RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13112
(302 letters)
>gnl|CDD|235532 PRK05610, rpsQ, 30S ribosomal protein S17; Reviewed.
Length = 84
Score = 38.2 bits (90), Expect = 4e-04
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 174 GKYFPKFTVMYAHDPDKICKTGDIVLIEE 202
GK + +AHD + K GD+V I E
Sbjct: 36 GKIVKRSKKYHAHDENNEAKIGDVVRIME 64
Score = 35.1 bits (82), Expect = 0.006
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 3/29 (10%)
Query: 106 VRYFPKFTVMYAHDPDKICKTGDIVLIEE 134
V+ K+ +AHD + K GD+V I E
Sbjct: 39 VKRSKKY---HAHDENNEAKIGDVVRIME 64
>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 = 37.5 bits (88), Expect = 5e-04
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 174 GKYFPKFTVMYAHDPDKICKTGDIVLIEE 202
GK + +AHD + CK GD+V I E
Sbjct: 31 GKIVKRTKKYHAHDENNECKVGDVVRIIE 59
Score = 33.6 bits (78), Expect = 0.013
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 107 RYFPKFTVMYAHDPDKICKTGDIVLIEE 134
+ + +AHD + CK GD+V I E
Sbjct: 32 KIVKRTKKYHAHDENNECKVGDVVRIIE 59
>gnl|CDD|177064 CHL00142, rps17, ribosomal protein S17; Validated.
Length = 84
Score = 34.6 bits (80), Expect = 0.007
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 13/68 (19%)
Query: 137 QKLTTLITHKVNK--VVYPLGDITDPITGKKVVGLRVDLGKYFPKFTVMYAHDPDKICKT 194
+K+ ++++K+NK VV PI GK + + KY HD + C
Sbjct: 5 EKIGIVVSNKMNKTIVVAVENRYKHPIYGKIITKTK----KY-------LVHDEENECNI 53
Query: 195 GDIVLIEE 202
GD VLIEE
Sbjct: 54 GDQVLIEE 61
Score = 33.1 bits (76), Expect = 0.026
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 116 YAHDPDKICKTGDIVLIEE 134
HD + C GD VLIEE
Sbjct: 43 LVHDEENECNIGDQVLIEE 61
>gnl|CDD|165527 PHA03269, PHA03269, envelope glycoprotein C; Provisional.
Length = 566
Score = 36.6 bits (84), Expect = 0.013
Identities = 15/84 (17%), Positives = 19/84 (22%), Gaps = 4/84 (4%)
Query: 26 DISFQERSQGSAKCDLMPTPRSPREREARPHAQPRKA----PGSAQRDRKQGSAKRDPMH 81
D + S D P S R+ P A A + S DP
Sbjct: 41 DPAPAPHQAASRAPDPAVAPTSAASRKPDLAQAPTPAASEKFDPAPAPHQAASRAPDPAV 100
Query: 82 NPTKPQERVARPYMQPRVANTRNE 105
P A +E
Sbjct: 101 APQLAAAPKPDAAEAFTSAAQAHE 124
Score = 27.8 bits (61), Expect = 7.7
Identities = 15/91 (16%), Positives = 23/91 (25%), Gaps = 4/91 (4%)
Query: 26 DISFQERSQGSAKCDLMPTPRSPREREARPHAQPRKAP----GSAQRDRKQGSAKRDPMH 81
D + S D P+ + A A S K DP
Sbjct: 83 DPAPAPHQAASRAPDPAVAPQLAAAPKPDAAEAFTSAAQAHEAPADAGTSAASKKPDPAA 142
Query: 82 NPTKPQERVARPYMQPRVANTRNEVRYFPKF 112
+ A +A T +++ P F
Sbjct: 143 HTQHSPPPFAYTRSMEHIACTHGGIQFIPYF 173
>gnl|CDD|109426 pfam00366, Ribosomal_S17, Ribosomal protein S17.
Length = 69
Score = 32.3 bits (74), Expect = 0.032
Identities = 14/53 (26%), Positives = 19/53 (35%), Gaps = 7/53 (13%)
Query: 89 RVARPYMQPRVANTRNEVRYFPKF-------TVMYAHDPDKICKTGDIVLIEE 134
V M+ + + PK+ AHDP K GD+V I E
Sbjct: 2 VVVSDKMEKTIVVRVERLVPHPKYGKYEKRTKKYPAHDPPCFRKVGDVVKIGE 54
Score = 32.3 bits (74), Expect = 0.034
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 7/48 (14%)
Query: 162 TGKKVVGLRVDLGKYFPKF-------TVMYAHDPDKICKTGDIVLIEE 202
+K + +RV+ PK+ AHDP K GD+V I E
Sbjct: 7 KMEKTIVVRVERLVPHPKYGKYEKRTKKYPAHDPPCFRKVGDVVKIGE 54
>gnl|CDD|223264 COG0186, RpsQ, Ribosomal protein S17 [Translation, ribosomal
structure and biogenesis].
