RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9793
(133 letters)
>gnl|CDD|235319 PRK04914, PRK04914, ATP-dependent helicase HepA; Validated.
Length = 956
Score = 35.2 bits (82), Expect = 0.006
Identities = 20/93 (21%), Positives = 42/93 (45%), Gaps = 16/93 (17%)
Query: 13 KVPYEILNKKFRAVQKTIDREVSYVQSAANELEKTIASSEKPPLTEVTRLLGGMFERLQA 72
+V +E LN++ AV + ++ V++ ++ K + +E + E ++
Sbjct: 845 QVEFESLNRQLSAVNRHTASKL--VKAVQQDIHKLLQKAEAQAEAQAR-------ELIEQ 895
Query: 73 LKRKAGESIGEELQVGHVCKRRIEHLKEHSGNV 105
K++A E + EL R+E LK + N+
Sbjct: 896 AKQEADEKLSAELS-------RLEALKAVNPNI 921
>gnl|CDD|215366 PLN02681, PLN02681, proline dehydrogenase.
Length = 455
Score = 32.8 bits (75), Expect = 0.041
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 5/69 (7%)
Query: 17 EILNKKFRAVQKTIDREVSYVQSA----ANELEKTIASSEKPPLT-EVTRLLGGMFERLQ 71
E ++ R + + ++ + Q + A+ A+SE PLT E RLL ERLQ
Sbjct: 164 ERVSDLLRWQDRDPNGKLPWKQWSFPLFADSSPLYHATSEPEPLTAEEERLLELAHERLQ 223
Query: 72 ALKRKAGES 80
L +A +
Sbjct: 224 KLCERAAQL 232
>gnl|CDD|236908 PRK11423, PRK11423, methylmalonyl-CoA decarboxylase; Provisional.
Length = 261
Score = 30.0 bits (68), Expect = 0.28
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 14/61 (22%)
Query: 32 REVSYVQSAANELEKTIASSEKPPLT-----EVTRLLGG-------MFERLQALKRKAGE 79
EV ++ ++ I+ EK PL E R+LG FER+Q L+R +
Sbjct: 182 VEVEELEDFTLQMAHHIS--EKAPLAIAVIKEQLRVLGEAHPMNPDEFERIQGLRRAVYD 239
Query: 80 S 80
S
Sbjct: 240 S 240
>gnl|CDD|204831 pfam12137, RapA_C, RNA polymerase recycling family C-terminal.
This domain is found in bacteria. This domain is about
360 amino acids in length. This domain is found
associated with pfam00271, pfam00176. The function of
this domain is not known, but structurally it forms an
alpha-beta fold in nature with a central beta-sheet
flanked by helices and loops, the beta-sheet being
mainly antiparallel and flanked by four alpha helices,
among which the two longer helices exhibit a coiled-coil
arrangement.
Length = 362
Score = 29.8 bits (68), Expect = 0.37
Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 13/75 (17%)
Query: 13 KVPYEILNKKFRAVQKTIDREVSYVQSAANELEKTIASSEK------PPLTE-----VTR 61
+V +E LNK+ V + R++ V++ ++E+ + +EK + E + +
Sbjct: 251 QVSFESLNKQLSPVNRHTARKL--VKALRPQIEQLLQKAEKLAEEQLEEIIEQAKQQMQQ 308
Query: 62 LLGGMFERLQALKRK 76
L RL+ALK
Sbjct: 309 QLSAELARLKALKAV 323
>gnl|CDD|237180 PRK12711, flgJ, flagellar rod assembly protein/muramidase FlgJ;
Reviewed.
Length = 392
Score = 29.5 bits (66), Expect = 0.44
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 29 TIDREVSYVQSAANELEKTIASSEKPPLTEVTR 61
TIDR V+ + +AA +L AS+ +P R
Sbjct: 359 TIDRAVAAIGNAAADLSNRYASTAEPAGLGTIR 391
>gnl|CDD|214922 smart00935, OmpH, Outer membrane protein (OmpH-like). This
family includes outer membrane proteins such as OmpH
among others. Skp (OmpH) has been characterized as a
molecular chaperone that interacts with unfolded
proteins as they emerge in the periplasm from the Sec
translocation machinery.
Length = 140
Score = 27.5 bits (62), Expect = 1.4
Identities = 15/80 (18%), Positives = 34/80 (42%)
Query: 7 LEHPTLKVPYEILNKKFRAVQKTIDREVSYVQSAANELEKTIASSEKPPLTEVTRLLGGM 66
E P K + L K+F+ Q +++ +Q +L+K A+ + + + L
Sbjct: 11 QESPAGKAAQKQLEKEFKKRQAELEKLEKELQKLKEKLQKDAATLSEAAREKKEKELQKK 70
Query: 67 FERLQALKRKAGESIGEELQ 86
+ Q ++K + + + Q
Sbjct: 71 VQEFQRKQQKLQQDLQKRQQ 90
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 27.1 bits (60), Expect = 3.2
Identities = 11/40 (27%), Positives = 20/40 (50%)
Query: 21 KKFRAVQKTIDREVSYVQSAANELEKTIASSEKPPLTEVT 60
K+ ++K D + ++Q+A L+ SS K L E+
Sbjct: 276 KETNGIEKAKDLALEHMQAAIQCLKFLPPSSAKDSLIEIA 315
>gnl|CDD|218498 pfam05206, TRM13, Methyltransferase TRM13. This is a family of
eukaryotic proteins which are responsible for
2'-O-methylation of tRNA at position 4. TRM13 shows no
sequence similarity to other known methyltransferases.
