397
Score = 64.1 bits (156), Expect = 5e-11
Identities = 29/63 (46%), Positives = 41/63 (65%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L ++ + +I+ AYRK ALK HPDKNPD+K+A E F +++A EVL + R
Sbjct: 4 DYYEVLGVSRSADKDEIKKAYRKLALKYHPDKNPDNKEAEEHFKEVNEAYEVLSNDDKRR 63
Query: 313 AYD 315
YD
Sbjct: 64 RYD 66
>gnl|CDD|237662 PRK14292, PRK14292, chaperone protein DnaJ; Provisional.
Length = 371
Score = 62.6 bits (152), Expect = 1e-10
Identities = 30/64 (46%), Positives = 40/64 (62%), Gaps = 1/64 (1%)
Query: 252 LDLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSAR 311
+D Y LL ++ S +I+SAYRK ALK HPD+N +K A E F +++A VL D R
Sbjct: 2 MDYYELLGVSRTASADEIKSAYRKLALKYHPDRNK-EKGAAEKFAQINEAYAVLSDAEKR 60
Query: 312 AAYD 315
A YD
Sbjct: 61 AHYD 64
>gnl|CDD|184599 PRK14277, PRK14277, chaperone protein DnaJ; Provisional.
Length = 386
Score = 62.1 bits (151), Expect = 2e-10
Identities = 30/70 (42%), Positives = 44/70 (62%), Gaps = 2/70 (2%)
Query: 246 MADIKDLDLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVL 305
MA KD Y +L + + +E++I+ AYR+ A K HPD NP DK+A + F +++A E+L
Sbjct: 1 MAAKKDY--YEILGVDRNATEEEIKKAYRRLAKKYHPDLNPGDKEAEQKFKEINEAYEIL 58
Query: 306 LDKSARAAYD 315
D RA YD
Sbjct: 59 SDPQKRAQYD 68
>gnl|CDD|184612 PRK14298, PRK14298, chaperone protein DnaJ; Provisional.
Length = 377
Score = 60.6 bits (147), Expect = 6e-10
Identities = 31/63 (49%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L L+ D S +DI+ AYRK A+K HPDKN + A E F +S+A VL D RA
Sbjct: 6 DYYEILGLSKDASVEDIKKAYRKLAMKYHPDKN-KEPDAEEKFKEISEAYAVLSDAEKRA 64
Query: 313 AYD 315
YD
Sbjct: 65 QYD 67
>gnl|CDD|240236 PTZ00037, PTZ00037, DnaJ_C chaperone protein; Provisional.
Length = 421
Score = 59.8 bits (145), Expect = 1e-09
Identities = 29/62 (46%), Positives = 38/62 (61%), Gaps = 4/62 (6%)
Query: 254 LYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARAA 313
LY +L L+ DC+ +I+ AYRK A+K HPDK D +K F +S+A EVL D R
Sbjct: 30 LYEVLNLSKDCTTSEIKKAYRKLAIKHHPDKGGDPEK----FKEISRAYEVLSDPEKRKI 85
Query: 314 YD 315
YD
Sbjct: 86 YD 87
>gnl|CDD|172774 PRK14286, PRK14286, chaperone protein DnaJ; Provisional.
Length = 372
Score = 59.2 bits (143), Expect = 2e-09
Identities = 26/67 (38%), Positives = 43/67 (64%)
Query: 249 IKDLDLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDK 308
+ + Y +L ++ ++++I+SAYRK A+K HPDKN +K++ E F ++A E+L D
Sbjct: 1 MSERSYYDILGVSKSANDEEIKSAYRKLAIKYHPDKNKGNKESEEKFKEATEAYEILRDP 60
Query: 309 SARAAYD 315
R AYD
Sbjct: 61 KKRQAYD 67
>gnl|CDD|237665 PRK14295, PRK14295, chaperone protein DnaJ; Provisional.
Length = 389
Score = 58.7 bits (142), Expect = 3e-09
Identities = 28/63 (44%), Positives = 38/63 (60%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L + D +E +I+ AYRK A + HPD N D KA E F +S+A +VL D+ R
Sbjct: 10 DYYKVLGVPKDATEAEIKKAYRKLAREYHPDANKGDAKAEERFKEISEAYDVLSDEKKRK 69
Query: 313 AYD 315
YD
Sbjct: 70 EYD 72
>gnl|CDD|225124 COG2214, CbpA, DnaJ-class molecular chaperone [Posttranslational
modification, protein turnover, chaperones].
Length = 237
Score = 57.1 bits (137), Expect = 3e-09
Identities = 31/67 (46%), Positives = 42/67 (62%), Gaps = 1/67 (1%)
Query: 250 KDLDLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKK-AIETFHLLSKAIEVLLDK 308
LD Y +L + + S ++I+ AYRK ALK HPD+NP D K A E F +++A E+L D
Sbjct: 4 DLLDYYEILGVPPNASLEEIKKAYRKLALKYHPDRNPGDPKVAEEKFKEINEAYEILSDP 63
Query: 309 SARAAYD 315
RA YD
Sbjct: 64 ERRAEYD 70
>gnl|CDD|237653 PRK14276, PRK14276, chaperone protein DnaJ; Provisional.
Length = 380
Score = 57.8 bits (140), Expect = 5e-09
Identities = 25/63 (39%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
+ Y L ++ D S+ +I+ AYRK + K HPD N + A E + + +A E L D RA
Sbjct: 5 EYYDRLGVSKDASQDEIKKAYRKLSKKYHPDIN-KEPGAEEKYKEVQEAYETLSDPQKRA 63
Query: 313 AYD 315
AYD
Sbjct: 64 AYD 66
>gnl|CDD|172773 PRK14285, PRK14285, chaperone protein DnaJ; Provisional.
Length = 365
Score = 57.7 bits (139), Expect = 5e-09
Identities = 29/63 (46%), Positives = 41/63 (65%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L L+ S+ +I+ AYRK A+K HPDKN +K+A F ++A EVL+D + RA
Sbjct: 4 DYYEILGLSKGASKDEIKKAYRKIAIKYHPDKNKGNKEAESIFKEATEAYEVLIDDNKRA 63
Query: 313 AYD 315
YD
Sbjct: 64 QYD 66
>gnl|CDD|172776 PRK14288, PRK14288, chaperone protein DnaJ; Provisional.
Length = 369
Score = 57.4 bits (138), Expect = 6e-09
Identities = 29/65 (44%), Positives = 43/65 (66%)
Query: 251 DLDLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSA 310
+L Y +LE+ +++ I+ +YRK ALK HPD+N DK+A E F L+++A VL D+
Sbjct: 2 ELSYYEILEVEKHSNQETIKKSYRKLALKYHPDRNAGDKEAEEKFKLINEAYGVLSDEKK 61
Query: 311 RAAYD 315
RA YD
Sbjct: 62 RALYD 66
>gnl|CDD|237663 PRK14293, PRK14293, chaperone protein DnaJ; Provisional.
Length = 374
Score = 55.8 bits (135), Expect = 2e-08
Identities = 24/63 (38%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L ++ D + +++ AYR+ A K HPD N + A + F +++A EVL D RA
Sbjct: 4 DYYEILGVSRDADKDELKRAYRRLARKYHPDVN-KEPGAEDRFKEINRAYEVLSDPETRA 62
Query: 313 AYD 315
YD
Sbjct: 63 RYD 65
>gnl|CDD|184603 PRK14282, PRK14282, chaperone protein DnaJ; Provisional.
Length = 369
Score = 54.8 bits (132), Expect = 5e-08
Identities = 22/64 (34%), Positives = 42/64 (65%), Gaps = 1/64 (1%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKK-AIETFHLLSKAIEVLLDKSAR 311
D Y +L ++ + ++++I+ AY++ + HPD++P+++K A + F + +A EVL D R
Sbjct: 5 DYYEILGVSRNATQEEIKRAYKRLVKEWHPDRHPENRKEAEQKFKEIQEAYEVLSDPQKR 64
Query: 312 AAYD 315
A YD
Sbjct: 65 AMYD 68
>gnl|CDD|172778 PRK14290, PRK14290, chaperone protein DnaJ; Provisional.
Length = 365
Score = 53.8 bits (129), Expect = 8e-08
Identities = 27/64 (42%), Positives = 40/64 (62%), Gaps = 1/64 (1%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDK-KAIETFHLLSKAIEVLLDKSAR 311
D Y +L + + S++DI+ A+R+ A K HPD +P +K +A E F +S+A EVL D R
Sbjct: 4 DYYKILGVDRNASQEDIKKAFRELAKKWHPDLHPGNKAEAEEKFKEISEAYEVLSDPQKR 63
Query: 312 AAYD 315
YD
Sbjct: 64 RQYD 67
>gnl|CDD|237656 PRK14280, PRK14280, chaperone protein DnaJ; Provisional.
Length = 376
Score = 53.6 bits (129), Expect = 1e-07
Identities = 27/63 (42%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L ++ S+ +I+ AYRK + K HPD N ++ A E F +S+A EVL D RA
Sbjct: 5 DYYEVLGVSKSASKDEIKKAYRKLSKKYHPDIN-KEEGADEKFKEISEAYEVLSDDQKRA 63
Query: 313 AYD 315
YD
Sbjct: 64 QYD 66
>gnl|CDD|237666 PRK14296, PRK14296, chaperone protein DnaJ; Provisional.
Length = 372
Score = 51.9 bits (124), Expect = 4e-07
Identities = 28/67 (41%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 249 IKDLDLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDK 308
+K D Y +L ++ SEQ+IR AYRK A + HPD N A + +++A +VLLDK
Sbjct: 1 MKKKDYYEVLGVSKTASEQEIRQAYRKLAKQYHPDLN-KSPDAHDKMVEINEAADVLLDK 59
Query: 309 SARAAYD 315
R YD
Sbjct: 60 DKRKQYD 66
>gnl|CDD|184604 PRK14283, PRK14283, chaperone protein DnaJ; Provisional.
Length = 378
Score = 51.7 bits (124), Expect = 4e-07
Identities = 24/63 (38%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L + + +++I+ AYRK A K HPD + +++ A E F +S+A VL D R
Sbjct: 6 DYYEVLGVDRNADKKEIKKAYRKLARKYHPDVS-EEEGAEEKFKEISEAYAVLSDDEKRQ 64
Query: 313 AYD 315
YD
Sbjct: 65 RYD 67
>gnl|CDD|237661 PRK14291, PRK14291, chaperone protein DnaJ; Provisional.
Length = 382
Score = 49.4 bits (118), Expect = 2e-06
Identities = 23/63 (36%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L ++ + ++++I+ AYR+ A K HPD N + +A E F +++A +VL D R
Sbjct: 4 DYYEILGVSRNATQEEIKKAYRRLARKYHPDFNK-NPEAEEKFKEINEAYQVLSDPEKRK 62
Query: 313 AYD 315
YD
Sbjct: 63 LYD 65
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an
RNA binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 41.3 bits (98), Expect = 3e-05
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 44 LTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAKLYELGLPNCPL 92
L K+FS +G + + + KK G A +EF ++A +A Y L
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQY---LNGVLF 46
Score = 41.3 bits (98), Expect = 3e-05
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 432 LTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAKLYELGLPNCPL 480
L K+FS +G + + + KK G A +EF ++A +A Y L
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQY---LNGVLF 46
>gnl|CDD|172788 PRK14300, PRK14300, chaperone protein DnaJ; Provisional.
Length = 372
Score = 45.0 bits (106), Expect = 6e-05
Identities = 25/63 (39%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L ++ S+ D++ AY K A + HPD D K A + F ++ A +VL D+ RA
Sbjct: 4 DYYQILGVSKTASQADLKKAYLKLAKQYHPD-TTDAKDAEKKFKEINAAYDVLKDEQKRA 62
Query: 313 AYD 315
AYD
Sbjct: 63 AYD 65
>gnl|CDD|234368 TIGR03835, termin_org_DnaJ, terminal organelle assembly protein
TopJ. This model describes TopJ (MG_200, CbpA), a DnaJ
homolog and probable assembly protein of the Mycoplasma
terminal organelle. The terminal organelle is involved
in both cytadherence and gliding motility [Cellular
processes, Chemotaxis and motility].
Length = 871
Score = 45.2 bits (106), Expect = 8e-05
Identities = 25/63 (39%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L + D EQ+I+ A+RK A K HPD+N A F +++A +VL + RA
Sbjct: 3 DYYEVLGIDRDADEQEIKKAFRKLAKKYHPDRN-KAPDAASIFAEINEANDVLSNPKKRA 61
Query: 313 AYD 315
YD
Sbjct: 62 NYD 64
>gnl|CDD|182347 PRK10266, PRK10266, curved DNA-binding protein CbpA; Provisional.
Length = 306
Score = 44.4 bits (105), Expect = 8e-05
Identities = 25/65 (38%), Positives = 36/65 (55%), Gaps = 5/65 (7%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPD--KNPDDKKAIETFHLLSKAIEVLLDKSA 310
D Y ++ + + I++AYR+ A K HPD K PD A F +++A EVL D+
Sbjct: 5 DYYAIMGVKPTDDLKTIKTAYRRLARKYHPDVSKEPD---AEARFKEVAEAWEVLSDEQR 61
Query: 311 RAAYD 315
RA YD
Sbjct: 62 RAEYD 66
>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in
RNA-binding protein 19 (RBM19) and RNA recognition
motif 3 in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes involved in ribosome biogenesis
by processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well conserved in yeast and its homologues exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 72
Score = 39.5 bits (93), Expect = 2e-04
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 11/61 (18%)
Query: 40 TRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRA------KLYELGLPNCPLT 93
T E L ++F K+G + L++ P R AL+EF AR+A K ++ + PL
Sbjct: 13 TEEELRELFEKFGSLGRLLLPPS-RTIALVEFLEPSDARKAFKSLAYKRFK----HVPLY 67
Query: 94 L 94
L
Sbjct: 68 L 68
Score = 39.5 bits (93), Expect = 2e-04
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 11/61 (18%)
Query: 428 TRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRA------KLYELGLPNCPLT 481
T E L ++F K+G + L++ P R AL+EF AR+A K ++ + PL
Sbjct: 13 TEEELRELFEKFGSLGRLLLPPS-RTIALVEFLEPSDARKAFKSLAYKRFK----HVPLY 67
Query: 482 L 482
L
Sbjct: 68 L 68
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex
in vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the
hnRNA in the nucleus and in processing of pre-mRNA such
as splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 39.1 bits (92), Expect = 2e-04
Identities = 23/51 (45%), Positives = 31/51 (60%), Gaps = 3/51 (5%)
Query: 36 TDVYTRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAKLYELG 86
TD ++E L +IFSKYGK IL IS K G ++F++ + AR A E G
Sbjct: 10 TDKVSKEDLEEIFSKYGK--ILGISLHK-GYGFVQFDNEEDARAAVAGENG 57
Score = 39.1 bits (92), Expect = 2e-04
Identities = 23/51 (45%), Positives = 31/51 (60%), Gaps = 3/51 (5%)
Query: 424 TDVYTRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAKLYELG 474
TD ++E L +IFSKYGK IL IS K G ++F++ + AR A E G
Sbjct: 10 TDKVSKEDLEEIFSKYGK--ILGISLHK-GYGFVQFDNEEDARAAVAGENG 57
>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily. RRM,
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), is a highly abundant domain
in eukaryotes found in proteins involved in
post-transcriptional gene expression processes
including mRNA and rRNA processing, RNA export, and RNA
stability. This domain is 90 amino acids in length and
consists of a four-stranded beta-sheet packed against
two alpha-helices. RRM usually interacts with ssRNA,
but is also known to interact with ssDNA as well as
proteins. RRM binds a variable number of nucleotides,
ranging from two to eight. The active site includes
three aromatic side-chains located within the conserved
RNP1 and RNP2 motifs of the domain. The RRM domain is
found in a variety heterogeneous nuclear
ribonucleoproteins (hnRNPs), proteins implicated in
regulation of alternative splicing, and protein
components of small nuclear ribonucleoproteins
(snRNPs).
Length = 72
Score = 39.2 bits (92), Expect = 2e-04
Identities = 16/45 (35%), Positives = 28/45 (62%), Gaps = 4/45 (8%)
Query: 40 TRESLTKIFSKYGKI-NILVI---SPKKRGSALLEFEHADSARRA 80
T E L ++FSK+G+I ++ ++ K +G A +EFE + A +A
Sbjct: 11 TEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKA 55
Score = 39.2 bits (92), Expect = 2e-04
Identities = 16/45 (35%), Positives = 28/45 (62%), Gaps = 4/45 (8%)
Query: 428 TRESLTKIFSKYGKI-NILVI---SPKKRGSALLEFEHADSARRA 468
T E L ++FSK+G+I ++ ++ K +G A +EFE + A +A
Sbjct: 11 TEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKA 55
>gnl|CDD|227694 COG5407, SEC63, Preprotein translocase subunit Sec63 [Intracellular
trafficking and secretion].
Length = 610
Score = 43.4 bits (102), Expect = 3e-04
Identities = 26/83 (31%), Positives = 40/83 (48%), Gaps = 10/83 (12%)
Query: 242 LSSIMADIKDL-----DLYGLLELTIDCSEQDIRSAYRKKALKCHPDK----NPDDKKAI 292
L S + +K D Y +L + D SE+DI+ YR ++K HPDK + +
Sbjct: 83 LISNIRTLKIEYRRGFDPYEILGIDQDTSERDIKKRYRMLSMKFHPDKAPPMVNELRSEY 142
Query: 293 E-TFHLLSKAIEVLLDKSARAAY 314
E + ++KA +L DK R Y
Sbjct: 143 EEKYKTITKAYGLLTDKKRRENY 165
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 39.1 bits (92), Expect = 3e-04
Identities = 16/47 (34%), Positives = 29/47 (61%), Gaps = 5/47 (10%)
Query: 40 TRESLTKIFSKYGKI-NILVISPKK----RGSALLEFEHADSARRAK 81
T E L ++FSK+GK+ ++ ++ K+ +G A +EFE + A +A
Sbjct: 12 TEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKAL 58
Score = 39.1 bits (92), Expect = 3e-04
Identities = 16/47 (34%), Positives = 29/47 (61%), Gaps = 5/47 (10%)
Query: 428 TRESLTKIFSKYGKI-NILVISPKK----RGSALLEFEHADSARRAK 469
T E L ++FSK+GK+ ++ ++ K+ +G A +EFE + A +A
Sbjct: 12 TEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKAL 58
>gnl|CDD|237667 PRK14299, PRK14299, chaperone protein DnaJ; Provisional.
Length = 291
Score = 42.6 bits (100), Expect = 3e-04
Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARA 312
D Y +L + + S+ +I+ A++K A K HPD N A E F +++A VL D R
Sbjct: 5 DYYAILGVPKNASQDEIKKAFKKLARKYHPDVN-KSPGAEEKFKEINEAYTVLSDPEKRR 63
Query: 313 AYDS 316
YD+
Sbjct: 64 IYDT 67
>gnl|CDD|222986 PHA03102, PHA03102, Small T antigen; Reviewed.
Length = 153
Score = 40.8 bits (96), Expect = 3e-04
Identities = 17/47 (36%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 257 LLELTIDC--SEQDIRSAYRKKALKCHPDKNPDDKKAIETFHLLSKA 301
LL L + +R AY +K L+ HPDK D++K E L K
Sbjct: 10 LLGLPRSAWGNLPLMRKAYLRKCLEFHPDKGGDEEKMKELNTLYKKF 56
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 38.7 bits (91), Expect = 4e-04
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 40 TRESLTKIFSKYGKINILVISPKK---RGSALLEFEHADSARRA 80
T E L + FS YGK+ + + K RG A +EF + A A
Sbjct: 11 TEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAA 54
Score = 38.7 bits (91), Expect = 4e-04
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 428 TRESLTKIFSKYGKINILVISPKK---RGSALLEFEHADSARRA 468
T E L + FS YGK+ + + K RG A +EF + A A
Sbjct: 11 TEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAA 54
>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an
RNA binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins. The RRM structure consists of four strands
and two helices arranged in an alpha/beta sandwich,
with a third helix present during RNA binding in some
cases The C-terminal beta strand (4th strand) and final
helix are hard to align and have been omitted in the
SEED alignment The LA proteins have an N terminal rrm
which is included in the seed. There is a second region
towards the C terminus that has some features
characteristic of a rrm but does not appear to have the
important structural core of a rrm. The LA proteins are
one of the main autoantigens in Systemic lupus
erythematosus (SLE), an autoimmune disease.
Length = 70
Score = 38.0 bits (89), Expect = 5e-04
Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 6/61 (9%)
Query: 39 YTRESLTKIFSKYGKINILVISP----KKRGSALLEFEHADSARRAK--LYELGLPNCPL 92
T E L +FSK+G I + I + +G A +EFE + A +A L L L
Sbjct: 10 TTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGREL 69
Query: 93 T 93
Sbjct: 70 R 70
Score = 38.0 bits (89), Expect = 5e-04
Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 6/61 (9%)
Query: 427 YTRESLTKIFSKYGKINILVISP----KKRGSALLEFEHADSARRAK--LYELGLPNCPL 480
T E L +FSK+G I + I + +G A +EFE + A +A L L L
Sbjct: 10 TTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGREL 69
Query: 481 T 481
Sbjct: 70 R 70
>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split
end) protein family. This subfamily corresponds to the
RRM3 domain in the Spen (split end) protein family
which includes RNA binding motif protein 15 (RBM15),
putative RNA binding motif protein 15B (RBM15B) and
similar proteins found in Metazoa. RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, is a novel mRNA export factor and is a
novel component of the NXF1 pathway. It binds to NXF1
and serves as receptor for the RNA export element RTE.
It also possess mRNA export activity and can facilitate
the access of DEAD-box protein DBP5 to mRNA at the
nuclear pore complex (NPC). RNA-binding protein 15B
(RBM15B), also termed one twenty-two 3 (OTT3), is a
paralog of RBM15 and therefore has post-transcriptional
regulatory activity. It is a nuclear protein sharing
with RBM15 the association with the splicing factor
compartment and the nuclear envelope as well as the
binding to mRNA export factors NXF1 and Aly/REF.
Members in this family belong to the Spen (split end)
protein family, which shares a domain architecture
comprising of three N-terminal RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 72
Score = 37.2 bits (87), Expect = 0.001
Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 40 TRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAK 81
+ L + F ++G I + R A +E+E ++A+ AK
Sbjct: 11 SLAELEREFDRFGAIR-RIDYDPGRNYAYIEYESIEAAQAAK 51
Score = 37.2 bits (87), Expect = 0.001
Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 428 TRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAK 469
+ L + F ++G I + R A +E+E ++A+ AK
Sbjct: 11 SLAELEREFDRFGAIR-RIDYDPGRNYAYIEYESIEAAQAAK 51
>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP
I), heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), and similar proteins. This subfamily
corresponds to the RRM2 of polypyrimidine tract-binding
protein 1 (PTB or hnRNP I), polypyrimidine
tract-binding protein 2 (PTBP2 or nPTB), regulator of
differentiation 1 (Rod1), heterogeneous nuclear
ribonucleoprotein L (hnRNP-L), heterogeneous nuclear
ribonucleoprotein L-like (hnRNP-LL), polypyrimidine
tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins, and RRM3 of
PTBPH1 and PTBPH2. PTB is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other
proteins, heterogeneous nuclear ribonucleoprotein
(hnRNP) H and KH-type splicing-regulatory protein
(KSRP), to the DCS RNA. The binding properties of PTBP2
and its reduced inhibitory activity on splicing imply
roles in controlling the assembly of other
splicing-regulatory proteins. Rod1 is a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset
of differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. This family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity
to other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain).
Although their biological roles remain unclear, both
PTBPH1 and PTBPH2 show significant sequence similarity
to PTB. However, in contrast to PTB, they have three
RRMs. .
Length = 85
Score = 36.8 bits (86), Expect = 0.003
Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 40 TRESLTKIFSKYGKINILVISPKKRG-SALLEFEHADSARRAK 81
T + L ++FS YG + ++I K G AL++F+ +SA AK
Sbjct: 14 TVDVLHQVFSPYGAVEKILIFEKNTGVQALVQFDSVESAENAK 56
Score = 36.8 bits (86), Expect = 0.003
Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 428 TRESLTKIFSKYGKINILVISPKKRG-SALLEFEHADSARRAK 469
T + L ++FS YG + ++I K G AL++F+ +SA AK
Sbjct: 14 TVDVLHQVFSPYGAVEKILIFEKNTGVQALVQFDSVESAENAK 56
>gnl|CDD|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM3 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. It contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 72
Score = 35.4 bits (82), Expect = 0.005
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 40 TRESLTKIFSKYGKINILVISPKKRGS-ALLEFEHADSARRA 80
T E L +F +GK+ +++ P G+ A++EF + AR A
Sbjct: 13 TAEELRDLFEPHGKLTRVLMPPA--GTIAIVEFANPQQARLA 52
Score = 35.4 bits (82), Expect = 0.005
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 428 TRESLTKIFSKYGKINILVISPKKRGS-ALLEFEHADSARRA 468
T E L +F +GK+ +++ P G+ A++EF + AR A
Sbjct: 13 TAEELRDLFEPHGKLTRVLMPPA--GTIAIVEFANPQQARLA 52
>gnl|CDD|227594 COG5269, ZUO1, Ribosome-associated chaperone zuotin [Translation,
ribosomal structure and biogenesis / Posttranslational
modification, protein turnover, chaperones].
