RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 042358
(193 letters)
>gnl|CDD|214357 CHL00079, rps9, ribosomal protein S9.
Length = 130
Score = 131 bits (333), Expect = 7e-40
Identities = 50/86 (58%), Positives = 61/86 (70%)
Query: 98 IFGTGRRKCAIARVVLQEGTGKFIINYRDAKEYLQGNPLWLQYIKVPLVTLGYETSYDVF 157
GTGRRK A+A+V L G+G+ IIN + A+EYLQ NP +L IK PL LG E YD+
Sbjct: 5 YIGTGRRKTAVAQVRLVPGSGEIIINGKPAEEYLQYNPNYLNAIKAPLKLLGLENKYDII 64
Query: 158 VKAHGGGLSGQAQAITLGVARALLKF 183
VK GGGL+GQA+AI LG+ARAL K
Sbjct: 65 VKVKGGGLTGQAEAIRLGLARALCKI 90
>gnl|CDD|178888 PRK00132, rpsI, 30S ribosomal protein S9; Reviewed.
Length = 130
Score = 124 bits (313), Expect = 8e-37
Identities = 41/90 (45%), Positives = 55/90 (61%), Gaps = 1/90 (1%)
Query: 94 AAQTIFGTGRRKCAIARVVLQEGTGKFIINYRDAKEYLQGNPLWLQYIKVPLVTLGYETS 153
A +GTGRRK A+ARV L+ G+GK +N RD +EY ++ PL E
Sbjct: 2 AEVQYYGTGRRKTAVARVRLKPGSGKITVNGRDLEEYF-PRETLRMVVRQPLELTETEGK 60
Query: 154 YDVFVKAHGGGLSGQAQAITLGVARALLKF 183
+DV+V GGG+SGQA AI G+ARALL++
Sbjct: 61 FDVYVTVKGGGISGQAGAIRHGIARALLEY 90
>gnl|CDD|201193 pfam00380, Ribosomal_S9, Ribosomal protein S9/S16. This family
includes small ribosomal subunit S9 from prokaryotes and
S16 from eukaryotes.
Length = 121
Score = 120 bits (304), Expect = 1e-35
Identities = 37/83 (44%), Positives = 48/83 (57%), Gaps = 1/83 (1%)
Query: 102 GRRKCAIARVVLQEGTGKFIINYRDAKEYLQGNPLWLQYIKVPLVTLGYETSYDVFVKAH 161
GRRK A+ARV L+ G+GK IN + +EY N I PL G +D+ V
Sbjct: 1 GRRKTAVARVWLKPGSGKITINGKPLEEYFP-NETLRMKILEPLELTGTLGKFDIVVTVK 59
Query: 162 GGGLSGQAQAITLGVARALLKFC 184
GGG+SGQA AI L +ARAL+ +
Sbjct: 60 GGGISGQAGAIRLAIARALVAYD 82
>gnl|CDD|223181 COG0103, RpsI, Ribosomal protein S9 [Translation, ribosomal
structure and biogenesis].
Length = 130
Score = 102 bits (257), Expect = 2e-28
Identities = 35/84 (41%), Positives = 47/84 (55%), Gaps = 1/84 (1%)
Query: 100 GTGRRKCAIARVVLQEGTGKFIINYRDAKEYLQGNPLWLQYIKVPLVTLGYETSYDVFVK 159
TG+RK A+ARV L G GK +N R + Y I PL+ G +D+ V
Sbjct: 8 TTGKRKSAVARVRLVPGKGKITVNGRPLELY-FPRETLRMKIMQPLLLTGTVGKFDIDVT 66
Query: 160 AHGGGLSGQAQAITLGVARALLKF 183
GGG+SGQA AI G+ARAL+++
Sbjct: 67 VKGGGISGQAGAIRHGIARALVEY 90
>gnl|CDD|179041 PRK00474, rps9p, 30S ribosomal protein S9P; Reviewed.
