RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11442
(1362 letters)
>gnl|CDD|202685 pfam03564, DUF1759, Protein of unknown function (DUF1759). This is a
family of proteins of unknown function. Most of the
members are gag-polyproteins.
Length = 146
Score = 87.0 bits (216), Expect = 7e-20
Identities = 46/139 (33%), Positives = 72/139 (51%), Gaps = 1/139 (0%)
Query: 1168 FSGEFSEFNVFYESFKSLIHDNKELDNTQKVQYLVSKLSGKALTVCAGVPATVDNYSIIF 1227
FSG+ E+ F+E F+SLIH +L QK YL S L G+A T+ +P T NY + +
Sbjct: 1 FSGDIKEWQAFWELFESLIHSKTDLPEIQKFNYLKSALEGEAATLVTHLPITAANYDVAW 60
Query: 1228 NNLVEKYQCKRSQAKAYLSNILNFKQIKGESPDQLNSLIDELCASVLALKKVDLDSLSDF 1287
L E+Y R ++ L+ ++ +S QL L DE + L+++ + D
Sbjct: 61 EALKERYDNPRVIIRSLLNKLMKLPSTNNDSVSQLRRLYDEANEIIRQLEQLGEN-ADDT 119
Query: 1288 MLAHITLSKIDSETARLFE 1306
+LAH+ L K+D E R +
Sbjct: 120 ILAHLLLQKLDEEIRRKWI 138
Score = 67.4 bits (165), Expect = 6e-13
Identities = 34/106 (32%), Positives = 55/106 (51%), Gaps = 3/106 (2%)
Query: 812 FSGEFSEFNVFYESFKSLIHDNKELDNTQKVQYLVSKLSGKALTVCAGVPATADNYSIIF 871
FSG+ E+ F+E F+SLIH +L QK YL S L G+A T+ +P TA NY + +
Sbjct: 1 FSGDIKEWQAFWELFESLIHSKTDLPEIQKFNYLKSALEGEAATLVTHLPITAANYDVAW 60
Query: 872 NNLVEKYQCKRSQAKAYLSNILNFKQIKGQNVNEVPELKKSVKTLV 917
L E+Y R ++ L+ ++ + N + V +L++
Sbjct: 61 EALKERYDNPRVIIRSLLNKLMK---LPSTNNDSVSQLRRLYDEAN 103
>gnl|CDD|147520 pfam05380, Peptidase_A17, Pao retrotransposon peptidase.
Corresponds to Merops family A17. These proteins are
homologous to aspartic proteinases encoded by
retroposons and retroviruses.
Length = 159
Score = 55.5 bits (134), Expect = 1e-08
Identities = 22/35 (62%), Positives = 29/35 (82%), Gaps = 1/35 (2%)
Query: 284 LIKAKSKVAPTKQLLSIPRLELCAALLLSRLYNSL 318
L+ AK++VAP K + SIPRLELCAALLL+RL ++
Sbjct: 111 LVAAKTRVAPLKTV-SIPRLELCAALLLTRLARAV 144
Score = 52.0 bits (125), Expect = 2e-07
Identities = 22/52 (42%), Positives = 32/52 (61%), Gaps = 4/52 (7%)
Query: 148 QFFISPSKVAPTKQLLSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTTFF 199
+ ++VAP K + SIPRLELCAALLL+RL ++ + +VK T+
Sbjct: 110 SLVAAKTRVAPLKTV-SIPRLELCAALLLTRLARAV---KPEHDVKPTDTYC 157
>gnl|CDD|147642 pfam05585, DUF1758, Putative peptidase (DUF1758). This is a
family of nematode proteins of unknown function.
However, it seems likely that these proteins act as
aspartic peptidases.
Length = 164
Score = 39.5 bits (92), Expect = 0.003
Identities = 20/54 (37%), Positives = 30/54 (55%)
Query: 11 NASGQLSSIRVIVDPGSQVSCITNDCVQRLGLKRYKCGISISGIGDNGVPDNKG 64
NA G + R++ D GS++S I+ C+ RLGL R I + GI + P +G
Sbjct: 5 NAQGARTKCRLLFDSGSELSYISERCINRLGLARTPSRILVIGISGDKAPQTRG 58
>gnl|CDD|133136 cd00303, retropepsin_like, Retropepsins; pepsin-like aspartate
proteases. The family includes pepsin-like aspartate
proteases from retroviruses, retrotransposons and
retroelements, as well as eukaryotic
dna-damage-inducible proteins (DDIs), and bacterial
aspartate peptidases. While fungal and mammalian
pepsins are bilobal proteins with structurally related
N and C-terminals, retropepsins are half as long as
their fungal and mammalian counterparts. The monomers
are structurally related to one lobe of the pepsin
molecule and retropepsins function as homodimers. The
active site aspartate occurs within a motif
(Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral
aspartyl protease is synthesized as part of the POL
polyprotein that contains an aspartyl protease, a
reverse transcriptase, RNase H, and an integrase. The
POL polyprotein undergoes specific enzymatic cleavage
to yield the mature proteins. In aspartate peptidases,
Asp residues are ligands of an activated water molecule
in all examples where catalytic residues have been
identified. This group of aspartate peptidases is
classified by MEROPS as the peptidase family A2
(retropepsin family, clan AA), subfamily A2A.