Length = 379
Score = 38.9 bits (90), Expect = 0.005
Identities = 30/75 (40%), Positives = 38/75 (50%), Gaps = 5/75 (6%)
Query: 248 DIKDLDLYGLLELTI---DCSEQDIRSAYRKKALKCHPDKNP--DDKKAIETFHLLSKAI 302
+ K +DLY LL L+ I A++KK K HPDK +K E F L+ KA
Sbjct: 39 NWKKVDLYALLGLSKYRTKAIPPQILKAHKKKVYKYHPDKTAAGGNKGCDEFFKLIQKAR 98
Query: 303 EVLLDKSARAAYDSV 317
EVL D+ R YDS
Sbjct: 99 EVLGDRKLRLQYDSN 113
>gnl|CDD|241138 cd12694, RRM2_hnRNPL_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM2 of heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), heterogeneous nuclear ribonucleoprotein
L-like (hnRNP-LL), and similar proteins. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both nuclear
and cytoplasmic roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL plays a critical and unique role in
the signal-induced regulation of CD45 and acts as a
global regulator of alternative splicing in activated T
cells. It is closely related in domain structure and
sequence to hnRNP-L, which contains three
RNA-recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 86
Score = 35.8 bits (83), Expect = 0.006
Identities = 16/42 (38%), Positives = 26/42 (61%)
Query: 40 TRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAK 81
T + + I + +GK+ +VI K A++EF+ DSA+RAK
Sbjct: 16 TVDVIYTICNPHGKVLRIVIFRKNGVQAMVEFDSVDSAQRAK 57
Score = 35.8 bits (83), Expect = 0.006
Identities = 16/42 (38%), Positives = 26/42 (61%)
Query: 428 TRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAK 469
T + + I + +GK+ +VI K A++EF+ DSA+RAK
Sbjct: 16 TVDVIYTICNPHGKVLRIVIFRKNGVQAMVEFDSVDSAQRAK 57
>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in
eukaryotic RNA-binding protein RBM24, RBM38 and similar
proteins. This subfamily corresponds to the RRM of
RBM24 and RBM38 from vertebrate, SUPpressor family
member SUP-12 from Caenorhabditis elegans and similar
proteins. Both, RBM24 and RBM38, are preferentially
expressed in cardiac and skeletal muscle tissues. They
regulate myogenic differentiation by controlling the
cell cycle in a p21-dependent or -independent manner.
RBM24, also termed RNA-binding region-containing
protein 6, interacts with the 3'-untranslated region
(UTR) of myogenin mRNA and regulates its stability in
C2C12 cells. RBM38, also termed CLL-associated antigen
KW-5, or HSRNASEB, or RNA-binding region-containing
protein 1(RNPC1), or ssDNA-binding protein SEB4, is a
direct target of the p53 family. It is required for
maintaining the stability of the basal and
stress-induced p21 mRNA by binding to their 3'-UTRs. It
also binds the AU-/U-rich elements in p63 3'-UTR and
regulates p63 mRNA stability and activity. SUP-12 is a
novel tissue-specific splicing factor that controls
muscle-specific splicing of the ADF/cofilin pre-mRNA in
C. elegans. All family members contain a conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 76
Score = 35.3 bits (82), Expect = 0.006
Identities = 17/46 (36%), Positives = 28/46 (60%), Gaps = 5/46 (10%)
Query: 40 TRESLTKIFSKYGKI-NILVISPKK----RGSALLEFEHADSARRA 80
T +SL K FS++G+I +VI+ ++ RG + F+ +SA RA
Sbjct: 13 TDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERA 58
Score = 35.3 bits (82), Expect = 0.006
Identities = 17/46 (36%), Positives = 28/46 (60%), Gaps = 5/46 (10%)
Query: 428 TRESLTKIFSKYGKI-NILVISPKK----RGSALLEFEHADSARRA 468
T +SL K FS++G+I +VI+ ++ RG + F+ +SA RA
Sbjct: 13 TDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERA 58
>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein
with serine-rich domain 1 (RNPS1) and similar proteins.
This subfamily corresponds to the RRM of RNPS1 and its
eukaryotic homologs. RNPS1, also termed RNA-binding
protein prevalent during the S phase, or SR-related
protein LDC2, was originally characterized as a general
pre-mRNA splicing activator, which activates both
constitutive and alternative splicing of pre-mRNA in
vitro.It has been identified as a protein component of
the splicing-dependent mRNP complex, or exon-exon
junction complex (EJC), and is directly involved in
mRNA surveillance. Furthermore, RNPS1 is a splicing
regulator whose activator function is controlled in
part by CK2 (casein kinase II) protein kinase
phosphorylation. It can also function as a
squamous-cell carcinoma antigen recognized by T cells-3
(SART3)-binding protein, and is involved in the
regulation of mRNA splicing. RNPS1 contains an
N-terminal serine-rich (S) domain, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and the
C-terminal arginine/serine/proline-rich (RS/P) domain.
.
Length = 73
Score = 35.2 bits (82), Expect = 0.006
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 5/49 (10%)
Query: 40 TRESLTKIFSKYGKI-NI-LVISPK---KRGSALLEFEHADSARRAKLY 83
++ L +IFS YG + ++ L I + RG A +EFE + A +A +
Sbjct: 11 NKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKH 59
Score = 35.2 bits (82), Expect = 0.006
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 5/49 (10%)
Query: 428 TRESLTKIFSKYGKI-NI-LVISPK---KRGSALLEFEHADSARRAKLY 471
++ L +IFS YG + ++ L I + RG A +EFE + A +A +
Sbjct: 11 NKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKH 59
>gnl|CDD|237659 PRK14287, PRK14287, chaperone protein DnaJ; Provisional.
Length = 371
Score = 38.5 bits (89), Expect = 0.007
Identities = 24/65 (36%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPD--KNPDDKKAIETFHLLSKAIEVLLDKSA 310
D Y +L + + S +++ AYRK A K HPD K PD A + F + +A + L D
Sbjct: 5 DYYEVLGVDRNASVDEVKKAYRKLARKYHPDVNKAPD---AEDKFKEVKEAYDTLSDPQK 61
Query: 311 RAAYD 315
+A YD
Sbjct: 62 KAHYD 66
>gnl|CDD|222912 PHA02624, PHA02624, large T antigen; Provisional.
Length = 647
Score = 38.4 bits (90), Expect = 0.008
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 254 LYGLLELTIDC--SEQDIRSAYRKKALKCHPDKNPDDKKA 291
L LL L + + +R AY +K + HPDK D++K
Sbjct: 13 LMDLLGLPMAAWGNLPLMRKAYLRKCKEYHPDKGGDEEKM 52
>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic
RNA-binding protein 18 and similar proteins. This
subfamily corresponds to the RRM of RBM18, a putative
RNA-binding protein containing a well-conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). The
biological role of RBM18 remains unclear. .
Length = 80
Score = 34.9 bits (81), Expect = 0.009
Identities = 18/50 (36%), Positives = 22/50 (44%), Gaps = 8/50 (16%)
Query: 40 TRESLTKIFSKYGKIN-----ILVISPKK---RGSALLEFEHADSARRAK 81
T L K+FSKYGKI P K RG + FE + A +A
Sbjct: 12 TEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKAL 61
Score = 34.9 bits (81), Expect = 0.009
Identities = 18/50 (36%), Positives = 22/50 (44%), Gaps = 8/50 (16%)
Query: 428 TRESLTKIFSKYGKIN-----ILVISPKK---RGSALLEFEHADSARRAK 469
T L K+FSKYGKI P K RG + FE + A +A
Sbjct: 12 TEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKAL 61
>gnl|CDD|214922 smart00935, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 140
Score = 36.0 bits (84), Expect = 0.011
Identities = 20/100 (20%), Positives = 45/100 (45%), Gaps = 10/100 (10%)
Query: 315 DSVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAEN--ERYKGYKVNKSEEEI--LQQE 370
+++ K +L+ KK + +LE+ EKE + E+ + SE ++E
Sbjct: 7 QKILQESPAGKAAQKQLEKEFKKRQAELEKLEKELQKLKEKLQKDAATLSEAAREKKEKE 66
Query: 371 IDRLRKEGSIRLQEEIKLMTEELNAA--KELSELNAKLNP 408
+ + +E Q + + + ++L +EL ++ K+N
Sbjct: 67 LQKKVQE----FQRKQQKLQQDLQKRQQEELQKILDKINK 102
>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP
I), heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), and similar proteins. This subfamily
corresponds to the RRM1 of the majority of family
members that include polypyrimidine tract-binding
protein 1 (PTB or hnRNP I), polypyrimidine
tract-binding protein 2 (PTBP2 or nPTB), regulator of
differentiation 1 (Rod1), heterogeneous nuclear
ribonucleoprotein L (hnRNP-L), heterogeneous nuclear
ribonucleoprotein L-like (hnRNP-LL), polypyrimidine
tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. Rod1 is
a mammalian polypyrimidine tract binding protein (PTB)
homolog of a regulator of differentiation in the
fission yeast Schizosaccharomyces pombe, where the nrd1
gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It might play a role controlling
differentiation in mammals. hnRNP-L is a higher
eukaryotic specific subunit of human KMT3a (also known
as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. The family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity
to other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain).
Although their biological roles remain unclear, both
PTBPH1 and PTBPH2 show significant sequence similarity
to PTB. However, in contrast to PTB, they have three
RRMs. In addition, this family also includes
RNA-binding motif protein 20 (RBM20) that is an
alternative splicing regulator associated with dilated
cardiomyopathy (DCM) and contains only one RRM. .
Length = 74
Score = 34.5 bits (80), Expect = 0.012
Identities = 12/41 (29%), Positives = 24/41 (58%), Gaps = 3/41 (7%)
Query: 40 TRESLTKIFSKYGKI-NILVISPKKRGSALLEFEHADSARR 79
T L + S +GK+ N+L++ + + AL+E + +SA+
Sbjct: 12 TESDLIALVSPFGKVTNVLLL--RGKNQALVEMDSVESAKS 50
Score = 34.5 bits (80), Expect = 0.012
Identities = 12/41 (29%), Positives = 24/41 (58%), Gaps = 3/41 (7%)
Query: 428 TRESLTKIFSKYGKI-NILVISPKKRGSALLEFEHADSARR 467
T L + S +GK+ N+L++ + + AL+E + +SA+
Sbjct: 12 TESDLIALVSPFGKVTNVLLL--RGKNQALVEMDSVESAKS 50
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 37.8 bits (88), Expect = 0.013
Identities = 45/192 (23%), Positives = 73/192 (38%), Gaps = 19/192 (9%)
Query: 298 LSKAIEVLLDKSARAAYDSVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAENERYKG- 356
LSK E + + R + R KL+ T ++ +E E E + E E K
Sbjct: 394 LSKVKEEERPREKEGTEEEERREITVYEKRIKKLEETVERLEE--ENSELKRELEELKRE 451
Query: 357 -YKVNKSEEEILQQEIDRLRKEGSIR-LQEEIKLMTEEL-NAAKELSELNAKLNPENYRL 413
K+ E ++ D++RK+ IR I+ + +EL K + EL KL
Sbjct: 452 IEKLESELERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKRVEELERKL---AELR 508
Query: 414 RIRWKSSSTDT------DVYTRESLTKIFSKYGKIN---ILVISPKKRGSALLEFEHADS 464
++R S + T E++ + +YG ILV P G+ E D
Sbjct: 509 KMRKLELSGKGTPVKVVEKLTLEAIEEAEEEYGIKEGDVILVEDPSGGGARTAEEL-IDK 567
Query: 465 ARRAKLYELGLP 476
RA + +
Sbjct: 568 KPRAIIRGEEMS 579
>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small
nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K)
and similar proteins. This subfamily corresponds to the
RRM of U11/U12-35K, also termed protein HM-1, or U1
snRNP-binding protein homolog, and is one of the
components of the U11/U12 snRNP, which is a subunit of
the minor (U12-dependent) spliceosome required for
splicing U12-type nuclear pre-mRNA introns. U11/U12-35K
is highly conserved among bilateria and plants, but
lacks in some organisms, such as Saccharomyces
cerevisiae and Caenorhabditis elegans. Moreover,
U11/U12-35K shows significant sequence homology to U1
snRNP-specific 70 kDa protein (U1-70K or snRNP70). It
contains a conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region, and Arg-Asp and Arg-Glu dipeptide
repeats rich domain, making U11/U12-35K a possible
functional analog of U1-70K. It may facilitate 5' splice
site recognition in the minor spliceosome and play a
role in exon bridging, interacting with components of
the major spliceosome bound to the pyrimidine tract of
an upstream U2-type intron. The family corresponds to
the RRM of U11/U12-35K that may directly contact the U11
or U12 snRNA through the RRM domain.
Length = 93
Score = 34.9 bits (81), Expect = 0.015
Identities = 24/85 (28%), Positives = 39/85 (45%), Gaps = 17/85 (20%)
Query: 33 STDTDVYTRESLTKIFSKYGKINIL-----VISPKKRGSALLEFEHADSARRA--KLYEL 85
S T T E+L ++FS+YG I L +++ +G A +E+EH A RA ++L
Sbjct: 12 SLQT---TEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDAHKL 68
Query: 86 GLPNCPLTLNYLNPDVEREESRKQP 110
+ + V+ E R P
Sbjct: 69 VIDGSEIF-------VDFERERTLP 86
Score = 34.9 bits (81), Expect = 0.015
Identities = 24/85 (28%), Positives = 39/85 (45%), Gaps = 17/85 (20%)
Query: 421 STDTDVYTRESLTKIFSKYGKINIL-----VISPKKRGSALLEFEHADSARRA--KLYEL 473
S T T E+L ++FS+YG I L +++ +G A +E+EH A RA ++L
Sbjct: 12 SLQT---TEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDAHKL 68
Query: 474 GLPNCPLTLNYLNPDVEREESRKQP 498
+ + V+ E R P
Sbjct: 69 VIDGSEIF-------VDFERERTLP 86
>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein
homolog TRA2-alpha, TRA2-beta and similar proteins.
This subfamily corresponds to the RRM of two mammalian
homologs of Drosophila transformer-2 (Tra2),
TRA2-alpha, TRA2-beta (also termed SFRS10), and similar
proteins found in eukaryotes. TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein that specifically
binds to gonadotropin-releasing hormone (GnRH) exonic
splicing enhancer on exon 4 (ESE4) and is necessary for
enhanced GnRH pre-mRNA splicing. It strongly stimulates
GnRH intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent
GnRH pre-mRNA splicing. TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. Both, TRA2-alpha and TRA2-beta, contains a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), flanked by the N- and C-terminal
arginine/serine (RS)-rich regions. .
Length = 78
Score = 34.1 bits (79), Expect = 0.020
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 6/51 (11%)
Query: 37 DVYTRE-SLTKIFSKYGKIN--ILVISPKK---RGSALLEFEHADSARRAK 81
+YT E L ++FS+YG I +V K RG + FE + A+ AK
Sbjct: 8 SLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAK 58
Score = 34.1 bits (79), Expect = 0.020
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 6/51 (11%)
Query: 425 DVYTRE-SLTKIFSKYGKIN--ILVISPKK---RGSALLEFEHADSARRAK 469
+YT E L ++FS+YG I +V K RG + FE + A+ AK
Sbjct: 8 SLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAK 58
>gnl|CDD|224259 COG1340, COG1340, Uncharacterized archaeal coiled-coil protein
[Function unknown].
Length = 294
Score = 36.6 bits (85), Expect = 0.020
Identities = 28/103 (27%), Positives = 45/103 (43%), Gaps = 4/103 (3%)
Query: 308 KSARAAYDSVIRR----KEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSE 363
+ R D + KE+ N+KL RK+++E E+R + R + E
Sbjct: 58 QELREERDEINEEVQELKEKRDEINAKLQELRKEYRELKEKRNEFNLGGRSIKSLEREIE 117
Query: 364 EEILQQEIDRLRKEGSIRLQEEIKLMTEELNAAKELSELNAKL 406
+Q+ L E L ++IK + +EL AK+ E N KL
Sbjct: 118 RLEKKQQTSVLTPEEERELVQKIKELRKELEDAKKALEENEKL 160
>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein A subfamily.
This subfamily corresponds to the RRM2 of hnRNP A0,
hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins.
hnRNP A0 is a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is
an abundant eukaryotic nuclear RNA-binding protein that
may modulate splice site selection in pre-mRNA
splicing. hnRNP A2/B1 is an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 73
Score = 33.4 bits (77), Expect = 0.028
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 40 TRESLTKIFSKYGKI---NILV--ISPKKRGSALLEFEHADSARRAKLY 83
T E L + FS+YG + I+ + KKRG A + F+ D + L
Sbjct: 12 TEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60
Score = 33.4 bits (77), Expect = 0.028
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 428 TRESLTKIFSKYGKI---NILV--ISPKKRGSALLEFEHADSARRAKLY 471
T E L + FS+YG + I+ + KKRG A + F+ D + L
Sbjct: 12 TEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60
>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM1 of RBM26, and
the RRM of RBM27. RBM26, also known as cutaneous T-cell
lymphoma (CTCL) tumor antigen se70-2, represents a
cutaneous lymphoma (CL)-associated antigen. It contains
two RNA recognition motifs (RRMs), also known as RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The RRMs may play some functional roles in
RNA-binding or protein-protein interactions. RBM27
contains only one RRM; its biological function remains
unclear. .
Length = 72
Score = 33.3 bits (77), Expect = 0.028
Identities = 12/44 (27%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 37 DVYTRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRA 80
++ L + FSK+G I + ++ SAL++F ++ A++A
Sbjct: 12 ELNNITKLNEHFSKFGTIVNIQVNYNPE-SALVQFSTSEEAKKA 54
Score = 33.3 bits (77), Expect = 0.028
Identities = 12/44 (27%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 425 DVYTRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRA 468
++ L + FSK+G I + ++ SAL++F ++ A++A
Sbjct: 12 ELNNITKLNEHFSKFGTIVNIQVNYNPE-SALVQFSTSEEAKKA 54
>gnl|CDD|189762 pfam00901, Orbi_VP5, Orbivirus outer capsid protein VP5.
cryoelectron microscopy indicates that VP5 is a trimer
implying that there are 360 copies of VP5 per virion.
Length = 507
Score = 36.2 bits (84), Expect = 0.038
Identities = 27/89 (30%), Positives = 42/89 (47%), Gaps = 19/89 (21%)
Query: 320 RKEEVKIRNSKLDATRKKFKEDLER------REKEAENERYKGY-----------KVNKS 362
++EEV+ +++K +KF EDLE E + E E K K+ K
Sbjct: 101 KEEEVREKHNK--KIIEKFGEDLEEVYKFMKGEAKVEEEEEKQMEILEKALKSYLKIVKE 158
Query: 363 EEEILQQEIDRLRKEGSIRLQEEIKLMTE 391
E + LQ+ L+KE R Q+E K++ E
Sbjct: 159 ENKSLQRLAKALQKESEERTQDETKMIEE 187
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA
repair protein alkB homolog 8 (ALKBH8) and similar
proteins. This subfamily corresponds to the RRM of
ALKBH8, also termed alpha-ketoglutarate-dependent
dioxygenase ABH8, or S-adenosyl-L-methionine-dependent
tRNA methyltransferase ABH8, expressed in various types
of human cancers. It is essential in urothelial
carcinoma cell survival mediated by NOX-1-dependent ROS
signals. ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation
of tRNA modification. ALKBH8 localizes to the
cytoplasm. It contains the characteristic AlkB domain
that is composed of a tRNA methyltransferase motif, a
motif homologous to the bacterial AlkB DNA/RNA repair
enzyme, and a dioxygenase catalytic core domain
encompassing cofactor-binding sites for iron and
2-oxoglutarate. In addition, unlike other AlkB
homologs, ALKBH8 contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a C-terminal
S-adenosylmethionine (SAM)-dependent methyltransferase
(MT) domain. .
Length = 80
Score = 33.0 bits (76), Expect = 0.041
Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 7/65 (10%)
Query: 40 TRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRA------KLYELGLPNCPLT 93
+RE L ++F KYG + LV+ P K + + + A A K EL N PL
Sbjct: 16 SREELLRVFEKYGTVEDLVMPPGK-PYCFVSYSSIEDAAAAYDALNGKELELPQQNKPLY 74
Query: 94 LNYLN 98
L+Y+
Sbjct: 75 LSYVE 79
Score = 33.0 bits (76), Expect = 0.041
Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 7/65 (10%)
Query: 428 TRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRA------KLYELGLPNCPLT 481
+RE L ++F KYG + LV+ P K + + + A A K EL N PL
Sbjct: 16 SREELLRVFEKYGTVEDLVMPPGK-PYCFVSYSSIEDAAAAYDALNGKELELPQQNKPLY 74
Query: 482 LNYLN 486
L+Y+
Sbjct: 75 LSYVE 79
>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl
cis-trans isomerase-like 4 (PPIase) and similar
proteins. This subfamily corresponds to the RRM of
PPIase, also termed cyclophilin-like protein PPIL4, or
rotamase PPIL4, a novel nuclear RNA-binding protein
encoded by cyclophilin-like PPIL4 gene. The precise
role of PPIase remains unclear. PPIase contains a
conserved N-terminal peptidyl-prolyl cistrans isomerase
(PPIase) motif, a central RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a lysine rich
domain, and a pair of bipartite nuclear targeting
sequences (NLS) at the C-terminus.
Length = 83
Score = 33.0 bits (76), Expect = 0.042
Identities = 20/48 (41%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 38 VYTRESLTKIFSKYGKI-NILVISPKKRGSAL----LEFEHADSARRA 80
V T E L IFS++GKI + VI KK G +L +EFE + A
Sbjct: 14 VTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61
Score = 33.0 bits (76), Expect = 0.042
Identities = 20/48 (41%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 426 VYTRESLTKIFSKYGKI-NILVISPKKRGSAL----LEFEHADSARRA 468
V T E L IFS++GKI + VI KK G +L +EFE + A
Sbjct: 14 VTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61
>gnl|CDD|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM1 of heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), heterogeneous nuclear ribonucleoprotein
L-like (hnRNP-LL), and similar proteins. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL plays a critical and unique role in
the signal-induced regulation of CD45 and acts as a
global regulator of alternative splicing in activated T
cells. It is closely related in domain structure and
sequence to hnRNP-L, which contains three
RNA-recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 80
Score = 32.7 bits (75), Expect = 0.062
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 44 LTKIFSKYGKINILVISPKKRGSALLEFEHADSARRA 80
L + S++G I+ + + PKKR AL+EFE A+
Sbjct: 19 LVEALSEFGPISYVTMMPKKR-QALVEFEDISDAKAC 54
Score = 32.7 bits (75), Expect = 0.062
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 432 LTKIFSKYGKINILVISPKKRGSALLEFEHADSARRA 468
L + S++G I+ + + PKKR AL+EFE A+
Sbjct: 19 LVEALSEFGPISYVTMMPKKR-QALVEFEDISDAKAC 54
>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in
serine/arginine-rich splicing factor 3 (SRSF3) and
similar proteins. This subfamily corresponds to the
RRM of two serine/arginine (SR) proteins,
serine/arginine-rich splicing factor 3 (SRSF3) and
serine/arginine-rich splicing factor 7 (SRSF7). SRSF3,
also termed pre-mRNA-splicing factor SRp20, modulates
alternative splicing by interacting with RNA
cis-elements in a concentration- and cell
differentiation-dependent manner. It is also involved
in termination of transcription, alternative RNA
polyadenylation, RNA export, and protein translation.
SRSF3 is critical for cell proliferation, and tumor
induction and maintenance. It can shuttle between the
nucleus and cytoplasm. SRSF7, also termed splicing
factor 9G8, plays a crucial role in both constitutive
splicing and alternative splicing of many pre-mRNAs.
Its localization and functions are tightly regulated by
phosphorylation. SRSF7 is predominantly present in the
nuclear and can shuttle between nucleus and cytoplasm.
It cooperates with the export protein, Tap/NXF1, helps
mRNA export to the cytoplasm, and enhances the
expression of unspliced mRNA. Moreover, SRSF7 inhibits
tau E10 inclusion through directly interacting with the
proximal downstream intron of E10, a clustering region
for frontotemporal dementia with Parkinsonism (FTDP)
mutations. Both SRSF3 and SRSF7 contain a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal RS domain rich in serine-arginine
dipeptides. The RRM domain is involved in RNA binding,
and the RS domain has been implicated in protein
shuttling and protein-protein interactions. .
