RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11684
(198 letters)
>gnl|CDD|129114 TIGR00002, S16, ribosomal protein S16. This model describes
ribosomal S16 of bacteria and organelles [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 78
Score = 69.6 bits (171), Expect = 4e-16
Identities = 37/123 (30%), Positives = 44/123 (35%), Gaps = 51/123 (41%)
Query: 47 IRLARYGCTNRPFYHIVVIHSSEHSVGLAHIDKKWSSKLYVRRCVNVKSSEHSVGLAHID 106
IRL R G RPFY IVV S
Sbjct: 3 IRLKRGGRKKRPFYRIVVADS--------------------------------------- 23
Query: 107 KKWSSKITRMRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHITSPVREL 166
R RR+ + IE+LG ++PL E V LN+ERI+YWL T VR L
Sbjct: 24 --------RSRRDGRYIEELGFYNPLTK---ESRVKLNVERIKYWLSKG-AQPTDTVRNL 71
Query: 167 FGK 169
K
Sbjct: 72 LKK 74
>gnl|CDD|216173 pfam00886, Ribosomal_S16, Ribosomal protein S16.
Length = 61
Score = 67.1 bits (165), Expect = 2e-15
Identities = 29/103 (28%), Positives = 37/103 (35%), Gaps = 48/103 (46%)
Query: 51 RYGCTNRPFYHIVVIHSSEHSVGLAHIDKKWSSKLYVRRCVNVKSSEHSVGLAHIDKKWS 110
R G RPFY IVV S
Sbjct: 1 RGGRKKRPFYRIVVADS------------------------------------------- 17
Query: 111 SKITRMRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLG 153
R R+ + IE+LGT++P+ QE V L+ ERI+YWLG
Sbjct: 18 ----RSPRDGRFIEELGTYNPIAKP-QEPEVKLDEERIKYWLG 55
>gnl|CDD|234588 PRK00040, rpsP, 30S ribosomal protein S16; Reviewed.
Length = 75
Score = 64.8 bits (159), Expect = 2e-14
Identities = 30/107 (28%), Positives = 39/107 (36%), Gaps = 48/107 (44%)
Query: 47 IRLARYGCTNRPFYHIVVIHSSEHSVGLAHIDKKWSSKLYVRRCVNVKSSEHSVGLAHID 106
IRLAR G RPFY IVV S
Sbjct: 4 IRLARGGAKKRPFYRIVVADS--------------------------------------- 24
Query: 107 KKWSSKITRMRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLG 153
R R+ + IE++G ++PL E+ V L+ ER+ YWLG
Sbjct: 25 --------RSPRDGRFIERVGFYNPLAKP-AEEEVKLDEERVLYWLG 62
>gnl|CDD|223306 COG0228, RpsP, Ribosomal protein S16 [Translation, ribosomal
structure and biogenesis].
Length = 87
Score = 58.0 bits (141), Expect = 1e-11
Identities = 32/107 (29%), Positives = 40/107 (37%), Gaps = 49/107 (45%)
Query: 47 IRLARYGCTNRPFYHIVVIHSSEHSVGLAHIDKKWSSKLYVRRCVNVKSSEHSVGLAHID 106
IRLAR G RPFY IVV S
Sbjct: 4 IRLARGGSKKRPFYRIVVADS--------------------------------------- 24
Query: 107 KKWSSKITRMRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLG 153
R R+ + IE+LGT++PL + E+ V L+ ERI YWL
Sbjct: 25 --------RSPRDGRFIERLGTYNPLLGK--EERVKLDEERILYWLS 61
>gnl|CDD|176950 CHL00005, rps16, ribosomal protein S16.
Length = 82
Score = 40.4 bits (95), Expect = 3e-05
Identities = 23/110 (20%), Positives = 34/110 (30%), Gaps = 53/110 (48%)
Query: 43 MSKSIRLARYGCTNRPFYHIVVIHSSEHSVGLAHIDKKWSSKLYVRRCVNVKSSEHSVGL 102
M K +RL R G + Y IV I
Sbjct: 1 MVK-LRLKRCGRKQQAVYRIVAIDV----------------------------------- 24
Query: 103 AHIDKKWSSKITRMRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWL 152
R RR + +E++G +DP+ N+ LN+ I Y+L
Sbjct: 25 ------------RSRREGRDLEKVGFYDPIKNQTY-----LNVPAILYFL 57
>gnl|CDD|184724 PRK14520, rpsP, 30S ribosomal protein S16; Provisional.
Length = 155
Score = 38.5 bits (90), Expect = 5e-04
Identities = 23/111 (20%), Positives = 37/111 (33%), Gaps = 50/111 (45%)
Query: 43 MSKSIRLARYGCTNRPFYHIVVIHSSEHSVGLAHIDKKWSSKLYVRRCVNVKSSEHSVGL 102
M+ I+L R G P Y IVV S
Sbjct: 1 MAVKIKLKRLGKIRNPQYRIVVADS----------------------------------- 25
Query: 103 AHIDKKWSSKITRMRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLG 153
R +R+ + IE++G + P + + L+ ++ ER +YWL
Sbjct: 26 ------------RTKRDGRAIEEIGRYHP---KEEPSLIEIDSERAQYWLS 61
>gnl|CDD|172991 PRK14525, rpsP, 30S ribosomal protein S16; Provisional.
