RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1616
(237 letters)
>gnl|CDD|185485 PTZ00156, PTZ00156, 60S ribosomal protein L11; Provisional.
Length = 172
Score = 219 bits (560), Expect = 5e-73
Identities = 109/194 (56%), Positives = 128/194 (65%), Gaps = 33/194 (17%)
Query: 43 KDKSKNVMREVKIRKLCLNICVGESGDRLTRAAKVLEQLTGQQPVFSKARYT-RSKG-RR 100
+ K +N MR+++I KL LNICVGESGDRLTRAAKVLEQLTGQ+PVFSKARYT RS G RR
Sbjct: 1 ESKKENPMRKIRIEKLVLNICVGESGDRLTRAAKVLEQLTGQKPVFSKARYTVRSFGIRR 60
Query: 101 NPGERASSFMKPLVVLALPGMYLFYKYNQYKQQQQEQNRR--KVTERELDHLNQKIHKAQ 158
N E+ + + + G + +E R KV E EL +
Sbjct: 61 N--EKIACH------VTVRG-----------DKAEEILERGLKVKEFEL----------K 91
Query: 159 SLCLHHSGNFGFGIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFNVAHRRRKTGIVGFQH 218
+GNFGFGIQEHIDLGIKYDPS GIYG+DFYVVLGRPGF VA R+RK VG H
Sbjct: 92 KRNFSDTGNFGFGIQEHIDLGIKYDPSTGIYGMDFYVVLGRPGFRVARRKRKQSKVGKSH 151
Query: 219 RLTKEDAMKWFQTK 232
R+TKE+AMKWF+T
Sbjct: 152 RVTKEEAMKWFKTT 165
>gnl|CDD|235259 PRK04219, rpl5p, 50S ribosomal protein L5P; Reviewed.
Length = 177
Score = 150 bits (381), Expect = 7e-46
Identities = 72/203 (35%), Positives = 107/203 (52%), Gaps = 48/203 (23%)
Query: 42 KKDKSKNVMREVKIRKLCLNICVGESGDRLTRAAKVLEQLTGQQPVFSKARYT-RSKG-- 98
+D N MR+ +I K+ +NI VGESG+RLT+A K+LE+LTGQ+PV ++A+ T G
Sbjct: 4 LEDWEMNPMRKPRIEKVVVNIGVGESGERLTKAEKLLEELTGQKPVRTRAKKTIPDFGIR 63
Query: 99 RRNP--------GERASSFMKPLVVLALPGMYLFYKYNQYKQQQQEQNRRKVTERELDHL 150
+ P GE+A F+K L+ +
Sbjct: 64 KGEPIGVKVTLRGEKAEEFLK---------------------------------TALEAV 90
Query: 151 NQKIHKAQSLCLHHSGNFGFGIQEHIDL-GIKYDPSIGIYGLDFYVVLGRPGFNVAHRRR 209
++ + +GN FGI+EHID G+KYDP IGI+G+D V L RPG+ VA RRR
Sbjct: 91 GNRLKASS---FDETGNVSFGIEEHIDFPGVKYDPEIGIFGMDVCVTLERPGYRVARRRR 147
Query: 210 KTGIVGFQHRLTKEDAMKWFQTK 232
K + +HR+TKE+A+++ +
Sbjct: 148 KRRKIPSRHRVTKEEAIEFLEEN 170
>gnl|CDD|223172 COG0094, RplE, Ribosomal protein L5 [Translation, ribosomal
structure and biogenesis].
Length = 180
Score = 118 bits (297), Expect = 3e-33
Identities = 60/193 (31%), Positives = 86/193 (44%), Gaps = 45/193 (23%)
Query: 42 KKDKSKNVMREVKIRKLCLNICVGES---GDRLTRAAKVLEQLTGQQPVFSKARYTRS-- 96
KK N M+ +I K+ +N+ VGE+ G RL +AAK LE +TGQ+PV +KA+ + +
Sbjct: 18 KKFGYSNPMQVPRIEKVVVNMGVGEAAADGKRLEKAAKDLELITGQKPVITKAKKSIAGF 77
Query: 97 KGRRN-P--------GERASSFMKPLVVLALPGMYLFYKYNQYKQQQQEQNRRKVTEREL 147
K R P GER F+ L+ +ALP + F R ++ +
Sbjct: 78 KIREGMPIGVKVTLRGERMYEFLDRLLNIALPRVRDF---------------RGLSPKSF 122
Query: 148 DHLNQKIHKAQSLCLHHSGNFGFGIQEHIDL-GIKYDPSIGIYGLDFYVVLGRPGFNVAH 206
D GN+ FGI+E I I YDP IGI G+D +V G A
Sbjct: 123 D---------------GRGNYSFGIKEQIIFPEIDYDPIIGIRGMDITIVTTAKGDVEAR 167
Query: 207 RRRKTGIVGFQHR 219
+ F+ R
Sbjct: 168 ALLSAFGIPFRKR 180
>gnl|CDD|201383 pfam00673, Ribosomal_L5_C, ribosomal L5P family C-terminus. This
region is found associated with pfam00281.