Length = 87
Score = 32.6 bits (75), Expect = 0.040
Identities = 13/29 (44%), Positives = 15/29 (51%)
Query: 174 GKYFPKFTVMYAHDPDKICKTGDIVLIEE 202
GKY + +AHD K GDIV I E
Sbjct: 38 GKYVRRSKKYHAHDECNEAKVGDIVRIAE 66
Score = 31.0 bits (71), Expect = 0.15
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 107 RYFPKFTVMYAHDPDKICKTGDIVLIEE 134
+Y + +AHD K GDIV I E
Sbjct: 39 KYVRRSKKYHAHDECNEAKVGDIVRIAE 66
>gnl|CDD|152354 pfam11919, DUF3437, Domain of unknown function (DUF3437). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 142 to 163 amino acids in length.
Length = 89
Score = 28.7 bits (65), Expect = 1.1
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 263 DYKKAPRRGWQEDKKDFTHRE 283
++KK + W EDKK FT +
Sbjct: 55 EFKKTHQDTWHEDKKKFTEDQ 75
>gnl|CDD|218658 pfam05616, Neisseria_TspB, Neisseria meningitidis TspB protein.
This family consists of several Neisseria meningitidis
TspB virulence factor proteins.
Length = 502
Score = 29.6 bits (66), Expect = 2.3
Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 28 SFQERSQGSAKCDLMPTPR---SPREREARPHAQPRKAPGSAQRDRKQGSAKRDPMHNP 83
+F SQG+ D+ PR +P EA P AQP A+ + + +P P
Sbjct: 298 TFGRDSQGNTTVDVQVIPRPDLTPGSAEA-PEAQPLPEVSPAENPANNPNPRENPGTRP 355
>gnl|CDD|236942 PRK11637, PRK11637, AmiB activator; Provisional.
Length = 428
Score = 28.9 bits (65), Expect = 3.3
Identities = 20/49 (40%), Positives = 25/49 (51%), Gaps = 11/49 (22%)
Query: 20 ETRLRDDISFQERSQGSAKCDLMPTPRSPREREARPHAQPRKAPGSAQR 68
E+RLRD I+ ER AK R+ EREAR A+ R A+R
Sbjct: 242 ESRLRDSIARAER---EAKA------RA--EREAREAARVRDKQKQAKR 279
>gnl|CDD|227298 COG4963, CpaE, Flp pilus assembly protein, ATPase CpaE
[Intracellular trafficking and secretion].
Length = 366
Score = 28.5 bits (64), Expect = 4.3
Identities = 23/131 (17%), Positives = 40/131 (30%), Gaps = 33/131 (25%)
Query: 158 TDPITGKKVVGLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNK 217
T +G K++ +L K Y ++L L+ +
Sbjct: 181 TRLASGLKLLAAPTELAK-------NYDLKTGA-------------VERLLDLLRGSFDF 220
Query: 218 VVYPLGDITDPITGKKVVGLRTAVLTAD-----------FYKELYELYGKNPQ--RKFDY 264
VV L +I T + + G V+ A+ EL L +P+ +
Sbjct: 221 VVVDLPNIWTDWTRQVLSGSDEIVIVAEPSLASLRNAKELLDELKRLRPNDPKPILVLNR 280
Query: 265 KKAPRRGWQED 275
P+R D
Sbjct: 281 VGVPKRPEPSD 291
>gnl|CDD|182221 PRK10070, PRK10070, glycine betaine transporter ATP-binding
subunit; Provisional.
Length = 400
Score = 28.5 bits (63), Expect = 4.3
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 248 KELYELYGKNPQRKFDY 264
K LY+++G++PQR F Y
Sbjct: 8 KNLYKIFGEHPQRAFKY 24
>gnl|CDD|181883 PRK09468, ompR, osmolarity response regulator; Provisional.
Length = 239
Score = 28.4 bits (64), Expect = 4.6
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 4/30 (13%)
Query: 40 DLMPTPRSPREREARPHA----QPRKAPGS 65
D +P P +PRE AR A Q + PG+
Sbjct: 102 DYLPKPFNPRELLARIRAVLRRQAPELPGA 131
>gnl|CDD|237284 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase;
Reviewed.
Length = 460
Score = 28.4 bits (63), Expect = 4.8
Identities = 11/76 (14%), Positives = 22/76 (28%), Gaps = 4/76 (5%)
Query: 30 QERSQGSAKCDLMPTPRSPREREARPHAQPRKAPGSAQRDRKQGSAKRDPMHNPTKPQER 89
Q ++ ++ P + + P KA + A P +P +P
Sbjct: 388 QVDAEAASAAPEEPAALASEAHDETEPEVPEKAAPIPDPAKPDELAVAGPGDDPAEPDGI 447
Query: 90 VARPYMQPRVANTRNE 105
Q ++ R
Sbjct: 448 RR----QDDFSSRRRR 459
>gnl|CDD|240130 cd04860, AE_Prim_S, AE_Prim_S: primase domain similar to that found
in the small subunit of archaeal and eukaryotic (A/E)
DNA primases. Primases are DNA-dependent RNA polymerases
which synthesis the short RNA primers required for DNA
replication. In addition to its catalytic role in
replication, DNA primase may play a role in coupling
replication to DNA damage repair and in checkpoint
control during S phase. In eukaryotes, this small
catalytically active primase subunit (p50) and a larger
primase subunit (p60), referred to jointly as the core
primase, associate with the B subunit and the DNA
polymerase alpha subunit in a complex, called Pol
alpha-pri. The function of the larger primase subunit is
unclear. Included in this group are Pfu41 and Pfu46,
these two proteins comprise the primase complex of the
archaea Pyrococcus furiosus; Pfu41 and Pfu46 have
sequence identity to the eukaryotic p50 and p60 primase
proteins respectively. Pfu41 preferentially uses dNTPs
as substrate. Pfu46 regulates the primase activity of
Pfu41.