Length = 134
Score = 61.0 bits (149), Expect = 2e-12
Identities = 31/92 (33%), Positives = 47/92 (51%), Gaps = 18/92 (19%)
Query: 101 TGRRKCAIARVVLQEGTGKFIINYRDAKEYLQGNPLWLQYIKV-------PLVTLGYE-- 151
+G+RK AIAR ++EG G+ IN G PL L ++ PL+ G +
Sbjct: 8 SGKRKTAIARATIREGKGRVRIN---------GVPLELIEPELARLKIMEPLILAGEDLR 58
Query: 152 TSYDVFVKAHGGGLSGQAQAITLGVARALLKF 183
+ D+ V GGG+ GQA A +AR L+++
Sbjct: 59 SKVDIDVNVEGGGIMGQADAARTAIARGLVEW 90
>gnl|CDD|132666 TIGR03627, arch_S9P, archaeal ribosomal protein S9P. This model
describes exclusively the archaeal ribosomal protein
S9P. Homologous eukaryotic and bacterial ribosomal
proteins are excluded from this model [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 130
Score = 58.1 bits (141), Expect = 3e-11
Identities = 32/84 (38%), Positives = 44/84 (52%), Gaps = 3/84 (3%)
Query: 101 TGRRKCAIARVVLQEGTGKFIINYRDAKEYLQGNPLWLQYIKVPLVTLGYETS-YDVFVK 159
+G+RK AIAR ++EG G+ IN + Y L I PL+ G D+ VK
Sbjct: 5 SGKRKTAIARATIREGKGRVRINGVPVELY--PPELARLKIMEPLILAGDIAKEVDIDVK 62
Query: 160 AHGGGLSGQAQAITLGVARALLKF 183
GGG+ GQA A +AR L++F
Sbjct: 63 VSGGGIMGQADAARTAIARGLVEF 86
>gnl|CDD|177799 PLN00210, PLN00210, 40S ribosomal protein S16; Provisional.
Length = 141
Score = 31.6 bits (72), Expect = 0.096
Identities = 27/99 (27%), Positives = 44/99 (44%), Gaps = 18/99 (18%)
Query: 94 AAQTIFGTGRRKCAIARVVLQEGTGKFIINYRDAKEYLQGNPLWLQY-----IKV--PLV 146
A +++ GR+K A+A + G G IN G P+ L K P++
Sbjct: 1 ATESVQCFGRKKTAVAVTYCKRGRGLIKIN---------GCPIELVQPEILRFKAFEPIL 51
Query: 147 TLGYE--TSYDVFVKAHGGGLSGQAQAITLGVARALLKF 183
LG D+ ++ GGG + Q AI +A+AL+ +
Sbjct: 52 LLGRHRFAGVDMRIRVKGGGHTSQIYAIRQSIAKALVAY 90
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 32.1 bits (74), Expect = 0.15
Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 7/43 (16%)
Query: 143 VPLVTLGYETSYDVFVKAHGGGLS-GQAQAITLGVARALLKFC 184
+PL+ G +T + GLS GQAQ + L ARALL+ C
Sbjct: 468 LPLLPQGLDTP----IGDQAAGLSVGQAQRLAL--ARALLQPC 504
>gnl|CDD|185437 PTZ00086, PTZ00086, 40S ribosomal protein S16; Provisional.
Length = 147
Score = 30.8 bits (70), Expect = 0.25
Identities = 27/86 (31%), Positives = 44/86 (51%), Gaps = 8/86 (9%)
Query: 102 GRRKCAIARVVLQEGTGKFIINYRDAKEYLQGNPLWLQYIKV--PLVTLGYE--TSYDVF 157
G++K A+A ++ +G G +N NP L+ KV PL+ +G E + D+
Sbjct: 15 GKKKTAVAVALVTKGKGLIRVN---GVPLDLINPETLR-AKVFEPLLLVGKERFSRLDIR 70
Query: 158 VKAHGGGLSGQAQAITLGVARALLKF 183
V+ GGG QA AI +A+ L+ +
Sbjct: 71 VRVRGGGQVAQAYAIRQAIAKGLVAY 96
>gnl|CDD|203338 pfam05856, ARPC4, ARP2/3 complex 20 kDa subunit (ARPC4). This
family consists of several eukaryotic ARP2/3 complex 20
kDa subunit (P20-ARC) proteins. The Arp2/3 protein
complex has been implicated in the control of actin
polymerisation in cells. The human complex consists of
seven subunits which include the actin related proteins
Arp2 and Arp3 it has been suggested that the complex
promotes actin assembly in lamellipodia and may
participate in lamellipodial protrusion.
Length = 168
Score = 29.9 bits (68), Expect = 0.57
Identities = 11/35 (31%), Positives = 22/35 (62%)
Query: 22 LTSSLSSLSFSSQISQKPGIPFVSLHRSKSISISP 56
LT++L +F SQ+ ++ P V ++ SK + ++P
Sbjct: 16 LTAALCLRNFPSQVVERHNKPEVEVNSSKELLLNP 50
>gnl|CDD|219916 pfam08580, KAR9, Yeast cortical protein KAR9. The KAR9 protein in
Saccharomyces cerevisiae is a cytoskeletal protein
required for karyogamy, correct positioning of the
mitotic spindle and for orientation of cytoplasmic
microtubules. KAR9 localises at the shmoo tip in mating
cells and at the tip of the growing bud in anaphase.