Length = 256
Score = 26.9 bits (60), Expect = 3.3
Identities = 9/27 (33%), Positives = 14/27 (51%), Gaps = 5/27 (18%)
Query: 80 SIGEELQVGHVCKR-----RIEHLKEH 101
S E ++G CKR R+ +LK+
Sbjct: 206 SDEEREEIGLKCKRLIDEGRVLYLKKK 232
>gnl|CDD|205932 pfam13758, Prefoldin_3, Prefoldin subunit. This family includes
prefoldin subunits that are not detected by pfam02996.
Length = 97
Score = 26.1 bits (58), Expect = 3.7
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 30 IDREVSYVQSAANELEKTIASSEK 53
I R + YV+ LEK + ++E
Sbjct: 71 ISRRIDYVKQNIATLEKRLEAAEN 94
>gnl|CDD|183017 PRK11177, PRK11177, phosphoenolpyruvate-protein
phosphotransferase; Provisional.
Length = 575
Score = 26.5 bits (59), Expect = 4.8
Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 57 TEVTRLLGG---MFERLQALKRKAGESIGEE 84
EV R L G +L+A+K KAGE+ GEE
Sbjct: 38 QEVERFLSGRAKASAQLEAIKTKAGETFGEE 68
>gnl|CDD|145800 pfam02831, gpW, gpW. gpW is a 68 residue protein known to be
present in phage particles. Extracts of phage-infected
cells lacking gpW contain DNA-filled heads, and active
tails, but no infectious virions. gpW is required for
the addition of gpFII to the head, which is, in turn,
required for the attachment of tails. Since gpFII and
tails are known to be attached at the connector, gpW is
also likely to assemble at this site. The addition of
gpW to filled heads increases the DNase resistance of
the packaged DNA, suggesting that gpW either forms a
plug at the connector to prevent ejection of the DNA,
or binds directly to the DNA. The large number of
positively charged residues in gpW (its calculated pI
is 10.8) is consistent with a role in DNA interaction.
Length = 68
Score = 24.8 bits (54), Expect = 6.0
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 21 KKFRAVQKTIDREVSYVQSAANELEKTIASSE 52
K+ +VQK R V Y ++ ++L+ IA E
Sbjct: 21 KRVVSVQKD-GRRVEYTATSLSDLKAYIAELE 51
>gnl|CDD|193454 pfam12981, DUF3865, Domain of Unknown Function with PDB structure
(DUF3865). Family based of PDB:3B5P encoded by
ZP_00108531 from nitrogen-fixing cyanobacterium Nostoc
punctiforme pcc 73102 is a CADD-like protein of unknown
function. Superposition between protein structures
encoded by CT610 from Chlamydia trachomatis (PDB code
1rwc), pyrroloquinolinquinone synthase C (PqqC, PDB code
1otv) and ZP_00108531 revealed that putative active
sites in CT610 and ZP_00108531 are identical. ( REF:
http://www.topsan.org/Proteins/JCSG/3B5P).
Length = 231
Score = 26.1 bits (57), Expect = 6.3
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 14 VPYEILNKKFRAVQKTIDREVSYVQSAANELEKT 47
+P +K R V DR+V YV A +E T
Sbjct: 112 IPSVATSKFLRTVLSLFDRQVDYVLGATYAIEAT 145
>gnl|CDD|191182 pfam05064, Nsp1_C, Nsp1-like C-terminal region. This family
probably forms a coiled-coil. This important region of
Nsp1 is involved in binding Nup82.
Length = 117
Score = 25.3 bits (56), Expect = 6.7
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 27 QKTIDREVSYVQSAANELEKTIASSEKPPLTEVTRLLGGM 66
Q ID+E+ +++S +ELE + E+ E+ LLG +
Sbjct: 74 QNRIDQELDFIESQQDELESLLDPYEE----EIEELLGNI 109
>gnl|CDD|214810 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 361
Score = 25.7 bits (57), Expect = 8.8
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 16 YEILNKKFRAVQKTIDREVSYVQSAANELEK 46
Y + F +++ I+R V+Y +SAA LE+
Sbjct: 46 YRFFDHDFFGMEEAIERFVNYFKSAAQGLEE 76
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
0.314 0.132 0.384
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,623,080
Number of extensions: 568489
Number of successful extensions: 502
Number of sequences better than 10.0: 1
Number of HSP's gapped: 502
Number of HSP's successfully gapped: 36
Length of query: 133
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 47
Effective length of database: 7,123,158
Effective search space: 334788426
Effective search space used: 334788426
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: 42 (22.0 bits)
S2: 53 (24.1 bits)