RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8582
(161 letters)
>gnl|CDD|191858 pfam07809, RTP801_C, RTP801 C-terminal region. The members of this
family are sequences similar to the C-terminal region of
RTP801, the protein product of a hypoxia-inducible
factor 1 (HIF-1)- responsive gene. Two members of this
family expressed by Drosophila melanogaster, Scylla and
Charybde, are designated by the GenBank as Hox targets.
RTP801 is thought to be involved in various cellular
processes. Its overexpression caused the apoptosis-
resistant phenotype in cycling cells, and apoptosis
sensitivity in growth arrested cells. Moreover, the
protein product of the mouse homolog of RTP801 (dig2) is
thought to be induced by diverse apoptotic signals, and
also by dexamethasone treatment.
Length = 116
Score = 153 bits (389), Expect = 4e-49
Identities = 62/116 (53%), Positives = 81/116 (69%), Gaps = 2/116 (1%)
Query: 38 LRAAKSAQLACGEVLLPSDLLPNVARDILRLAEVEPYGLKGCTLFINFETD-QECRKIAT 96
LR AK L C EVLLP+DL P +A+++LRL+E EP GL+GCT+ + FE + + CR+IA
Sbjct: 1 LRKAKQRHLRCTEVLLPADLTPRIAQELLRLSESEPCGLRGCTIDVEFEDEPKNCRRIAQ 60
Query: 97 ITCDPNTVSTFELYLTLRQDFRHSWHSLLPQFLKNLTKGGTIMISRGFTLEKKRLY 152
I DP+TV TFEL L LRQD R W S+L F +L +G T+ +S GF L KK+LY
Sbjct: 61 IKVDPSTVPTFELTLVLRQDSR-GWTSILGLFSTSLGRGQTLTLSPGFRLIKKKLY 115
>gnl|CDD|165574 PHA03330, PHA03330, putative primase; Provisional.
Length = 771
Score = 28.6 bits (63), Expect = 1.9
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 35 EQELRAAKSAQLACGEVLLPSDLLPNVARDI-LRLAEVEPY 74
E E A+ AQ EV LP + N+ DI +R A EP+
Sbjct: 353 EWEAETAEGAQCCWHEVCLPGRSITNILLDIDIRAAGAEPH 393
>gnl|CDD|227017 COG4671, COG4671, Predicted glycosyl transferase [General function
prediction only].
Length = 400
Score = 28.1 bits (63), Expect = 2.3
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 29 FLSNRLEQELRAAKSAQLACGEVLLPSDLLP 59
+ R EQ +RA + +L +VLLP +L P
Sbjct: 322 RAAPREEQLIRAQRLEELGLVDVLLPENLTP 352
>gnl|CDD|185272 PRK15374, PRK15374, pathogenicity island 1 effector protein SipB;
Provisional.
Length = 593
Score = 28.0 bits (62), Expect = 2.5
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 124 LLPQFLKNLTKGGTIMISRGF 144
L+P LK L + G+ + ++G
Sbjct: 452 LVPNVLKQLAQNGSKLFTQGM 472
>gnl|CDD|136438 PRK07594, PRK07594, type III secretion system ATPase SsaN;
Validated.
Length = 433
Score = 28.0 bits (62), Expect = 2.7
Identities = 17/51 (33%), Positives = 25/51 (49%)
Query: 28 IFLSNRLEQELRAAKSAQLACGEVLLPSDLLPNVARDILRLAEVEPYGLKG 78
+ L++ L + RAA+ LA GE + + P V + RL E G KG
Sbjct: 248 VLLADSLTRYARAAREIALAAGETAVSGEYPPGVFSALPRLLERTGMGEKG 298
>gnl|CDD|199881 cd02850, E_set_Cellulase_N, N-terminal Early set domain associated
with the catalytic domain of cellulase. E or "early"
set domains are associated with the catalytic domain of
cellulases at the N-terminal end. Cellulases are
O-glycosyl hydrolases (GHs) that hydrolyze beta 1-4
glucosidic bonds in cellulose. They are usually
categorized into either exoglucanases, which
sequentially release terminal sugar units from the
cellulose chain, or endoglucanases, which also attack
the chain internally. The N-terminal domain of cellulase
may be related to the immunoglobulin and/or fibronectin
type III superfamilies. These domains are associated
with different types of catalytic domains at either the
N-terminal or C-terminal end and may be involved in
homodimeric/tetrameric/dodecameric interactions. Members
of this family include members of the alpha amylase
family, sialidase, galactose oxidase, cellulase,
cellulose, hyaluronate lyase, chitobiase, and chitinase,
among others.
