RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 031794
(153 letters)
>gnl|CDD|185507 PTZ00191, PTZ00191, 60S ribosomal protein L23a; Provisional.
Length = 145
Score = 161 bits (408), Expect = 1e-51
Identities = 93/140 (66%), Positives = 108/140 (77%), Gaps = 2/140 (1%)
Query: 14 KAQATKVAKAVKSGPTFKKKAKKMRTSVTFHRPKTLKKDRNPKYPRISAPPRNKLDHYQI 73
K +A K AKA K G K K +K+RTSV F RPKTL+ + PKYPR P KLD Y I
Sbjct: 8 KKKAKKAAKAAKKGV--KVKKRKVRTSVRFFRPKTLRLPKKPKYPRRVKPASKKLDKYSI 65
Query: 74 LKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGTKKA 133
+KYPLTTE AMKKIEDNNTLVFIVD RA+K +IK AV+K+Y+++ KVNTLI PDG KKA
Sbjct: 66 IKYPLTTEKAMKKIEDNNTLVFIVDQRANKTQIKKAVEKLYDVKVVKVNTLITPDGLKKA 125
Query: 134 YVRLTPDYDALDVANKIGII 153
Y+RL+PD DALDVANKIGII
Sbjct: 126 YIRLSPDVDALDVANKIGII 145
>gnl|CDD|237750 PRK14548, PRK14548, 50S ribosomal protein L23P; Provisional.
Length = 84
Score = 103 bits (258), Expect = 1e-29
Identities = 44/83 (53%), Positives = 61/83 (73%)
Query: 71 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGT 130
Y I+KYPL TE AM IE N L FIVD RA K IK AV+++++++ +KVNTLI P G
Sbjct: 2 YSIIKYPLVTEKAMNLIEKENKLTFIVDRRATKPDIKRAVEELFDVKVEKVNTLITPKGE 61
Query: 131 KKAYVRLTPDYDALDVANKIGII 153
KKAYV+L +YDA ++A+++G+
Sbjct: 62 KKAYVKLAEEYDAEEIASRLGVF 84
>gnl|CDD|132675 TIGR03636, L23_arch, archaeal ribosomal protein L23. This model
describes the archaeal ribosomal protein L23P and
rigorously excludes the bacterial counterpart L23. In
order to capture every known instance of archaeal L23P,
the trusted cutoff is set lower than a few of the
highest scoring eukaryotic cytosolic ribosomal
counterparts [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 77
Score = 95.7 bits (239), Expect = 6e-27
Identities = 39/77 (50%), Positives = 55/77 (71%)
Query: 77 PLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGTKKAYVR 136
PL TE AM IE N L FIVD +A K IK AV+K+++++ +KVNTLI P G KKAYV+
Sbjct: 1 PLVTEKAMNLIEKENKLTFIVDRKATKGDIKRAVEKLFDVKVEKVNTLITPRGEKKAYVK 60
Query: 137 LTPDYDALDVANKIGII 153
L +Y A ++A+++G+
Sbjct: 61 LAEEYAAEEIASRLGVF 77
>gnl|CDD|223167 COG0089, RplW, Ribosomal protein L23 [Translation, ribosomal
structure and biogenesis].
Length = 94
Score = 80.7 bits (200), Expect = 8e-21
Identities = 35/86 (40%), Positives = 49/86 (56%), Gaps = 3/86 (3%)
Query: 70 HYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDG 129
Y ++K P+ TE AM +E N VFIVD A K +IK AV++++ ++ +KVNTL
Sbjct: 1 LYDVIKSPVVTEKAMLLMEKENKYVFIVDPDATKPEIKAAVEELFGVKVEKVNTLNTKGK 60
Query: 130 TKKAYVR---LTPDYDALDVANKIGI 152
TK+A V+ L DY V K G
Sbjct: 61 TKRAGVKRIGLRKDYKKAYVTLKEGQ 86
>gnl|CDD|235586 PRK05738, rplW, 50S ribosomal protein L23; Reviewed.
Length = 92
Score = 63.6 bits (156), Expect = 3e-14
Identities = 26/83 (31%), Positives = 38/83 (45%), Gaps = 13/83 (15%)
Query: 71 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRP--- 127
Y ++K P+ TE + +E N VF V A K +IK AV+K++ ++ + VNTL
Sbjct: 1 YDVIKRPVITEKSTLLMEKQNKYVFEVAPDATKPEIKAAVEKLFGVKVESVNTLNVKGKT 60
Query: 128 ----------DGTKKAYVRLTPD 140
KKA V L
Sbjct: 61 KRFGRRIGKRSDWKKAIVTLAEG 83
>gnl|CDD|144021 pfam00276, Ribosomal_L23, Ribosomal protein L23.
Length = 90
Score = 61.6 bits (150), Expect = 2e-13
Identities = 36/90 (40%), Positives = 51/90 (56%), Gaps = 14/90 (15%)
Query: 73 ILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGT-- 130
++KYP+ TE AM +E N VFIVD +A+K +IKDAV+ ++ ++ +KVNTLI P
Sbjct: 2 VIKYPIITEKAMNLLEKPNQYVFIVDKKANKTEIKDAVEHIFGVKVEKVNTLILPGKVKR 61
Query: 131 -----------KKAYVRLTPDYDALDVANK 149
KKA V L D L A++
Sbjct: 62 NGQYLGRKKSYKKAIVTLEEG-DILPFASR 90
>gnl|CDD|202819 pfam03939, Ribosomal_L23eN, Ribosomal protein L23, N-terminal
domain. The N-terminal domain appears to be specific
to the eukaryotic ribosomal proteins L25, L23, and
L23a.