Length = 95
Score = 68.7 bits (169), Expect = 3e-15
Identities = 37/129 (28%), Positives = 52/129 (40%), Gaps = 45/129 (34%)
Query: 103 GERASSFMKPLVVLALPGMYLFYKYNQYKQQQQEQNRRKVTERELDHLNQKIHKAQSLCL 162
GE+ F+ L+ +ALP + F R ++ + D
Sbjct: 10 GEKMYEFLDRLINVALPRIRDF---------------RGLSPKSFDG------------- 41
Query: 163 HHSGNFGFGIQEHIDL-GIKYDPSIGIYGLDFYVVLGRPGFNVAHRRRKTGIVGFQHR-L 220
GN+ FGI+EHI IKYDP IGI+G+D +V KT + R L
Sbjct: 42 --RGNYSFGIKEHIIFPEIKYDPIIGIFGMDITIV----------TTAKT---DKEARAL 86
Query: 221 TKEDAMKWF 229
KE M +F
Sbjct: 87 LKELGMPFF 95
>gnl|CDD|109342 pfam00281, Ribosomal_L5, Ribosomal protein L5.
Length = 56
Score = 59.3 bits (144), Expect = 3e-12
Identities = 21/49 (42%), Positives = 35/49 (71%), Gaps = 2/49 (4%)
Query: 48 NVMREVKIRKLCLNICVGESGDR--LTRAAKVLEQLTGQQPVFSKARYT 94
NVM K+ K+ +N+ VGE+GD L +AA LE+++GQ+P+ +KA+ +
Sbjct: 1 NVMEVPKLEKIVVNMGVGEAGDNKILEKAALELEEISGQKPIITKAKKS 49
>gnl|CDD|178791 PRK00010, rplE, 50S ribosomal protein L5; Validated.
Length = 179
Score = 43.9 bits (105), Expect = 1e-05
Identities = 34/89 (38%), Positives = 48/89 (53%), Gaps = 18/89 (20%)
Query: 47 KNVMREVKIRKLCLNICVGE-SGDR--LTRAAKVLEQLTGQQPVFSKARYTRS----KGR 99
KNVM+ K+ K+ LN+ VGE D+ L A + L +TGQ+PV +KA+ +S K R
Sbjct: 23 KNVMQVPKLEKIVLNMGVGEAVADKKLLENAVEDLTLITGQKPVVTKAK--KSIAGFKLR 80
Query: 100 RN-P--------GERASSFMKPLVVLALP 119
P GER F+ L+ +ALP
Sbjct: 81 EGMPIGCKVTLRGERMYEFLDRLINIALP 109
Score = 26.6 bits (60), Expect = 9.0
Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 16/50 (32%)
Query: 5 KIRKLCLNICVGESGDRLTRAAKTKAVDPA----------KPVAKKGKKD 44
K+ K+ LN+ VGE+ A K ++ A KPV K KK
Sbjct: 30 KLEKIVLNMGVGEA------VADKKLLENAVEDLTLITGQKPVVTKAKKS 73
>gnl|CDD|214356 CHL00078, rpl5, ribosomal protein L5.
Length = 181
Score = 32.9 bits (76), Expect = 0.073
Identities = 25/91 (27%), Positives = 49/91 (53%), Gaps = 22/91 (24%)
Query: 47 KNVMREVKIRKLCLNICVGESGDRLTRAAKVLEQ-------LTGQQPVFSKARYTRS--K 97
KN+ + K++K+ +N +GE+ ++ +K+LE +TGQ+P+ ++A+ + K
Sbjct: 24 KNIHQVPKLKKIVINRGLGEA----SQNSKILESSIKELTIITGQKPIITRAKKAIAGFK 79
Query: 98 GRRN-P--------GERASSFMKPLVVLALP 119
R P G++ +F+ L+ LALP
Sbjct: 80 IREKMPVGVSVTLRGDKMYAFLDRLINLALP 110
>gnl|CDD|234175 TIGR03348, VI_IcmF, type VI secretion protein IcmF. Members of
this protein family are IcmF homologs and tend to be
associated with type VI secretion systems [Cellular
processes, Pathogenesis].
