RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 030945
(168 letters)
>gnl|CDD|185507 PTZ00191, PTZ00191, 60S ribosomal protein L23a; Provisional.
Length = 145
Score = 166 bits (423), Expect = 9e-54
Identities = 93/143 (65%), Positives = 107/143 (74%), Gaps = 1/143 (0%)
Query: 26 KADPKVQALKTAKAVKSGRTFKKAKKIRTSVTFHRPKTLKKDRNPKYPRISAPPRNKLDH 85
K +A K AKA K G K +K+RTSV F RPKTL+ + PKYPR P KLD
Sbjct: 4 AKKAKKKAKKAAKAAKKG-VKVKKRKVRTSVRFFRPKTLRLPKKPKYPRRVKPASKKLDK 62
Query: 86 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGT 145
Y I+KYPLTTE AMKKIEDNNTLVFIVD RA+K +IK AV+K+YD++ KVNTLI PDG
Sbjct: 63 YSIIKYPLTTEKAMKKIEDNNTLVFIVDQRANKTQIKKAVEKLYDVKVVKVNTLITPDGL 122
Query: 146 KKAYVRLTPDSDALDVANKIGII 168
KKAY+RL+PD DALDVANKIGII
Sbjct: 123 KKAYIRLSPDVDALDVANKIGII 145
>gnl|CDD|237750 PRK14548, PRK14548, 50S ribosomal protein L23P; Provisional.
Length = 84
Score = 104 bits (262), Expect = 5e-30
Identities = 44/83 (53%), Positives = 60/83 (72%)
Query: 86 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGT 145
Y I+KYPL TE AM IE N L FIVD RA K IK AV++++D++ +KVNTLI P G
Sbjct: 2 YSIIKYPLVTEKAMNLIEKENKLTFIVDRRATKPDIKRAVEELFDVKVEKVNTLITPKGE 61
Query: 146 KKAYVRLTPDSDALDVANKIGII 168
KKAYV+L + DA ++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 = 96.9 bits (242), Expect = 4e-27
Identities = 39/77 (50%), Positives = 54/77 (70%)
Query: 92 PLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVR 151
PL TE AM IE N L FIVD +A K IK AV+K++D++ +KVNTLI P G KKAYV+
Sbjct: 1 PLVTEKAMNLIEKENKLTFIVDRKATKGDIKRAVEKLFDVKVEKVNTLITPRGEKKAYVK 60
Query: 152 LTPDSDALDVANKIGII 168
L + A ++A+++G+
Sbjct: 61 LAEEYAAEEIASRLGVF 77
>gnl|CDD|223167 COG0089, RplW, Ribosomal protein L23 [Translation, ribosomal
structure and biogenesis].
Length = 94
Score = 82.3 bits (204), Expect = 3e-21
Identities = 34/86 (39%), Positives = 48/86 (55%), Gaps = 3/86 (3%)
Query: 85 HYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDG 144
Y ++K P+ TE AM +E N VFIVD A K +IK AV++++ ++ +KVNTL
Sbjct: 1 LYDVIKSPVVTEKAMLLMEKENKYVFIVDPDATKPEIKAAVEELFGVKVEKVNTLNTKGK 60
Query: 145 TKKAYVR---LTPDSDALDVANKIGI 167
TK+A V+ L D V K G
Sbjct: 61 TKRAGVKRIGLRKDYKKAYVTLKEGQ 86
>gnl|CDD|235586 PRK05738, rplW, 50S ribosomal protein L23; Reviewed.
Length = 92
Score = 66.7 bits (164), Expect = 3e-15
Identities = 26/85 (30%), Positives = 38/85 (44%), Gaps = 13/85 (15%)
Query: 86 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRP--- 142
Y ++K P+ TE + +E N VF V A K +IK AV+K++ ++ + VNTL
Sbjct: 1 YDVIKRPVITEKSTLLMEKQNKYVFEVAPDATKPEIKAAVEKLFGVKVESVNTLNVKGKT 60
Query: 143 ----------DGTKKAYVRLTPDSD 157
KKA V L
Sbjct: 61 KRFGRRIGKRSDWKKAIVTLAEGQK 85
>gnl|CDD|144021 pfam00276, Ribosomal_L23, Ribosomal protein L23.
Length = 90
Score = 63.5 bits (155), Expect = 6e-14
Identities = 36/90 (40%), Positives = 51/90 (56%), Gaps = 14/90 (15%)
Query: 88 ILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGT-- 145
++KYP+ TE AM +E N VFIVD +A+K +IKDAV+ ++ ++ +KVNTLI P
Sbjct: 2 VIKYPIITEKAMNLLEKPNQYVFIVDKKANKTEIKDAVEHIFGVKVEKVNTLILPGKVKR 61
Query: 146 -----------KKAYVRLTPDSDALDVANK 164
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 = 60.4 bits (147), Expect = 4e-13
Identities = 35/52 (67%), Positives = 37/52 (71%)
Query: 29 PKVQALKTAKAVKSGRTFKKAKKIRTSVTFHRPKTLKKDRNPKYPRISAPPR 80
PK +ALK KAV G KK +KIRTSVTF RPKTLK RNPKYPR S P R
Sbjct: 1 PKAKALKAKKAVLKGVHGKKKRKIRTSVTFRRPKTLKLPRNPKYPRKSVPHR 52
>gnl|CDD|176971 CHL00030, rpl23, ribosomal protein L23.