Length = 86
Score = 26.1 bits (58), Expect = 3.8
Identities = 8/26 (30%), Positives = 12/26 (46%), Gaps = 2/26 (7%)
Query: 85 FETDQECRKIATITCDPNTVSTFELY 110
+ + K+A + D STFEL
Sbjct: 9 YLPNAP--KVAVVVGDETAASTFELV 32
>gnl|CDD|144788 pfam01318, Bromo_coat, Bromovirus coat protein.
Length = 165
Score = 26.8 bits (59), Expect = 4.0
Identities = 14/41 (34%), Positives = 23/41 (56%)
Query: 22 IEDSASIFLSNRLEQELRAAKSAQLACGEVLLPSDLLPNVA 62
++ ++ +S +L EL + + L G VLL LLP+VA
Sbjct: 37 VKAKETVAVSIKLPDELSSEANKALKVGRVLLWLGLLPSVA 77
>gnl|CDD|238946 cd01988, Na_H_Antiporter_C, The C-terminal domain of a subfamily
of Na+ /H+ antiporter existed in bacteria and archea .
Na+/H+ exchange proteins eject protons from cells,
effectively eliminating excess acid from actively
metabolising cells. Na+ /H+ exchange activity is also
crucial for the regulation of cell volume, and for the
reabsorption of NaCl across renal, intestinal, and
other epithelia. These antiports exchange Na+ for H+ in
an electroneutral manner, and this activity is carried
out by a family of Na+ /H+ exchangers, or NHEs, which
are known to be present in both prokaryotic and
eukaryotic cells. These exchangers are
highly-regulated (glyco)phosphoproteins, which, based
on their primary structure, appear to contain 10-12
membrane-spanning regions (M) at the N-terminus and a
large cytoplasmic region at the C-terminus. The
transmembrane regions M3-M12 share identity wit h other
members of the family. The M6 and M7 regions are highly
conserved. Thus, this is thought to be the region that
is involved in the transport of sodium and hydrogen
ions. The cytoplasmic region or C-terminal has homology
with a family universal stress protein.Usp is a small
cytoplasmic bacterial protein whose expression is
enhanced when the cell is exposed to stress agents. Usp
enhances the rate of cell survival during prolonged
exposure to such conditions, and may provide a general
"stress endurance" activity.
Length = 132
Score = 26.1 bits (58), Expect = 6.0
Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 6/69 (8%)
Query: 2 EVLPNPVVFANNYEAFQQEDIEDSASIFLSNRLEQELRAAKSAQLACGEVLLPSDLLPNV 61
E++P V+ N+ + Q ++ + L Q R A S + ++ ++
Sbjct: 29 EIIPLNVIEVPNHSSPSQLEVNVQRA---RKLLRQAERIAASLGVPVHTIIRIDH---DI 82
Query: 62 ARDILRLAE 70
A ILR A+
Sbjct: 83 ASGILRTAK 91
>gnl|CDD|187839 cd09708, Csf4_U, CRISPR/Cas system-associated DinG family helicase
Csf4. 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;
DinG family DNA helicase.
Length = 632
Score = 26.9 bits (59), Expect = 7.0
Identities = 17/52 (32%), Positives = 21/52 (40%), Gaps = 1/52 (1%)
Query: 11 ANNYEAFQQEDIEDSASIFLSNRLEQELRAAKSAQLACGEVLLPSDLLPNVA 62
N + F ED ED + +E A KS LAC +L LLP
Sbjct: 182 TLNPQDFVTEDEEDKRWVTSLVE-SREYYARKSRILACTHTMLKWGLLPQPD 232
>gnl|CDD|182007 PRK09634, nusB, transcription antitermination protein NusB;
Provisional.