Length = 1169
Score = 30.8 bits (70), Expect = 0.83
Identities = 18/98 (18%), Positives = 35/98 (35%), Gaps = 25/98 (25%)
Query: 113 LVVLALPGMYLFYKYNQYKQQQQEQNRRKVTER---------ELDHLNQKIHKAQSLCLH 163
+++L L ++ ++ QQ + E+ L + ++A +L L
Sbjct: 40 VLLLVWLLWLLIRQWRARRRNQQLLAALAAPTKLKADAAAEAEIRELRARFNEALAL-LK 98
Query: 164 HSGNFGFGIQEHIDLGIKYDPSIGIYGLDFYVVLGRPG 201
S G +Y L +Y+V+G PG
Sbjct: 99 RSRLGGRR---------------YLYDLPWYLVIGPPG 121
>gnl|CDD|215323 PLN02598, PLN02598, omega-6 fatty acid desaturase.
Length = 421
Score = 30.2 bits (68), Expect = 0.92
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 3/66 (4%)
Query: 78 LEQLTGQQPVFSKARYTRSKGRRNPGERASSFMKPLVVLALPGMYLFYKYNQYKQQQQEQ 137
L T QP F ++ + R RA M PL A G +LF+ ++ K + QE
Sbjct: 190 LVMDTAWQP-FRPHQFDNADPLRKAMMRA--GMGPLWWWASIGHWLFWHFDLNKFRPQEV 246
Query: 138 NRRKVT 143
R K++
Sbjct: 247 PRVKIS 252
>gnl|CDD|179310 PRK01622, PRK01622, OxaA-like protein precursor; Validated.
Length = 256
Score = 29.7 bits (67), Expect = 1.1
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 128 NQYKQQQQEQNRRKVTERELDHLNQKIHKAQSL 160
+QYK Q+ Q + V + ELD + K+ + L
Sbjct: 81 SQYKSQRGMQEKMAVMKPELDKIQAKLKVTKDL 113
>gnl|CDD|223839 COG0768, FtsI, Cell division protein FtsI/penicillin-binding
protein 2 [Cell envelope biogenesis, outer membrane].
Length = 599
Score = 29.3 bits (66), Expect = 1.8
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 5/60 (8%)
Query: 90 KARYTRSKGRRNPGERAS-SFMKPLVVLALPGMYLFY----KYNQYKQQQQEQNRRKVTE 144
K R + K R R + F+ ++ AL + LFY + + Y ++ +N+R V
Sbjct: 1 KKRKKKKKKGRLFRRRLNLLFLIIFLLFALLILRLFYLQIVQGDDYAKEAANRNQRTVPI 60
>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
subunit. This is a family of proteins which are
subunits of the eukaryotic translation initiation
factor 3 (eIF3). In yeast it is called Hcr1. The
Saccharomyces cerevisiae protein eIF3j (HCR1) has been
shown to be required for processing of 20S pre-rRNA and
binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p.
Length = 242
Score = 28.5 bits (64), Expect = 2.8
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 25 AAKTKAVDPAKPVAKKGKKDKSKNVMREVKIRK 57
+ KA AK AKK K K + + + ++
Sbjct: 45 KEEEKAKVAAKAKAKKALKAKIEEKEKAKREKE 77
>gnl|CDD|153335 cd07651, F-BAR_PombeCdc15_like, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Schizosaccharomyces pombe
Cdc15, and similar proteins. F-BAR domains are
dimerization modules that bind and bend membranes and
are found in proteins involved in membrane dynamics and
actin reorganization. This subfamily is composed of
Schizosaccharomyces pombe Cdc15 and Imp2, and similar
proteins. These proteins contain an N-terminal F-BAR
domain and a C-terminal SH3 domain. S. pombe Cdc15 and
Imp2 play both distinct and overlapping roles in the
maintenance and strengthening of the contractile ring at
the division site, which is required in cell division.
