RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10000
(193 letters)
>gnl|CDD|240326 PTZ00241, PTZ00241, 40S ribosomal protein S11; Provisional.
Length = 158
Score = 221 bits (565), Expect = 1e-74
Identities = 103/155 (66%), Positives = 120/155 (77%), Gaps = 7/155 (4%)
Query: 45 ETERAFQKQPTIFLARKPTYKKKS---LRYHKTVGLGFKTPREAIDGTYIDKKCPFTGNV 101
+TERAFQKQ +F K KKK+ +RY K VGLGFKTP+EAI+G YIDKKCPFTGNV
Sbjct: 5 QTERAFQKQEGVFQNSKRLLKKKTSKGVRYWKKVGLGFKTPKEAIEGKYIDKKCPFTGNV 64
Query: 102 SIRGRILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVV 161
SIRGRIL G+V KM+RTI+IRRDYLHY+KKYNR+EKRH+N+ VH SP F DV+ GD+V
Sbjct: 65 SIRGRILRGVVISTKMKRTIIIRRDYLHYVKKYNRYEKRHKNIPVHCSPCF-DVKEGDIV 123
Query: 162 TVGECRPLSKTVRFNVLKVTKGT---GSKKAFKKF 193
VG+CRPLSKTVRFNVLKV K +K F F
Sbjct: 124 VVGQCRPLSKTVRFNVLKVEKNEIIGNVRKQFVLF 158
>gnl|CDD|236296 PRK08572, rps17p, 30S ribosomal protein S17P; Reviewed.
Length = 108
Score = 120 bits (303), Expect = 1e-35
Identities = 47/111 (42%), Positives = 66/111 (59%), Gaps = 5/111 (4%)
Query: 73 KTVGLGFKTPREAIDGTYIDKKCPFTGNVSIRGRILIGIVRKMKMQRTIVIRRDYLHYIK 132
+ +GL K P E D D CPF G + +RG++L G V KM +T+V+ R+YLHY+
Sbjct: 1 RNIGLDVKPPEEECD----DPNCPFHGTLPVRGQVLEGTVVSDKMHKTVVVEREYLHYVP 56
Query: 133 KYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVGECRPLSKTVRFNVLKVTKG 183
KY R+EKR + H P D ++GD V + ECRPLSKT F V++ +
Sbjct: 57 KYERYEKRRSRIHAHNPPCI-DAKVGDKVKIAECRPLSKTKSFVVVEKKER 106
>gnl|CDD|132669 TIGR03630, arch_S17P, archaeal ribosomal protein S17P. This model
describes exclusively the archaeal ribosomal protein
S17P. It excludes the homologous ribosomal protein S17
from bacteria, and is not intended for use on eukaryotic
sequences, where some instances of ribosomal proteins
S11 score above the trusted cutoff [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 102
Score = 113 bits (286), Expect = 3e-33
Identities = 46/106 (43%), Positives = 66/106 (62%), Gaps = 5/106 (4%)
Query: 75 VGLGFKTPREAIDGTYIDKKCPFTGNVSIRGRILIGIVRKMKMQRTIVIRRDYLHYIKKY 134
+G+ K P + D KCPF G++ +RG+IL G+V KM +T+V+ R+YL+Y +KY
Sbjct: 1 IGIPVKPPERECN----DPKCPFHGHLKVRGQILEGVVVSDKMNKTVVVEREYLYYDRKY 56
Query: 135 NRFEKRHRNMSVHLSPAFRDVEIGDVVTVGECRPLSKTVRFNVLKV 180
R+E+R + H P DV+ GD+V +GE RPLSKT F VL
Sbjct: 57 ERYERRRSKIHAHNPPCI-DVKEGDIVIIGETRPLSKTKSFVVLGK 101
>gnl|CDD|109426 pfam00366, Ribosomal_S17, Ribosomal protein S17.
Length = 69
Score = 94.7 bits (236), Expect = 5e-26
Identities = 36/71 (50%), Positives = 47/71 (66%), Gaps = 2/71 (2%)
Query: 110 GIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVGECRPL 169
G+V KM++TIV+R + L KY ++EKR + H P FR V GDVV +GECRPL
Sbjct: 1 GVVVSDKMEKTIVVRVERLVPHPKYGKYEKRTKKYPAHDPPCFRKV--GDVVKIGECRPL 58
Query: 170 SKTVRFNVLKV 180
SKT RF V++V
Sbjct: 59 SKTKRFRVVRV 69
>gnl|CDD|223264 COG0186, RpsQ, Ribosomal protein S17 [Translation, ribosomal
structure and biogenesis].
Length = 87
Score = 90.0 bits (224), Expect = 5e-24
Identities = 29/83 (34%), Positives = 49/83 (59%), Gaps = 2/83 (2%)
Query: 98 TGNVSIRGRILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEI 157
G + +RGR+L G+V KM +T+V+ + Y KY ++ +R + H + ++
Sbjct: 1 HGKLRVRGRVLEGVVVSDKMDKTVVVEVERKVYHPKYGKYVRRSKKYHAH-DECN-EAKV 58
Query: 158 GDVVTVGECRPLSKTVRFNVLKV 180
GD+V + E RPLSKT RF V+++
Sbjct: 59 GDIVRIAETRPLSKTKRFVVVEI 81
>gnl|CDD|235532 PRK05610, rpsQ, 30S ribosomal protein S17; Reviewed.