Length = 73
Score = 32.2 bits (74), Expect = 0.079
Identities = 13/41 (31%), Positives = 19/41 (46%)
Query: 40 TRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRA 80
T+ L F KYG + + ++ G A +EFE A A
Sbjct: 12 TKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDA 52
Score = 32.2 bits (74), Expect = 0.079
Identities = 13/41 (31%), Positives = 19/41 (46%)
Query: 428 TRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRA 468
T+ L F KYG + + ++ G A +EFE A A
Sbjct: 12 TKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDA 52
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 35.1 bits (82), Expect = 0.084
Identities = 24/112 (21%), Positives = 51/112 (45%), Gaps = 24/112 (21%)
Query: 313 AYDSVIRRKE----EVKIRNSKLDATRKKFK----------EDLERREKEAENERYKGYK 358
A + + + + E++ R ++L K+ E LE+RE+E E + +
Sbjct: 62 AKEEIHKLRNEFEKELRERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKE---KE 118
Query: 359 VNKSEEEI--LQQEIDRLRKEGSIRLQEEIKLMTEELNAAKE--LSELNAKL 406
+ + ++E+ ++E++ L +E L+ L EE AKE L ++ +
Sbjct: 119 LEQKQQELEKKEEELEELIEEQLQELERISGLTAEE---AKEILLEKVEEEA 167
Score = 34.4 bits (80), Expect = 0.14
Identities = 26/99 (26%), Positives = 50/99 (50%), Gaps = 19/99 (19%)
Query: 319 RRKEEVKIRNSKLDATRKKF---KEDLERREKEAEN---------ERYKGYKVNKSEEEI 366
R+ E ++ R +L+ K+ +++LE++E+E E ER G +++E +
Sbjct: 100 RKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQELERISGLTAEEAKEIL 159
Query: 367 LQQEIDRLRKEGSIRLQEEIKLMTEELNAAKELSELNAK 405
L++ + R E ++ IK + EE AKE ++ AK
Sbjct: 160 LEKVEEEARHEAAVL----IKEIEEE---AKEEADKKAK 191
Score = 33.6 bits (78), Expect = 0.24
Identities = 23/111 (20%), Positives = 49/111 (44%), Gaps = 5/111 (4%)
Query: 308 KSARAAYDSVI---RRKEEVKIRNSKLDATRK--KFKEDLERREKEAENERYKGYKVNKS 362
K A ++ +++ E + + L+A + K + + E+ +E NE K K
Sbjct: 34 KEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQ 93
Query: 363 EEEILQQEIDRLRKEGSIRLQEEIKLMTEELNAAKELSELNAKLNPENYRL 413
+EE L ++++ L K ++E +L ++ K+ EL + + L
Sbjct: 94 KEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQEL 144
Score = 31.7 bits (73), Expect = 1.0
Identities = 25/84 (29%), Positives = 45/84 (53%), Gaps = 5/84 (5%)
Query: 325 KIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEI--LQQEIDRLRKEGSIRL 382
KI +K+ ++ K LE +KEAE K + +++EEI L+ E ++ +E L
Sbjct: 27 KIAEAKIKEAEEEAKRILEEAKKEAEA--IKKEALLEAKEEIHKLRNEFEKELRERRNEL 84
Query: 383 QE-EIKLMTEELNAAKELSELNAK 405
Q+ E +L+ +E N ++L L +
Sbjct: 85 QKLEKRLLQKEENLDRKLELLEKR 108
>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain. This is a family of proteins of
approximately 300 residues, found in plants and
vertebrates. They contain a highly conserved DDRGK
motif.
Length = 189
Score = 33.9 bits (78), Expect = 0.093
Identities = 26/99 (26%), Positives = 43/99 (43%), Gaps = 11/99 (11%)
Query: 308 KSARAAYDSVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEIL 367
+ R A + +EE K K + RK+ +E E REK+ E E K + +E
Sbjct: 18 RQQREAEE---EEREERKKLEEKREGERKEEEELEEEREKKKEEEERKEREEQARKE--- 71
Query: 368 QQEIDRLRKEGSIRLQEEIKLMTEELNAAKELSELNAKL 406
Q+E ++L+ + + KL +E E +EL
Sbjct: 72 QEEYEKLKSSFVVEEEGTDKLSADE-----ESNELLEDF 105
>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM2 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), is an RNA-binding protein expressed
in the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver.
It is involved in the regulation of mRNA splicing
probably via its complex formation with RNA-binding
protein with a serine-rich domain (RNPS1), a
pre-mRNA-splicing factor. SART3 has also been
identified as a nuclear Tat-interacting protein that
regulates Tat transactivation activity through direct
interaction and functions as an important cellular
factor for HIV-1 gene expression and viral replication.
In addition, SART3 is required for U6 snRNP targeting
to Cajal bodies. It binds specifically and directly to
the U6 snRNA, interacts transiently with the U6 and
U4/U6 snRNPs, and promotes the reassembly of U4/U6
snRNPs after splicing in vitro. SART3 contains an
N-terminal half-a-tetratricopeptide repeat (HAT)-rich
domain, a nuclearlocalization signal (NLS) domain, and
two C-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 32.0 bits (73), Expect = 0.11
Identities = 16/45 (35%), Positives = 27/45 (60%), Gaps = 4/45 (8%)
Query: 40 TRESLTKIFSKYGKINILVI----SPKKRGSALLEFEHADSARRA 80
T+E L K+F K+G + + + S K +G A +E+E+ SA +A
Sbjct: 15 TKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQA 59
Score = 32.0 bits (73), Expect = 0.11
Identities = 16/45 (35%), Positives = 27/45 (60%), Gaps = 4/45 (8%)
Query: 428 TRESLTKIFSKYGKINILVI----SPKKRGSALLEFEHADSARRA 468
T+E L K+F K+G + + + S K +G A +E+E+ SA +A
Sbjct: 15 TKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQA 59
>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, is an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 77
Score = 31.9 bits (73), Expect = 0.12
Identities = 17/49 (34%), Positives = 30/49 (61%), Gaps = 5/49 (10%)
Query: 32 SSTDTDVYTRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRA 80
+ T+ Y LT+ FS+YG + +VI ++RG AL+ F+ ++A+ A
Sbjct: 16 DESVTEQY----LTRHFSRYGPVVHVVID-RQRGQALVFFDKVEAAQAA 59
Score = 31.9 bits (73), Expect = 0.12
Identities = 17/49 (34%), Positives = 30/49 (61%), Gaps = 5/49 (10%)
Query: 420 SSTDTDVYTRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRA 468
+ T+ Y LT+ FS+YG + +VI ++RG AL+ F+ ++A+ A
Sbjct: 16 DESVTEQY----LTRHFSRYGPVVHVVID-RQRGQALVFFDKVEAAQAA 59
>gnl|CDD|240882 cd12436, RRM1_2_MATR3_like, RNA recognition motif 1 and 2 in the
matrin 3 family of nuclear proteins. This subfamily
corresponds to the RRM of the matrin 3 family of
nuclear proteins consisting of Matrin 3 (MATR3),
nuclear protein 220 (NP220) and similar proteins. MATR3
is a highly conserved inner nuclear matrix protein that
has been implicated in various biological processes.
NP220 is a large nucleoplasmic DNA-binding protein that
binds to cytidine-rich sequences, such as CCCCC (G/C),
in double-stranded DNA (dsDNA). Both, Matrin 3 and
NP220, contain two RNA recognition motif (RRM), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a Cys2-His2 zinc
finger-like motif at the C-terminal region. .
Length = 76
Score = 31.5 bits (72), Expect = 0.13
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 39 YTRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSAR 78
YT L K+ +GK++ + P + A +E E + A+
Sbjct: 13 YTEAELLKLAEPFGKVDHYIFLPNRN-KAFIEMESPEDAQ 51
Score = 31.5 bits (72), Expect = 0.13
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 427 YTRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSAR 466
YT L K+ +GK++ + P + A +E E + A+
Sbjct: 13 YTEAELLKLAEPFGKVDHYIFLPNRN-KAFIEMESPEDAQ 51
>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA
binding motif protein 15B (RBM15B) from vertebrate.
This subgroup corresponds to the RRM2 of RBM15B, also
termed one twenty-two 3 (OTT3), a paralog of RNA
binding motif protein 15 (RBM15), also known as
One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear
envelope as well as the binding to mRNA export factors
NXF1 and Aly/REF. RBM15B belongs to the Spen (split
end) protein family, which shares a domain architecture
comprising of three N-terminal RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 85
Score = 31.9 bits (72), Expect = 0.13
Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 4/43 (9%)
Query: 44 LTKIFSKYGKINILVISPKKRGS----ALLEFEHADSARRAKL 82
L + F KYG I +VI RG A L+F++ D A RAK+
Sbjct: 25 LRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKV 67
Score = 31.9 bits (72), Expect = 0.13
Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 4/43 (9%)
Query: 432 LTKIFSKYGKINILVISPKKRGS----ALLEFEHADSARRAKL 470
L + F KYG I +VI RG A L+F++ D A RAK+
Sbjct: 25 LRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKV 67
>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM2 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy
suppressor of sporulation protein Msa1. It is a
putative RNA-binding protein encoded by a novel gene,
msa1, from the fission yeast Schizosaccharomyces pombe.
Msa1 may be involved in the inhibition of sexual
differentiation by controlling the expression of
Ste11-regulated genes, possibly through the
pheromone-signaling pathway. Like RIM4, Msa1 also
contains two RRMs, both of which are essential for the
function of Msa1. .
Length = 80
Score = 31.5 bits (72), Expect = 0.15
Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 40 TRESLTKIFSKYGKI---NILVISPKKRGSALLEFEHADSARRA 80
T+E L + FS++GKI N++ + A ++FE +A RA
Sbjct: 16 TKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARA 59
Score = 31.5 bits (72), Expect = 0.15
Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 428 TRESLTKIFSKYGKI---NILVISPKKRGSALLEFEHADSARRA 468
T+E L + FS++GKI N++ + A ++FE +A RA
Sbjct: 16 TKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARA 59
>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC. All proteins in this family for
which functions are known are part of an exonuclease
complex with sbcD homologs. This complex is involved in
the initiation of recombination to regulate the levels
of palindromic sequences in DNA. 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 = 1042
Score = 34.6 bits (79), Expect = 0.15
Identities = 22/104 (21%), Positives = 40/104 (38%), Gaps = 9/104 (8%)
Query: 315 DSVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEI--LQQEID 372
+ + + + +L + RK+ E+ ++ ++ N+S+E+I LQ
Sbjct: 535 QTYAQLETSEEDVYHQLTSERKQRASLKEQMQEIQQSFSILTQCDNRSKEDIPNLQNITV 594
Query: 373 RLRKEGSIRLQEEIKLMTEELNAAKELSELNAKLNPENYRLRIR 416
RL+ + E L A E L KL PE +R
Sbjct: 595 RLQDLTEKLSEAEDML-------ACEQHALLRKLQPEQDLQDVR 631
>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM3 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 82
Score = 31.4 bits (72), Expect = 0.17
Identities = 12/44 (27%), Positives = 25/44 (56%), Gaps = 5/44 (11%)
Query: 39 YTRESLTKIFSKYGKIN--ILVISP---KKRGSALLEFEHADSA 77
T E L ++FS++G++ +V +G+A ++F+ +SA
Sbjct: 12 ATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESA 55
Score = 31.4 bits (72), Expect = 0.17
Identities = 12/44 (27%), Positives = 25/44 (56%), Gaps = 5/44 (11%)
Query: 427 YTRESLTKIFSKYGKIN--ILVISP---KKRGSALLEFEHADSA 465
T E L ++FS++G++ +V +G+A ++F+ +SA
Sbjct: 12 ATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESA 55
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins.
This subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can
accumulate in the perinucleolar compartment, a dynamic
nuclear substructure that harbors PTB. Raver-1 also
modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes,
particularly in differentiated muscle tissue. Raver-2
is a novel member of the heterogeneous nuclear
ribonucleoprotein (hnRNP) family. It shows high
sequence homology to raver-1. Raver-2 exerts a
spatio-temporal expression pattern during embryogenesis
and is mainly limited to differentiated neurons and
glia cells. Although it displays nucleo-cytoplasmic
shuttling in heterokaryons, raver2 localizes to the
nucleus in glia cells and neurons. Raver-2 can interact
with PTB and may participate in PTB-mediated
RNA-processing. However, there is no evidence
indicating that raver-2 can bind to cytoplasmic
proteins. Both, raver-1 and raver-2, contain three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. They binds to RNA through the
RRMs. In addition, the two [SG][IL]LGxxP motifs serve
as the PTB-binding motifs in raver1. However, raver-2
interacts with PTB through the SLLGEPP motif only. .
Length = 92
Score = 31.5 bits (72), Expect = 0.18
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 44 LTKIFSKYGKINILVISPKK----RGSALLEFEHADSARRAK 81
L K+FS+ GK ++ RG A +E+ A+ A A+
Sbjct: 20 LRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQ 61
Score = 31.5 bits (72), Expect = 0.18
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 432 LTKIFSKYGKINILVISPKK----RGSALLEFEHADSARRAK 469
L K+FS+ GK ++ RG A +E+ A+ A A+
Sbjct: 20 LRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQ 61
>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 157
Score = 33.0 bits (76), Expect = 0.18
Identities = 20/98 (20%), Positives = 42/98 (42%), Gaps = 15/98 (15%)
Query: 314 YDSVIRRKEEVKIRNSKLDATRKKFKEDLERREKE--AENERYKGYKVNKSEEEI----- 366
V+ K +L+ KK + +L+++EKE E ++ + SEE
Sbjct: 23 VQKVLSESPAGKAAQKQLEKEFKKLQAELQKKEKELQKEEQKLQKQAATLSEEARKAKQQ 82
Query: 367 --------LQQEIDRLRKEGSIRLQEEIKLMTEELNAA 396
LQQ+ ++E + QE ++ + ++++ A
Sbjct: 83 ELQQKQQELQQKQQAAQQELQQKQQELLQPIYDKIDKA 120
>gnl|CDD|241224 cd12780, RRM1_hnRNPL, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein L (hnRNP-L).
This subgroup corresponds to the RRM1 of hnRNP-L, a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-L shows significant sequence homology
to polypyrimidine tract-binding protein (PTB or hnRNP
I). Both, hnRNP-L and PTB, are localized in the nucleus
but excluded from the nucleolus. hnRNP-L is an
RNA-binding protein with three RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 31.2 bits (70), Expect = 0.19
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 37 DVYTRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAKLY 83
D L + ++G I+ +V+ PKKR AL+EFE + A A Y
Sbjct: 12 DGVVEADLVEALQEFGTISYVVVMPKKR-QALVEFEDMNGACNAVNY 57
Score = 31.2 bits (70), Expect = 0.19
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 425 DVYTRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAKLY 471
D L + ++G I+ +V+ PKKR AL+EFE + A A Y
Sbjct: 12 DGVVEADLVEALQEFGTISYVVVMPKKR-QALVEFEDMNGACNAVNY 57
>gnl|CDD|241137 cd12693, RRM2_PTBP1_like, RNA recognition motif 2 in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I)
and similar proteins. This subfamily corresponds to
the RRM2 of polypyrimidine tract-binding protein 1 (PTB
or hnRNP I), polypyrimidine tract-binding protein 2
(PTBP2 or nPTB), regulator of differentiation 1 (Rod1),
and similar proteins found in Metazoa. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. PTBP2
also contains four RRMs. ROD1 coding protein Rod1 is a
mammalian PTB homolog of a regulator of differentiation
in the fission yeast Schizosaccharomyces pombe, where
the nrd1 gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It may play a role controlling differentiation
in mammals. All members in this family contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 96
Score = 31.6 bits (72), Expect = 0.19
Identities = 17/44 (38%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 40 TRESLTKIFSKYGKI-NILVISPKKRGSALLEFEHADSARRAKL 82
T + L +IFSK+G + I+ + + AL++F A SA+ AKL
Sbjct: 16 TLDVLHQIFSKFGTVLKIITFTKNNQFQALIQFADAVSAQAAKL 59
Score = 31.6 bits (72), Expect = 0.19
Identities = 17/44 (38%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 428 TRESLTKIFSKYGKI-NILVISPKKRGSALLEFEHADSARRAKL 470
T + L +IFSK+G + I+ + + AL++F A SA+ AKL
Sbjct: 16 TLDVLHQIFSKFGTVLKIITFTKNNQFQALIQFADAVSAQAAKL 59
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit B (eIF-3B) and
similar proteins. This subfamily corresponds to the
RRM domain in eukaryotic translation initiation factor
3 (eIF-3), a large multisubunit complex that plays a
central role in the initiation of translation by
binding to the 40 S ribosomal subunit and promoting the
binding of methionyl-tRNAi and mRNA. eIF-3B, also
termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta,
eIF-3 p110, or eIF-3 p116, is the major scaffolding
subunit of eIF-3. It interacts with eIF-3 subunits A,
G, I, and J. eIF-3B contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
involved in the interaction with eIF-3J. The
interaction between eIF-3B and eIF-3J is crucial for
the eIF-3 recruitment to the 40 S ribosomal subunit.
eIF-3B also binds directly to domain III of the
internal ribosome-entry site (IRES) element of
hepatitis-C virus (HCV) RNA through its N-terminal RRM,
which may play a critical role in both cap-dependent
and cap-independent translation. Additional research
has shown that eIF-3B may function as an oncogene in
glioma cells and can be served as a potential
therapeutic target for anti-glioma therapy. This family
also includes the yeast homolog of eIF-3 subunit B
(eIF-3B, also termed PRT1 or eIF-3 p90) that interacts
with the yeast homologs of eIF-3 subunits A(TIF32),
G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast,
eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A
(TIF32) and eIF-3J (HCR1). In contrast to its human
homolog, yeast eIF-3B (PRT1) may have potential to bind
its total RNA through its RRM domain. .
Length = 84
Score = 31.0 bits (71), Expect = 0.22
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 6/43 (13%)
Query: 44 LTKIFSKYGKINILVI------SPKKRGSALLEFEHADSARRA 80
L KIFSK+G I+ I + K +G A +EF + A+ A
Sbjct: 24 LRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEA 66
Score = 31.0 bits (71), Expect = 0.22
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 6/43 (13%)
Query: 432 LTKIFSKYGKINILVI------SPKKRGSALLEFEHADSARRA 468
L KIFSK+G I+ I + K +G A +EF + A+ A
Sbjct: 24 LRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEA 66
>gnl|CDD|240754 cd12308, RRM1_Spen, RNA recognition motif 1 in the Spen (split
end) protein family. This subfamily corresponds to the
RRM1 domain in the Spen (split end) family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B), and similar
proteins found in Metazoa. RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, is a novel mRNA export factor and component
of the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possesses mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RNA-binding protein 15B (RBM15B),
also known as one twenty-two 3 (OTT3), is a paralog of
RBM15 and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15
the association with the splicing factor compartment
and the nuclear envelope as well as the binding to mRNA
export factors NXF1 and Aly/REF. Members in this family
belong- to the Spen (split end) protein family, which
share a domain architecture comprising of three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. .
Length = 79
Score = 31.1 bits (71), Expect = 0.24
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 37 DVYTRESLTKIFSKYGKINILVI--SPKKRGSALLEFEHADSARRAK 81
D + L F K+G +++ V+ +R A + F H + AR AK
Sbjct: 15 DEDIEDVLYHEFKKFGDVSVRVLHDGEDER-VAYVNFRHPEDAREAK 60
Score = 31.1 bits (71), Expect = 0.24
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 425 DVYTRESLTKIFSKYGKINILVI--SPKKRGSALLEFEHADSARRAK 469
D + L F K+G +++ V+ +R A + F H + AR AK
Sbjct: 15 DEDIEDVLYHEFKKFGDVSVRVLHDGEDER-VAYVNFRHPEDAREAK 60
>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1,
2, 3, 4 family. These eukaryotic proteins recognize the
poly-A of mRNA and consists of four tandem RNA
recognition domains at the N-terminus (rrm: pfam00076)
followed by a PABP-specific domain (pfam00658) at the
C-terminus. The protein is involved in the transport of
mRNA's from the nucleus to the cytoplasm. There are four
paralogs in Homo sapiens which are expressed in testis
(GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ),
broadly expressed (SP:P11940_PABP1) and of unknown
tissue range (SP:Q15097_PABP2).
Length = 562
Score = 33.6 bits (77), Expect = 0.25
Identities = 47/197 (23%), Positives = 86/197 (43%), Gaps = 25/197 (12%)
Query: 285 NPDD-KKAIETFH---LLSKAIEVLL---DKSAR-AAYDSVIRRKEEVKIRNSKLDATRK 336
NP D ++A+ET + L K I ++ D S R + ++ + + + N L T
Sbjct: 51 NPADAERALETMNFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFS 110
Query: 337 KFKEDLERREKEAENERYKGY-KVNKSEEEILQQEIDRLRKEGSIRLQEEIKLMTEELNA 395
KF L + EN + +GY V+ +EE + I ++ G + +E+ +
Sbjct: 111 KFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKV--NGMLLNDKEVYV---GRFI 165
Query: 396 AKELSELNAKLNPENYRLRIRWKSSSTDTDVYTRESLTKIFSKYGKINILVI----SPKK 451
K E A + L ++ + D V + L ++F+K+G+I + S +
Sbjct: 166 KK--HEREAAPLKKFTNLYVK----NLDPSV-NEDKLRELFAKFGEITSAAVMKDGSGRS 218
Query: 452 RGSALLEFEHADSARRA 468
RG A + FE + A +A
Sbjct: 219 RGFAFVNFEKHEDAAKA 235
Score = 32.9 bits (75), Expect = 0.49
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 12/57 (21%)
Query: 36 TDVY--------TRESLTKIFSKYGKINILVI----SPKKRGSALLEFEHADSARRA 80
T++Y + L ++F+K+G+I + S + RG A + FE + A +A
Sbjct: 179 TNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKA 235
>gnl|CDD|220368 pfam09730, BicD, Microtubule-associated protein Bicaudal-D. BicD
proteins consist of three coiled-coiled domains and are
involved in dynein-mediated minus end-directed transport
from the Golgi apparatus to the endoplasmic reticulum
(ER). For full functioning they bind with GSK-3beta
pfam05350 to maintain the anchoring of microtubules to
the centromere. It appears that amino-acid residues
437-617 of BicD and the kinase activity of GSK-3 are
necessary for the formation of a complex between BicD
and GSK-3beta in intact cells.
Length = 711
Score = 33.7 bits (77), Expect = 0.25
Identities = 26/122 (21%), Positives = 54/122 (44%), Gaps = 17/122 (13%)
Query: 284 KNPDDKKAIETFHLLSKAIEVLLDKSARAAYDSVIRRKEEVKIRNSKLDATRKKFKEDLE 343
K+ + + + + E+L K R A V K E+K ++ + +++++++ +
Sbjct: 330 KDRGSHEDGDYYEVDINGPEILECK-YRVAVSEVGELKAELKALKARYNELQERYEDEKD 388
Query: 344 RREKEAENERYKGYKVNKSEEEILQQEIDRLRKEGSIRLQEEIKLMTE-------ELNAA 396
R E +N K + KS E +E S L++E++ +T LNAA
Sbjct: 389 RLRNEIQNLAEKLLSLEKSSHE---------DQERSGDLEKELRKLTHVAGESQGSLNAA 439
Query: 397 KE 398
++
Sbjct: 440 QD 441
>gnl|CDD|184732 PRK14539, PRK14539, 50S ribosomal protein L11/unknown domain fusion
protein; Provisional.