Length = 52
Score = 60.0 bits (146), Expect = 4e-13
Identities = 34/53 (64%), Positives = 37/53 (69%), Gaps = 1/53 (1%)
Query: 13 PKAQATKVAKAVKSGPTFKKKAKKMRTSVTFHRPKTLKKDRNPKYPRISAPPR 65
PKA+A K KAV G KK +K+RTSVTF RPKTLK RNPKYPR S P R
Sbjct: 1 PKAKALKAKKAVLKG-VHGKKKRKIRTSVTFRRPKTLKLPRNPKYPRKSVPHR 52
>gnl|CDD|176971 CHL00030, rpl23, ribosomal protein L23.
Length = 93
Score = 41.4 bits (98), Expect = 9e-06
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 71 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRP 127
+KYP+ T+ +++ +E N F VD + K +IK ++ + ++ VN+ P
Sbjct: 1 MDGIKYPVFTDKSIRLLE-KNQYTFDVDSGSTKTEIKHWIELFFGVKVIAVNSHRLP 56
>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed.
Length = 158
Score = 35.9 bits (83), Expect = 0.002
Identities = 19/65 (29%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 68 LDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRP 127
++ +++K P+ TE + + N F VD RA+K +IK AV+ +++++ KVN
Sbjct: 1 MNINEVIKKPILTEKSYSLMSKN-VYTFKVDRRANKIEIKKAVEFIFKVKVLKVNIFNVD 59
Query: 128 DGTKK 132
K+
Sbjct: 60 KKPKR 64
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 28.1 bits (63), Expect = 1.8
Identities = 9/30 (30%), Positives = 17/30 (56%)
Query: 93 LVFIVDIRADKRKIKDAVKKMYEIQTKKVN 122
+VF+VD ++ I+D + +Y+I T
Sbjct: 75 IVFVVDSATFQKNIRDVAEFLYDILTDLEK 104
>gnl|CDD|211393 cd11381, NSA2, pre-ribosomal protein NSA2 (Nop seven-associated 2).
NSA2 appears to be a protein required for the
maturation of 27S pre-rRNA in yeast; it has been
characterized in mammalian cells as a nucleolar protein
that might play a role in the regulation of the cell
cycle and in cell proliferation.
Length = 257
Score = 27.6 bits (62), Expect = 3.0
Identities = 18/42 (42%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 22 KAVKSGPTFKKKAKKMRTSVTFHRPKTLKKDRNPKYPRISAP 63
K VK+G KK K+M T VTF +K PKY R P
Sbjct: 131 KVVKTGKRKKKSWKRMVTKVTFVGEGFTRK--PPKYERFIRP 170
>gnl|CDD|224162 COG1241, MCM2, Predicted ATPase involved in replication control,
Cdc46/Mcm family [DNA replication, recombination, and
repair].
Length = 682
Score = 27.7 bits (62), Expect = 3.1
Identities = 11/66 (16%), Positives = 26/66 (39%), Gaps = 6/66 (9%)
Query: 71 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVK------KMYEIQTKKVNTL 124
+L+ P +K D L+ ++ +KI K + E++++ + L
Sbjct: 49 GLLLENPEEIIPLFEKALDEIALLLFPEVDRSLKKIHVRFKNLPNRLSIRELRSEHIGKL 108
Query: 125 IRPDGT 130
+ +G
Sbjct: 109 VSVEGI 114
>gnl|CDD|224942 COG2031, AtoE, Short chain fatty acids transporter [Lipid
metabolism].
Length = 446
Score = 27.3 bits (61), Expect = 3.2
Identities = 11/40 (27%), Positives = 17/40 (42%)
Query: 1 MAPKVDSSKKGDPKAQATKVAKAVKSGPTFKKKAKKMRTS 40
MAP + + DPK V A K + A+++ S
Sbjct: 210 MAPSKGETVEIDPKLLGDDVKTAAKLLEKDRTPAERLENS 249
>gnl|CDD|213858 TIGR03764, ICE_PFGI_1_parB, integrating conjugative element,
PFGI_1 class, ParB family protein. Members of this
protein family carry the ParB-type nuclease domain and
are found in integrating conjugative elements (ICE) in
the same class as PFGI-1 of Pseudomonas fluorescens
Pf-5.
Length = 258
Score = 26.5 bits (59), Expect = 6.5
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 4/28 (14%)
Query: 44 HRPKTLKKDRNPKYPRISAPPRNK-LDH 70
P+T RNPKY I A R + LD
Sbjct: 21 DNPRTT---RNPKYDEIKASIRERGLDQ 45
>gnl|CDD|218942 pfam06218, NPR2, Nitrogen permease regulator 2. This family of
regulators are involved in post-translational control of
nitrogen permease.
Length = 400
Score = 26.5 bits (59), Expect = 6.8
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 5/50 (10%)
Query: 67 KLDHYQILKYPLTTESAMKKIEDNN---TLVFIVDIRADKRKIKDAVKKM 113
K + Y+I+ YP+ E+ K N F+ AD + AVK++
Sbjct: 58 KANKYRIIGYPVNIEN--SKYARNAFLFNFCFVFPYDADTSPYEPAVKRL 105
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.314 0.130 0.362
Gapped
Lambda K H
0.267 0.0750 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,479,494
Number of extensions: 658079
Number of successful extensions: 660
Number of sequences better than 10.0: 1
Number of HSP's gapped: 641
Number of HSP's successfully gapped: 59
Length of query: 153
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 64
Effective length of database: 6,990,096
Effective search space: 447366144
Effective search space used: 447366144
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 (22.0 bits)
S2: 55 (24.9 bits)