Length = 84
Score = 47.8 bits (115), Expect = 7e-08
Identities = 28/81 (34%), Positives = 40/81 (49%), Gaps = 14/81 (17%)
Query: 106 RILIGIVRKMKMQRTIVIR--RDYLHYIKKYNRFEKRHRNMSVHLSPAFRD----VEIGD 159
+ L G V KM +TIV+ R H Y + KR + H D +IGD
Sbjct: 7 KTLQGRVVSDKMDKTIVVLVERRVKH--PLYGKIVKRSKKYHAH------DENNEAKIGD 58
Query: 160 VVTVGECRPLSKTVRFNVLKV 180
VV + E RPLSKT R+ ++++
Sbjct: 59 VVRIMETRPLSKTKRWRLVEI 79
>gnl|CDD|213841 TIGR03635, S17_bact, 30S ribosomal protein S17. This model
describes the bacterial ribosomal small subunit protein
S17, while excluding cytosolic eukaryotic homologs and
archaeal homologs. The model finds many, but not,
chloroplast and mitochondrial counterparts to bacterial
S17 [Protein synthesis, Ribosomal proteins: synthesis
and modification].
Length = 71
Score = 47.1 bits (113), Expect = 7e-08
Identities = 27/78 (34%), Positives = 38/78 (48%), Gaps = 14/78 (17%)
Query: 106 RILIGIVRKMKMQRTIVIR--RDYLHYIKKYNRFEKRHRNMSVHLSPAFRD----VEIGD 159
+ L G+V KM +TIV+ R H Y + KR + H D ++GD
Sbjct: 2 KTLQGVVVSDKMDKTIVVLVERRVKH--PLYGKIVKRTKKYHAH------DENNECKVGD 53
Query: 160 VVTVGECRPLSKTVRFNV 177
VV + E RPLSKT R+ +
Sbjct: 54 VVRIIETRPLSKTKRWRL 71
>gnl|CDD|177064 CHL00142, rps17, ribosomal protein S17; Validated.
Length = 84
Score = 40.4 bits (95), Expect = 4e-05
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 108 LIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVGECR 167
IGIV KM +TIV+ + + Y + + + VH + IGD V + E R
Sbjct: 6 KIGIVVSNKMNKTIVVAVENRYKHPIYGKIITKTKKYLVH--DEENECNIGDQVLIEETR 63
Query: 168 PLSKTVRFNVLKV 180
PLSKT R+ + ++
Sbjct: 64 PLSKTKRWILKEI 76
>gnl|CDD|151362 pfam10915, DUF2709, Protein of unknown function (DUF2709). This
bacterial family of proteins has no known function.
Length = 238
Score = 29.1 bits (65), Expect = 1.2
Identities = 18/68 (26%), Positives = 25/68 (36%), Gaps = 16/68 (23%)
Query: 47 ERAFQKQPTIFLARKPTYKKKS----------LRYHKT---VGLGFKTPREAIDGTYIDK 93
E+ Q QP +F+ K Y+ + +T + G E YI
Sbjct: 32 EQKLQLQPVLFVRDKVIYQSAEDAIALLEAEGKLWRETEIQISSGKPEVNEQTKKIYI-- 89
Query: 94 KCPFTGNV 101
CPFTG V
Sbjct: 90 -CPFTGKV 96
>gnl|CDD|115526 pfam06875, PRF, Plethodontid receptivity factor PRF. This family
consists of several plethodontid receptivity factor
(PRF) proteins which seem to be specific to Plethodon
jordani (Jordan's salamander). PRF is a courtship
pheromone produced by males increase female receptivity.
Length = 214
Score = 28.9 bits (64), Expect = 1.5
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 96 PFTGNVSIRGRILIGIVRKMKMQRTIVIRRDYLHYIKKY 134
PF G+ R ++ G+V K +R + +RD+ +KY
Sbjct: 172 PFEGSAYFRKKLRGGVVCKEYKERVFLTKRDFEFLAEKY 210
>gnl|CDD|100055 cd04650, LbH_FBP, Ferripyochelin Binding Protein (FBP): FBP is an
outer membrane protein which plays a role in iron
acquisition. It binds iron when it is complexed with
pyochelin. It adopts the left-handed parallel beta-helix
(LbH) structure, and contains imperfect tandem repeats
of a hexapeptide repeat motif
(X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing
hexapeptide repeats are often enzymes showing
acyltransferase activity. Acyltransferase activity has
not been observed in this group.
Length = 154
Score = 28.3 bits (63), Expect = 1.9
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 5/45 (11%)
Query: 121 IVIRRDYLH-YIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVG 164
VIR D YI KY+ ++ N+S+H + EIGD VT+G
Sbjct: 31 AVIRGDNDSIYIGKYSNVQE---NVSIHTDHGYP-TEIGDYVTIG 71
>gnl|CDD|187872 cd09741, Csx1_III-U, CRISPR/Cas system-associated protein Csx1.