Length = 92
Score = 34.2 bits (79), Expect = 0.056
Identities = 13/62 (20%), Positives = 25/62 (40%), Gaps = 2/62 (3%)
Query: 18 SIRVIVDPGSQVSCITNDCVQRLGLKRY--KCGISISGIGDNGVPDNKGAVSCTLATSNK 75
+R +VD G+ V+ I+ ++LGL + + G + V + T+ K
Sbjct: 9 PVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGK 68
Query: 76 VI 77
Sbjct: 69 TF 70
>gnl|CDD|222288 pfam13650, Asp_protease_2, Aspartyl protease. This family
consists of predicted aspartic proteases, typically
from 180 to 230 amino acids in length, in MEROPS clan
AA. This model describes the well-conserved 121-residue
C-terminal region. The poorly conserved, variable
length N-terminal region usually contains a predicted
transmembrane helix.
Length = 89
Score = 33.0 bits (76), Expect = 0.15
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 18 SIRVIVDPGSQVSCITNDCVQRLGLKRYKCGISISGIGDNGV 59
+R ++D G+ + ++ +RLGLK K NG
Sbjct: 9 PVRFLLDTGASGTLLSRSLAERLGLKPTK-LTIGRVSTANGT 49
>gnl|CDD|238822 cd01644, RT_pepA17, RT_pepA17: Reverse transcriptase (RTs) in
retrotransposons. This subfamily represents the RT
domain of a multifunctional enzyme. C-terminal to the RT
domain is a domain homologous to aspartic proteinases
(corresponding to Merops family A17) encoded by
retrotransposons and retroviruses. RT catalyzes DNA
replication from an RNA template and is responsible for
the replication of retroelements.
Length = 213
Score = 35.0 bits (81), Expect = 0.17
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 6/66 (9%)
Query: 58 GVPDNKGAVSCTLATSNKVIFSENKGCFELRKWASNSQQLLNTVPHEHCEVPLRQNEEST 117
AV+ + ++I KG F LRKWASNSQ++L+ +P E V L ++ + T
Sbjct: 147 STDTLNEAVN----VAKRLIALLKKGGFNLRKWASNSQEVLDDLPEE--RVLLDRDSDVT 200
Query: 118 FKILSV 123
K L +
Sbjct: 201 EKTLGL 206
>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex
non-fungal. The approx. 70 residue Med15 domain of the
ARC-Mediator co-activator is a three-helix bundle with
marked similarity to the KIX domain. The sterol
regulatory element binding protein (SREBP) family of
transcription activators use the ARC105 subunit to
activate target genes in the regulation of cholesterol
and fatty acid homeostasis. In addition, Med15 is a
critical transducer of gene activation signals that
control early metazoan development.
Length = 768
Score = 35.4 bits (81), Expect = 0.28
Identities = 40/181 (22%), Positives = 67/181 (37%), Gaps = 42/181 (23%)
Query: 389 PQQLVSHPLWWHGPQFLSSPDHQWPSGQGQNVNEVPELKKSVKTLVVTDSA--------- 439
P S P + SP PS Q +++ P +++++ +V+
Sbjct: 437 PGGPGSQPPQSVSGGMIPSPPALMPSPSPQ-MSQSPASQRTIQQDMVSPGGPLNTPGQSS 495
Query: 440 --TAESSNDLHDSFQKYSQLSKVQRVFAYILRFIHNVRNRHAKLQ-GPLQIDGLN---SS 493
+ + + +KY QLSK +I +R AK+ +I L+ S
Sbjct: 496 VNSPANPQEEQLYREKYKQLSK----------YIEPLRRMIAKIDNDEGRIKDLSKMKSL 545
Query: 494 LDLLTN------LEQAFHFKQVLTSLKND----------SPLKDASLRKLTPFIDDAGLI 537
LD+L+N LE + L LKN +PL +A L L + + L
Sbjct: 546 LDILSNPSSRCPLETLQKCEIALEKLKNQMGTPTPPPLCNPLLEAVLANLQSPVFNHTLY 605
Query: 538 R 538
R
Sbjct: 606 R 606
>gnl|CDD|222878 PHA02562, 46, endonuclease subunit; Provisional.