Length = 196
Score = 32.6 bits (74), Expect = 0.29
Identities = 28/85 (32%), Positives = 43/85 (50%), Gaps = 7/85 (8%)
Query: 282 PDKNPDD-KKAIETFHLLSKAIEVLLDKSARAAYDSVIRRKEEVKIRNSKLDATRKKFKE 340
PD N DD ++A+ T +K + VL++ YD V++ KEE K +K A K +
Sbjct: 111 PDLNTDDVEEAMHTIAGTAKNMGVLVE-----GYDDVVKAKEEAKAA-AKAAALAKAKEA 164
Query: 341 DLERREKEAENERYKGYKVNKSEEE 365
L+ E E + + K +VN EE
Sbjct: 165 SLKSAEAELKASKGKSIEVNVIGEE 189
>gnl|CDD|240735 cd12289, RRM_LARP6, RNA recognition motif in La-related protein 6
(LARP6) and similar proteins. This subfamily
corresponds to the RRM of LARP6, also termed Acheron
(Achn), a novel member of the lupus antigen (La)
family. It is expressed predominantly in neurons and
muscle in vertebrates. LARP6 functions as a key
regulatory protein that may play a role in mediating a
variety of developmental and homeostatic processes in
animals, including myogenesis, neurogenesis and
possibly metastasis. LARP6 binds to
Ca2+/calmodulin-dependent serine protein kinase (CASK),
and forms a complex with inhibitor of differentiation
transcription factors. It is structurally related to
the La autoantigen and contains a La motif (LAM),
nuclear localization and export (NLS and NES) signals,
and an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 93
Score = 31.1 bits (71), Expect = 0.30
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 19/60 (31%)
Query: 40 TRESLTKIFSKYGKIN-ILVISPKK------RGS------------ALLEFEHADSARRA 80
T ES+ ++FS G I I ++ P + + A++EFE ++AR+A
Sbjct: 14 TIESVLELFSTCGVIALIRILRPGRTIPPDLKRYSSRHPQLGTKECAVVEFEKLEAARKA 73
Score = 31.1 bits (71), Expect = 0.30
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 19/60 (31%)
Query: 428 TRESLTKIFSKYGKIN-ILVISPKK------RGS------------ALLEFEHADSARRA 468
T ES+ ++FS G I I ++ P + + A++EFE ++AR+A
Sbjct: 14 TIESVLELFSTCGVIALIRILRPGRTIPPDLKRYSSRHPQLGTKECAVVEFEKLEAARKA 73
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 33.5 bits (77), Expect = 0.31
Identities = 25/97 (25%), Positives = 52/97 (53%), Gaps = 11/97 (11%)
Query: 316 SVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRLR 375
+ R +E++ + +L+ +KK KE + E ER++ Y+ K+ ++E++RL+
Sbjct: 325 GIEERIKELEEKEERLEELKKKLKE--LEKRLEELEERHELYEEAKA----KKEELERLK 378
Query: 376 KEGSIRLQEEIKLMTEELNAAK-----ELSELNAKLN 407
K + E+++ EEL AK E+S++ A++
Sbjct: 379 KRLTGLTPEKLEKELEELEKAKEEIEEEISKITARIG 415
Score = 30.4 bits (69), Expect = 2.7
Identities = 23/75 (30%), Positives = 33/75 (44%), Gaps = 2/75 (2%)
Query: 340 EDLERREKEAEN--ERYKGYKVNKSEEEILQQEIDRLRKEGSIRLQEEIKLMTEELNAAK 397
E+LE R KE E Y K + E E ++E+ +L +E +E + K
Sbjct: 588 EELEERLKELEPFYNEYLELKDAEKELEREEKELKKLEEELDKAFEELAETEKRLEELRK 647
Query: 398 ELSELNAKLNPENYR 412
EL EL K + E Y
Sbjct: 648 ELEELEKKYSEEEYE 662
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 33.2 bits (76), Expect = 0.33
Identities = 34/141 (24%), Positives = 52/141 (36%), Gaps = 20/141 (14%)
Query: 35 DTDVYTRESLTKIFSKYGKINILVISPKKRGS--ALLEFEHADSARRAKLYELGLPN--- 89
DV L +IF+ YGK+ +V K AL+EFE +SA+ AK L
Sbjct: 109 TLDV-----LYQIFNPYGKVLRIVTF-TKNNVFQALVEFESVNSAQHAK---AALNGADI 159
Query: 90 ----CPLTLNYLNPDVEREESRKQPKNPVFSNIDFSGPRD-SDSKNVESSNGSDSDSTPN 144
C L + Y P + + ++N D G RD + + P+
Sbjct: 160 YNGCCTLKIEYAKPTRLNVK-YNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPS 218
Query: 145 LFPSANKSSNIFPSADKSSNL 165
+ SS+ P A +
Sbjct: 219 SYGHDGYSSHGGPLAPLAGGD 239
Score = 32.1 bits (73), Expect = 0.71
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 423 DTDVYTRESLTKIFSKYGKINILVISPKKRGS--ALLEFEHADSARRAKL 470
DV L +IF+ YGK+ +V K AL+EFE +SA+ AK
Sbjct: 109 TLDV-----LYQIFNPYGKVLRIVTF-TKNNVFQALVEFESVNSAQHAKA 152
>gnl|CDD|236512 PRK09430, djlA, Dna-J like membrane chaperone protein; Provisional.
Length = 267
Score = 32.9 bits (76), Expect = 0.34
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 253 DLYGLLELTIDCSEQDIRSAYRKKALKCHPDK 284
D Y +L ++ +Q+I+ AYRK + HPDK
Sbjct: 201 DAYKVLGVSESDDDQEIKRAYRKLMSEHHPDK 232
>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear
ribonucleoprotein 70 kDa (U1-70K) and similar proteins.
This subfamily corresponds to the RRM of U1-70K, also
termed snRNP70, a key component of the U1 snRNP
complex, which is one of the key factors facilitating
the splicing of pre-mRNA via interaction at the 5'
splice site, and is involved in regulation of
polyadenylation of some viral and cellular genes,
enhancing or inhibiting efficient poly(A) site usage.
U1-70K plays an essential role in targeting the U1
snRNP to the 5' splice site through protein-protein
interactions with regulatory RNA-binding splicing
factors, such as the RS protein ASF/SF2. Moreover,
U1-70K protein can specifically bind to stem-loop I of
the U1 small nuclear RNA (U1 snRNA) contained in the U1
snRNP complex. It also mediates the binding of U1C,
another U1-specific protein, to the U1 snRNP complex.
U1-70K contains a conserved RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region at the N-terminal half, and two
serine/arginine-rich (SR) domains at the C-terminal
half. The RRM is responsible for the binding of
stem-loop I of U1 snRNA molecule. Additionally, the
most prominent immunodominant region that can be
recognized by auto-antibodies from autoimmune patients
may be located within the RRM. The SR domains are
involved in protein-protein interaction with SR
proteins that mediate 5' splice site recognition. For
instance, the first SR domain is necessary and
sufficient for ASF/SF2 Binding. The family also
includes Drosophila U1-70K that is an essential
splicing factor required for viability in flies, but
its SR domain is dispensable. The yeast U1-70k doesn't
contain easily recognizable SR domains and shows low
sequence similarity in the RRM region with other U1-70k
proteins and therefore not included in this family. The
RRM domain is dispensable for yeast U1-70K function.
Length = 91
Score = 30.7 bits (70), Expect = 0.40
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 5/46 (10%)
Query: 40 TRESLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRA 80
T L + F +YG I + + + K RG A +EFEH + A
Sbjct: 14 TESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAA 59
Score = 30.7 bits (70), Expect = 0.40
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 5/46 (10%)
Query: 428 TRESLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRA 468
T L + F +YG I + + + K RG A +EFEH + A
Sbjct: 14 TESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAA 59
>gnl|CDD|240903 cd12457, RRM_XMAS2, RNA recognition motif in X-linked male
sterile 2 (Xmas-2) and similar proteins. This
subfamily corresponds to the RRM in Xmas-2, the
Drosophila homolog of yeast Sac3p protein, together
with E(y)2, the Drosophila homologue of yeast Sus1p
protein, forming an endogenous complex that is required
in the regulation of mRNA transport and also involved
in the efficient transcription regulation of the
heat-shock protein 70 (hsp70) loci. All family members
are found in insects and contain an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), followed by
a PCI domain.
Length = 71
Score = 30.0 bits (68), Expect = 0.40
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 46 KIFSKYGKINILVISPKKRGSALLEFEHADSARRA 80
K F ++G+I + + P KR + +E+ D A RA
Sbjct: 20 KYFRRFGRIVRITLRP-KRHTCTVEYSSEDEAERA 53
Score = 30.0 bits (68), Expect = 0.40
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 434 KIFSKYGKINILVISPKKRGSALLEFEHADSARRA 468
K F ++G+I + + P KR + +E+ D A RA
Sbjct: 20 KYFRRFGRIVRITLRP-KRHTCTVEYSSEDEAERA 53
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 33.1 bits (76), Expect = 0.41
Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 10/81 (12%)
Query: 336 KKFKEDLERREKEAENERYKGYKVNKSEEEI--LQQEIDRLRKEGSIRLQEEIKLMTEEL 393
KE+LE +E E + E + L++E D L + L+ +I+ + ++
Sbjct: 860 NGKKEELEEELEELEAA------LRDLESRLGDLKKERDELEAQLR-ELERKIEELEAQI 912
Query: 394 NAAKE-LSELNAKLNPENYRL 413
++ LSEL AKL L
Sbjct: 913 EKKRKRLSELKAKLEALEEEL 933
Score = 33.1 bits (76), Expect = 0.45
Identities = 30/120 (25%), Positives = 52/120 (43%), Gaps = 23/120 (19%)
Query: 312 AAYDSVIRRK----EEVKIRNSKLDATRKKFKEDLERREKEAEN-ERYK----------G 356
A +D + EEV+ +LD + ++ LER +E E ERY+ G
Sbjct: 166 AEFDRKKEKALEELEEVEENIERLDLIIDEKRQQLERLRREREKAERYQALLKEKREYEG 225
Query: 357 Y----KVNKSEEEI--LQQEIDRLRKEGSIRLQEEIKLMTEELNAA-KELSELNAKLNPE 409
Y + E + +++++ L +E +L EEI + + L + L ELN K+
Sbjct: 226 YELLKEKEALERQKEAIERQLASLEEELE-KLTEEISELEKRLEEIEQLLEELNKKIKDL 284
>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split
end) protein family. This subfamily corresponds to the
RRM2 domain in the Spen (split end) protein family
which includes RNA binding motif protein 15 (RBM15),
putative RNA binding motif protein 15B (RBM15B), and
similar proteins found in Metazoa. RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, is a novel mRNA export factor and component
of the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possess mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RNA-binding protein 15B (RBM15B),
also termed one twenty-two 3 (OTT3), is a paralog of
RBM15 and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15
the association with the splicing factor compartment
and the nuclear envelope as well as the binding to mRNA
export factors NXF1 and Aly/REF. Members in this family
belong to the Spen (split end) protein family, which
share a domain architecture comprising of three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. .
Length = 79
Score = 30.4 bits (69), Expect = 0.42
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 40 TRESLTKIFSKYGKINILVISPKKRGS----ALLEFEHADSARRAKL 82
T E L + F +YG + + I RG A ++F + D A RAK+
Sbjct: 15 TEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKV 61
Score = 30.4 bits (69), Expect = 0.42
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 428 TRESLTKIFSKYGKINILVISPKKRGS----ALLEFEHADSARRAKL 470
T E L + F +YG + + I RG A ++F + D A RAK+
Sbjct: 15 TEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKV 61
>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain. Axonemal
dynein light chain proteins play a dynamic role in
flagellar and cilia motility. Eukaryotic cilia and
flagella are complex organelles consisting of a core
structure, the axoneme, which is composed of nine
microtubule doublets forming a cylinder that surrounds a
pair of central singlet microtubules. This
ultra-structural arrangement seems to be one of the most
stable micro-tubular assemblies known and is responsible
for the flagellar and ciliary movement of a large number
of organisms ranging from protozoan to mammals. This
light chain interacts directly with the N-terminal half
of the heavy chains.
Length = 189
Score = 32.2 bits (74), Expect = 0.43
Identities = 13/65 (20%), Positives = 30/65 (46%), Gaps = 3/65 (4%)
Query: 335 RKKFKEDLERREKEAENERYKGYKVNKSEEEI--LQQEIDRLRKEGSIRLQEEIKLMTEE 392
RK + + + E E E ++ + + + E+ + L+ +++ + K Q E K +E
Sbjct: 113 RKALQAEQGKSELEQEIKKLEE-EKEELEKRVAELEAKLEAIEKREEEERQIEEKRHADE 171
Query: 393 LNAAK 397
+ K
Sbjct: 172 IAFLK 176
Score = 28.3 bits (64), Expect = 7.9
Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 24/93 (25%)
Query: 300 KAIEVLLDKSARAAY-----DSVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAENERY 354
KA++ KS + ++ V +KL+A K+ +E E++ E +R+
Sbjct: 114 KALQAEQGKSELEQEIKKLEEEKEELEKRVAELEAKLEAIEKREEE-----ERQIEEKRH 168
Query: 355 KGYKVNKSEEEILQQEIDRLRKEGSIRLQEEIK 387
EI L+K+ +L+ +++
Sbjct: 169 -------------ADEIAFLKKQNQ-QLKSQLE 187
>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional.
Length = 508
Score = 32.8 bits (75), Expect = 0.43
Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 1/80 (1%)
Query: 320 RKEEVKIRNSKLDATRKKFKE-DLERREKEAENERYKGYKVNKSEEEILQQEIDRLRKEG 378
R E++ ++L+ K +LE E E + + + E+ + + L E
Sbjct: 96 RAEKLDNLENQLEEREKALSARELELEELEKQLDNELYRVAGLTPEQARKLLLKLLDAEL 155
Query: 379 SIRLQEEIKLMTEELNAAKE 398
+ +K + EE + E
Sbjct: 156 EEEKAQRVKKIEEEADLEAE 175
Score = 30.1 bits (68), Expect = 3.1
Identities = 34/134 (25%), Positives = 55/134 (41%), Gaps = 10/134 (7%)
Query: 304 VLLDKSARAAYDSVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSE 363
VLL K R A ++ +E K KL+A + KE L R + E + E
Sbjct: 23 VLLKKRQRLAKEAERILQEAQKEAEEKLEAALLEAKELLLRERNQQRQE-------ARRE 75
Query: 364 EEILQQEIDRL--RKEGSIRLQEEIKLMTEELNAAKE-LSELNAKLNPENYRLRIRWKSS 420
E LQ+E +RL ++E E++ + +L ++ LS +L +L
Sbjct: 76 REELQREEERLVQKEEQLDARAEKLDNLENQLEEREKALSARELELEELEKQLDNELYRV 135
Query: 421 STDTDVYTRESLTK 434
+ T R+ L K
Sbjct: 136 AGLTPEQARKLLLK 149
>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor. This
model describes the sex-lethal family of splicing
factors found in Dipteran insects. The sex-lethal
phenotype, however, may be limited to the Melanogasters
and closely related species. In Drosophila the protein
acts as an inhibitor of splicing. This subfamily is most
closely related to the ELAV/HUD subfamily of splicing
factors (TIGR01661).
Length = 346
Score = 32.7 bits (74), Expect = 0.44
Identities = 27/96 (28%), Positives = 44/96 (45%), Gaps = 18/96 (18%)
Query: 2 TEELNAAKELSELNAKLNPENYRLRIRWK----SSSTDTDVY--------TRESLTKIFS 49
E ++ + + LN + N RL++ + S DT++Y T + L IF
Sbjct: 157 GSEADSQRAIKNLNG-ITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFG 215
Query: 50 KYGKI---NIL--VISPKKRGSALLEFEHADSARRA 80
KYG+I NIL ++ RG A + F + A+ A
Sbjct: 216 KYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEA 251
Score = 32.7 bits (74), Expect = 0.44
Identities = 27/96 (28%), Positives = 44/96 (45%), Gaps = 18/96 (18%)
Query: 390 TEELNAAKELSELNAKLNPENYRLRIRWK----SSSTDTDVY--------TRESLTKIFS 437
E ++ + + LN + N RL++ + S DT++Y T + L IF
Sbjct: 157 GSEADSQRAIKNLNG-ITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFG 215
Query: 438 KYGKI---NIL--VISPKKRGSALLEFEHADSARRA 468
KYG+I NIL ++ RG A + F + A+ A
Sbjct: 216 KYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEA 251
>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 = 32.7 bits (75), Expect = 0.47
Identities = 30/131 (22%), Positives = 56/131 (42%), Gaps = 8/131 (6%)
Query: 284 KNPDDKKAIETFHL----LSKAIEVLLDKSARAAYDSVIR-RKEEVKIRNSKLDATRKKF 338
D + I + LSK + L + ++ ++EE+ + + R +
Sbjct: 157 LKDDLESLIASAKEELDQLSKKLA-ELKAEEEEELERALKEKREELLSKLEEELLARLES 215
Query: 339 KEDLERREKEAENERYKGYKVNKSEEEILQQEIDRLRKEGSIRLQEEIKLMTEELNAAKE 398
KE ++ E ER K ++ K EE L+QE++R + +L+ E+ L EL +
Sbjct: 216 KEAALEKQLRLEFEREK-EELRKKYEEKLRQELERQAEAHEQKLKNELALQAIELQ-REF 273
Query: 399 LSELNAKLNPE 409
E+ K+ E
Sbjct: 274 NKEIKEKVEEE 284
>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain is
found at the N terminus of SMC proteins. The SMC
(structural maintenance of chromosomes) superfamily
proteins have ATP-binding domains at the N- and
C-termini, and two extended coiled-coil domains
separated by a hinge in the middle. The eukaryotic SMC
proteins form two kind of heterodimers: the SMC1/SMC3
and the SMC2/SMC4 types. These heterodimers constitute
an essential part of higher order complexes, which are
involved in chromatin and DNA dynamics. This family also
includes the RecF and RecN proteins that are involved in
DNA metabolism and recombination.
Length = 1162
Score = 33.0 bits (75), Expect = 0.49
Identities = 37/163 (22%), Positives = 56/163 (34%), Gaps = 17/163 (10%)
Query: 289 KKAIETFHLLSKAIEVLLDKSAR----AAYDSVIRRKEEVKIRNSKLDATRKKFKEDLER 344
+K ++ L A E KS + +E + KL+ KK KE++E
Sbjct: 281 EKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEE 340
Query: 345 REKEAENERYKGYKVNKSEE---------EILQQEIDRLRKEGSIRLQEEIKL----MTE 391
EKE + K + EE E L++E+ +K S RL KL +
Sbjct: 341 LEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELEL 400
Query: 392 ELNAAKELSELNAKLNPENYRLRIRWKSSSTDTDVYTRESLTK 434
+ KE L E L+ K + TK
Sbjct: 401 KNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEELEESLETK 443
Score = 32.2 bits (73), Expect = 0.80
Identities = 19/101 (18%), Positives = 38/101 (37%), Gaps = 9/101 (8%)
Query: 318 IRRKEEVKIRNSKLDATRKKFKEDLERREKEA--------ENERYKGYKVNKSEEEILQQ 369
+ + E K + L+ + K+A + E + + ++ ++
Sbjct: 179 LIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEENLLYLDYLKLNEE 238
Query: 370 EIDRLRKEGSIRLQEEIKLMTEELNAAKELSELNAKLNPEN 410
ID L++ QEEI+ +EL +E+ K N E
Sbjct: 239 RIDLLQELLRDE-QEEIESSKQELEKEEEILAQVLKENKEE 278
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 32.8 bits (75), Expect = 0.54
Identities = 24/113 (21%), Positives = 47/113 (41%), Gaps = 13/113 (11%)
Query: 308 KSARAAYDSVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAEN--ERYKGYK------- 358
++ + + + EE + R L+ + ++ ER E+E E E + +
Sbjct: 789 QALQEELEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELE 848
Query: 359 ----VNKSEEEILQQEIDRLRKEGSIRLQEEIKLMTEELNAAKELSELNAKLN 407
+ E E L++E++ L E E +L E+ +EL EL ++L
Sbjct: 849 EELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELA 901
Score = 31.2 bits (71), Expect = 1.7
Identities = 22/116 (18%), Positives = 48/116 (41%), Gaps = 2/116 (1%)
Query: 320 RKEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRLRKEGS 379
EE++ +L + KE++E E E R + + ++E E L++ ++ L+++
Sbjct: 275 ELEELREELEELQEELLELKEEIEELEGEISLLRER-LEELENELEELEERLEELKEKIE 333
Query: 380 IRLQEEIKLMTEELNAAKELSELNAKLNPENYRLRIRWKSSSTDTDVYTRESLTKI 435
+E + T + L+EL +L + + RE L ++
Sbjct: 334 ALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEAL-REELAEL 388
Score = 28.9 bits (65), Expect = 7.7
Identities = 32/116 (27%), Positives = 47/116 (40%), Gaps = 3/116 (2%)
Query: 288 DKKAIETFHLLSKAIEVLLDKSARAAYDSVIRRKEEVKIRNSKLDATRKKFKEDLERREK 347
+ E + L + L A + + EE++ S+L+ ++ +E+LE E
Sbjct: 208 QAEKAERYQELKAELRELELALLLAKLKELRKELEELEEELSRLEEELEELQEELE--EA 265
Query: 348 EAENERYKGYKVNKSEEEILQQEIDRLRKEGSIRLQEEIKLMTEEL-NAAKELSEL 402
E E E K EE QE KE L+ EI L+ E L EL EL
Sbjct: 266 EKEIEELKSELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEEL 321
>gnl|CDD|216525 pfam01486, K-box, K-box region. The K-box region is commonly found
associated with SRF-type transcription factors see
pfam00319. The K-box is a possible coiled-coil
structure. Possible role in multimer formation.
Length = 100
Score = 30.2 bits (69), Expect = 0.57
Identities = 19/49 (38%), Positives = 29/49 (59%), Gaps = 4/49 (8%)
Query: 361 KSEEEILQQEIDRLRKEGSIRLQEEI-KLMTEELNA--AKELSELNAKL 406
+S+ E LQQE +L+K+ LQ E L+ E+L + KEL +L +L
Sbjct: 11 ESKYENLQQEAAKLKKQNEN-LQREQRHLLGEDLGSLSLKELQQLEQQL 58
>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible
RNA binding protein (CIRBP), RNA binding motif protein
3 (RBM3) and similar proteins. This subfamily
corresponds to the RRM domain of two structurally
related heterogenous nuclear ribonucleoproteins, CIRBP
(also termed CIRP or A18 hnRNP) and RBM3 (also termed
RNPL), both of which belong to a highly conserved cold
shock proteins family. The cold shock proteins can be
induced after exposure to a moderate cold-shock and
other cellular stresses such as UV radiation and
hypoxia. CIRBP and RBM3 may function in
posttranscriptional regulation of gene expression by
binding to different transcripts, thus allowing the
cell to response rapidly to environmental signals.
However, the kinetics and degree of cold induction are
different between CIRBP and RBM3. Tissue distribution
of their expression is different. CIRBP and RBM3 may be
differentially regulated under physiological and stress
conditions and may play distinct roles in cold
responses of cells. CIRBP, also termed glycine-rich
RNA-binding protein CIRP, is localized in the nucleus
and mediates the cold-induced suppression of cell cycle
progression. CIRBP also binds DNA and possibly serves
as a chaperone that assists in the folding/unfolding,
assembly/disassembly and transport of various proteins.
RBM3 may enhance global protein synthesis and the
formation of active polysomes while reducing the levels
of ribonucleoprotein complexes containing microRNAs.
RBM3 may also serve to prevent the loss of muscle mass
by its ability to decrease cell death. Furthermore,
RBM3 may be essential for cell proliferation and
mitosis. Both, CIRBP and RBM3, contain an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), that
is involved in RNA binding, and C-terminal glycine-rich
domain (RGG motif) that probably enhances RNA-binding
via protein-protein and/or protein-RNA interactions.
Like CIRBP, RBM3 can also bind to both RNA and DNA via
its RRM domain. .
Length = 80
Score = 29.8 bits (67), Expect = 0.60
Identities = 16/46 (34%), Positives = 28/46 (60%), Gaps = 5/46 (10%)
Query: 40 TRESLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRA 80
+SL ++FSKYG+I+ +V+ + + RG + FE+ D A+ A
Sbjct: 13 NEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDA 58
Score = 29.8 bits (67), Expect = 0.60
Identities = 16/46 (34%), Positives = 28/46 (60%), Gaps = 5/46 (10%)
Query: 428 TRESLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRA 468
+SL ++FSKYG+I+ +V+ + + RG + FE+ D A+ A
Sbjct: 13 NEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDA 58
>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA
branch site protein p14 (SF3B14) and similar proteins.
This subfamily corresponds to the RRM of SF3B14 (also
termed p14), a 14 kDa protein subunit of SF3B which is
a multiprotein complex that is an integral part of the
U2 small nuclear ribonucleoprotein (snRNP) and the
U11/U12 di-snRNP. SF3B is essential for the accurate
excision of introns from pre-messenger RNA and has been
involved in the recognition of the pre-mRNA's branch
site within the major and minor spliceosomes. SF3B14
associates directly with another SF3B subunit called
SF3B155. It is also present in both U2- and
U12-dependent spliceosomes and may contribute to branch
site positioning in both the major and minor
spliceosome. Moreover, SF3B14 interacts directly with
the pre-mRNA branch adenosine early in spliceosome
assembly and within the fully assembled spliceosome.
SF3B14 contains one well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 77
Score = 29.9 bits (68), Expect = 0.62
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 40 TRESLTKIFSKYGKI-NILV-ISPKKRGSALLEFEHADSARRA 80
+ E L +F KYG I I + + + RG+A + +E A+ A
Sbjct: 15 SSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNA 57
Score = 29.9 bits (68), Expect = 0.62
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 428 TRESLTKIFSKYGKI-NILV-ISPKKRGSALLEFEHADSARRA 468
+ E L +F KYG I I + + + RG+A + +E A+ A
Sbjct: 15 SSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNA 57
>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM3 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. PABP-1 possesses an A-rich sequence in its
5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammalian,
such as ovary and testis. It may play an important role
in germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes the yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 80
Score = 29.8 bits (68), Expect = 0.64
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 12/57 (21%)
Query: 36 TDVY--------TRESLTKIFSKYGKINILVI----SPKKRGSALLEFEHADSARRA 80
T+VY E L ++F KYGKI + K +G + FE+ ++A++A
Sbjct: 2 TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKA 58
Score = 29.8 bits (68), Expect = 0.64
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 12/57 (21%)
Query: 424 TDVY--------TRESLTKIFSKYGKINILVI----SPKKRGSALLEFEHADSARRA 468
T+VY E L ++F KYGKI + K +G + FE+ ++A++A
Sbjct: 2 TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKA 58
>gnl|CDD|193187 pfam12711, Kinesin-relat_1, Kinesin motor. This family is closely
related to Kinesin-related, pfam06548.