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;
Protein of this family often fused to HTH domain; Some
proteins could have an additional fusion with
RecB-family nuclease domain; Core domain appears to have
a Rossmann-like fold; loosely associated with CRISPR/Cas
systems; also known as NE0113 family.
Length = 219
Score = 28.1 bits (63), Expect = 2.4
Identities = 8/41 (19%), Positives = 18/41 (43%)
Query: 122 VIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVT 162
++ R++ Y + Y R + +H+ E+ D+ T
Sbjct: 49 LLAREFGRYYRGYQRPALKFDERHIHVIEDVSGEELDDIRT 89
>gnl|CDD|205873 pfam13698, DUF4156, Domain of unknown function (DUF4156). The
function of this family is unknown but members are
annotated as putative lipoprotein outer membrane
proteins.
Length = 87
Score = 26.8 bits (60), Expect = 2.4
Identities = 9/29 (31%), Positives = 12/29 (41%)
Query: 145 SVHLSPAFRDVEIGDVVTVGECRPLSKTV 173
+V L+P V I D V C+ L
Sbjct: 1 AVQLTPEGVQVRIVDSQPVSNCQFLGTVT 29
>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional.
Length = 1113
Score = 28.0 bits (63), Expect = 3.8
Identities = 11/21 (52%), Positives = 12/21 (57%), Gaps = 3/21 (14%)
Query: 153 RDVEIGDVVTVGECRPLSKTV 173
R V IGD VT+G S TV
Sbjct: 937 RPVRIGDTVTIGT---FSGTV 954
>gnl|CDD|173440 PTZ00151, PTZ00151, translationally controlled tumor-like protein;
Provisional.
Length = 172
Score = 26.6 bits (59), Expect = 6.4
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 108 LIGIVRKMKMQRTIVIRRDYLHYIKKY 134
+I IV K+Q T +++Y YIKKY
Sbjct: 69 VIDIVDAFKLQSTPFTKKEYSTYIKKY 95
>gnl|CDD|224032 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains
DnaJ-type Zn finger domain [DNA replication,
recombination, and repair].
Length = 715
Score = 27.4 bits (61), Expect = 6.5
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 151 AFRDVEIGDVVTV-GECRPLSKTVRFNVLKVTKGTGSKKA 189
A+ ++E+GD+V V GE ++ + + K TG + A
Sbjct: 255 AYPEIEVGDIVEVIGEVTRRDGRLQIEIEAMEKLTGDEAA 294
>gnl|CDD|233690 TIGR02025, BchH, magnesium chelatase, H subunit. This model
represents the H subunit of the magnesium chelatase
complex responsible for magnesium insertion into the
protoporphyrin IX ring in the biosynthesis of both
chlorophyll and bacteriochlorophyll. In
chlorophyll-utilizing species, this gene is known as
ChlH, while in bacteriochlorophyll-utilizing spoecies it
is called BchH. Subunit H is the largest (~140kDa) of
the three subunits (the others being BchD/ChlD and
BchI/ChlI), and is known to bind protoporphyrin IX.
Subunit H is homologous to the CobN subunit of
cobaltochelatase and by anology with that enzyme,
subunit H is believed to also bind the magnesium ion
which is inserted into the ring. In conjunction with the
hydrolysis of ATP by subunits I and D, a conformation
change is believed to happen in subunit H causing the
magnesium ion insertion into the distorted
protoporphyrin ring [Biosynthesis of cofactors,
prosthetic groups, and carriers, Chlorophyll and
bacteriochlorphyll].
Length = 1224
Score = 27.0 bits (60), Expect = 6.9
Identities = 12/70 (17%), Positives = 23/70 (32%), Gaps = 10/70 (14%)
Query: 71 YHKTVGLGFKTPREAIDGTYIDKKCPFTGNVSIRGRILIGIVRKMKMQRTIVIRRDYLHY 130
YH F+T +E + + C R+ G++ + R ++ + HY
Sbjct: 210 YHPDAKGFFETVKEYLAWYKKREGCRAPKA----PRV--GLL----LLRKHLLTENQAHY 259
Query: 131 IKKYNRFEKR 140
E
Sbjct: 260 DNLIRELEAA 269
>gnl|CDD|223735 COG0663, PaaY, Carbonic anhydrases/acetyltransferases, isoleucine
patch superfamily [General function prediction only].
Length = 176
Score = 26.4 bits (59), Expect = 8.3
Identities = 9/22 (40%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 143 NMSVHLSPAFRDVEIGDVVTVG 164
+ +H P + V IGD VT+G
Sbjct: 62 GVVIHADPGY-PVTIGDDVTIG 82
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
0.323 0.139 0.403
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,967,128
Number of extensions: 948564
Number of successful extensions: 755
Number of sequences better than 10.0: 1
Number of HSP's gapped: 744
Number of HSP's successfully gapped: 24
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 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 56 (25.3 bits)