Length = 232
Score = 28.0 bits (63), Expect = 5.4
Identities = 11/59 (18%), Positives = 17/59 (28%), Gaps = 17/59 (28%)
Query: 261 KFDYKKAPRRGWQEDKKDFTHRE--------SYIRYHEFDDDDQ---------PYAVYK 302
++ E +RE YIR+ F ++ P AVY
Sbjct: 1 PSLFRYYYLNYGLEIPDYLENREFGFTLFDGVYIRHLSFSSAEELRKYLLRNVPRAVYS 59
>gnl|CDD|237075 PRK12360, PRK12360, 4-hydroxy-3-methylbut-2-enyl diphosphate
reductase; Provisional.
Length = 281
Score = 28.2 bits (63), Expect = 6.2
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 8/54 (14%)
Query: 99 VANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVY 152
+ N+ EV P DK C +I EL + + +I K ++V+
Sbjct: 143 IVNSIEEVENIPF--------LDKACVVAQTTIIPELWEDILNVIKLKSKELVF 188
>gnl|CDD|221517 pfam12300, DUF3628, Protein of unknown function (DUF3628). This
domain family is found in bacteria, and is typically
between 153 and 183 amino acids in length. The family is
found in association with pfam00270, pfam00271.
Length = 180
Score = 27.7 bits (61), Expect = 6.2
Identities = 15/55 (27%), Positives = 22/55 (40%)
Query: 43 PTPRSPREREARPHAQPRKAPGSAQRDRKQGSAKRDPMHNPTKPQERVARPYMQP 97
P PR+R R +P + S Q G++ P+ KP A+ QP
Sbjct: 123 PGEEVPRKRRRRRRGRPVEGAESVQNAAGNGASPVTPVQVVAKPVRVAAKSGSQP 177
>gnl|CDD|223065 PHA03378, PHA03378, EBNA-3B; Provisional.
Length = 991
Score = 28.1 bits (62), Expect = 6.8
Identities = 17/65 (26%), Positives = 19/65 (29%)
Query: 43 PTPRSPREREARPHAQPRKAPGSAQRDRKQGSAKRDPMHNPTKPQERVARPYMQPRVANT 102
P P R P P PG AQR R P P + + A P A
Sbjct: 691 PGTMQPPPRAPTPMRPPAAPPGRAQRPAAATGRARPPAAAPGRARPPAAAPGRARPPAAA 750
Query: 103 RNEVR 107
R
Sbjct: 751 PGRAR 755
>gnl|CDD|222536 pfam14092, DUF4270, Domain of unknown function (DUF4270). This
family of lipoproteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are typically between 444 and 534 amino
acids in length.
Length = 432
Score = 28.0 bits (63), Expect = 7.3
Identities = 12/50 (24%), Positives = 19/50 (38%), Gaps = 8/50 (16%)
Query: 139 LTTLITHKVNKV------VYPLGDITDPITGKKVVGL--RVDLGKYFPKF 180
+ T T ++ V LG TDP+ G +++L P F
Sbjct: 20 VVTKSTVALDSVQTNGLSTGYLGKYTDPVFGTTTASFLTQLNLPSGNPTF 69
>gnl|CDD|184092 PRK13501, PRK13501, transcriptional activator RhaR; Provisional.
Length = 290
Score = 27.6 bits (61), Expect = 7.9
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 1 MTPPLRLESRDYVLS 15
M PL LESRDY+LS
Sbjct: 1 MRAPLLLESRDYLLS 15
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 28.0 bits (62), Expect = 8.5
Identities = 15/55 (27%), Positives = 19/55 (34%), Gaps = 5/55 (9%)
Query: 43 PTPRSP----REREARPHAQPRKAPGSAQRDRKQGSAKRDPMHNPTKPQERVARP 93
P PR R RP A P+ A A D +G + +P P P
Sbjct: 2573 PAPRPSEPAVTSRARRPDAPPQSARPRAPVD-DRGDPRGPAPPSPLPPDTHAPDP 2626
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
0.319 0.138 0.417
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,891,778
Number of extensions: 1532928
Number of successful extensions: 1395
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1390
Number of HSP's successfully gapped: 49
Length of query: 302
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 206
Effective length of database: 6,679,618
Effective search space: 1376001308
Effective search space used: 1376001308
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 (21.7 bits)
S2: 59 (26.5 bits)