Length = 86
Score = 29.9 bits (68), Expect = 0.65
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 321 KEEVKIRNSKLDATRK--KFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRLRK 376
KEE+K+ +++ + +F + R +E R + + + E E+L +EI LR
Sbjct: 30 KEEIKLLREQVEHNPEVTRFALENIRLREE--LRRLQNFYE-QGEREMLLEEISELRD 84
>gnl|CDD|203301 pfam05659, RPW8, Arabidopsis broad-spectrum mildew resistance
protein RPW8. This family consists of several
broad-spectrum mildew resistance proteins from
Arabidopsis thaliana. Plant disease resistance (R) genes
control the recognition of specific pathogens and
activate subsequent defence responses. The Arabidopsis
thaliana locus Resistance To Powdery Mildew 8 (RPW8)
contains two naturally polymorphic, dominant R genes,
RPW8.1 and RPW8.2, which individually control resistance
to a broad range of powdery mildew pathogens. They
induce localised, salicylic acid-dependent defences
similar to those induced by R genes that control
specific resistance. Apparently, broad-spectrum
resistance mediated by RPW8 uses the same mechanisms as
specific resistance.
Length = 147
Score = 30.9 bits (70), Expect = 0.66
Identities = 15/49 (30%), Positives = 24/49 (48%)
Query: 370 EIDRLRKEGSIRLQEEIKLMTEELNAAKELSELNAKLNPENYRLRIRWK 418
+ID+L KE ++ I+ + L A L E A+L N + R+K
Sbjct: 52 QIDKLSKESDDPFRKVIEDLKRLLEKAVSLVEKYAELRRRNLLKKYRYK 100
>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits.
U2AF65 specifically recognizes the intron
polypyrimidine tract upstream of the 3' splice site and
promotes binding of U2 snRNP to the pre-mRNA
branchpoint. U2AF65 also plays an important role in the
nuclear export of mRNA. It facilitates the formation of
a messenger ribonucleoprotein export complex,
containing both the NXF1 receptor and the RNA
substrate. Moreover, U2AF65 interacts directly and
specifically with expanded CAG RNA, and serves as an
adaptor to link expanded CAG RNA to NXF1 for RNA
export. U2AF65 contains an N-terminal RS domain rich in
arginine and serine, followed by a proline-rich segment
and three C-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The N-terminal RS domain
stabilizes the interaction of U2 snRNP with the branch
point (BP) by contacting the branch region, and further
promotes base pair interactions between U2 snRNA and
the BP. The proline-rich segment mediates
protein-protein interactions with the RRM domain of the
small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2
are sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The
family also includes Splicing factor U2AF 50 kDa
subunit (dU2AF50), the Drosophila ortholog of U2AF65.
dU2AF50 functions as an essential pre-mRNA splicing
factor in flies. It associates with intronless mRNAs
and plays a significant and unexpected role in the
nuclear export of a large number of intronless mRNAs.
Length = 89
Score = 29.8 bits (68), Expect = 0.73
Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 42 ESLTKIFSKYGKI-NILVISPKKR-------GSALLEFEHADSARRAKL 82
E + + KYGK+ ++++ P+ G +EF + A++A+L
Sbjct: 26 EDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQL 74
Score = 29.8 bits (68), Expect = 0.73
Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 430 ESLTKIFSKYGKI-NILVISPKKR-------GSALLEFEHADSARRAKL 470
E + + KYGK+ ++++ P+ G +EF + A++A+L
Sbjct: 26 EDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQL 74
>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar
protein interacting with the FHA domain of pKI-67
(NIFK) and similar proteins. This subgroup corresponds
to the RRM of NIFK and Nop15p. NIFK, also termed MKI67
FHA domain-interacting nucleolar phosphoprotein, or
nucleolar phosphoprotein Nopp34, is a putative
RNA-binding protein interacting with the forkhead
associated (FHA) domain of pKi-67 antigen in a
mitosis-specific and phosphorylation-dependent manner.
It is nucleolar in interphase but associates with
condensed mitotic chromosomes. This family also
includes Saccharomyces cerevisiae YNL110C gene encoding
ribosome biogenesis protein 15 (Nop15p), also termed
nucleolar protein 15. Both, NIFK and Nop15p, contain an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 29.5 bits (67), Expect = 0.76
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 42 ESLTKIFSKYGKI-NILVISPKK----RGSALLEFEHADSAR 78
L K FS++G + + + KK +G A +EFE + A+
Sbjct: 14 PELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAK 55
Score = 29.5 bits (67), Expect = 0.76
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 430 ESLTKIFSKYGKI-NILVISPKK----RGSALLEFEHADSAR 466
L K FS++G + + + KK +G A +EFE + A+
Sbjct: 14 PELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAK 55
>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate
heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP
C1/C2). This subgroup corresponds to the RRM of
heterogeneous nuclear ribonucleoprotein C (hnRNP)
proteins C1 and C2, produced by a single coding
sequence. They are the major constituents of the
heterogeneous nuclear RNA (hnRNA) ribonucleoprotein
(hnRNP) complex in vertebrates. They bind hnRNA
tightly, suggesting a central role in the formation of
the ubiquitous hnRNP complex. They are involved in the
packaging of hnRNA in the nucleus and in processing of
pre-mRNA such as splicing and 3'-end formation. hnRNP C
proteins contain two distinct domains, an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal auxiliary domain that includes the
variable region, the basic region and the KSG box rich
in repeated Lys-Ser-Gly sequences, the leucine zipper,
and the acidic region. The RRM is capable of binding
poly(U). The KSG box may bind to RNA. The leucine
zipper may be involved in dimer formation. The acidic
and hydrophilic C-teminus harbors a putative nucleoside
triphosphate (NTP)-binding fold and a protein kinase
phosphorylation site. .
Length = 71
Score = 29.2 bits (65), Expect = 0.76
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 35 DTDVYTRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRA 80
+T V + + IFSKYGKI V +G A +++ + +AR A
Sbjct: 10 NTLVVKKSDVEAIFSKYGKI---VGCSVHKGFAFVQYVNERNARAA 52
Score = 29.2 bits (65), Expect = 0.76
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 423 DTDVYTRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRA 468
+T V + + IFSKYGKI V +G A +++ + +AR A
Sbjct: 10 NTLVVKKSDVEAIFSKYGKI---VGCSVHKGFAFVQYVNERNARAA 52
>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core
protein A1, an abundant eukaryotic nuclear RNA-binding
protein that may modulate splice site selection in
pre-mRNA splicing. hnRNP A1 has been characterized as a
splicing silencer, often acting in opposition to an
activating hnRNP H. It silences exons when bound to
exonic elements in the alternatively spliced
transcripts of c-src, HIV, GRIN1, and beta-tropomyosin.
hnRNP A1 can shuttle between the nucleus and the
cytoplasm. Thus, it may be involved in transport of
cellular RNAs, including the packaging of pre-mRNA into
hnRNP particles and transport of poly A+ mRNA from the
nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has
high affinity with AU-rich elements, whereas the
nuclear hnRNP A1 has high affinity with a
polypyrimidine stretch bordered by AG at the 3' ends of
introns. hnRNP A1 is also involved in the replication
of an RNA virus, such as mouse hepatitis virus (MHV),
through an interaction with the
transcription-regulatory region of viral RNA. Moreover,
hnRNP A1, together with the scaffold protein septin 6,
serves as host proteins to form a complex with NS5b and
viral RNA, and further play important roles in the
replication of Hepatitis C virus (HCV). hnRNP A1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. The RRMs of hnRNP A1 play an important role
in silencing the exon and the glycine-rich domain is
responsible for protein-protein interactions. .
Length = 77
Score = 29.6 bits (66), Expect = 0.82
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 44 LTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARR 79
L F +YGKI ++ I S KKRG A + F+ DS +
Sbjct: 17 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 57
Score = 29.6 bits (66), Expect = 0.82
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 432 LTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARR 467
L F +YGKI ++ I S KKRG A + F+ DS +
Sbjct: 17 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 57
>gnl|CDD|223618 COG0544, Tig, FKBP-type peptidyl-prolyl cis-trans isomerase
(trigger factor) [Posttranslational modification,
protein turnover, chaperones].
Length = 441
Score = 31.9 bits (73), Expect = 0.89
Identities = 22/88 (25%), Positives = 41/88 (46%), Gaps = 9/88 (10%)
Query: 328 NSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEE--------ILQQEIDRLRKEGS 379
L+ ++K +++LER KEA E+ K ++ E +++ EID L K+
Sbjct: 259 EDTLEELKEKLRKNLERELKEATLEKRKEQLLDALVEANDFDLPESLVEAEIDNLLKQAL 318
Query: 380 IRLQE-EIKLMTEELNAAKELSELNAKL 406
+LQ+ I + + +EL E +
Sbjct: 319 QQLQQQGIDSLEASGESEEELREEFKEE 346
>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA
recognition motif 1 (hRBMY), testis-specific
heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T)
and similar proteins. This subfamily corresponds to
the RRM domain of hnRNP G, also termed glycoprotein p43
or RBMX, an RNA-binding motif protein located on the X
chromosome. It is expressed ubiquitously and has been
implicated in the splicing control of several
pre-mRNAs. Moreover, hnRNP G may function as a
regulator of transcription for SREBP-1c and GnRH1.
Research has shown that hnRNP G may also act as a
tumor-suppressor since it upregulates the Txnip gene
and promotes the fidelity of DNA end-joining activity.
In addition, hnRNP G appears to play a critical role in
proper neural development of zebrafish and frog
embryos. The family also includes several paralogs of
hnRNP G, such as hRBMY and hnRNP G-T (also termed
RNA-binding motif protein, X-linked-like-2). Both,
hRBMY and hnRNP G-T, are exclusively expressed in
testis and critical for male fertility. Like hnRNP G,
hRBMY and hnRNP G-T interact with factors implicated in
the regulation of pre-mRNA splicing, such as
hTra2-beta1 and T-STAR. Although members in this family
share a high conserved N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), they appear to recognize
different RNA targets. For instance, hRBMY interacts
specifically with a stem-loop structure in which the
loop is formed by the sequence CA/UCAA. In contrast,
hnRNP G associates with single stranded RNA sequences
containing a CCA/C motif. In addition to the RRM, hnRNP
G contains a nascent transcripts targeting domain (NTD)
in the middle region and a novel auxiliary RNA-binding
domain (RBD) in its C-terminal region. The C-terminal
RBD exhibits distinct RNA binding specificity, and
would play a critical role in the regulation of
alternative splicing by hnRNP G. .
Length = 80
Score = 29.5 bits (67), Expect = 0.92
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 5/46 (10%)
Query: 40 TRESLTKIFSKYGKIN--ILVISP---KKRGSALLEFEHADSARRA 80
T + L +FSK+G++ +L+ P + RG + FE + A A
Sbjct: 14 TEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAA 59
Score = 29.5 bits (67), Expect = 0.92
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 5/46 (10%)
Query: 428 TRESLTKIFSKYGKIN--ILVISP---KKRGSALLEFEHADSARRA 468
T + L +FSK+G++ +L+ P + RG + FE + A A
Sbjct: 14 TEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAA 59
>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the
U1A/U2B"/SNF protein family. This subfamily
corresponds to the RRM1 of U1A/U2B"/SNF protein family
which contains Drosophila sex determination protein SNF
and its two mammalian counterparts, U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2
small nuclear ribonucleoprotein B" (U2 snRNP B" or
U2B"), all of which consist of two RNA recognition
motifs (RRMs), connected by a variable, flexible
linker. SNF is an RNA-binding protein found in the U1
and U2 snRNPs of Drosophila where it is essential in
sex determination and possesses a novel dual RNA
binding specificity. SNF binds with high affinity to
both Drosophila U1 snRNA stem-loop II (SLII) and U2
snRNA stem-loop IV (SLIV). It can also bind to poly(U)
RNA tracts flanking the alternatively spliced
Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal
protein (SXL). U1A is an RNA-binding protein associated
with the U1 snRNP, a small RNA-protein complex involved
in pre-mRNA splicing. U1A binds with high affinity and
specificity to stem-loop II (SLII) of U1 snRNA. It is
predominantly a nuclear protein that shuttles between
the nucleus and the cytoplasm independently of
interactions with U1 snRNA. Moreover, U1A may be
involved in RNA 3'-end processing, specifically
cleavage, splicing and polyadenylation, through
interacting with a large number of non-snRNP proteins.
U2B", initially identified to bind to stem-loop IV
(SLIV) at the 3' end of U2 snRNA, is a unique protein
that comprises of the U2 snRNP. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. Moreover, U2B" does not
require an auxiliary protein for binding to RNA, and
its nuclear transport is independent of U2 snRNA
binding. .
Length = 78
Score = 29.0 bits (66), Expect = 1.0
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 41 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAK 81
+ SL +FS++G + +I+ + K RG A + F+ +SA A
Sbjct: 17 KRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNAL 59
Score = 29.0 bits (66), Expect = 1.0
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 429 RESLTKIFSKYGKI-NILVI-SPKKRGSALLEFEHADSARRAK 469
+ SL +FS++G + +I+ + K RG A + F+ +SA A
Sbjct: 17 KRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNAL 59
>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM2 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 76
Score = 29.1 bits (66), Expect = 1.0
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 40 TRESLTKIFSKYGKINILVI----SPKKRGSALLEFEHADSARRA 80
T L K+FS +G + + I KK+G A ++F A +A
Sbjct: 12 TEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKA 56
Score = 29.1 bits (66), Expect = 1.0
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 428 TRESLTKIFSKYGKINILVI----SPKKRGSALLEFEHADSARRA 468
T L K+FS +G + + I KK+G A ++F A +A
Sbjct: 12 TEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKA 56
>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2
protein homolog beta (TRA-2 beta) and similar proteins.
This subgroup corresponds to the RRM of TRA2-beta or
TRA-2-beta, also termed splicing factor,
arginine/serine-rich 10 (SFRS10), or transformer-2
protein homolog B, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. It contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. TRA2-beta
specifically binds to two types of RNA sequences, the
CAA and (GAA)2 sequences, through the RRMs in different
RNA binding modes. .
Length = 89
Score = 29.2 bits (65), Expect = 1.2
Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 40 TRESLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRAK 81
T L ++FSKYG I + I S + RG A + FE+ D A+ AK
Sbjct: 22 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 68
Score = 29.2 bits (65), Expect = 1.2
Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 428 TRESLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRAK 469
T L ++FSKYG I + I S + RG A + FE+ D A+ AK
Sbjct: 22 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 68
>gnl|CDD|165099 PHA02732, PHA02732, hypothetical protein; Provisional.
Length = 1467
Score = 31.6 bits (71), Expect = 1.2
Identities = 38/149 (25%), Positives = 62/149 (41%), Gaps = 13/149 (8%)
Query: 115 FSNIDFSGPR-DSDSKNVESSNGSDSDSTPNLFPSANKSSNIFPSADKSSNLFPTADKSS 173
+S I + R D+D+ S + +P F S S IF ++ SS + P S
Sbjct: 1040 WSEIGYVAIRVDTDNIFYVSYFAASQGPSPFTFVSP---SYIFLNSWASSYVAPGFLGSP 1096
Query: 174 HLFPIADKSSNLF---PSADKSSNIFSS-SSKPRNVFPSGLFPSANVSSNIFASSDRTLP 229
+ P ++ + K N+FS V + L+ ++ S + A L
Sbjct: 1097 YALPYFMNQTSALVGNTALPKGLNVFSGYMFGAGTVASAFLYMNSTPQSPVLAL----LL 1152
Query: 230 EPHISWSFPAIPLS-SIMADIKDLDLYGL 257
P+IS+ F A+ L SI AD L+G+
Sbjct: 1153 APYISYKFNALSLGFSITADAAIFSLFGI 1181
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 31.4 bits (72), Expect = 1.2
Identities = 15/70 (21%), Positives = 40/70 (57%), Gaps = 6/70 (8%)
Query: 324 VKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRLR--KEGSIR 381
+ ++L+ +K +++++R EK+ NE + V K+ EE++++E ++L + +
Sbjct: 812 LAAELARLEKELEKLEKEIDRIEKKLSNEGF----VAKAPEEVVEKEKEKLAEYQVKLAK 867
Query: 382 LQEEIKLMTE 391
L+E + ++
Sbjct: 868 LEERLAVLKA 877
>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin. Trichoplein
or mitostatin, was first defined as a meiosis-specific
nuclear structural protein. It has since been linked
with mitochondrial movement. It is associated with the
mitochondrial outer membrane, and over-expression leads
to reduction in mitochondrial motility whereas lack of
it enhances mitochondrial movement. The activity appears
to be mediated through binding the mitochondria to the
actin intermediate filaments (IFs).
Length = 349
Score = 31.4 bits (72), Expect = 1.2
Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 2/83 (2%)
Query: 335 RKKFKEDLERREKEAENERYKGYKVNKSEEEI-LQQEIDRLRKEGSIRLQEEIKLMTEEL 393
R + KE E+ + E + Y+ K+E E + E ++E + E
Sbjct: 137 RIERKE-EEKEREREEELKILEYQREKAEREEEREAERRERKEEKEREVARLRAQQEEAE 195
Query: 394 NAAKELSELNAKLNPENYRLRIR 416
+ +EL EL A L E Y + R
Sbjct: 196 DEREELDELRADLYQEEYERKER 218
Score = 29.9 bits (68), Expect = 3.7
Identities = 29/132 (21%), Positives = 50/132 (37%), Gaps = 20/132 (15%)
Query: 301 AIEVLLDKSARAAYDSVIRRKEEVKIR-----NSKLDATR------KKFKEDLERREKEA 349
++ L + Y+ R+KE+ + +L R K+ + ER E+EA
Sbjct: 200 ELDELRADLYQEEYERKERQKEKEEAEKRRRQKQELQRAREEQIEEKEERLQEERAEEEA 259
Query: 350 ENERYKGYKVNKSEEEILQQEIDRLRKEGSIRLQEEIKLMTEE------LNAAKELSELN 403
E ER + +EE+ +QE R+ + + E++ EE +EL E
Sbjct: 260 ERERML--EKQAEDEEL-EQENAEKRRMKRLEHRRELEQQIEEKEERRAAEREEELEEGE 316
Query: 404 AKLNPENYRLRI 415
E R
Sbjct: 317 RLREEEAERQAR 328
Score = 29.1 bits (66), Expect = 5.6
Identities = 22/95 (23%), Positives = 40/95 (42%), Gaps = 13/95 (13%)
Query: 318 IRRKEEVKI---RNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRL 374
R + + R K R++ + L+ + +E E R + Y+ E E + + I+R+
Sbjct: 49 EERLKALAEEEERERKRKEERREGRAVLQEQIEEREKRRQEEYEERLQEREQMDEIIERI 108
Query: 375 RKEGS----------IRLQEEIKLMTEELNAAKEL 399
++E +L+EEI EE KE
Sbjct: 109 QEEDEAEAQEKREKQKKLREEIDEFNEERIERKEE 143
Score = 28.7 bits (65), Expect = 8.2
Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 8/79 (10%)
Query: 322 EEVKIRNSKLDATR------KKFKEDLERREKEAENERYKGYKVNKSEEEILQ--QEIDR 373
EE++ N KL A + + +E + +E E ER + + + L +E +R
Sbjct: 4 EELRELNEKLRAAKVNKERDAQIEEKKRIKAEEKEEERRIDEMMEEERLKALAEEEERER 63
Query: 374 LRKEGSIRLQEEIKLMTEE 392
RKE + ++ EE
Sbjct: 64 KRKEERREGRAVLQEQIEE 82
>gnl|CDD|233830 TIGR02350, prok_dnaK, chaperone protein DnaK. Members of this
family are the chaperone DnaK, of the DnaK-DnaJ-GrpE
chaperone system. All members of the seed alignment were
taken from completely sequenced bacterial or archaeal
genomes and (except for Mycoplasma sequence) found
clustered with other genes of this systems. This model
excludes DnaK homologs that are not DnaK itself, such as
the heat shock cognate protein HscA (TIGR01991).
However, it is not designed to distinguish among DnaK
paralogs in eukaryotes. Note that a number of dnaK genes
have shadow ORFs in the same reverse (relative to dnaK)
reading frame, a few of which have been assigned
glutamate dehydrogenase activity. The significance of
this observation is unclear; lengths of such shadow ORFs
are highly variable as if the presumptive protein
product is not conserved [Protein fate, Protein folding
and stabilization].
Length = 595
Score = 31.5 bits (72), Expect = 1.3
Identities = 28/105 (26%), Positives = 43/105 (40%), Gaps = 21/105 (20%)
Query: 307 DKSARAAYDSVIRRKEEVKIRN---SKLDATRKKFKEDLERREKEAENERYKGYKVNKSE 363
+ A A D +RKEE++ RN S K KE G K+ E
Sbjct: 509 EAEANAEEDK--KRKEEIEARNNADSLAYQAEKTLKE--------------AGDKLPAEE 552
Query: 364 EEILQQEIDRLRKEGSIRLQEEIKLMTEELNAAKELSELNAKLNP 408
+E +++ + L++ EEIK TEEL + L +L +
Sbjct: 553 KEKIEKAVAELKEALKGEDVEEIKAKTEELQ--QALQKLAEAMYQ 595
>gnl|CDD|237551 PRK13902, alaS, alanyl-tRNA synthetase; Provisional.
Length = 900
Score = 31.4 bits (72), Expect = 1.3
Identities = 23/112 (20%), Positives = 49/112 (43%), Gaps = 21/112 (18%)
Query: 300 KAIEVLLDKSARAAYDSVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKV 359
+ I+ L D AA E + + +L T ++F E+ + ++K E E+ +
Sbjct: 736 EYIQELEDLLKEAA--------EILGVPPEQLPKTVERFFEEWKEQKK--EIEKLR---- 781
Query: 360 NKSEEEILQQEIDRLRKEGSIRLQEEIKLMTEELNA-AKELSELNAKLNPEN 410
+E+ + L + + +K++ EE++A EL ++ +L E
Sbjct: 782 ----KELAELLASELLSKA-EEVG-GVKVVVEEVDADEDELRKIANELAKEG 827
>gnl|CDD|217817 pfam03961, DUF342, Protein of unknown function (DUF342). This
family of bacterial proteins has no known function. The
proteins are in the region of 500-600 amino acid
residues in length.
Length = 450
Score = 31.1 bits (71), Expect = 1.4
Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 323 EVKIRNSKLDATRKKFKEDLERREKEAEN-----ERYKGYKVNKSEEEILQQEIDRLRKE 377
EV + +L K+ +E+L+ E+E E ++ + E +Q +++L +
Sbjct: 324 EVGVDFPELKEELKELEEELKELEEELEKIKKLLKKLPKKARGQLPPEKREQ-LEKLLET 382
Query: 378 GSIRLQEEIKLMTEELNAAKE 398
+L EE++ + EEL KE
Sbjct: 383 -KEKLSEELEELEEELKELKE 402
>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1,
RRM2) in Arabidopsis thaliana CTC-interacting domain
protein CID8, CID9, CID10, CID11, CID12, CID 13 and
similar proteins. This subgroup corresponds to the RRM
domains found in A. thaliana CID8, CID9, CID10, CID11,
CID12, CID 13 and mainly their plant homologs. These
highly related RNA-binding proteins contain an
N-terminal PAM2 domain (PABP-interacting motif 2), two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a basic region that resembles a bipartite nuclear
localization signal. The biological role of this family
remains unclear.
Length = 77
Score = 28.9 bits (65), Expect = 1.4
Identities = 12/44 (27%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 40 TRESLTKIFSKYGKINILVISPKKRGS---ALLEFEHADSARRA 80
+ + L + FS G++ + + ++ S A +EF A+SA A
Sbjct: 13 SEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSA 56
Score = 28.9 bits (65), Expect = 1.4
Identities = 12/44 (27%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 428 TRESLTKIFSKYGKINILVISPKKRGS---ALLEFEHADSARRA 468
+ + L + FS G++ + + ++ S A +EF A+SA A
Sbjct: 13 SEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSA 56
>gnl|CDD|144972 pfam01576, Myosin_tail_1, Myosin tail. The myosin molecule is a
multi-subunit complex made up of two heavy chains and
four light chains it is a fundamental contractile
protein found in all eukaryote cell types. This family
consists of the coiled-coil myosin heavy chain tail
region. The coiled-coil is composed of the tail from two
molecules of myosin. These can then assemble into the
macromolecular thick filament. The coiled-coil region
provides the structural backbone the thick filament.
