RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11384
(137 letters)
>gnl|CDD|216410 pfam01283, Ribosomal_S26e, Ribosomal protein S26e.
Length = 113
Score = 183 bits (466), Expect = 4e-61
Identities = 77/106 (72%), Positives = 85/106 (80%)
Query: 1 MTCKRRNGGRSKHGRGHVNPVRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDITEASYYQ 60
M KRRN GRSK RGHV PVRCTNC RCVPKDKAIK+FV+RNIVEAAA RD++EAS Y+
Sbjct: 1 MPKKRRNNGRSKKNRGHVKPVRCTNCGRCVPKDKAIKRFVVRNIVEAAAARDLSEASVYE 60
Query: 61 SYQLPKLYAKLHYCVSCAIHSKVVRNRSKSDRRIRTPPQRNFPRSV 106
Y LPKLY KL YCVSCAIHSK+VR RS+ DR+IRTPP R R
Sbjct: 61 GYALPKLYVKLQYCVSCAIHSKIVRVRSREDRKIRTPPPRFRRRKD 106
>gnl|CDD|185497 PTZ00172, PTZ00172, 40S ribosomal protein S26; Provisional.
Length = 108
Score = 165 bits (420), Expect = 3e-54
Identities = 78/102 (76%), Positives = 87/102 (85%)
Query: 1 MTCKRRNGGRSKHGRGHVNPVRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDITEASYYQ 60
MT KRRN GRSKHGRGHV PVRC+NC RCVPKDKAIK+FV+RNIV+AA+VRDI EAS Y
Sbjct: 1 MTSKRRNNGRSKHGRGHVKPVRCSNCGRCVPKDKAIKRFVVRNIVDAASVRDIAEASVYY 60
Query: 61 SYQLPKLYAKLHYCVSCAIHSKVVRNRSKSDRRIRTPPQRNF 102
Y LPKLY K YCVSCAIHS+VVR RS+ DR+IRTPP+R F
Sbjct: 61 GYPLPKLYMKQQYCVSCAIHSRVVRVRSREDRKIRTPPKRPF 102
>gnl|CDD|215093 PLN00186, PLN00186, ribosomal protein S26; Provisional.
Length = 109
Score = 157 bits (400), Expect = 2e-51
Identities = 72/104 (69%), Positives = 86/104 (82%), Gaps = 1/104 (0%)
Query: 1 MTCKRRNGGRSKHGRGHVNPVRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDITEASYYQ 60
MT KRRNGGR+KHGRGHV +RC+NC +CVPKDKAIK+F++RNIVE AA+RD+ EA Y
Sbjct: 1 MTKKRRNGGRNKHGRGHVKRIRCSNCGKCVPKDKAIKRFLVRNIVEQAALRDVQEACVYD 60
Query: 61 SYQLPKLYAKLHYCVSCAIHSKVVRNRSKSDRRIRTPPQRNFPR 104
Y LPKLYAK+ YC+SCAIHS+VVR RS+ +RRIR PP R F R
Sbjct: 61 GYTLPKLYAKVQYCISCAIHSRVVRVRSRENRRIREPPPR-FRR 103
>gnl|CDD|227167 COG4830, RPS26B, Ribosomal protein S26 [Translation, ribosomal
structure and biogenesis].
Length = 108
Score = 127 bits (320), Expect = 4e-39
Identities = 62/101 (61%), Positives = 76/101 (75%)
Query: 1 MTCKRRNGGRSKHGRGHVNPVRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDITEASYYQ 60
M KRRN GR+K GRGHV VRC NC + VPKDKAIK+ IR+ VEAAA RD++EAS Y
Sbjct: 1 MPKKRRNRGRNKKGRGHVKYVRCDNCGKAVPKDKAIKRTAIRSPVEAAAARDLSEASIYS 60
Query: 61 SYQLPKLYAKLHYCVSCAIHSKVVRNRSKSDRRIRTPPQRN 101
Y +PK Y KL YCVSCAIH+++VR RS+ +R+IR P R+
Sbjct: 61 EYAVPKTYNKLQYCVSCAIHARIVRVRSREERKIRAPFNRD 101
>gnl|CDD|181785 PRK09335, PRK09335, 30S ribosomal protein S26e; Provisional.