Length = 562
Score = 33.4 bits (77), Expect = 0.81
Identities = 21/96 (21%), Positives = 41/96 (42%), Gaps = 15/96 (15%)
Query: 1239 SQAKAYLSNILNFKQIKGESPDQLNSLIDELCASVLALKKVDLDSLSDFMLAHI------ 1292
Q K Y NI ++ GE+ + + DEL +K +++ L+D +L +
Sbjct: 195 QQIKTYNKNIEEQRKKNGENIARKQNKYDELVEEAKTIKA-EIEELTDELLNLVMDIEDP 253
Query: 1293 --TLSKIDSETARLFEMSLKSGEIPTFSKVHNFLKD 1326
L+K+++ A++ +I F KV +
Sbjct: 254 SAALNKLNTAAAKI------KSKIEQFQKVIKMYEK 283
>gnl|CDD|133147 cd05480, NRIP_C, NRIP_C; putative nuclear receptor interacting
protein. Proteins in this family have been described
as probable nuclear receptor interacting proteins. The
C-terminal domain of this family is homologous to the
retroviral aspartyl protease domain. The domain is
structurally related to one lobe of the pepsin
molecule. The conserved active site aspartate occurs
within a motif (Asp-Thr/Ser-Gly), as it does in pepsin.
Asp residues are ligands of an activated water molecule
in all examples where catalytic residues have been
identified. This group of aspartate peptidases is
classified by MEROPS as the peptidase family A2
(retropepsin family, clan AA), subfamily A2A.
Length = 103
Score = 31.4 bits (71), Expect = 0.81
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 19 IRVIVDPGSQVSCITNDCVQRLGLKR 44
+R +VD G Q + I+ C+ RLGLK
Sbjct: 10 LRALVDTGCQYNLISAACLDRLGLKE 35
>gnl|CDD|149409 pfam08337, Plexin_cytopl, Plexin cytoplasmic RasGAP domain. This
family features the C-terminal regions of various
plexins. Plexins are receptors for semaphorins, and
plexin signalling is important in path finding and
patterning of both neurons and developing blood vessels.
The cytoplasmic region, which has been called a SEX
domain in some members of this family, is involved in
downstream signalling pathways, by interaction with
proteins such as Rac1, RhoD, Rnd1 and other plexins. This
domain acts as a RasGAP domain.
Length = 538
Score = 32.4 bits (74), Expect = 2.0
Identities = 25/78 (32%), Positives = 35/78 (44%), Gaps = 12/78 (15%)
Query: 1032 PYHRKHPLLLPKIHI---------ISSWLKLLNIIVFMFRFIHFLPRRDFISVSDR-NFA 1081
P H HPLL + ++ + +LLN F+ FIH L + SV DR N A
Sbjct: 20 PGHETHPLLRDLVPESRRPTVEQGLTQFSQLLNNKSFLLTFIHTLESQRSFSVRDRCNVA 79
Query: 1082 EIALIKALQRQF-FAKDI 1098
+ L AL + + DI
Sbjct: 80 SL-LTVALHGKLEYCTDI 96
>gnl|CDD|238637 cd01312, Met_dep_hydrolase_D, Metallo-dependent hydrolases, subgroup
D is part of the superfamily of metallo-dependent
hydrolases, a large group of proteins that show
conservation in their 3-dimensional fold (TIM barrel) and
in details of their active site. The vast majority of the
members have a conserved metal binding site, involving
four histidines and one aspartic acid residue. In the
common reaction mechanism, the metal ion (or ions)
deprotonate a water molecule for a nucleophilic attack on
the substrate. The function of this subgroup is unknown.
Length = 381
Score = 31.7 bits (72), Expect = 3.3
Identities = 43/178 (24%), Positives = 63/178 (35%), Gaps = 25/178 (14%)
Query: 1153 AEKSKVRLPA--LELPSFSGEFSE----FNVFYESFKSLIHDNKELDNTQKVQYLVSKLS 1206
A+K + L LE E F F+ESF L K + L
Sbjct: 172 AKKLNLPLSTHFLESKEEREWLEESKGWFKHFWESFLKLPKPKKLATAIDFLDML--GGL 229
Query: 1207 GKALTVCAGVPATVDNYSIIFNNLVEKYQCKRS-----QAKAYLSNILNFKQIKGESPDQ 1261
G ++ V A ++ I+ + C RS K +S + D
Sbjct: 230 GTRVSFVHCVYANLEEAEILASRGASIALCPRSNRLLNGGKLDVSELKKAGIPVSLGTDG 289
Query: 1262 LNS-----LIDELCASVLALKKVDLDSLSDFMLAHITLSKIDSETARLFEMSLKSGEI 1314
L+S L+DEL A + + DL L+ +L TL AR + L +GEI
Sbjct: 290 LSSNISLSLLDELRALLDLHPEEDLLELASELLLMATLG-----GAR--ALGLNNGEI 340
>gnl|CDD|232811 TIGR00073, hypB, hydrogenase accessory protein HypB. A GTP hydrolase
for assembly of nickel metallocenter of hydrogenase. A
similar protein, ureG, is an accessory protein for
urease, which also uses nickel. hits scoring 75 and above
are safe as orthologs. [SS 1/05/04 I changed the role_ID
and process GO from protein folding to to protein
modification, since a protein folding role has not been
established, but HypB is implicated in insertion of
nickel into the large subunit of NiFe hydrogenases.]