Cdc15 is a component of the actomyosin ring and is
required in normal cytokinesis. Imp2 colocalizes with
the medial ring during septation and is required for
normal septation. 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 = 236
Score = 28.0 bits (63), Expect = 3.7
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 5/34 (14%)
Query: 126 KYNQYKQQQQEQNRRKVTERELDHLNQKIHKAQS 159
K N Y Q Q +EL+ N K++KAQS
Sbjct: 136 KINSYTLQSQ-----LTWGKELEKNNAKLNKAQS 164
>gnl|CDD|200485 cd11347, AmyAc_1, Alpha amylase catalytic domain found in an
uncharacterized protein family. The Alpha-amylase
family comprises the largest family of glycoside
hydrolases (GH), with the majority of enzymes acting on
starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 391
Score = 28.4 bits (64), Expect = 3.8
Identities = 24/84 (28%), Positives = 33/84 (39%), Gaps = 23/84 (27%)
Query: 69 DRLT-RAAKVLEQLTGQQPVFSK--ARYTRSKGRRNPGE-RASSFMKP-------LVVLA 117
DRL A+V+ + R+ N E RA++ P L+ L
Sbjct: 279 DRLRHGDAEVVRYHLSADLDYQSHLVRFIE-----NHDEPRAAAKFGPERHRAAALITLT 333
Query: 118 LPGMYLFYKYNQYKQQQQEQNRRK 141
LPGM LF+ Q Q + RRK
Sbjct: 334 LPGMRLFH-------QGQLEGRRK 350
>gnl|CDD|213021 cd10916, CE4_PuuE_HpPgdA_like, Catalytic domain of bacterial PuuE
allantoinases, Helicobacter pylori peptidoglycan
deacetylase (HpPgdA), and similar proteins. This family
is a member of the very large and functionally diverse
carbohydrate esterase 4 (CE4) superfamily. It contains
bacterial PuuE (purine utilization E) allantoinases, a
peptidoglycan deacetylase from Helicobacter pylori
(HpPgdA), Escherichia coli ArnD, and many
uncharacterized homologs from all three kingdoms of
life. PuuE allantoinase appears to be metal-independent
and specifically catalyzes the hydrolysis of
(S)-allantoin into allantoic acid. Different from PuuE
allantoinase, HpPgdA has the ability to bind a metal ion
at the active site and is responsible for a
peptidoglycan modification that counteracts the host
immune response. Both PuuE allantoinase and HpPgdA
function as a homotetramer. The monomer is composed of a
7-stranded barrel with detectable sequence similarity to
the 6-stranded barrel NodB homology domain of
polysaccharide deacetylase (DCA)-like proteins in the
CE4 superfamily, which removes N-linked or O-linked
acetyl groups from cell wall polysaccharides. However,
in contrast with the typical DCAs, PuuE allantoinase and
HpPgdA might not exhibit a solvent-accessible
polysaccharide binding groove and only recognize a small
substrate molecule. ArnD catalyzes the deformylation of
4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol to
4-amino-4-deoxy-L-arabinose-phosphoundecaprenol.
Length = 247
Score = 27.7 bits (62), Expect = 5.6
Identities = 9/19 (47%), Positives = 15/19 (78%)
Query: 69 DRLTRAAKVLEQLTGQQPV 87
+ L R+ ++LE+LTGQ+P
Sbjct: 98 EVLLRSLELLEELTGQRPT 116
>gnl|CDD|211620 TIGR01038, L22_arch, ribosomal protein
L22(archaeal)/L17(eukaryotic/archaeal). This model
describes the ribosomal protein of the eukaryotic
cytosol and of the Archaea, variously designated as L17,
L22, and L23. The corresponding bacterial homolog,
described by a separate model, is designated L22
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 150
Score = 27.0 bits (60), Expect = 5.9
Identities = 13/56 (23%), Positives = 20/56 (35%), Gaps = 1/56 (1%)
Query: 46 SKNVMREVKI-RKLCLNICVGESGDRLTRAAKVLEQLTGQQPVFSKARYTRSKGRR 100
+K R +++ K G L +A K LE + + RY G R
Sbjct: 12 AKARGRNLRVSFKNARETARAIRGMELDKARKYLEDVIEMKRAVPFRRYNGKVGHR 67
>gnl|CDD|147845 pfam05914, RIB43A, RIB43A. This family consists of several
RIB43A-like eukaryotic proteins. Ciliary and flagellar
microtubules contain a specialised set of
protofilaments, termed ribbons, that are composed of
tubulin and several associated proteins. RIB43A was
first characterized in the unicellular biflagellate,
Chlamydomonas reinhardtii although highly related
sequences are present in several higher eukaryotes
including humans. The function of this protein is
unknown although the structure of RIB43A and its
association with the specialised protofilament ribbons
and with basal bodies is relevant to the proposed role
of ribbons in forming and stabilising doublet and
triplet microtubules and in organising their
three-dimensional structure. Human RIB43A homologues
could represent a structural requirement in centriole
replication in dividing cells.