Length = 626
Score = 29.8 bits (67), Expect = 0.97
Identities = 15/81 (18%), Positives = 26/81 (32%), Gaps = 5/81 (6%)
Query: 16 SPAISPLTSSLSSLSFSSQISQKPGIPFVSLHRSKSISISP-KNDKTPKLVVSATEAAPA 74
+I +SS SS + PG S S+ + K+D+ +++ P
Sbjct: 391 GSSIDTPSSSPSSSVIMTPPDSGPG----SNVSSRRVGTPGSKSDRVGAVLLRRMNIKPT 446
Query: 75 ELETTDLKKYVKSRLPGGFAA 95
D K S +
Sbjct: 447 LASIPDEKPSNISVFEDSETS 467
>gnl|CDD|233187 TIGR00921, 2A067, The (Largely Archaeal Putative)
Hydrophobe/Amphiphile Efflux-3 (HAE3) Family.
Characterized members of the RND superfamily all
probably catalyze substrate efflux via an H+ antiport
mechanism. These proteins are found ubiquitously in
bacteria, archaea and eukaryotes. They fall into seven
phylogenetic families, this family (2.A.6.7) consists of
uncharacterised putative transporters, largely in the
Archaea [Transport and binding proteins, Unknown
substrate].
Length = 719
Score = 29.0 bits (65), Expect = 1.8
Identities = 18/87 (20%), Positives = 28/87 (32%), Gaps = 1/87 (1%)
Query: 9 PSSTMAMSPAISPLTSSLSSLSFSSQISQKPGIPFVSL-HRSKSISISPKNDKTPKLVVS 67
+ M P PL ++ + + F+S H I + K+D K VV
Sbjct: 96 AADIMRQIPGNFPLPVTMPEVRPLMSEYPRSKEMFLSKDHTVAIIIVQLKSDADYKQVVP 155
Query: 68 ATEAAPAELETTDLKKYVKSRLPGGFA 94
LE T+ + G A
Sbjct: 156 IYNDVERSLERTNPPSGKFLDVTGSPA 182
>gnl|CDD|212081 cd11512, SLC6sbd_NET, Na(+)- and Cl(-)-dependent norepinephrine
transporter NET; solute-binding domain. NET (also
called NAT1, NET1), is a transmembrane transporter that
transports the neurotransmitter norepinephrine from
synaptic spaces into presynaptic neurons. Human NET is
encoded by the SLC6A2 gene. NET is expressed in brain,
peripheral nervous system, adrenal gland, and placenta.
NET may play a role in diseases or disorders including
depression, orthostatic intolerance, anorexia nervosa,
cardiovascular diseases, alcoholism, and
attention-deficit hyperactivity disorder. This subgroup
belongs to the solute carrier 6 (SLC6) transporter
family.
Length = 560
Score = 28.0 bits (62), Expect = 3.3
Identities = 22/64 (34%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 92 GFAAQTIFG--TGRRKCAIARVVLQEGTGKFIINYRDAKEYLQGNPLWLQYIKVPLVTLG 149
GFA +I G K I V EG G I Y +A L G+ W + L+TLG
Sbjct: 303 GFAIFSILGYMAHEHKVKIEDVA-TEGAGLVFILYPEAISTLSGSTFWAVVFFIMLLTLG 361
Query: 150 YETS 153
++S
Sbjct: 362 IDSS 365
>gnl|CDD|239501 cd03407, Band_7_4, A subgroup of the band 7 domain of flotillin
(reggie) like proteins. This subgroup contains proteins
similar to stomatin, prohibitin, flotillin, HlfK/C and
podicin. Many of these band 7 domain-containing
proteins are lipid raft-associated. Individual proteins
of this band 7 domain family may cluster to form
membrane microdomains which may in turn recruit
multiprotein complexes. Microdomains formed from
flotillin proteins may in addition be dynamic units with
their own regulatory functions. Flotillins have been
implicated in signal transduction, vesicle trafficking,
cytoskeleton rearrangement and are known to interact
with a variety of proteins. Stomatin interacts with and
regulates members of the degenerin/epithelia Na+ channel
family in mechanosensory cells of Caenorhabditis elegans
and vertebrate neurons and participates in trafficking
of Glut1 glucose transporters. Prohibitin may act as a
chaperone for the stabilization of mitochondrial
proteins. Prokaryotic HflK/C plays a role in the
decision between lysogenic and lytic cycle growth during
lambda phage infection. Flotillins have been implicated
in the progression of prion disease, in the pathogenesis
of neurodegenerative diseases such as Parkinson's and
Alzheimer's disease and, in cancer invasion and
metastasis. Mutations in the podicin gene give rise to
autosomal recessive steroid resistant nephritic
syndrome.
Length = 262
Score = 27.7 bits (62), Expect = 3.8
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 161 HGGGLSGQAQAITLGVARALLKFCTSVPGI 190
G G + Q QAI G+ ++L +VPG+
Sbjct: 187 QGVGAAEQRQAIADGLRESILSLADAVPGM 216
>gnl|CDD|200134 TIGR01842, type_I_sec_PrtD, type I secretion system ABC
transporter, PrtD family. Type I protein secretion is a
system in some Gram-negative bacteria to export proteins
(often proteases) across both inner and outer membranes
to the extracellular medium. This is one of three
proteins of the type I secretion apparatus. Targeted
proteins are not cleaved at the N-terminus, but rather
carry signals located toward the extreme C-terminus to
direct type I secretion [Protein fate, Protein and
peptide secretion and trafficking].