[Protein fate, Protein modification and repair].
Length = 208
Score = 30.8 bits (70), Expect = 3.5
Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 5/62 (8%)
Query: 1270 CASVLALKKVDLDSLSDFMLAHI--TLSKIDSETARLFEMSLKSGEIPTFSKVHNFLKDQ 1327
A ++ + K DL F + + KI+ E A + MSLK+GE + FL+ Q
Sbjct: 149 EADLIVINKADLAEAVGFDVEKMKADAKKINPE-AEIILMSLKTGE--GLDEWLEFLEGQ 205
Query: 1328 VK 1329
VK
Sbjct: 206 VK 207
>gnl|CDD|151560 pfam11116, DUF2624, Protein of unknown function (DUF2624). This
family is conserved in the Bacillaceae family. Several
members are named as YqfT. The function is not known.
Length = 84
Score = 28.8 bits (65), Expect = 4.4
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 878 YQCKRSQAKAYLSNILNFKQIKGQNVNEVPELKKSVKTLVVTDSATAESSNDLHDSFQK 936
R+QAK ++ +L K I N +E +L K + +T TA+ N+L F K
Sbjct: 29 IPITRAQAKQ-IAKLLRGKNINIFNESERSKLLKELAK--ITSPQTAQEVNELFAQFVK 84
>gnl|CDD|182817 PRK10895, PRK10895, lipopolysaccharide ABC transporter ATP-binding
protein; Provisional.
Length = 241
Score = 30.6 bits (69), Expect = 5.3
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 5/40 (12%)
Query: 624 HNPSNLGNSYLGAERRFYSLERKLHANPSLL-----FSGV 658
H ++G S G ERR + R L ANP + F+GV
Sbjct: 129 HLRDSMGQSLSGGERRRVEIARALAANPKFILLDEPFAGV 168
>gnl|CDD|237283 PRK13106, ubiA, prenyltransferase; Reviewed.
Length = 300
Score = 30.5 bits (69), Expect = 7.0
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 237 KILVIVLRVIYFPSNLFLIRYGGMVLSFSPLLIGQSYP 274
K L+ +++F S + R+ ++LS LI SYP
Sbjct: 99 KALITAGLILFFASAYLVNRW-ALLLSPIVALIAMSYP 135
>gnl|CDD|130734 TIGR01673, holin_LLH, phage holin, LL-H family. This model
represents a putative phage holin from a number of phage
and prophage regions of Gram-positive bacteria. Like
other holins, it is small (about 100 amino acids) with
stretches of hydrophobic sequence and is encoded adjacent
to lytic enzymes [Mobile and extrachromosomal element
functions, Prophage functions].
Length = 108
Score = 28.7 bits (64), Expect = 7.2
Identities = 13/48 (27%), Positives = 19/48 (39%), Gaps = 3/48 (6%)
Query: 1232 EKYQCKRSQAKAYLSNILNFKQIKGESPDQLNSLIDELCASVLALKKV 1279
K QA Y++ L I S Q+ I+ A+V +KK
Sbjct: 63 GGGAEKLEQAFNYITEELKKAHIPKPSDAQIEGAIE---AAVAEMKKN 107
>gnl|CDD|144068 pfam00336, DNA_pol_viral_C, DNA polymerase (viral) C-terminal
domain.
Length = 245
Score = 29.5 bits (66), Expect = 9.8
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 9/64 (14%)
Query: 334 SDSNIVLAWLRTAPHLLQTYVANRVVEINKLADGCKWYHVPTSENPCDCASRGLLPQQLV 393
+D+++VL+ T+ L AN ++ G + +VP++ NP D SRGLL +
Sbjct: 147 TDNSVVLSRKYTSFPWLLGCAANWILR------GTSFVYVPSALNPADDPSRGLLG---L 197
Query: 394 SHPL 397
PL
Sbjct: 198 LRPL 201
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 0.135 0.393
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 67,831,369
Number of extensions: 6724990
Number of successful extensions: 5160
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5155
Number of HSP's successfully gapped: 35
Length of query: 1362
Length of database: 10,937,602
Length adjustment: 109
Effective length of query: 1253
Effective length of database: 6,103,016
Effective search space: 7647079048
Effective search space used: 7647079048
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: 65 (28.9 bits)