Length = 379
Score = 27.7 bits (62), Expect = 6.6
Identities = 8/34 (23%), Positives = 16/34 (47%)
Query: 131 KQQQQEQNRRKVTERELDHLNQKIHKAQSLCLHH 164
+QQ QE+ + K E++ D L+ ++
Sbjct: 165 EQQVQERQQAKAAEKQADTLHDQLRVELDHRAQE 198
Score = 26.9 bits (60), Expect = 9.3
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 133 QQQEQNRRKVTERELDHLNQKIHKAQ 158
++QE+ RK ++LD NQ++ K Q
Sbjct: 325 ERQERRLRKELRKQLDSANQQLAKEQ 350
>gnl|CDD|221296 pfam11894, DUF3414, Protein of unknown function (DUF3414). This
family of proteins are functionally uncharacterized.
This protein is found in eukaryotes. Proteins in this
family are typically between 764 to 2011 amino acids in
length. This protein has a conserved LLG sequence motif.
Length = 1612
Score = 27.3 bits (61), Expect = 8.4
Identities = 10/38 (26%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 141 KVTERELDHLNQKIHKAQSLCLHHSGNFGFGIQEHIDL 178
+ ++ L L ++I K + L ++ G G EHI
Sbjct: 166 GLIKQLLSLLKEQIDKQKILGQLNTNR-GLGFIEHIKF 202
>gnl|CDD|233028 TIGR00571, dam, DNA adenine methylase (dam). All proteins in this
family for which functions are known are DNA-adenine
methyltransferases. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University). The DNA adenine methylase (dam) of
E. coli and related species is instrumental in
distinguishing the newly synthesized strand during DNA
replication for methylation-directed mismatch repair.
This family includes several phage methylases and a
number of different restriction enzyme chromosomal
site-specific modification systems [DNA metabolism, DNA
replication, recombination, and repair].
Length = 266
Score = 26.9 bits (60), Expect = 8.4
Identities = 17/75 (22%), Positives = 24/75 (32%), Gaps = 20/75 (26%)
Query: 99 RRNPGERASSFMKPLVVL---ALPGMYLFYKYNQ-------YKQQQQEQNRRKVTERELD 148
P ERA F+ L G+Y + K + YK E+ L
Sbjct: 98 STEPFERALLFL----YLNRSCFNGLYRYNKKGEFNVPFGRYK------TPNFFDEKNLR 147
Query: 149 HLNQKIHKAQSLCLH 163
H +K+ LC
Sbjct: 148 HFAEKLQNTTFLCGS 162
>gnl|CDD|220716 pfam10359, Fmp27_WPPW, RNA pol II promoter Fmp27 protein domain.
Fmp27_WPPW is a conserved domain of a family of proteins
involved in RNA polymerase II transcription initiation.
It contains characteristic HQR and WPPW sequence motifs.
and is towards the C-terminal in members which contain
Fmp27_SW pfam10305.
Length = 470
Score = 27.3 bits (61), Expect = 8.6
Identities = 6/35 (17%), Positives = 15/35 (42%)
Query: 129 QYKQQQQEQNRRKVTERELDHLNQKIHKAQSLCLH 163
+ ++ Q+ + E EL L +++ + L
Sbjct: 188 ELNDTEELQSDLEELEEELSVLKERLEFLEKLLED 222
>gnl|CDD|236795 PRK10920, PRK10920, putative uroporphyrinogen III
C-methyltransferase; Provisional.
Length = 390
Score = 27.0 bits (60), Expect = 8.9
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 129 QYKQQQQEQNRRKVTERELDHLNQKI 154
Q K Q ++ ++LD L QK+
Sbjct: 97 QAKALDQANRQQAALAKQLDELQQKV 122
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 0.138 0.408
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,046,520
Number of extensions: 1116160
Number of successful extensions: 1165
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1154
Number of HSP's successfully gapped: 44
Length of query: 237
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 143
Effective length of database: 6,768,326
Effective search space: 967870618
Effective search space used: 967870618
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: 57 (25.6 bits)