Length = 95
Score = 67.0 bits (164), Expect = 1e-15
Identities = 30/99 (30%), Positives = 53/99 (53%), Gaps = 4/99 (4%)
Query: 1 MTCKRRNGGRSKHGRGHVNPVRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDITEASYYQ 60
M KR N GR K +GHV V+C NC R VP+DKA+ + + V+ +++ +
Sbjct: 1 MPKKRENRGRRKGDKGHVGYVQCDNCGRRVPRDKAVCVTKMYSPVDPQLAKELEKKGAI- 59
Query: 61 SYQLPKLYAKLHYCVSCAIHSKVVRNRSKSDRRIRTPPQ 99
+ + YCV+CA+H +++ R + +R+ + P +
Sbjct: 60 ---IARYPVTKCYCVNCAVHLGIIKIRPEEERKKKAPLR 95
>gnl|CDD|173877 cd08512, PBP2_NikA_DppA_OppA_like_7, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 476
Score = 29.1 bits (66), Expect = 0.62
Identities = 10/42 (23%), Positives = 16/42 (38%), Gaps = 6/42 (14%)
Query: 35 AIKKFVIRNIVEAAAVR------DITEASYYQSYQLPKLYAK 70
+K+ +IR++ EAA R D A + L
Sbjct: 200 KLKRVIIRHVPEAATRRLLLERGDADIARNLPPDDVAALEGN 241
>gnl|CDD|235828 PRK06556, PRK06556, vitamin B12-dependent ribonucleotide reductase;
Validated.
Length = 953
Score = 29.2 bits (66), Expect = 0.63
Identities = 22/62 (35%), Positives = 28/62 (45%), Gaps = 9/62 (14%)
Query: 4 KRRNGGRSKHGRGHVNPVRCTNCARCVP-KDKAIKKFVIRNIVEAAAVRDITEASYYQSY 62
K +G RS GHV + A P AI K V N+ E A V DI E Y + +
Sbjct: 628 KPASGERSISPMGHVRMM-----AAVQPFLSGAISKTV--NMPEDATVEDIEEV-YLEGW 679
Query: 63 QL 64
+L
Sbjct: 680 KL 681
>gnl|CDD|221801 pfam12838, Fer4_7, 4Fe-4S dicluster domain. Superfamily includes
proteins containing domains which bind to iron-sulfur
clusters. Members include bacterial ferredoxins,
various dehydrogenases, and various reductases.
Structure of the domain is an alpha-antiparallel beta
sandwich. Domain contains two 4Fe4S clusters.
Length = 48
Score = 26.8 bits (59), Expect = 0.99
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 5 RRNGGRSKHGRGHVNPVRCTNCARCV 30
+ K G ++P +CT C CV
Sbjct: 17 TLDEEGGKKGTVEIDPDKCTGCGACV 42
>gnl|CDD|235428 PRK05355, PRK05355, 3-phosphoserine/phosphohydroxythreonine
aminotransferase; Provisional.
Length = 360
Score = 28.5 bits (65), Expect = 1.0
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 3/44 (6%)
Query: 34 KAIK---KFVIRNIVEAAAVRDITEASYYQSYQLPKLYAKLHYC 74
KAIK K+ N+ ++ T +QL A +HY
Sbjct: 105 KAIKEAKKYGEVNVAASSEDDGFTYIPPLDEWQLSDDAAYVHYT 148
>gnl|CDD|227598 COG5273, COG5273, Uncharacterized protein containing DHHC-type Zn
finger [General function prediction only].
Length = 309
Score = 27.8 bits (62), Expect = 1.8
Identities = 11/31 (35%), Positives = 12/31 (38%), Gaps = 9/31 (29%)
Query: 2 TCKRRNGGRSKHGRGHVNPVRCTNCARCVPK 32
TC RS H C+ C RCV K
Sbjct: 114 TCNIYKPPRSHH---------CSICNRCVLK 135
>gnl|CDD|224318 COG1400, SEC65, Signal recognition particle 19 kDa protein
[Intracellular trafficking and secretion].