Length = 93
Score = 42.6 bits (101), Expect = 5e-06
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 86 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRP 142
+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 = 38.6 bits (90), Expect = 4e-04
Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 83 LDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRP 142
++ +++K P+ TE + + N F VD RA+K +IK AV+ ++ ++ KVN
Sbjct: 1 MNINEVIKKPILTEKSYSLMSKN-VYTFKVDRRANKIEIKKAVEFIFKVKVLKVNIFNVD 59
Query: 143 DGTKK 147
K+
Sbjct: 60 KKPKR 64
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 30.7 bits (70), Expect = 0.32
Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 6/59 (10%)
Query: 13 RRRTMAPPKGETKKADPKVQALKTAKAVKSGRTFKKAKKIRTSVTFHRPKTLKKDRNPK 71
R +T AP + +T K KV A + K K K K+ R + K + K R P
Sbjct: 377 RPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDT------KNIGKRRKPS 429
>gnl|CDD|224942 COG2031, AtoE, Short chain fatty acids transporter [Lipid
metabolism].
Length = 446
Score = 30.0 bits (68), Expect = 0.57
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 15 RTMAPPKGETKKADPKVQALKTAKAVKSG 43
MAP KGET + DPK+ A K
Sbjct: 208 YMMAPSKGETVEIDPKLLGDDVKTAAKLL 236
>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 = 28.4 bits (64), Expect = 1.5
Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 11/86 (12%)
Query: 47 KKAKKIRTSVTFH-RPKTLKKDRNPKYPRISAPPRNKLDHYQILKYPLTTESAMKKIEDN 105
K + TS+ + + K + P KL ++L+Y + A
Sbjct: 23 GKVRSTVTSIEPNVASFYSNSSKGKKLTLVDVPGHEKL-RDKLLEYLKASLKA------- 74
Query: 106 NTLVFIVDIRADKKKIKDAVKKMYDI 131
+VF+VD +K I+D + +YDI
Sbjct: 75 --IVFVVDSATFQKNIRDVAEFLYDI 98
>gnl|CDD|224162 COG1241, MCM2, Predicted ATPase involved in replication control,
Cdc46/Mcm family [DNA replication, recombination, and
repair].
Length = 682
Score = 28.5 bits (64), Expect = 2.2
Identities = 11/66 (16%), Positives = 26/66 (39%), Gaps = 6/66 (9%)
Query: 86 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVK------KMYDIQAKKVNTL 139
+L+ P +K D L+ ++ KKI K + +++++ + L
Sbjct: 49 GLLLENPEEIIPLFEKALDEIALLLFPEVDRSLKKIHVRFKNLPNRLSIRELRSEHIGKL 108
Query: 140 IRPDGT 145
+ +G
Sbjct: 109 VSVEGI 114
>gnl|CDD|234263 TIGR03568, NeuC_NnaA, UDP-N-acetyl-D-glucosamine 2-epimerase,
UDP-hydrolysing. This family of enzymes catalyzes the
combined epimerization and UDP-hydrolysis of
UDP-N-acetylglucosamine to N-acetylmannosamine. This is
in contrast to the related enzyme WecB (TIGR00236) which
retains the UDP moiety. NeuC acts in concert with NeuA
and NeuB to synthesize CMP-N5-acetyl-neuraminate.
Length = 365
Score = 27.1 bits (61), Expect = 4.7
Identities = 11/42 (26%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 111 IVDIRADKKKIKDAVKKMYDIQ-AKKVNTLIRPDGTKKAYVR 151
++D+ DK++I A++K+ D K + + P G + R
Sbjct: 319 VIDVDPDKEEIVKAIEKLLDPAFKKSLKNVKNPYGDGNSSER 360
>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 = 26.9 bits (60), Expect = 6.0
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 5/50 (10%)
Query: 82 KLDHYQILKYPLTTESAMKKIEDNN---TLVFIVDIRADKKKIKDAVKKM 128
K + Y+I+ YP+ E+ K N F+ AD + AVK++
Sbjct: 58 KANKYRIIGYPVNIEN--SKYARNAFLFNFCFVFPYDADTSPYEPAVKRL 105
>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 = 26.1 bits (58), Expect = 9.7
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 4/28 (14%)
Query: 59 HRPKTLKKDRNPKYPRISAPPRNK-LDH 85
P+T RNPKY I A R + LD
Sbjct: 21 DNPRTT---RNPKYDEIKASIRERGLDQ 45
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.132 0.372
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,361,137
Number of extensions: 741643
Number of successful extensions: 952
Number of sequences better than 10.0: 1
Number of HSP's gapped: 935
Number of HSP's successfully gapped: 51
Length of query: 168
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 78
Effective length of database: 6,945,742
Effective search space: 541767876
Effective search space used: 541767876
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (24.9 bits)