RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15100
(165 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 90.6 bits (226), Expect = 6e-25
Identities = 31/52 (59%), Positives = 35/52 (67%)
Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
FT EQL LE +F+ RY S ER LA L LTE QVK+WFQNRR KWK+
Sbjct: 6 TFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved
in the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 81.9 bits (203), Expect = 1e-21
Identities = 30/53 (56%), Positives = 33/53 (62%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
FT EQL LE +F+ Y S ER LA L LTE QVKIWFQNRR K K+
Sbjct: 7 FTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 78.4 bits (194), Expect = 3e-20
Identities = 29/51 (56%), Positives = 34/51 (66%)
Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95
+FT EQL LE +F+ Y S ER LA L L+E QVK+WFQNRR KWK
Sbjct: 7 SFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 54.8 bits (132), Expect = 4e-10
Identities = 23/52 (44%), Positives = 33/52 (63%)
Query: 47 TYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
T EQL+ LE +F+ Y S R+ L+L L++ V+IWFQN+R K KK+
Sbjct: 59 TDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110
>gnl|CDD|223031 PHA03273, PHA03273, envelope glycoprotein C; Provisional.
Length = 486
Score = 30.4 bits (68), Expect = 0.48
Identities = 20/101 (19%), Positives = 39/101 (38%), Gaps = 6/101 (5%)
Query: 1 MTTSASTGTTTMSSATSAKTPPVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKT 60
M ++ +T T T S+ TS S N ++E + +
Sbjct: 44 MQSTPATPTHTTSNLTSPFGTGTD----NSTNANGTESTTQASQPHSHETTITCTKSLIS 99
Query: 61 TRYL-SVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG 100
Y SV ++ ++ +E +++I+ N+RT + PG
Sbjct: 100 VPYYKSVDMNCTTSVGVNYSEYRLEIYL-NQRTPFSGTPPG 139
>gnl|CDD|234253 TIGR03547, muta_rot_YjhT, mutatrotase, YjhT family. Members of
this protein family contain multiple copies of the
beta-propeller-forming Kelch repeat. All are full-length
homologs to YjhT of Escherichia coli, which has been
identified as a mutarotase for sialic acid. This protein
improves bacterial ability to obtain host sialic acid,
and thus serves as a virulence factor. Some bacteria
carry what appears to be a cyclically permuted homolog
of this protein.
Length = 346
Score = 29.6 bits (67), Expect = 0.62
Identities = 17/82 (20%), Positives = 25/82 (30%), Gaps = 25/82 (30%)
Query: 87 FQNRRTKWKKQNPGMDVNSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSGTAHYPYAAAA 146
F + +W K P +P S G A G ++G ++ A
Sbjct: 224 FTGGKLEWNKL--------PPLPPPKSSSQEGLA-----------GAFAGISNGVLLVAG 264
Query: 147 AAYFH------HLGAHHTHGGL 162
A F G + H GL
Sbjct: 265 GANFPGAQENYKNGKLYAHEGL 286
>gnl|CDD|205996 pfam13825, Paramyxo_PNT, Paramyxovirus structural protein V/P
N-terminus. This family consists of several
Paramyxoviridae structural protein P and V sequences.
From a structural point of view, P is the
best-characterized protein of the replicative complex. P
is organised into two moieties that are functionally and
structurally distinct: a C-terminal moiety (PCT) and an
N-terminal moiety (PNT). PCT is the most conserved in
sequence and contains all regions required for virus
transcription, whereas PNT, which is poorly conserved,
provides several additional functions required for
replication. P protein plays a crucial role in the
enzyme by positioning L onto the N/RNA template through
an interaction with the C-terminal domain of N. Without
P, L is not functional. The N, P, and L proteins of SeV
and measles and mumps viruses are functionally
equivalent. However, sequence identity between proteins
from these viruses is limited, and the viruses have been
placed in different genera (Respirovirus, Morbilivirus,
and Rubulavirus, respectively). SeV P protein (568 aa)
is a modular protein with distinct functional domains.
The N-terminal part of P (PNT) is a chaperone for N and
prevents it from binding to non-viral RNA in the
infected cell.