Length = 88
Score = 36.1 bits (83), Expect = 0.002
Identities = 24/112 (21%), Positives = 38/112 (33%), Gaps = 50/112 (44%)
Query: 43 MSKSIRLARYGCTNRPFYHIVVIHSSEHSVGLAHIDKKWSSKLYVRRCVNVKSSEHSVGL 102
M+ +RL+R G PFYH+V S
Sbjct: 1 MAVVLRLSRAGTHKAPFYHVVATDS----------------------------------- 25
Query: 103 AHIDKKWSSKITRMRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGT 154
R R+ + +E +G +DP + E+ + L +ERI +WL
Sbjct: 26 ------------RNARDGKYLEDVGIYDP--TKRPER-IELKVERIEHWLKA 62
>gnl|CDD|237744 PRK14521, rpsP, 30S ribosomal protein S16; Provisional.
Length = 186
Score = 37.1 bits (86), Expect = 0.002
Identities = 26/112 (23%), Positives = 36/112 (32%), Gaps = 50/112 (44%)
Query: 43 MSKSIRLARYGCTNRPFYHIVVIHSSEHSVGLAHIDKKWSSKLYVRRCVNVKSSEHSVGL 102
M+ IRL R+G + FY IV S
Sbjct: 1 MAVKIRLQRHGRKGKAFYWIVAADS----------------------------------- 25
Query: 103 AHIDKKWSSKITRMRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGT 154
R R+ + IE++GT++P N V LN +R YWL
Sbjct: 26 ------------RAPRDGKFIEKIGTYNPNTNPAT---VDLNFDRAVYWLMN 62
>gnl|CDD|172990 PRK14524, rpsP, 30S ribosomal protein S16; Provisional.
Length = 94
Score = 32.9 bits (75), Expect = 0.023
Identities = 28/126 (22%), Positives = 43/126 (34%), Gaps = 51/126 (40%)
Query: 47 IRLARYGCTNRPFYHIVVIHSSEHSVGLAHIDKKWSSKLYVRRCVNVKSSEHSVGLAHID 106
IRL R G +PFY IVV+ S
Sbjct: 4 IRLTRMGKRKQPFYRIVVVDS--------------------------------------- 24
Query: 107 KKWSSKITRMRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHITSPVREL 166
R RR+ IE LG ++PL Y+ + +++ER W+ + VR++
Sbjct: 25 --------RKRRDGAYIESLGYYNPLKEPYE---IKVDVERAVEWI-LKGAQPSDTVRDI 72
Query: 167 FGKLNI 172
K +
Sbjct: 73 LRKFGV 78
>gnl|CDD|172989 PRK14523, rpsP, 30S ribosomal protein S16; Provisional.
Length = 137
Score = 30.2 bits (67), Expect = 0.38
Identities = 13/18 (72%), Positives = 13/18 (72%)
Query: 47 IRLARYGCTNRPFYHIVV 64
IRLAR G PFYHIVV
Sbjct: 4 IRLARGGSKKNPFYHIVV 21
>gnl|CDD|225274 COG2411, COG2411, Uncharacterized conserved protein [Function
unknown].
Length = 188
Score = 29.7 bits (67), Expect = 0.69
Identities = 10/29 (34%), Positives = 12/29 (41%)
Query: 51 RYGCTNRPFYHIVVIHSSEHSVGLAHIDK 79
R G V IHS + +G A I K
Sbjct: 29 RLGKIVLKPGSEVYIHSGGYIIGKAKIKK 57
>gnl|CDD|153357 cd07673, F-BAR_FCHO2, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of FCH domain Only 2
protein. F-BAR domains are dimerization modules that
bind and bend membranes and are found in proteins
involved in membrane dynamics and actin reorganization.
The specific function of FCH domain Only 2 (FCHO2) is
still unknown. It contains an N-terminal F-BAR domain
and a C-terminal domain of unknown function named SAFF
which is also present in FCHO1 and endophilin
interacting protein 1. F-BAR domains form banana-shaped
dimers with a positively-charged concave surface that
binds to negatively-charged lipid membranes. They can
induce membrane deformation in the form of long tubules.
Length = 269
Score = 28.1 bits (62), Expect = 3.2
Identities = 15/50 (30%), Positives = 31/50 (62%), Gaps = 3/50 (6%)
Query: 103 AHIDKKWSSKITRMRRNDQPIEQLGTFDPLPNEYQ---EKLVSLNIERIR 149
A I++ +S +T++ ++ QLGTF P+ + ++ EKL + ++E +R
Sbjct: 39 ATIEEAYSRSMTKLAKSASNYSQLGTFAPVWDVFKTSTEKLANCHLELVR 88
>gnl|CDD|162022 TIGR00754, bfr, bacterioferritin. Bacterioferritin, predominantly
an iron-storage protein restricted to Bacteria, has also
been designated cytochrome b1 and cytochrome
b-557.Bacterioferritin is a homomultimer most species.