Length = 544
Score = 27.3 bits (61), Expect = 5.9
Identities = 14/34 (41%), Positives = 16/34 (47%), Gaps = 3/34 (8%)
Query: 148 LGYETSYDVFVKAHGGGLS-GQAQAITLGVARAL 180
L YD + G LS GQ Q I +ARAL
Sbjct: 438 LRLPDGYDTVIGPGGATLSGGQRQRI--ALARAL 469
>gnl|CDD|227321 COG4988, CydD, ABC-type transport system involved in cytochrome bd
biosynthesis, ATPase and permease components [Energy
production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 559
Score = 27.2 bits (61), Expect = 6.9
Identities = 15/30 (50%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 154 YDVFVKAHGGGLS-GQAQAITLGVARALLK 182
D + G GLS GQAQ L +ARALL
Sbjct: 446 LDTVIGEGGAGLSGGQAQ--RLALARALLS 473
>gnl|CDD|233596 TIGR01846, type_I_sec_HlyB, type I secretion system ABC
transporter, HlyB family. Type I protein secretion is a
system in some Gram-negative bacteria to export proteins
(often proteases) across both inner and outer membranes
to the extracellular medium. This is one of three
proteins of the type I secretion apparatus. Targeted
proteins are not cleaved at the N-terminus, but rather
carry signals located toward the extreme C-terminus to
direct type I secretion [Protein fate, Protein and
peptide secretion and trafficking].
Length = 694
Score = 27.0 bits (60), Expect = 7.9
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 3/29 (10%)
Query: 154 YDVFVKAHGGGLS-GQAQAITLGVARALL 181
Y+ V G LS GQ Q I + ARAL+
Sbjct: 583 YNTEVGEKGANLSGGQRQRIAI--ARALV 609
>gnl|CDD|213980 TIGR04367, HpnR_B12_rSAM, hopanoid C-3 methylase HpnR. Members of
this are family are a B12-binding domain/radical SAM
domain protein required for 3-methylhopanoid production.
Activity was confirmed by mutant phenotype by disrupting
this gene in Methylococcus capsulatus strain Bath. This
protein family should only occur in genomes that encode
a squalene-hopene cyclase (see TIGR01507) [Fatty acid
and phospholipid metabolism, Biosynthesis].
Length = 490
Score = 27.0 bits (60), Expect = 7.9
Identities = 16/43 (37%), Positives = 20/43 (46%), Gaps = 4/43 (9%)
Query: 77 ETTDLKKYVKSRLPGGFAAQTIFGTGRRKCAIARVVLQEGTGK 119
E DL K K RLPG F +F G +AR +L+ G
Sbjct: 76 EVIDLAKETKRRLPGCF----VFVGGHSASFVARELLEHAEGA 114
>gnl|CDD|227773 COG5486, COG5486, Predicted metal-binding integral membrane protein
[Function unknown].
Length = 283
Score = 26.7 bits (59), Expect = 8.5
Identities = 7/29 (24%), Positives = 12/29 (41%), Gaps = 2/29 (6%)
Query: 156 VFVKAHGGGLSGQAQAITLGVARALLKFC 184
F+ +H + A LG+ L +C
Sbjct: 196 SFLFSHWRFRAKPVGAFRLGLRHGL--YC 222
>gnl|CDD|178748 PLN03209, PLN03209, translocon at the inner envelope of
chloroplast subunit 62; Provisional.
Length = 576
Score = 26.8 bits (59), Expect = 10.0
Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 7/72 (9%)
Query: 16 SPAISPLTSSLSSLSF------SSQISQKPGIPFVSLHR-SKSISISPKNDKTPKLVVSA 68
S AI+ + +SL+ F Q+ + PG R +S+ I + K +A
Sbjct: 8 SSAITTIPTSLTKCGFIEKPFLHGQLLRFPGFSKHPHSRKLRSLDIKAQASGATKFSSAA 67
Query: 69 TEAAPAELETTD 80
EA P EL+T D
Sbjct: 68 IEAIPKELDTKD 79
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 0.131 0.373
Gapped
Lambda K H
0.267 0.0584 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,581,947
Number of extensions: 872394
Number of successful extensions: 815
Number of sequences better than 10.0: 1
Number of HSP's gapped: 808
Number of HSP's successfully gapped: 31
Length of query: 193
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 101
Effective length of database: 6,857,034
Effective search space: 692560434
Effective search space used: 692560434
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: 56 (25.7 bits)