Length = 859
Score = 31.2 bits (71), Expect = 1.5
Identities = 27/95 (28%), Positives = 43/95 (45%), Gaps = 8/95 (8%)
Query: 309 SARAAYDSVIRRKEE----VKIRNSKLDATRKKFKEDLERREKEAENERYK-GYKVNKSE 363
S R + K E + N+++ R KF+ + R +E E + K K+++ E
Sbjct: 275 SLREQLEEESEAKAELERQLSKANAEIQQWRSKFESEGALRAEELEELKKKLNQKISELE 334
Query: 364 E--EILQQEIDRLRKEGSIRLQEEIKLMTEELNAA 396
E E + D L K S RLQ E++ + EL A
Sbjct: 335 EAAEAANAKCDSLEKTKS-RLQSELEDLQIELERA 368
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 30.8 bits (70), Expect = 1.5
Identities = 11/74 (14%), Positives = 24/74 (32%)
Query: 68 LLEFEHADSARRAKLYELGLPNCPLTLNYLNPDVEREESRKQPKNPVFSNIDFSGPRDSD 127
L E E A +++ + + L+ N E ++ + K + D
Sbjct: 63 LEEAERAHKSKKENKLAIEDADKSTNLDASNEGDEDDDEEDEIKRKRIEEDARNSDADDS 122
Query: 128 SKNVESSNGSDSDS 141
+ +S + D
Sbjct: 123 DSSSDSDSSDDDSD 136
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 31.3 bits (70), Expect = 1.5
Identities = 34/126 (26%), Positives = 60/126 (47%), Gaps = 9/126 (7%)
Query: 275 KKALKCHPDKNPDDKKAIETFHLLSKAIEVL--LDKSARAAYDSVIRRKEEVKIRNSKLD 332
++A K DKN +KA E IE + L + + ++ EE KI+ +L
Sbjct: 1567 EEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELK 1626
Query: 333 ATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRLRKEGSIRLQEEIKLMTEE 392
++ K+ + ++KEAE E+ K ++ K+EEE ++++ + EE K EE
Sbjct: 1627 KAEEEKKKVEQLKKKEAE-EKKKAEELKKAEEE------NKIKAAEEAKKAEEDKKKAEE 1679
Query: 393 LNAAKE 398
A+E
Sbjct: 1680 AKKAEE 1685
Score = 31.3 bits (70), Expect = 1.8
Identities = 18/78 (23%), Positives = 38/78 (48%)
Query: 315 DSVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRL 374
+ + + +EE KI+ ++ ++ K+ E +K E+E+ + K EE + E +
Sbjct: 1650 EELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKK 1709
Query: 375 RKEGSIRLQEEIKLMTEE 392
++ + EE+K EE
Sbjct: 1710 KEAEEKKKAEELKKAEEE 1727
Score = 30.5 bits (68), Expect = 3.0
Identities = 22/101 (21%), Positives = 46/101 (45%), Gaps = 1/101 (0%)
Query: 300 KAIEVLLDKSARAAYDSVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKV 359
KA E+ + + + + +++ E K + +L ++ K K+AE ++ K +
Sbjct: 1621 KAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEA 1680
Query: 360 NKSEEEILQQEIDRLRKEGSIRLQEEI-KLMTEELNAAKEL 399
K+EE+ + ++ + EE+ K EE A+EL
Sbjct: 1681 KKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEEL 1721
Score = 29.3 bits (65), Expect = 6.1
Identities = 21/87 (24%), Positives = 34/87 (39%), Gaps = 6/87 (6%)
Query: 315 DSVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRL 374
D ++ EE K K DA +KK +E + E + +EE + E
Sbjct: 1318 DEAKKKAEEAK---KKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEE---KAEAAEK 1371
Query: 375 RKEGSIRLQEEIKLMTEELNAAKELSE 401
+KE + + + K EE A E +
Sbjct: 1372 KKEEAKKKADAAKKKAEEKKKADEAKK 1398
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 31.0 bits (71), Expect = 1.6
Identities = 24/84 (28%), Positives = 43/84 (51%), Gaps = 5/84 (5%)
Query: 325 KIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEI--LQQEIDRLRKEGSIRL 382
+I KL + + K +E +KEAE K + +++EE+ L+ E++R KE L
Sbjct: 21 RIAEKKLGSAEELAKRIIEEAKKEAET--LKKEALLEAKEEVHKLRAELERELKERRNEL 78
Query: 383 Q-EEIKLMTEELNAAKELSELNAK 405
Q E +L+ E +++ L+ K
Sbjct: 79 QRLERRLLQREETLDRKMESLDKK 102
Score = 30.3 bits (69), Expect = 2.6
Identities = 21/93 (22%), Positives = 42/93 (45%), Gaps = 11/93 (11%)
Query: 321 KEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRLRKEGSI 380
KEEV ++L+ K+ + +L+R E+ EE L ++++ L K+
Sbjct: 57 KEEVHKLRAELERELKERRNELQRLERR-----------LLQREETLDRKMESLDKKEEN 105
Query: 381 RLQEEIKLMTEELNAAKELSELNAKLNPENYRL 413
++E +L +E N ++ EL + + L
Sbjct: 106 LEKKEKELSNKEKNLDEKEEELEELIAEQREEL 138
Score = 29.9 bits (68), Expect = 3.5
Identities = 26/106 (24%), Positives = 51/106 (48%), Gaps = 12/106 (11%)
Query: 303 EVLLDK---SARAAYDSVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKV 359
E LD+ S +++ ++++E+ + LD ++ +E E+ E ER G
Sbjct: 89 EETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEE--LIAEQREELERISGLTQ 146
Query: 360 NKSEEEILQQEIDRLRKEGSIRLQEEIKLMTEELNAAKELSELNAK 405
+++E +L++ + R E + IK + EE AKE ++ AK
Sbjct: 147 EEAKEILLEEVEEEARHEAAKL----IKEIEEE---AKEEADKKAK 185
>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant
Mei2-like proteins. This subgroup corresponds to the
RRM1 of Mei2-like proteins that represent an ancient
eukaryotic RNA-binding proteins family. Their
corresponding Mei2-like genes appear to have arisen
early in eukaryote evolution, been lost from some
lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. Members in this family contain
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RRM (RRM3) is unique to
Mei2-like proteins and it is highly conserved between
plants and fungi. Up to date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 77
Score = 28.4 bits (64), Expect = 1.6
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 42 ESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAK 81
E L +F ++G I L + K RG ++ + +ARRAK
Sbjct: 16 EELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAK 55
Score = 28.4 bits (64), Expect = 1.6
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 430 ESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAK 469
E L +F ++G I L + K RG ++ + +ARRAK
Sbjct: 16 EELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAK 55
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related
protein 7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S),
an oligopyrimidine-binding protein that binds to the
highly conserved 3'-terminal U-rich stretch (3'
-UUU-OH) of 7SK RNA. LARP7 is a stable component of the
7SK small nuclear ribonucleoprotein (7SK snRNP). It
intimately associates with all the nuclear 7SK and is
required for 7SK stability. LARP7 also acts as a
negative transcriptional regulator of cellular and
viral polymerase II genes, acting by means of the 7SK
snRNP system. It plays an essential role in the
inhibition of positive transcription elongation factor
b (P-TEFb)-dependent transcription, which has been
linked to the global control of cell growth and
tumorigenesis. LARP7 contains a La motif (LAM) and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), at
the N-terminal region, which mediates binding to the
U-rich 3' terminus of 7SK RNA. LARP7 also carries
another putative RRM domain at its C-terminus. .
Length = 80
Score = 28.5 bits (64), Expect = 1.8
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 5/46 (10%)
Query: 40 TRESLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRA 80
T E L +FSKYG + + + + +G A +EFE + A++A
Sbjct: 12 THEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKA 57
Score = 28.5 bits (64), Expect = 1.8
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 5/46 (10%)
Query: 428 TRESLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRA 468
T E L +FSKYG + + + + +G A +EFE + A++A
Sbjct: 12 THEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKA 57
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 30.8 bits (71), Expect = 1.9
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 298 LSKAIEVLLDKSARAAYDSVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAENER 353
L A++ L + + AY I K+E R + LDA +++ E L E+E E+E+
Sbjct: 241 LKAAVKELAEAKLKEAYQ--ITDKQE---REAALDAIKEEVLEALAAEEEEEEDEK 291
>gnl|CDD|187635 cd08930, SDR_c8, classical (c) SDR, subgroup 8. This subgroup has
a fairly well conserved active site tetrad and domain
size of the classical SDRs, but has an atypical
NAD-binding motif ([ST]G[GA]XGXXG). SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 250
Score = 30.4 bits (69), Expect = 2.1
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 8/47 (17%)
Query: 37 DVYTRESLTKI----FSKYGKINILV----ISPKKRGSALLEFEHAD 75
D+ ++ES+ ++ K+G+I+IL+ SPK GS EF +
Sbjct: 60 DITSKESIKELIESYLEKFGRIDILINNAYPSPKVWGSRFEEFPYEQ 106
Score = 30.4 bits (69), Expect = 2.1
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 8/47 (17%)
Query: 425 DVYTRESLTKI----FSKYGKINILV----ISPKKRGSALLEFEHAD 463
D+ ++ES+ ++ K+G+I+IL+ SPK GS EF +
Sbjct: 60 DITSKESIKELIESYLEKFGRIDILINNAYPSPKVWGSRFEEFPYEQ 106
>gnl|CDD|227606 COG5281, COG5281, Phage-related minor tail protein [Function
unknown].
Length = 833
Score = 30.8 bits (69), Expect = 2.3
Identities = 23/118 (19%), Positives = 38/118 (32%), Gaps = 23/118 (19%)
Query: 310 ARAAYDSVIRRKEEVKIRNSKLDATR------------KKFKEDLERRE--KEAENERYK 355
A Y + + + N++ D K D E+R +E N+
Sbjct: 389 AELNYAAADQAANQEGALNAREDEAEVLSTQEERRDILKNLLADAEKRTARQEELNKALA 448
Query: 356 ----GYKVNKSE---EEILQQEIDRLRKEGSIRLQEEIKLMTEELNAAKELSELNAKL 406
++ E+ILQ+E K + +E MT L A + A L
Sbjct: 449 KAKILQADKAAKAYQEDILQREAQSRGKTAAAERSQE--QMTAALKALLAFQQQIADL 504
>gnl|CDD|226513 COG4026, COG4026, Uncharacterized protein containing TOPRIM domain,
potential nuclease [General function prediction only].
Length = 290
Score = 30.3 bits (68), Expect = 2.3
Identities = 26/109 (23%), Positives = 47/109 (43%), Gaps = 18/109 (16%)
Query: 314 YDSVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDR 373
Y + EE+K + +L +++ ++LE E +E E +Q+ + R
Sbjct: 130 YMDLKEDYEELKEKLEELQKEKEELLKELEELE---------------AEYEEVQERLKR 174
Query: 374 LRKEGSIRLQEEIKLMTEEL-NAAKELSELNAKLN-PENYRLRIRWKSS 420
L E S RL+E +K + E+ + K EL + PE + K +
Sbjct: 175 LEVENS-RLEEMLKKLPGEVYDLKKRWDELEPGVELPEEELISDLVKET 222
Score = 30.3 bits (68), Expect = 2.4
Identities = 28/131 (21%), Positives = 53/131 (40%), Gaps = 30/131 (22%)
Query: 311 RAAYDSVIRRKEEVKIRNSKLDATRKKFKEDLERREKEA---ENERYKGYKVNKSEEEIL 367
RA ++ R E + ++ + ++K +E + EKE E E + E E +
Sbjct: 118 RAGLKTLQRVPEYMDLKEDYEE-LKEKLEELQK--EKEELLKELEELEA------EYEEV 168
Query: 368 QQEIDRLRKEGSIRLQEEIKLMTEELNAAKELSELNAKLNPENYRLRIRWKSSSTDTDVY 427
Q+ + RL E S RL+E +K + E+ Y L+ RW ++
Sbjct: 169 QERLKRLEVENS-RLEEMLKKLPGEV-----------------YDLKKRWDELEPGVELP 210
Query: 428 TRESLTKIFSK 438
E ++ + +
Sbjct: 211 EEELISDLVKE 221
>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52
motif-containing protein 1 (RDM1) and similar proteins.
This subfamily corresponds to the RRM of RDM1, also
termed RAD52 homolog B, a novel factor involved in the
cellular response to the anti-cancer drug cisplatin in
vertebrates. RDM1 contains a small RD motif that shares
with the recombination and repair protein RAD52, and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
RD motif is responsible for the acidic pH-dependent
DNA-binding properties of RDM1. It interacts with ss-
and dsDNA, and may act as a DNA-damage recognition
factor by recognizing the distortions of the double
helix caused by cisplatin-DNA adducts in vitro. In
addition, due to the presence of RRM, RDM1 can bind to
RNA as well as DNA. .
Length = 81
Score = 28.1 bits (63), Expect = 2.4
Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 6/63 (9%)
Query: 24 RLRIRWKSSSTDTDVYTRESLTKIFSKYGKINILVISPKKRGS-----ALLEFEHADSAR 78
L + W S T+ ESL FS++G + + + P + A ++F A +A
Sbjct: 2 TLYV-WGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAAS 60
Query: 79 RAK 81
RA+
Sbjct: 61 RAQ 63
Score = 28.1 bits (63), Expect = 2.4
Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 6/63 (9%)
Query: 412 RLRIRWKSSSTDTDVYTRESLTKIFSKYGKINILVISPKKRGS-----ALLEFEHADSAR 466
L + W S T+ ESL FS++G + + + P + A ++F A +A
Sbjct: 2 TLYV-WGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAAS 60
Query: 467 RAK 469
RA+
Sbjct: 61 RAQ 63
>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP A and
hnRNP D subfamilies and similar proteins. This
subfamily corresponds to the RRM1 in the hnRNP A
subfamily which includes hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in
mRNA stability in mammalian cells. hnRNP A1 is an
abundant eukaryotic nuclear RNA-binding protein that
may modulate splice site selection in pre-mRNA
splicing. hnRNP A2/B1 is an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. The hnRNP D subfamily includes hnRNP D0,
hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a
UUAG-specific nuclear RNA binding protein that may be
involved in pre-mRNA splicing and telomere elongation.
hnRNP A/B is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus, plays an
important role in apoB mRNA editing. hnRNP DL (or hnRNP
D-like) is a dual functional protein that possesses
DNA- and RNA-binding properties. It has been implicated
in mRNA biogenesis at the transcriptional and
post-transcriptional levels. All members in this
subfamily contain two putative RRMs and a glycine- and
tyrosine-rich C-terminus. The family also contains
DAZAP1 (Deleted in azoospermia-associated protein 1),
RNA-binding protein Musashi homolog Musashi-1,
Musashi-2 and similar proteins. They all harbor two
RRMs. .
Length = 72
Score = 27.9 bits (63), Expect = 2.4
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 8/53 (15%)
Query: 33 STDTDVYTRESLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRA 80
S DT T ESL + FSKYG++ VI + + RG + F S +
Sbjct: 7 SWDT---TEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKV 56
Score = 27.9 bits (63), Expect = 2.4
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 8/53 (15%)
Query: 421 STDTDVYTRESLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRA 468
S DT T ESL + FSKYG++ VI + + RG + F S +
Sbjct: 7 SWDT---TEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKV 56
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 30.2 bits (69), Expect = 2.5
Identities = 18/56 (32%), Positives = 33/56 (58%), Gaps = 8/56 (14%)
Query: 320 RKEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRLR 375
R E ++ RNS+L+ ++ + L R+ EAENE+ + E E L+ E+++L+
Sbjct: 2 RLEALEERNSELEEQIRQLELKL--RDLEAENEKLE------RELERLKSELEKLK 49
>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM2 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are
putative RNA-binding proteins carrying three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and TEL characteristic motifs that allow sequence and
putative functional discrimination between the terminal
EAR1-like proteins and Mei2-like proteins. .
Length = 71
Score = 27.9 bits (62), Expect = 2.5
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 40 TRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAK 81
+ E+L IF YG + L +P KR +EF A +A
Sbjct: 14 SSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKAL 55
Score = 27.9 bits (62), Expect = 2.5
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 428 TRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAK 469
+ E+L IF YG + L +P KR +EF A +A
Sbjct: 14 SSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKAL 55
>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 1 (SRSF1 or
ASF-1), serine/arginine-rich splicing factor 9 (SRSF9
or SRp30C), and plant pre-mRNA-splicing factor SF2
(SR1). SRSF1 is a shuttling SR protein involved in
constitutive and alternative splicing,
nonsense-mediated mRNA decay (NMD), mRNA export and
translation. It also functions as a splicing-factor
oncoprotein that regulates apoptosis and proliferation
to promote mammary epithelial cell transformation.
SRSF9 has been implicated in the activity of many
elements that control splice site selection, the
alternative splicing of the glucocorticoid receptor
beta in neutrophils and in the gonadotropin-releasing
hormone pre-mRNA. It can also interact with other
proteins implicated in alternative splicing, including
YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both,
SRSF1 and SRSF9, contain two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
RS domains rich in serine-arginine dipeptides. In
contrast, SF2 contains two N-terminal RRMs and a
C-terminal PSK domain rich in proline, serine and
lysine residues. .
Length = 72
Score = 27.7 bits (62), Expect = 2.5
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 36 TDVYTRESLTKIFSKYGKINILVISPKKRGS--ALLEFEHADSARRA 80
D+ R+ + +F KYG I + + ++RG A +EFE A A
Sbjct: 9 GDIRERD-IEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDA 54
Score = 27.7 bits (62), Expect = 2.5
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 424 TDVYTRESLTKIFSKYGKINILVISPKKRGS--ALLEFEHADSARRA 468
D+ R+ + +F KYG I + + ++RG A +EFE A A
Sbjct: 9 GDIRERD-IEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDA 54
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 28.3 bits (64), Expect = 2.5
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 6/54 (11%)
Query: 35 DTDVYTRESLTKIFSKYGKINILVISPKKRGSA------LLEFEHADSARRAKL 82
+ D ++ + + KYGK+ +++ A +EF AD A +A
Sbjct: 14 EIDEDLKDEIEEECEKYGKVLNVIVHEVASSEADDAVRIFVEFSDADEAIKAVR 67
Score = 28.3 bits (64), Expect = 2.5
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 6/54 (11%)
Query: 423 DTDVYTRESLTKIFSKYGKINILVISPKKRGSA------LLEFEHADSARRAKL 470
+ D ++ + + KYGK+ +++ A +EF AD A +A
Sbjct: 14 EIDEDLKDEIEEECEKYGKVLNVIVHEVASSEADDAVRIFVEFSDADEAIKAVR 67
>gnl|CDD|182904 PRK11020, PRK11020, hypothetical protein; Provisional.
Length = 118
Score = 28.8 bits (65), Expect = 2.6
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 7/65 (10%)
Query: 321 KEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRLRKEGSI 380
K E+K + +LDA R K R + E Y + E+ L+ EI RL++ S
Sbjct: 4 KNEIKRLSDRLDAIRHKLAAASLRGDAEK-------YAQFEKEKATLEAEIARLKEVQSQ 56
Query: 381 RLQEE 385
+L +E
Sbjct: 57 KLSKE 61
>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), yeast ortholog
mRNA 3'-end-processing protein RNA15 and similar
proteins. This subfamily corresponds to the RRM domain
of CSTF2, its tau variant and eukaryotic homologs.
CSTF2, also termed cleavage stimulation factor 64 kDa
subunit (CstF64), is the vertebrate conterpart of yeast
mRNA 3'-end-processing protein RNA15. It is expressed
in all somatic tissues and is one of three cleavage
stimulatory factor (CstF) subunits required for
polyadenylation. CstF64 contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
CstF77-binding domain, a repeated MEARA helical region
and a conserved C-terminal domain reported to bind the
transcription factor PC-4. During polyadenylation, CstF
interacts with the pre-mRNA through the RRM of CstF64
at U- or GU-rich sequences within 10 to 30 nucleotides
downstream of the cleavage site. CSTF2T, also termed
tauCstF64, is a paralog of the X-linked cleavage
stimulation factor CstF64 protein that supports
polyadenylation in most somatic cells. It is expressed
during meiosis and subsequent haploid differentiation
in a more limited set of tissues and cell types,
largely in meiotic and postmeiotic male germ cells, and
to a lesser extent in brain. The loss of CSTF2T will
cause male infertility, as it is necessary for
spermatogenesis and fertilization. Moreover, CSTF2T is
required for expression of genes involved in
morphological differentiation of spermatids, as well as
for genes having products that function during
interaction of motile spermatozoa with eggs. It
promotes germ cell-specific patterns of polyadenylation
by using its RRM to bind to different sequence elements
downstream of polyadenylation sites than does CstF64.
The family also includes yeast ortholog mRNA
3'-end-processing protein RNA15 and similar proteins.
RNA15 is a core subunit of cleavage factor IA (CFIA),
an essential transcriptional 3'-end processing factor
from Saccharomyces cerevisiae. RNA recognition by CFIA
is mediated by an N-terminal RRM, which is contained in
the RNA15 subunit of the complex. The RRM of RNA15 has
a strong preference for GU-rich RNAs, mediated by a
binding pocket that is entirely conserved in both yeast
and vertebrate RNA15 orthologs.
Length = 75
Score = 28.0 bits (63), Expect = 2.7
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 5/46 (10%)
Query: 40 TRESLTKIFSKYGK-INI-LVISP---KKRGSALLEFEHADSARRA 80
T E L +IFS+ G ++ LV K +G EFE ++A A
Sbjct: 11 TEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASA 56
Score = 28.0 bits (63), Expect = 2.7
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 5/46 (10%)
Query: 428 TRESLTKIFSKYGK-INI-LVISP---KKRGSALLEFEHADSARRA 468
T E L +IFS+ G ++ LV K +G EFE ++A A
Sbjct: 11 TEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASA 56
>gnl|CDD|235780 PRK06330, PRK06330, transcript cleavage factor/unknown domain
fusion protein; Validated.
Length = 718
Score = 30.5 bits (69), Expect = 2.7
Identities = 11/20 (55%), Positives = 18/20 (90%)
Query: 381 RLQEEIKLMTEELNAAKELS 400
RLQEEI++++EE+N A+ L+
Sbjct: 620 RLQEEIRVLSEEINRARILT 639
>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM3 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 28.0 bits (63), Expect = 2.7
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 10/50 (20%)
Query: 40 TRESLTKIFSKYGKINILVISPKKR---------GSALLEFEHADSARRA 80
+ L IFSK+G++ + I PKK+ G A + F+ A SA A
Sbjct: 13 DEDDLRGIFSKFGEVESIRI-PKKQDEKQGRLNNGFAFVTFKDASSAENA 61
Score = 28.0 bits (63), Expect = 2.7
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 10/50 (20%)
Query: 428 TRESLTKIFSKYGKINILVISPKKR---------GSALLEFEHADSARRA 468
+ L IFSK+G++ + I PKK+ G A + F+ A SA A
Sbjct: 13 DEDDLRGIFSKFGEVESIRI-PKKQDEKQGRLNNGFAFVTFKDASSAENA 61
>gnl|CDD|226889 COG4487, COG4487, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 438
Score = 30.2 bits (68), Expect = 2.7
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 4/78 (5%)
Query: 336 KKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRLRKEGSIRLQEEIK----LMTE 391
+ LE EKEA +R + K E L++++ +KE E+IK + +
Sbjct: 38 SRILNTLEEFEKEANEKRAQYRSAKKKELSQLEEQLINQKKEQKNLFNEQIKQFELALQD 97
Query: 392 ELNAAKELSELNAKLNPE 409
E+ + L LN + + E
Sbjct: 98 EIAKLEALELLNLEKDKE 115
Score = 30.2 bits (68), Expect = 3.0
Identities = 30/123 (24%), Positives = 58/123 (47%), Gaps = 5/123 (4%)
Query: 285 NPDDKKAIETFHLLSKAIEVLLDKSARAAYDSVIRRKEEVKIRNSKLDATRKKFKEDLER 344
D+ + E L E++ K + ++ + E K+ S L+ R+KF+E L
Sbjct: 121 KELDELSKELQKQLQNTAEIIEKKRENNKNEERLKFENEKKLEES-LELEREKFEEQLH- 178
Query: 345 REKEAENERYKGYKVNKSEEEILQQEIDRLRKEGSIRLQ-EEIKLMTEELNAAKELSELN 403
E + E + + +S+ IL +++ R + GS ++Q E ++L E +K S++N
Sbjct: 179 -EANLDLEFKENEEQRESKWAIL-KKLKRRAELGSQQVQGEALELPNESFIRSKFPSDIN 236
Query: 404 AKL 406
K
Sbjct: 237 EKA 239
>gnl|CDD|215969 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 427
Score = 30.2 bits (69), Expect = 2.8
Identities = 20/113 (17%), Positives = 44/113 (38%), Gaps = 26/113 (23%)
Query: 289 KKAIETFHLLSKAIEVLLDKSARAAYDSVIRRKEEVKIRNSKLDATRKKFKEDLERREKE 348
+K E H+L ++ L +++ +D KK K++L E
Sbjct: 330 EKLEERLHILEGLLKALNK------------IDFVIEVIRGSID--LKKAKKELIEELSE 375
Query: 349 AENERYKGYKVNKSEEEILQQEIDRLRKEGSIRLQEEIKLMTEELNAAKELSE 401
+ + +L + RL KE +L++EI+ + +E+ +++
Sbjct: 376 IQADY------------LLDMRLRRLTKEEIEKLEKEIEELEKEIAELEKILA 416
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins.
This subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can
accumulate in the perinucleolar compartment, a dynamic
nuclear substructure that harbors PTB. Raver-1 also
modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes,
particularly in differentiated muscle tissue. Raver-2
is a novel member of the heterogeneous nuclear
ribonucleoprotein (hnRNP) family. It shows high
sequence homology to raver-1. Raver-2 exerts a
spatio-temporal expression pattern during embryogenesis
and is mainly limited to differentiated neurons and
glia cells. Although it displays nucleo-cytoplasmic
shuttling in heterokaryons, raver2 localizes to the
nucleus in glia cells and neurons. Raver-2 can interact
with PTB and may participate in PTB-mediated
RNA-processing. However, there is no evidence
indicating that raver-2 can bind to cytoplasmic
proteins. Both, raver-1 and raver-2, contain three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. They binds to RNA through the
RRMs. In addition, the two [SG][IL]LGxxP motifs serve
as the PTB-binding motifs in raver1. However, raver-2
interacts with PTB through the SLLGEPP motif only. .
Length = 77
Score = 28.0 bits (63), Expect = 2.9
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 5/48 (10%)
Query: 39 YTRESLTKIFSKYGKIN--ILVISPK---KRGSALLEFEHADSARRAK 81
+T E ++ S +G + LV S +G +E+ SA +AK
Sbjct: 11 FTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAK 58
Score = 28.0 bits (63), Expect = 2.9
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 5/48 (10%)
Query: 427 YTRESLTKIFSKYGKIN--ILVISPK---KRGSALLEFEHADSARRAK 469
+T E ++ S +G + LV S +G +E+ SA +AK
Sbjct: 11 FTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAK 58
>gnl|CDD|224691 COG1777, COG1777, Predicted transcriptional regulators
[Transcription].
Length = 217
Score = 29.7 bits (67), Expect = 3.0
Identities = 18/101 (17%), Positives = 38/101 (37%), Gaps = 9/101 (8%)
Query: 312 AAYDSVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEI 371
D R E K+ S + +L R E E + + ++ L + +
Sbjct: 99 EEDDLESERSEVSKLFKSP------EGISELISRLLEINREIEELSRAQTELQKQLNELM 152
Query: 372 DRLRKE-GSIRLQEEIKLMTEEL--NAAKELSELNAKLNPE 409
DR+++E +++ E L N A ++ E + + +
Sbjct: 153 DRIKEEIEDKDGDMTERIVLEYLLKNGAADVEETSRRTVLK 193
>gnl|CDD|232945 TIGR00376, TIGR00376, DNA helicase, putative. The gene product may
represent a DNA helicase. Eukaryotic members of this
family have been characterized as binding certain
single-stranded G-rich DNA sequences (GGGGT and GGGCT).
A number of related proteins are characterized as
helicases [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 30.2 bits (68), Expect = 3.1
Identities = 22/120 (18%), Positives = 44/120 (36%), Gaps = 8/120 (6%)
Query: 305 LLDKSARAAYDSVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEE 364
LL + + + D +I + + R+K E +E R K+ + + S+
Sbjct: 237 LLKSNKQHSLDYLIENHPK----YQIVADIREKIDELIEERNKKLKP--SPQKRRGLSDI 290
Query: 365 EILQQEIDRLRKEGSIRLQEEIKLMTEELNAAKELSELNAKLNPENYRLRIRWKSSSTDT 424
+IL++ ++E +I M E + K + L L R+ + S
Sbjct: 291 KILRK--ALKKREARGIESLKIASMAEWIETNKSIDRLLKLLPEIEERIENEILAESDVV 348
>gnl|CDD|151173 pfam10669, Phage_Gp23, Protein gp23 (Bacteriophage A118). This is
the highly conserved family of the major tail subunit
protein.
Length = 121
Score = 28.9 bits (64), Expect = 3.1
Identities = 12/56 (21%), Positives = 31/56 (55%)
Query: 322 EEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRLRKE 377
++ KI ++ R K + + E+R+KE++ ER K ++ ++ ++ D + ++
Sbjct: 39 DDSKIVRVEMKEERDKMETEREKRDKESKEERDKFISTMNEQQRLMDKQNDMMGQQ 94
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein. Members of this
protein family have a signal peptide, a strongly
conserved SH3 domain, a variable region, and then a
C-terminal hydrophobic transmembrane alpha helix region.
Length = 198
Score = 29.6 bits (67), Expect = 3.2
Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 8/65 (12%)
Query: 358 KVNKSEEEI--LQQEIDRLRKEGS------IRLQEEIKLMTEELNAAKELSELNAKLNPE 409
++ + +EE+ LQ+++ L++E L+ E++ + +EL K+LS +L+ E
Sbjct: 74 ELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQLSANAIELDEE 133
Query: 410 NYRLR 414
N LR
Sbjct: 134 NRELR 138
>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger
CCHC-type and RNA-binding motif-containing protein 1
(ZCRB1) and similar proteins. This subfamily
corresponds to the RRM of ZCRB1, also termed MADP-1, or
U11/U12 small nuclear ribonucleoprotein 31 kDa protein
(U11/U12 snRNP 31 or U11/U12-31K), a novel
multi-functional nuclear factor, which may be involved
in morphine dependence, cold/heat stress, and
hepatocarcinoma. It is located in the nucleoplasm, but
outside the nucleolus. ZCRB1 is one of the components
of U11/U12 snRNPs that bind to U12-type pre-mRNAs and
form a di-snRNP complex, simultaneously recognizing the
5' splice site and branchpoint sequence. ZCRB1 is
characterized by an RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCHC-type Zinc finger
motif. In addition, it contains core nucleocapsid
motifs, and Lys- and Glu-rich domains. .
Length = 78
Score = 27.7 bits (62), Expect = 3.2
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 5/46 (10%)
Query: 40 TRESLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRA 80
T L KIFSKYGK+ + I + K +G A + F + A +
Sbjct: 14 TNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKC 59
Score = 27.7 bits (62), Expect = 3.2
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 5/46 (10%)
Query: 428 TRESLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRA 468
T L KIFSKYGK+ + I + K +G A + F + A +
Sbjct: 14 TNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKC 59
>gnl|CDD|150838 pfam10226, DUF2216, Uncharacterized conserved proteins (DUF2216).
This is the conserved N-terminal half of a proteins
which are found from worms to humans. some annotation
suggests it might be PKR, the Hepatitis delta
antigen-interacting protein A, but this could not be
confirmed.
Length = 195
Score = 29.4 bits (66), Expect = 3.2
Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 18/76 (23%)
Query: 339 KEDLERREKEAENERYKGYKVNKSEEEILQQEIDRLRKEGSIRLQEEIKLMTEELNAAKE 398
KE+L RR + E E+ I++ L +E + RLQ LN +
Sbjct: 19 KEELVRRLRREEAEKMSA---------IVEH--GNLMREVNRRLQGH-------LNEIRG 60
Query: 399 LSELNAKLNPENYRLR 414
L ++N KL +N LR
Sbjct: 61 LKDVNQKLQEDNQELR 76
>gnl|CDD|129694 TIGR00606, rad50, rad50. All proteins in this family for which
functions are known are involvedin recombination,
recombinational repair, and/or non-homologous end
joining.They are components of an exonuclease complex
with MRE11 homologs. This family is distantly related to
the SbcC family of bacterial proteins.This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University).
Length = 1311
Score = 30.4 bits (68), Expect = 3.3
Identities = 22/127 (17%), Positives = 56/127 (44%), Gaps = 16/127 (12%)
Query: 319 RRKEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQ---------Q 369
+ +E++ L T + KE LE++++E + + ++ S + IL+ +
Sbjct: 426 EQADEIRDEKKGLGRTIELKKEILEKKQEELKFVIKELQQLEGSSDRILELDQELRKAER 485
Query: 370 EIDRLRKEGSI--RLQEEIKLMTEELNAAKELSELNAKLNPENYRLRIRWKSSSTDTDVY 427
E+ + K +E L E+ + ++L +L+ ++ N ++ T ++
Sbjct: 486 ELSKAEKNSLTETLKKEVKSLQNEKADLDRKLRKLDQEMEQLN-----HHTTTRTQMEML 540
Query: 428 TRESLTK 434
T++ + K
Sbjct: 541 TKDKMDK 547
>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM2 of RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, a novel mRNA export factor and component of
the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possesses mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RBM15 belongs to the Spen (split
end) protein family, which contain three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal SPOC (Spen paralog and ortholog
C-terminal) domain. This family also includes a
RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is
N-terminally fused to megakaryoblastic leukemia 1
protein (MKL1) at the C-terminus in a translocation
involving chromosome 1 and 22, resulting in acute
megakaryoblastic leukemia. The fusion protein could
interact with the mRNA export machinery. Although it
maintains the specific transactivator function of MKL1,
the fusion protein cannot activate RTE-mediated mRNA
expression and has lost the post-transcriptional
activator function of RBM15. However, it has
transdominant suppressor function contributing to its
oncogenic properties. .
Length = 87
Score = 28.0 bits (62), Expect = 3.3
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 37 DVYTRES-LTKIFSKYGKINILVISPKKRGS----ALLEFEHADSARRAKL 82
D+ E+ L + F ++G I + I RG L+FE+ D A RAKL
Sbjct: 16 DITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKL 66
Score = 28.0 bits (62), Expect = 3.3
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 425 DVYTRES-LTKIFSKYGKINILVISPKKRGS----ALLEFEHADSARRAKL 470
D+ E+ L + F ++G I + I RG L+FE+ D A RAKL
Sbjct: 16 DITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKL 66
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 30.0 bits (68), Expect = 3.3
Identities = 22/113 (19%), Positives = 40/113 (35%), Gaps = 3/113 (2%)
Query: 319 RRKEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRLRKEG 378
+ EV + + +D+ +KF+ + K+AE + K K EE ++I+R
Sbjct: 46 KTAVEV-TKLAAVDSELRKFQTREAAKVKDAEAQLLKDPAEKKREERKAAKKIERSTPSL 104
Query: 379 SIRLQEEIKLMTEELNAAKELSELNAKLNPENYRL-RIRWKSSSTDTDVYTRE 430
R +E+K EE+ A E E + +
Sbjct: 105 IERKTQEVKDSGEEI-AEMMRDEKVPIRELEEIPPEFVALYKQEIQSPTRLNL 156
>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the
peroxisome proliferator-activated receptor gamma
coactivator 1A (PGC-1alpha) family of regulated
coactivators. This subfamily corresponds to the RRM of
PGC-1alpha, PGC-1beta, and PGC-1-related coactivator
(PRC), which serve as mediators between environmental
or endogenous signals and the transcriptional machinery
governing mitochondrial biogenesis. They play an
important integrative role in the control of
respiratory gene expression through interacting with a
number of transcription factors, such as NRF-1, NRF-2,
ERR, CREB and YY1. All family members are multi-domain
proteins containing the N-terminal activation domain,
an LXXLL coactivator signature, a tetrapeptide motif
(DHDY) responsible for HCF binding, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In contrast
to PGC-1alpha and PRC, PGC-1beta possesses two
glutamic/aspartic acid-rich acidic domains, but lacks
most of the arginine/serine (SR)-rich domain that is
responsible for the regulation of RNA processing. .
Length = 89
Score = 28.1 bits (63), Expect = 3.4
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 40 TRESLTKIFSKYGKINILVISPKKRGS--ALLEFEHADSARRA 80
TR L + F +G+I + + + G + + +A A RA
Sbjct: 15 TRSELRQRFQPFGEIEEITLHFRDDGDNYGFVTYRYACDAFRA 57
Score = 28.1 bits (63), Expect = 3.4
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 428 TRESLTKIFSKYGKINILVISPKKRGS--ALLEFEHADSARRA 468
TR L + F +G+I + + + G + + +A A RA
Sbjct: 15 TRSELRQRFQPFGEIEEITLHFRDDGDNYGFVTYRYACDAFRA 57
>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1
small nuclear ribonucleoprotein A (U1A). This subgroup
corresponds to the RRM1 of U1A (also termed U1 snRNP A
or U1-A), an RNA-binding protein associated with the U1
snRNP, a small RNA-protein complex involved in pre-mRNA
splicing. U1A binds with high affinity and specificity
to stem-loop II (SLII) of U1 snRNA. It is predominantly
a nuclear protein and it also shuttles between the
nucleus and the cytoplasm independently of interactions
with U1 snRNA. U1A may be involved in RNA 3'-end
processing, specifically cleavage, splicing and
polyadenylation, through interacting with a large number
of non-snRNP proteins, including polypyrimidine tract
binding protein (PTB), polypyrimidine-tract binding
protein-associated factor (PSF), and
non-POU-domain-containing, octamer-binding (NONO), DEAD
(Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also
binds to a flavivirus NS5 protein and plays an important
role in virus replication. U1A contains two RNA
recognition motifs (RRMs); the N-terminal RRM (RRM1)
binds tightly and specifically to the U1 snRNA SLII and
its own 3'-UTR, while in contrast, the C-terminal RRM
(RRM2) does not appear to associate with any RNA and may
be free to bind other proteins. U1A also contains a
proline-rich region, and a nuclear localization signal
(NLS) in the central domain that is responsible for its
nuclear import. .
Length = 89
Score = 28.1 bits (62), Expect = 3.5
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 41 RESLTKIFSKYGKINILVISP--KKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 96
++SL IFS++G+I +++S K RG A + F+ SA A G P + P+ + Y
Sbjct: 21 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 80
Query: 97 LNPD 100
D
Sbjct: 81 AKTD 84
Score = 28.1 bits (62), Expect = 3.5
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 429 RESLTKIFSKYGKINILVISP--KKRGSALLEFEHADSARRAKLYELGLP--NCPLTLNY 484
++SL IFS++G+I +++S K RG A + F+ SA A G P + P+ + Y
Sbjct: 21 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 80
Query: 485 LNPD 488
D
Sbjct: 81 AKTD 84
>gnl|CDD|232831 TIGR00115, tig, trigger factor. Trigger factor is a
ribosome-associated molecular chaperone and is the first
chaperone to interact with nascent polypeptide. Trigger
factor can bind at the same time as the signal
recognition particle (SRP), but is excluded by the SRP
receptor (FtsY). The central domain of trigger factor
has peptidyl-prolyl cis/trans isomerase activity. This
protein is found in a single copy in virtually every
bacterial genome [Protein fate, Protein folding and
stabilization].
Length = 408
Score = 29.8 bits (68), Expect = 3.6
Identities = 26/100 (26%), Positives = 44/100 (44%), Gaps = 16/100 (16%)
Query: 323 EVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEE--------ILQQEIDRL 374
+ L+ + +++LER +KE + K ++K E +++QEIDRL
Sbjct: 244 SLGEEFETLEELKADIRKNLEREKKERAKNKLKEQLLDKLVENNEFELPESLVEQEIDRL 303
Query: 375 RKEGSIRLQ------EEIKLMTEEL--NAAKELSELNAKL 406
++ +LQ EE TEE +E +E KL
Sbjct: 304 LEQALQQLQQQGIDLEEYLKDTEEELREEFREEAERRVKL 343
>gnl|CDD|234402 TIGR03928, T7_EssCb_Firm, type VII secretion protein EssC,
C-terminal domain. This model describes the C-terminal
domain, or longer subunit, of the Firmicutes type VII
secretion protein EssC. This protein (homologous to EccC
in Actinobacteria) and the WXG100 target proteins are
the only homologous parts of type VII secretion between
Firmicutes and Actinobacteria [Protein fate, Protein and
peptide secretion and trafficking].
Length = 1296
Score = 30.0 bits (68), Expect = 3.7
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 9/62 (14%)
Query: 335 RKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRLRKEGSIRLQ--EEIKLMTEE 392
+KK+K+D+E+R + Y+ Y K +E LQ ++ R EE+K M E
Sbjct: 86 KKKYKKDVEKRNR-----SYRLYLDKKRKE--LQALSEKQRHVLHYHNPSVEELKEMVEN 138
Query: 393 LN 394
+N
Sbjct: 139 VN 140
>gnl|CDD|213060 cd12091, FANCM_ID, insert domain of FANCM helicase and similar
proteins. FANCM and related proteins, like Mph1 and
Fml1, are DNA junction-specific helicases/translocases
that bind to and process perturbed replication forks and
intermediates of homologous recombination. FANCM
contains an N-terminal superfamily 2 helicase (SF2)
domain, although FANCM, in contrast to other members of
this family, does not exhibit DNA helicase activity. The
SF2 helicase domain is comprised of 3 structural
domains, the 2 generally conserved helicase domains and
a helical domain inserted between the two domains. FANCM
is a component of the Fanconi anaemia (FA) core complex.
FA is a rare genetic disease in humans that is
associated with progressive bone marrow failure, a
variety of developmental abnormalities, and a high
incidence of cancer. A key role of this complex is to
monoubiquitination of FANCD2 and FANCI during S-phase
and in response to DNA damage. The role of FANCM during
this process seems to be the recruitment of the complex
to chromatin.
Length = 122
Score = 28.4 bits (64), Expect = 3.7
Identities = 22/72 (30%), Positives = 32/72 (44%), Gaps = 7/72 (9%)
Query: 274 RKKALKCHPDKNPDDKKAIE-TFHLLSK---AIEVLLDKSARAAYDSVIRRKEEVKIRNS 329
R K P N K +IE F LL A+E+LL+ R YD + E K + S
Sbjct: 41 RDKFRANPPGNNEGQKGSIEGDFALLISLAHAMELLLEHGIRPFYDYLKEIATETKSKKS 100
Query: 330 KLDATRKKFKED 341
K ++K+ +
Sbjct: 101 K---SKKELANN 109
>gnl|CDD|227318 COG4985, COG4985, ABC-type phosphate transport system, auxiliary
component [Inorganic ion transport and metabolism].
Length = 289
Score = 29.5 bits (66), Expect = 4.0
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 341 DLERREKEAENERYKGYKVNKSEEEILQQEIDRLRKEGSIRLQEEIKLMTEEL-NAAKEL 399
+L++R E E R + K+ + + ++ +++RLR E RLQ +L E + E
Sbjct: 165 ELQKRLLEVETLRDQVDKMVEQQVRVINSQLERLRLEKR-RLQLNGQLDDEFQQHYVAEK 223
Query: 400 SELNAKL 406
SEL +L
Sbjct: 224 SELQKRL 230
>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein
RBM8A, RBM8B nd similar proteins. This subfamily
corresponds to the RRM of RBM8, also termed binder of
OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is
one of the components of the exon-exon junction complex
(EJC). It has two isoforms, RBM8A and RBM8B, both of
which are identical except that RBM8B is 16 amino acids
shorter at its N-terminus. RBM8, together with other
EJC components (such as Magoh, Aly/REF, RNPS1, Srm160,
and Upf3), plays critical roles in postsplicing
processing, including nuclear export and cytoplasmic
localization of the mRNA, and the nonsense-mediated
mRNA decay (NMD) surveillance process. RBM8 binds to
mRNA 20-24 nucleotides upstream of a spliced exon-exon
junction. It is also involved in spliced mRNA nuclear
export, and the process of nonsense-mediated decay of
mRNAs with premature stop codons. RBM8 forms a specific
heterodimer complex with the EJC protein Magoh which
then associates with Aly/REF, RNPS1, DEK, and SRm160 on
the spliced mRNA, and inhibits ATP turnover by
eIF4AIII, thereby trapping the EJC core onto RNA. RBM8
contains an N-terminal putative bipartite nuclear
localization signal, one RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), in the central region, and
a C-terminal serine-arginine rich region (SR domain)
and glycine-arginine rich region (RG domain). .
Length = 88
Score = 27.6 bits (62), Expect = 4.2
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 5/46 (10%)
Query: 40 TRESLTKIFSKYGKINILVISPKKR-----GSALLEFEHADSARRA 80
E + F+++G+I L ++ +R G AL+E+E A+ A
Sbjct: 19 QEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAA 64
Score = 27.6 bits (62), Expect = 4.2
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 5/46 (10%)
Query: 428 TRESLTKIFSKYGKINILVISPKKR-----GSALLEFEHADSARRA 468
E + F+++G+I L ++ +R G AL+E+E A+ A
Sbjct: 19 QEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAA 64
>gnl|CDD|191634 pfam06886, TPX2, Targeting protein for Xklp2 (TPX2). This family
represents a conserved region approximately 60 residues
long within the eukaryotic targeting protein for Xklp2
(TPX2). Xklp2 is a kinesin-like protein localised on
centrosomes throughout the cell cycle and on spindle
pole microtubules during metaphase. In Xenopus, it has
been shown that Xklp2 protein is required for centrosome
separation and maintenance of spindle bi-polarity. TPX2
is a microtubule-associated protein that mediates the
binding of the C-terminal domain of Xklp2 to
microtubules. It is phosphorylated during mitosis in a
microtubule-dependent way.
Length = 57
Score = 27.0 bits (60), Expect = 4.4
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 335 RKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRLRKE 377
R +F + LE +EK E E+ + K EEE + I +LRKE
Sbjct: 10 RAEFDKKLEEKEKALEAEKEEAEARQKEEEE---EAIKQLRKE 49
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 29.5 bits (67), Expect = 4.5
Identities = 25/129 (19%), Positives = 48/129 (37%), Gaps = 5/129 (3%)
Query: 274 RKKALKCHPDKNPDDKKAIETFHLLSKAIEVLLDKSARAAYDSVIRRKEEVKIRNSKLDA 333
+K A K H K K E LS + + +AR A + +E + SK
Sbjct: 353 KKIAEKLHTSKR---KVRREVLPFLSIIFKHNPELAARLAAFLELTEEEIEFLTGSKKAT 409
Query: 334 TRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRL--RKEGSIRLQEEIKLMTE 391
+ K + +++E E + K ++E ++E ++ + E + E
Sbjct: 410 KKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEE 469
Query: 392 ELNAAKELS 400
E K+ +
Sbjct: 470 EEKKKKQAT 478
>gnl|CDD|235582 PRK05729, valS, valyl-tRNA synthetase; Reviewed.
Length = 874
Score = 29.7 bits (68), Expect = 5.3
Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 16/71 (22%)
Query: 331 LDATRKKFKEDLERREKEAE-------NERYKGYKVNKSEEEILQQEIDRLRKEGSIRLQ 383
++A + +++L + EKE E NE + V K+ EE++++E ++L + +
Sbjct: 809 VEAELARLEKELAKLEKEIERVEKKLSNEGF----VAKAPEEVVEKEREKLAE-----YE 859
Query: 384 EEIKLMTEELN 394
E++ + E L
Sbjct: 860 EKLAKLKERLA 870
>gnl|CDD|241160 cd12716, RRM1_2_NP220, RNA recognition motif 1 and 2 in
vertebrate nuclear protein 220 (NP220). This subgroup
corresponds to RRM1 and RRM2 of NP220, also termed zinc
finger protein 638 (ZN638), or cutaneous T-cell
lymphoma-associated antigen se33-1, or zinc finger
matrin-like protein, a large nucleoplasmic DNA-binding
protein that binds to cytidine-rich sequences, such as
CCCCC (G/C), in double-stranded DNA (dsDNA). NP220
contains multiple domains, including MH1, MH2, and MH3,
domains homologous to the acidic nuclear protein matrin
3; RS, an arginine/serine-rich domain commonly found in
pre-mRNA splicing factors; PstI-HindIII, a domain
essential for DNA binding; acidic repeat, a domain with
nine repeats of the sequence LVTVDEVIEEEDL; and a
Cys2-His2 zinc finger-like motif that is also present
in matrin 3. It may be involved in packaging,
transferring, or processing transcripts. This subgroup
corresponds to the domain of MH2 that contains two
tandem RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains).
Length = 76
Score = 27.1 bits (60), Expect = 5.3
Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 37 DVYTRESLTKIFSKYGKIN-ILVISPKKRGSALLEFEHADSARRAKLY 83
Y+ E + + +GK+ IL++S K+ A LE + ++A Y
Sbjct: 11 KGYSEEEIYNLAKPFGKLKDILILSSHKK--AYLEMNNKEAAEAMVKY 56
Score = 27.1 bits (60), Expect = 5.3
Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 425 DVYTRESLTKIFSKYGKIN-ILVISPKKRGSALLEFEHADSARRAKLY 471
Y+ E + + +GK+ IL++S K+ A LE + ++A Y
Sbjct: 11 KGYSEEEIYNLAKPFGKLKDILILSSHKK--AYLEMNNKEAAEAMVKY 56
>gnl|CDD|219083 pfam06548, Kinesin-related, Kinesin-related. This family
represents a region within kinesin-related proteins from
higher plants. Many family members also contain the
pfam00225 domain. Kinesins are ATP-driven microtubule
motor proteins that produce directed force. Some family
members are associated with the phragmoplast, a
structure composed mainly of microtubules that executes
cytokinesis in higher plants.
Length = 488
Score = 29.5 bits (66), Expect = 5.4
Identities = 15/55 (27%), Positives = 29/55 (52%)
Query: 323 EVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRLRKE 377
E K+ S + + KE +E + + E E +K + + E+E+L +EI L+ +
Sbjct: 183 EHKLLKSDYENHPEVLKETIELKRIQEELESFKNFYFDMGEKEVLLEEIQDLKSQ 237
>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase.
Members of this protein family are polyribonucleotide
nucleotidyltransferase, also called polynucleotide
phosphorylase. Some members have been shown also to have
additional functions as guanosine pentaphosphate
synthetase and as poly(A) polymerase (see model
TIGR02696 for an exception clade, within this family)
[Transcription, Degradation of RNA].