Length = 93
Score = 26.2 bits (58), Expect = 3.5
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 28 RCVPKDKAIKKFVIRNIVEAA 48
R VPK+ A++ + I EA
Sbjct: 21 RRVPKELAVENPSLEEIAEAL 41
>gnl|CDD|150776 pfam10141, ssDNA-exonuc_C, Single-strand DNA-specific exonuclease,
C terminal domain. Members of this set of prokaryotic
domains are found in a set of single-strand DNA-specific
exonucleases, including RecJ. Their exact function has
not, as yet, been determined.
Length = 195
Score = 26.5 bits (59), Expect = 4.0
Identities = 8/28 (28%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 36 IKKFVIRNIVEAAAVRDITEASYYQSYQ 63
I+ ++ + + A RD+TE+ YQ+
Sbjct: 148 IEDGLM-TVNKNAEKRDLTESPTYQARL 174
>gnl|CDD|205417 pfam13237, Fer4_10, 4Fe-4S dicluster domain. This family
includes proteins containing domains which bind to
iron-sulfur clusters. Members include bacterial
ferredoxins, various dehydrogenases, and various
reductases. The structure of the domain is an
alpha-antiparallel beta sandwich.
Length = 51
Score = 24.7 bits (53), Expect = 6.4
Identities = 8/26 (30%), Positives = 11/26 (42%)
Query: 5 RRNGGRSKHGRGHVNPVRCTNCARCV 30
R + G ++P RC C CV
Sbjct: 22 GAGAIRDEGGAVEIDPDRCIGCGACV 47
>gnl|CDD|146444 pfam03805, CLAG, Cytoadherence-linked asexual protein. Clag
(cytoadherence linked asexual gene) is a malaria surface
protein which has been shown to be involved in the
binding of Plasmodium falciparum infected erythrocytes
to host endothelial cells, a process termed
cytoadherence. The cytoadherence phenomenon is
associated with the sequestration of infected
erythrocytes in the blood vessels of the brain, cerebral
malaria. Clag is a multi-gene family in Plasmodium
falciparum with at least 9 members identified to date.
Orthologous proteins in the rodent malaria species
Plasmodium chabaudi (Lawson D Unpubl. obs.) suggest that
the gene family is found in other malaria species and
may play a more generic role in cytoadherence.
Length = 1282
Score = 26.6 bits (59), Expect = 6.4
Identities = 15/70 (21%), Positives = 32/70 (45%), Gaps = 4/70 (5%)
Query: 55 EASYYQSYQLPKLYAKLHYCV-SCAIHSKVVRNRSKSDRRIRTPPQRNFPRS-VSLTEGT 112
+ S+ + +L L+ L CV C +S+ +N+S ++ + F S ++ +GT
Sbjct: 445 QLSFTEEVELKDLFENLVKCVEKC--YSRDRKNKSSENKIKSIFSNKEFDSSKCNICKGT 502
Query: 113 VTAMVLSSQN 122
+ Q+
Sbjct: 503 FLYINNKFQD 512
>gnl|CDD|184290 PRK13738, PRK13738, conjugal transfer pilus assembly protein
TraW; Provisional.
Length = 209
Score = 25.9 bits (57), Expect = 8.5
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 34 KAIKKFVIRNIVEAAAVRDITEASYYQSY 62
A K+ VIRN + AV I A Y+S
Sbjct: 56 DAFKERVIRNSLRPPAVPGIGRAEKYRSR 84
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
0.321 0.132 0.393
Gapped
Lambda K H
0.267 0.0748 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,550,037
Number of extensions: 533937
Number of successful extensions: 515
Number of sequences better than 10.0: 1
Number of HSP's gapped: 514
Number of HSP's successfully gapped: 31
Length of query: 137
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 50
Effective length of database: 7,078,804
Effective search space: 353940200
Effective search space used: 353940200
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: 54 (24.5 bits)