In Neisseria gonorrhoeae, Synechocystis PCC6803,
Magnetospirillum magnetotacticum, and Pseudomonas
aeruginosa, two types of subunit are found in a
heteromultimeric complex, with each species having one
member of each type. At present, both types of subunit
are including in this single model [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 157
Score = 27.5 bits (61), Expect = 3.3
Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 18/85 (21%)
Query: 101 GLAHI-DKKWSSKITRMRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHI 159
GL + D ++ I M+ D+ IE++ + LPN Q ++ ++R I
Sbjct: 36 GLKELADHEYHESIDEMKHADEIIERILFLEGLPN-LQ------DLGKLR---------I 79
Query: 160 TSPVRELFG-KLNIDLTNLCDLRPS 183
VRE+ L ++L L L+ +
Sbjct: 80 GETVREMLEADLALELDVLNRLKEA 104
>gnl|CDD|217905 pfam04114, Gaa1, Gaa1-like, GPI transamidase component. GPI
(glycosyl phosphatidyl inositol) transamidase is a
multi-protein complex. Gpi16, Gpi8 and Gaa1 for a
sub-complex of the GPI transamidase. GPI transamidase
that adds glycosylphosphatidylinositols (GPIs) to newly
synthesised proteins.
Length = 498
Score = 27.9 bits (62), Expect = 3.4
Identities = 19/67 (28%), Positives = 25/67 (37%), Gaps = 20/67 (29%)
Query: 152 LGTSDIHITSPVRE-----LFGKL-NIDLTNLCD--------------LRPSQWLANSNF 191
L S S E L G+L N+DL NL L+PS +NS F
Sbjct: 104 LELSSTEDFSEYVEVSYEGLNGQLPNLDLFNLAQRITEHEGFMKYSLHLQPSDQHSNSGF 163
Query: 192 WFNSQQV 198
W + +
Sbjct: 164 WQRLKIL 170
>gnl|CDD|215342 PLN02636, PLN02636, acyl-coenzyme A oxidase.
Length = 686
Score = 27.5 bits (61), Expect = 5.1
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 119 NDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIH 158
N Q ++ TFDPL +E+ + + N I++W+G + +H
Sbjct: 187 NVQGLQTTATFDPLTDEFV--INTPNDGAIKWWIGNAAVH 224
>gnl|CDD|187834 cd09703, Cas6-I-III, CRISPR/Cas system-associated RAMP superfamily
protein Cas6. 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;
Cas6 is an endoribonuclease that generates crRNAs,
predicted subunit of Cascade complex; RAMP superfamily
protein; Possesses double RRM/ferredoxin fold; also
known as Cse3 family.
Length = 188
Score = 26.6 bits (59), Expect = 7.7
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 9/56 (16%)
Query: 115 RMRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHITSPVRELFGKL 170
R+R P+EQ+ PL + SL+I R LG I P LF ++
Sbjct: 61 RIR---IPVEQVPLVLPLAGK------SLDIGGHRLRLGAPSIRALQPAPSLFARI 107
>gnl|CDD|131854 TIGR02807, cas6_var, CRISPR-associated protein Cas6, subtype MYXAN.
Members of this protein family resemble the Cas6
proteins described by TIGR01877 in having a C-terminal
motif GXGXXXXXGXG, where the single X of each GXG is
hydrophobic and the spacer XXXXX has at least one Lys or
Arg. Examples are found in cas gene operons of CRISPR
regions in Anabaena variabilis ATCC 29413, Leptospira
interrogans, Gemmata obscuriglobus UQM 2246, and twice
in Myxococcus xanthus DK 1622. Oddly, an orphan member
is found in Thiobacillus denitrificans ATCC 25259, whose
genome does not seem to contain other evidence of CRISPR
repeats or cas genes [Mobile and extrachromosomal
element functions, Other].
Length = 190
Score = 26.6 bits (59), Expect = 8.2
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 9/56 (16%)
Query: 115 RMRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHITSPVRELFGKL 170
R+R P+EQ+ PL + SL+I R LG I P LF ++
Sbjct: 64 RIR---IPVEQVPLVLPLAGK------SLDIGGHRLRLGAPSIRALQPASSLFARI 110
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
0.322 0.134 0.427
Gapped
Lambda K H
0.267 0.0609 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,882,696
Number of extensions: 871565
Number of successful extensions: 623
Number of sequences better than 10.0: 1
Number of HSP's gapped: 616
Number of HSP's successfully gapped: 31
Length of query: 198
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 106
Effective length of database: 6,857,034
Effective search space: 726845604
Effective search space used: 726845604
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (25.6 bits)