Length = 207
Score = 26.4 bits (59), Expect = 7.4
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 58 LPNVARDILRLAEVE 72
LP + RDILRLA VE
Sbjct: 146 LPRIDRDILRLAVVE 160
>gnl|CDD|236608 PRK09652, PRK09652, RNA polymerase sigma factor RpoE; Provisional.
Length = 182
Score = 25.9 bits (58), Expect = 7.9
Identities = 18/58 (31%), Positives = 24/58 (41%), Gaps = 13/58 (22%)
Query: 15 EAFQQEDIEDSASIFLSNRLEQELRAAKSAQLACGEVLLPSDLLPNVARDILRLAEVE 72
A DI + LS LEQ +RAA + LP +L R + L E+E
Sbjct: 99 LADALRDISTPENELLSAELEQRVRAAIES--------LPEEL-----RTAITLREIE 143
>gnl|CDD|205803 pfam13625, Helicase_C_3, Helicase conserved C-terminal domain.
This domain family is found in a wide variety of
helicases and helicase-related proteins.
Length = 128
Score = 25.6 bits (57), Expect = 8.2
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 49 GEVLLPSDLLPNVARDILRLAEVEPYGL 76
+LLP P +AR + AE+E G
Sbjct: 8 LTILLPGPPTPELARALAAFAELESPGH 35
>gnl|CDD|132511 TIGR03471, HpnJ, hopanoid biosynthesis associated radical SAM
protein HpnJ. The sequences represented by this model
are members of the radical SAM superfamily of enzymes
(pfam04055). These enzymes utilize an iron-sulfur redox
cluster and S-adenosylmethionine to carry out diverse
radical mediated reactions. The member of this clade
from Acidithiobacillus ferrooxidans ATCC 23270
(AFE_0975) is found in the same locus as squalene-hopene
cyclase (SHC, TIGR01507) and other genes associated with
the biosynthesis of hopanoid natural products.
Similarly, in Ralstonia eutropha JMP134 (Reut_B4901)
this gene is adjacent to HpnAB, IspH and HpnH
(TIGR03470), although SHC itself is elsewhere in the
genome. Notably, this gene (here named HpnJ) and three
others form a conserved set (HpnIJKL) which occur in a
subset of all genomes containing the SHC enzyme. This
relationship was discerned using the method of partial
phylogenetic profiling. This group includes Zymomonas
mobilis, the organism where the initial hopanoid
biosynthesis locus was described consisting of the genes
HpnA-E and SHC (HpnF). Continuing past SHC are found a
phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and
another radical SAM enzyme (ZMO0874), HpnH. Although
discontinuous in Z. mobilis, we continue the gene symbol
sequence with HpnIJKL. One of the well-described
hopanoid intermediates is bacteriohopanetetrol. In the
conversion from hopene several reactions must occur in
the side chain for which a radical mechanism might be
reasonable. These include the four (presumably
anaerobic) hydroxylations and a methyl shift.
Length = 472
Score = 26.2 bits (58), Expect = 9.8
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 126 PQFLKNLTKGGTIMISRGFTLEKKRL 151
Q LKN+ KG T+ I+R FT + +L
Sbjct: 310 QQILKNIKKGLTVEIARRFTRDCHKL 335
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
0.320 0.136 0.395
Gapped
Lambda K H
0.267 0.0814 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,232,341
Number of extensions: 732817
Number of successful extensions: 655
Number of sequences better than 10.0: 1
Number of HSP's gapped: 653
Number of HSP's successfully gapped: 20
Length of query: 161
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 72
Effective length of database: 6,990,096
Effective search space: 503286912
Effective search space used: 503286912
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 (21.8 bits)
S2: 55 (24.8 bits)