Length = 684
Score = 29.4 bits (67), Expect = 5.6
Identities = 19/101 (18%), Positives = 44/101 (43%), Gaps = 15/101 (14%)
Query: 281 HPDKNPDDKKAIETFHLLSKAIEVLLDKSARAAYDSVIRRKEEVKIRNSKLDATRKKFKE 340
P+ + + K ++ E+ + + AY I K+E R + LDA +++ E
Sbjct: 226 APEVDEELKAKVK---------ELAYEAGLKEAYQ--ITEKQE---RYAALDAIKEEVLE 271
Query: 341 DLERREKEAENERYKGYKVNKSEEEILQQEIDRLRKEGSIR 381
L E E E E + ++ ++ +++ ++ + + R
Sbjct: 272 ALAEEE-EEEEEADREKEIKEAFKDLEKKIVRERILKEGKR 311
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 29.3 bits (66), Expect = 5.6
Identities = 18/92 (19%), Positives = 43/92 (46%)
Query: 316 SVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRLR 375
S + + E++ +L+ ++ +E+L + E + + + + E +L++ +
Sbjct: 491 SREKEEAELREEIEELEKELRELEEELIELLELEEALKEELEEKLEKLENLLEELEELKE 550
Query: 376 KEGSIRLQEEIKLMTEELNAAKELSELNAKLN 407
K +L+EE++ + + L KEL E L
Sbjct: 551 KLQLQQLKEELRQLEDRLQELKELLEELRLLR 582
Score = 29.3 bits (66), Expect = 5.7
Identities = 21/104 (20%), Positives = 41/104 (39%), Gaps = 4/104 (3%)
Query: 308 KSARAAYDSVIRRKEEVKIRNSKLDATRKKFKE--DLERREKEAENERYKGYKVN--KSE 363
K + RKEE++ +L +KK KE + + +E N +
Sbjct: 572 KELLEELRLLRTRKEELEELRERLKELKKKLKELEERLSQLEELLQSLELSEAENELEEA 631
Query: 364 EEILQQEIDRLRKEGSIRLQEEIKLMTEELNAAKELSELNAKLN 407
EE L+ E+++L + + + L E + +E+ +L
Sbjct: 632 EEELESELEKLNLQAELEELLQAALEELEEKVEELEAEIRRELQ 675
>gnl|CDD|223327 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 843
Score = 29.6 bits (67), Expect = 5.8
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 336 KKFKEDLERREKEAENERYKGYKVNKSEEEIL--QQEIDRLRKEGSIRLQEEIKLMTEEL 393
K +D RR+ ER+ ++ + EE++L +++I L E L+E+I EL
Sbjct: 483 KLVPDDYIRRQTLKNAERFTTPELKELEEKLLDAEEKILALEYELFDELREKILAHINEL 542
Query: 394 -NAAKELSELNA 404
AK L+EL+
Sbjct: 543 QALAKALAELDV 554
>gnl|CDD|234883 PRK00979, PRK00979, tetrahydromethanopterin S-methyltransferase
subunit H; Provisional.
Length = 308
Score = 29.1 bits (66), Expect = 5.9
Identities = 12/59 (20%), Positives = 23/59 (38%), Gaps = 5/59 (8%)
Query: 193 SNIFSSSSKPRNVFPSGLFPSANVSSNI---FASSDRTL--PEPHISWSFPAIPLSSIM 246
N S+ R F ++ +N+ +D L P + +FPA+ ++ I
Sbjct: 227 HNAPSAWDWLREFKGKEAFAVCDIGANLVARILGADFLLYGPIENAEEAFPAVAMTDIF 285
>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM1 of the p54nrb/PSF/PSP1 family, including 54
kDa nuclear RNA- and DNA-binding protein (p54nrb or
NonO or NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in
vertebrates. p54nrb is a multi-functional protein
involved in numerous nuclear processes including
transcriptional regulation, splicing, DNA unwinding,
nuclear retention of hyperedited double-stranded RNA,
viral RNA processing, control of cell proliferation,
and circadian rhythm maintenance. PSF is also a
multi-functional protein that binds RNA,
single-stranded DNA (ssDNA), double-stranded DNA
(dsDNA) and many factors, and mediates diverse
activities in the cell. PSP1 is a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. The cellular function
of PSP1 remains unknown currently. This subfamily also
includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65.
D. melanogaster NONA is involved in eye development and
behavior, and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contain a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 71
Score = 26.9 bits (60), Expect = 6.0
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 40 TRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAKLYEL 85
T E ++FSKYG+++ V K++G + + +A +AK EL
Sbjct: 14 TEEEFKELFSKYGEVS-EVFLNKEKGFGFIRLDTRTNAEKAK-AEL 57
Score = 26.9 bits (60), Expect = 6.0
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 428 TRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAKLYEL 473
T E ++FSKYG+++ V K++G + + +A +AK EL
Sbjct: 14 TEEEFKELFSKYGEVS-EVFLNKEKGFGFIRLDTRTNAEKAK-AEL 57
>gnl|CDD|240889 cd12443, RRM_MCM3A_like, RNA recognition motif in 80 kDa
MCM3-associated protein (Map80) and similar proteins.
This subfamily corresponds to the RRM of Map80, also
termed germinal center-associated nuclear protein
(GANP), involved in the nuclear localization pathway of
MCM3, a protein necessary for the initiation of DNA
replication and also involves in controls that ensure
DNA replication is initiated once per cell cycle. Map80
contains one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). .
Length = 73
Score = 27.0 bits (60), Expect = 6.2
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 41 RESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAK 81
++ L + F K+GK+ V ++ SA++ F SA AK
Sbjct: 15 KDWLERHFGKFGKV-ARVYCNPRKKSAVVHFFDHASAALAK 54
Score = 27.0 bits (60), Expect = 6.2
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 429 RESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRAK 469
++ L + F K+GK+ V ++ SA++ F SA AK
Sbjct: 15 KDWLERHFGKFGKV-ARVYCNPRKKSAVVHFFDHASAALAK 54
>gnl|CDD|203371 pfam06005, DUF904, Protein of unknown function (DUF904). This
family consists of several bacterial and archaeal
hypothetical proteins of unknown function.
Length = 72
Score = 26.9 bits (60), Expect = 6.3
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 8/49 (16%)
Query: 358 KVNKSEEEI--LQQEIDRLR------KEGSIRLQEEIKLMTEELNAAKE 398
K+ ++ E I LQ EI+ L+ E + L+EE K + EE NA +
Sbjct: 12 KIQQAVETIALLQMEIEELKEENEQLSEENEELEEENKKLKEERNAWQS 60
>gnl|CDD|237418 PRK13534, PRK13534, 7-cyano-7-deazaguanine tRNA-ribosyltransferase;
Provisional.
Length = 639
Score = 29.2 bits (66), Expect = 6.5
Identities = 25/94 (26%), Positives = 39/94 (41%), Gaps = 32/94 (34%)
Query: 332 DATRKKFKEDLE---RREKEAENERYKGYKVNKSEEEILQQEIDRLRKEGSIRLQEEIKL 388
D +R+K +EDLE R KEA + E+ L + +GS K
Sbjct: 128 DVSREKAEEDLEETLERAKEAIEIK---------EKLALNGTV-----QGSTYPDLRQK- 172
Query: 389 MTEELNAAKELSELNAKLNP--------ENYRLR 414
+A+E+S++N + P E+YR R
Sbjct: 173 ------SAEEMSKMNFDIYPIGAVVPLMESYRYR 200
>gnl|CDD|224004 COG1078, COG1078, HD superfamily phosphohydrolases [General
function prediction only].
Length = 421
Score = 28.9 bits (65), Expect = 6.8
Identities = 25/145 (17%), Positives = 45/145 (31%), Gaps = 17/145 (11%)
Query: 287 DDKKAIETFHLLSKAIEVLLDKSARAAYDSVIRR-------KEEVKIRNSKLDATRKKFK 339
D E F L + L + ++RR K +V +++ L ++
Sbjct: 256 DLDFDAEEFRRLDDFELLALLRDLLDLDRELLRRLFNRDLYKRDVILKDLALRFLNRELL 315
Query: 340 EDLERREKE-------AENERYKGYKVNKSEEEILQQEIDRLRKEGSIRLQEEIKLMTEE 392
+ L+ ++ AE + Y V +I + +KL +
Sbjct: 316 KTLDFVQEIRDLESEVAEAKGDPEYYV---IVDINIPYDIFRPGSELPESEVNVKLKDGK 372
Query: 393 LNAAKELSELNAKLNPENYRLRIRW 417
L E+S L LN R
Sbjct: 373 LKELSEISPLVKALNEARRRRARYG 397
>gnl|CDD|220013 pfam08777, RRM_3, RNA binding motif. This domain is found in
protein La which functions as an RNA chaperone during
RNA polymerase III transcription, and can also stimulate
translation initiation. It contains a five stranded beta
sheet which forms an atypical RNA recognition motif.
Length = 102
Score = 27.3 bits (61), Expect = 6.8
Identities = 16/75 (21%), Positives = 36/75 (48%), Gaps = 9/75 (12%)
Query: 40 TRESLTKIFSKYGKINILVISPKKRG--SALLEFEHADSARRA----KLYELGLPNCPLT 93
+RE + + FS++G++ + G + F+ ++A++A +L + +T
Sbjct: 14 SREDIKEAFSQHGEVKYVDF---LEGDKEGYVRFKTPEAAKKALEKATEAKLKIKEAEVT 70
Query: 94 LNYLNPDVEREESRK 108
L L + E+E +K
Sbjct: 71 LELLEGEEEKEYWKK 85
Score = 27.3 bits (61), Expect = 6.8
Identities = 16/75 (21%), Positives = 36/75 (48%), Gaps = 9/75 (12%)
Query: 428 TRESLTKIFSKYGKINILVISPKKRG--SALLEFEHADSARRA----KLYELGLPNCPLT 481
+RE + + FS++G++ + G + F+ ++A++A +L + +T
Sbjct: 14 SREDIKEAFSQHGEVKYVDF---LEGDKEGYVRFKTPEAAKKALEKATEAKLKIKEAEVT 70
Query: 482 LNYLNPDVEREESRK 496
L L + E+E +K
Sbjct: 71 LELLEGEEEKEYWKK 85
>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila
melanogaster sex determination protein SNF and similar
proteins. This subgroup corresponds to the RRM1 of SNF
(Sans fille), also termed U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an
RNA-binding protein found in the U1 and U2 snRNPs of
Drosophila. It is essential in Drosophila sex
determination and possesses a novel dual RNA binding
specificity. SNF binds with high affinity to both
Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA
stem-loop IV (SLIV). It can also bind to poly(U) RNA
tracts flanking the alternatively spliced Sex-lethal
(Sxl) exon, as does Drosophila Sex-lethal protein
(SXL). SNF contains two RNA recognition motifs (RRMs);
it can self-associate through RRM1, and each RRM can
recognize poly(U) RNA binding independently. .
Length = 78
Score = 26.8 bits (59), Expect = 7.5
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 41 RESLTKIFSKYGKINILVI--SPKKRGSALLEFEHADSARRAKLYELGLP 88
++SL IFS++G+I +V + K RG A + F+ SA A G P
Sbjct: 17 KKSLYAIFSQFGQILDIVALKTLKMRGQAFVVFKDISSATNALRSMQGFP 66
Score = 26.8 bits (59), Expect = 7.5
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 429 RESLTKIFSKYGKINILVI--SPKKRGSALLEFEHADSARRAKLYELGLP 476
++SL IFS++G+I +V + K RG A + F+ SA A G P
Sbjct: 17 KKSLYAIFSQFGQILDIVALKTLKMRGQAFVVFKDISSATNALRSMQGFP 66
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 28.9 bits (66), Expect = 7.8
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 7/64 (10%)
Query: 342 LERREKEAENERYKGYKVNKSEEEILQQEIDRLRKEGSIRLQEEIKLMTEELNAAKELSE 401
LER EK+A+ G K K+E E+L++ ++ L + R ++L EE K L
Sbjct: 144 LERLEKKAK----GGDKEAKAELELLEKLLEHLEEGKPAR---TLELTDEEEKLLKSLQL 196
Query: 402 LNAK 405
L AK
Sbjct: 197 LTAK 200
>gnl|CDD|185594 PTZ00395, PTZ00395, Sec24-related protein; Provisional.
Length = 1560
Score = 28.9 bits (64), Expect = 7.9
Identities = 28/132 (21%), Positives = 48/132 (36%), Gaps = 2/132 (1%)
Query: 96 YLNPDVEREESRKQP-KNPVFSNIDFSGPRDSDSKNVESSNGSDSDSTPNLFPSANKSSN 154
NP + P NP SN +S P +S+ + S L + S+
Sbjct: 419 NSNPGYNNAPNSNTPYNNPPNSNTPYSNPPNSNPPYSNLPYSNTPYSNAPLSNAPPSSAK 478
Query: 155 IFPSADKSSNLFPTADKSSHLFPIADKSS-NLFPSADKSSNIFSSSSKPRNVFPSGLFPS 213
SA ++ A++ + P A++ + N F A +S +S+P P G +
Sbjct: 479 DHHSAYHAAYQHRAANQPAANLPTANQPAANNFHGAAGNSVGNPFASRPFGSAPYGGNAA 538
Query: 214 ANVSSNIFASSD 225
N A +
Sbjct: 539 TTADPNGIAKRE 550
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 28.7 bits (65), Expect = 8.2
Identities = 28/105 (26%), Positives = 47/105 (44%), Gaps = 15/105 (14%)
Query: 308 KSARAAYDSVIRRKEEVKIRNSKLDAT----RKKFKEDLERREKEAENERYKGYKVNKSE 363
S + A D RR+E N + T +KK ++ L+ +E E + K +K
Sbjct: 559 DSMQKAIDETERRREIQMAYNEEHGITPQTIKKKIRDILDGEYEEDEYKAKIEKKASKMS 618
Query: 364 EEILQQEIDRLRK-----------EGSIRLQEEIKLMTEELNAAK 397
++ L++ I +L K E + RL++EIK + EEL
Sbjct: 619 KKELEKLIKKLEKEMKEAAKNLEFEEAARLRDEIKELKEELLGKS 663
>gnl|CDD|224397 COG1480, COG1480, Predicted membrane-associated HD superfamily
hydrolase [General function prediction only].
Length = 700
Score = 28.9 bits (65), Expect = 8.3
Identities = 17/103 (16%), Positives = 31/103 (30%), Gaps = 19/103 (18%)
Query: 343 ERREKEAENERYKGYKVNKSEEEILQQEIDRLRKEGSIRLQEEIKLMTEELNAAKELSEL 402
E K A + YK + EI Q + + + +N K E
Sbjct: 69 EEERKAASDSVEPVYKRDA---EITQNIVQ------------LYQNFFDAINEVKRSLEE 113
Query: 403 NAKLNPENYRLRIRWK----SSSTDTDVYTRESLTKIFSKYGK 441
N N E +++ T+T + E + + +
Sbjct: 114 NEDENTEYSLKQVKQLKDRLLRDTNTVDISEERILTLLELDSE 156
>gnl|CDD|222549 pfam14111, DUF4283, Domain of unknown function (DUF4283). This
domain family is found in plants, and is approximately
100 amino acids in length. Considering the very diverse
range of other domains it is associated with it is
possible that this domain is a binding/guiding region.
There are two highly conserved tryptophan residues.
Length = 153
Score = 27.9 bits (63), Expect = 8.4
Identities = 13/53 (24%), Positives = 19/53 (35%), Gaps = 3/53 (5%)
Query: 28 RWKSSSTDTDVYTRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRA 80
RW S R + K + G + + + G L EFE + A R
Sbjct: 22 RWLSPRGPDLEALRSWMAKAWGLKGGLGVASLG---DGLFLFEFESEEDAERV 71
Score = 27.9 bits (63), Expect = 8.4
Identities = 13/53 (24%), Positives = 19/53 (35%), Gaps = 3/53 (5%)
Query: 416 RWKSSSTDTDVYTRESLTKIFSKYGKINILVISPKKRGSALLEFEHADSARRA 468
RW S R + K + G + + + G L EFE + A R
Sbjct: 22 RWLSPRGPDLEALRSWMAKAWGLKGGLGVASLG---DGLFLFEFESEEDAERV 71
>gnl|CDD|173958 cd08199, EEVS, 2-epi-5-epi-valiolone synthase (EEVS).
2-epi-5-epi-valiolone synthases catalyze the cyclization
of sedoheptulose 7-phosphate to 2-epi-5-epi-valiolone in
the biosynthesis of C(7)N-aminocyclitol-containing
products. The cyclization product, 2-epi-5-epi-valiolone
((2S,3S,4S,5R)-5-(hydroxymethyl)cyclohexanon-2,3,4,
5-tetrol), is a precursor of the valienamine moiety. The
valienamine unit is responsible for their biological
activities as various glycosidic hydrolases inhibitors.
Two important microbial secondary metabolites, i.e.,
validamycin and acarbose, are used in agricultural and
biomedical applications. Validamycine A is an antifungal
antibiotic which has a strong trehalase inhibitory
activity and has been used to control sheath blight
disease in rice caused by Rhizoctonia solani. Acarbose
is an alpha-glucosidase inhibitor used for the treatment
of type II insulin-independent diabetes. Salbostatin
produced by Streptomyces albus also belongs to this
family. It exhibits strong trehalase inhibitory
activity.
Length = 354
Score = 28.8 bits (65), Expect = 8.5
Identities = 17/35 (48%), Positives = 19/35 (54%), Gaps = 5/35 (14%)
Query: 226 RTLPEPHISWSFPAIPLSSI-MADIKDLDLYGLLE 259
TLPE HI I I MA IKD +L+ LLE
Sbjct: 164 ATLPERHIRNGLAEI----IKMAVIKDAELFELLE 194
>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM2 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 79
Score = 26.6 bits (59), Expect = 8.5
Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 5/46 (10%)
Query: 40 TRESLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRA 80
+ L K+FSK+G+++ + + S K +G A + F + A +A
Sbjct: 15 KEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKA 60
Score = 26.6 bits (59), Expect = 8.5
Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 5/46 (10%)
Query: 428 TRESLTKIFSKYGKINILVI-----SPKKRGSALLEFEHADSARRA 468
+ L K+FSK+G+++ + + S K +G A + F + A +A
Sbjct: 15 KEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKA 60
>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast
nucleolar protein 3 (Npl3p) and similar proteins. This
subfamily corresponds to the RRM1 of Npl3p, also termed
mitochondrial targeting suppressor 1 protein, or
nuclear polyadenylated RNA-binding protein 1. Npl3p is
a major yeast RNA-binding protein that competes with
3'-end processing factors, such as Rna15, for binding
to the nascent RNA, protecting the transcript from
premature termination and coordinating transcription
termination and the packaging of the fully processed
transcript for export. It specifically recognizes a
class of G/U-rich RNAs. Npl3p is a multi-domain protein
containing two central RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a short
linker and a C-terminal domain rich in glycine,
arginine and serine residues. .
Length = 67
Score = 26.2 bits (58), Expect = 8.9
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 7/58 (12%)
Query: 42 ESLTKIFSKYGKI-NILVISPKKRGSALLEFEHADSARRAK--LYELGLPNCPLTLNY 96
++ +IFS YG + + +IS A +EFE +SA RAK ++ L N PL + Y
Sbjct: 14 SAIREIFSPYGAVKEVKMIS----NFAFVEFESLESAIRAKDSVHGKVLNNNPLYVTY 67
Score = 26.2 bits (58), Expect = 8.9
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 7/58 (12%)
Query: 430 ESLTKIFSKYGKI-NILVISPKKRGSALLEFEHADSARRAK--LYELGLPNCPLTLNY 484
++ +IFS YG + + +IS A +EFE +SA RAK ++ L N PL + Y
Sbjct: 14 SAIREIFSPYGAVKEVKMIS----NFAFVEFESLESAIRAKDSVHGKVLNNNPLYVTY 67
>gnl|CDD|237560 PRK13922, PRK13922, rod shape-determining protein MreC;
Provisional.
Length = 276
Score = 28.4 bits (64), Expect = 8.9
Identities = 10/38 (26%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 369 QEIDRLRKEGSIRLQEEIKLMTEELNAAKELSELNAKL 406
+ LR+E + L++E+ + L ++L NA+L
Sbjct: 69 ASLFDLREE-NEELKKELLELESRLQELEQLEAENARL 105
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 28.7 bits (65), Expect = 9.0
Identities = 24/109 (22%), Positives = 40/109 (36%), Gaps = 9/109 (8%)
Query: 297 LLSKAIEVLLDKSARAA--YDSVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAENERY 354
L K +EV AA D ++ ++ K + + LE+R ++
Sbjct: 40 LGKKLVEVT------AAVDEDETPKKNPVLREEKRKPAKSILSLQALLEKRPSRTNSQDA 93
Query: 355 KGYKVNKSEEEILQQEIDRLRKEGSIRLQEEIKLMTEELNA-AKELSEL 402
N E + E KE + E K++ +EL+ EL EL
Sbjct: 94 LLQAENALPEWKKELEKPSEPKEEEPKAAAESKVVQKELDELRDELKEL 142
>gnl|CDD|177556 PHA03195, PHA03195, tegument protein VP11/12; Provisional.
Length = 746
Score = 28.8 bits (64), Expect = 9.0
Identities = 27/114 (23%), Positives = 38/114 (33%), Gaps = 6/114 (5%)
Query: 96 YLNPDVEREESRKQPKNPVFSNIDFSGPRDSDSKNVESS------NGSDSDSTPNLFPSA 149
Y NP + +E PV D+S P++ D S+ DSD TP + PS
Sbjct: 559 YTNPLLGPDEEVDASPQPVDPVSDYSAPKNPDYMRPRSTLVEEIWQLRDSDYTPYMRPSR 618
Query: 150 NKSSNIFPSADKSSNLFPTADKSSHLFPIADKSSNLFPSADKSSNIFSSSSKPR 203
+ P P D NL S S + + +PR
Sbjct: 619 AGRPRVRVEDQTLEPGSPKGCYPPANSPENDVKDNLPDSPPISPEVVYGTFRPR 672
>gnl|CDD|187767 cd09636, Cas1_I-II-III, CRISPR/Cas system-associated protein Cas1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas1 is the most universal CRISPR system protein thought
to be involved in spacer integration; Cas1 is
metal-dependent deoxyribonuclease, also binds RNA; Shown
to possess a unique fold consisting of a N-terminal
beta-strand domain and a C-terminal alpha-helical
domain.
Length = 260
Score = 28.4 bits (64), Expect = 9.4
Identities = 24/113 (21%), Positives = 40/113 (35%), Gaps = 10/113 (8%)
Query: 316 SVIRRKEEVKIRNSKLDATRKKFKEDLERREKEAENE---RYKGYKVNKSEEEI-LQQEI 371
SV R+ + K K +E +E + + + KSE + + +
Sbjct: 81 SVFTRRAQYK-AYLNPAKRLKLAREFVEGKLANQAALLRYLTRRREDLKSELAEYIAELL 139
Query: 372 DRLRKEGSIRLQEEIKLMTEELNAAKELSELNAKLNPENYRLRIRWKSSSTDT 424
L SI +LM E NAA+ A+L P+ + R + D
Sbjct: 140 KELDNANSIE-----ELMGIEGNAARAYYAALAQLLPDEFGFNGRSRRPPKDP 187
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 28.9 bits (65), Expect = 9.5
Identities = 17/92 (18%), Positives = 33/92 (35%), Gaps = 5/92 (5%)
Query: 328 NSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQE-----IDRLRKEGSIRL 382
+L+A + +F E+ E + + + EE+ Q E +++ ++E
Sbjct: 430 RQQLEAGKLEFNEEEYELELRLGRLKQRLDSATATPEELEQLEINDEALEKAQEEQEQAE 489
Query: 383 QEEIKLMTEELNAAKELSELNAKLNPENYRLR 414
+L +E K E L RL
Sbjct: 490 ANVEQLQSELRQLRKRRDEALEALQRAERRLL 521
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 28.6 bits (65), Expect = 9.9
Identities = 23/93 (24%), Positives = 45/93 (48%), Gaps = 1/93 (1%)
Query: 321 KEEVKIRNSKLDATRKKFKEDLERREKEAENERYKGYKVNKSEEEILQQEIDRLRKEGSI 380
+E + +L+ ++K +E+ ++ +EAE E + K K E + + +E+ +L+K G
Sbjct: 543 LKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEADEIIKELRQLQKGGYA 602
Query: 381 RLQE-EIKLMTEELNAAKELSELNAKLNPENYR 412
++ E+ + LN A E E K E
Sbjct: 603 SVKAHELIEARKRLNKANEKKEKKKKKQKEKQE 635
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
0.311 0.129 0.356
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,549,021
Number of extensions: 2482626
Number of successful extensions: 3506
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3227
Number of HSP's successfully gapped: 546
Length of query: 512
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 411
Effective length of database: 6,457,848
Effective search space: 2654175528
Effective search space used: 2654175528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 61 (27.4 bits)