Length = 309
Score = 29.0 bits (65), Expect = 0.94
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 4 SASTGTTTMSSATSAKTPPVRRNRGRSPNTQTPSEDLVPESAFTYE 49
SAS+GT T S +T T ++ S + + V +SA +
Sbjct: 233 SASSGTETESLSTGGATQSALKSTWGSSEPNASAGN-VRQSASNAK 277
>gnl|CDD|185763 cd09240, BRO1_Alix, Protein-interacting, N-terminal, Bro1-like
domain of mammalian Alix and related domains. This
family contains the N-terminal, Bro1-like domain of
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), also called apoptosis-linked gene-2
interacting protein 1 (AIP1). It belongs to the
BRO1_Alix_like superfamily which also includes the
Bro1-like domains of His-Domain type N23 protein
tyrosine phosphatase (HD-PTP, also known as PTPN23),
RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1
and Rim20 (also known as PalA) from Saccharomyces
cerevisiae, Ustilago maydis Rim23 (also known as PalC),
and related domains. Alix, HD-PTP, Brox, Bro1, Rim20,
and Rim23, interact with the ESCRT (Endosomal Sorting
Complexes Required for Transport) system. Alix
participates in membrane remodeling processes during
the budding of enveloped viruses, vesicle budding
inside late endosomal multivesicular bodies (MVBs), and
the abscission reactions of mammalian cell division. It
also functions in apoptosis. Bro1-like domains are
boomerang-shaped, and part of the domain is a
tetratricopeptide repeat (TPR)-like structure.
Bro1-like domains bind components of the ESCRT-III
complex: CHMP4, in the case of Alix. The Alix Bro1-like
domain can also bind human immunodeficiency virus type
1 (HIV-1) nucleocapsid and Rab5-specfic GAP (RabGAP5,
also known as Rab-GAPLP). In addition to this Bro1-like
domain, Alix has a middle V-shaped (V) domain. The Alix
V-domain is a dimerization domain, and carries a
binding site for the retroviral late assembly (L)
domain YPXnL motif, which is partially conserved in the
superfamily. Alix also has a C-terminal proline-rich
region (PRR) that binds multiple partners including
Tsg101 (tumor susceptibility gene 101, a component of
ESCRT-1) and the apoptotic protein ALG-2.
Length = 346
Score = 28.8 bits (65), Expect = 1.3
Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 23/48 (47%)
Query: 48 YEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95
Y+QL A+E KF +E+Q+++ F WK
Sbjct: 70 YDQLCAIEPKF------------------PFSESQIQVTF-----TWK 94
>gnl|CDD|172552 PRK14061, PRK14061, unknown domain/lipoate-protein ligase A fusion
protein; Provisional.
Length = 562
Score = 27.8 bits (61), Expect = 3.5
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNSPTVP 109
RL L LSL++ + Q +RT+W +Q+P + S VP
Sbjct: 166 RLMLLLSLAIGVVLTRTLLQGKRTRW-QQSPFLLTASKPVP 205
>gnl|CDD|193556 cd05681, M20_dipept_like_4, Uncharacterized M20 Dipeptidases.
Peptidase M20 family, unknown dipeptidase-like subfamily
3 (inferred by homology to be dipeptidases). M20
dipeptidases include a large variety of bacterial
enzymes including cytosolic nonspecific dipeptidase
(CNDP), Xaa-methyl-His dipeptidase (anserinase),and
canosinase. These dipeptidases have been shown to act on
a wide range of dipeptides, but not larger peptides. For
example, anserinase mainly catalyzes the hydrolysis of
N-alpha-acetylhistidine while carnosinase degrades
beta-alanyl-L-histidine.
Length = 430
Score = 27.2 bits (61), Expect = 4.2
Identities = 14/40 (35%), Positives = 17/40 (42%), Gaps = 10/40 (25%)
Query: 108 VPTCPGGSHSGPAFPFHPALSGP------GGHYSGTAHYP 141
+P G +GP +PF AL P G S AH P
Sbjct: 373 LPNSAG---TGPMYPFTDALKAPIVAIGIGYAGSR-AHAP 408
>gnl|CDD|233200 TIGR00940, 2a6301s01, Tmonovalent cation:proton antiporter. This
family of proteins constists of bacterial multicomponent
K+:H+ and Na+:H+ antiporters. The best characterized
systems are the PhaABCDEFG system of Rhizobium meliloti
which functions in pH adaptation and as a K+ efflux
system and the MnhABCDEFG system of Staphylococcus
aureus which functions as a Na+:H+ antiporter [Transport
and binding proteins, Cations and iron carrying
compounds].
Length = 793
Score = 27.1 bits (60), Expect = 5.8
Identities = 15/36 (41%), Positives = 15/36 (41%)
Query: 126 ALSGPGGHYSGTAHYPYAAAAAAYFHHLGAHHTHGG 161
L P HY G YA AA A HL H T G
Sbjct: 314 GLGSPSYHYQGDDSKIYALAAVAAVFHLINHATFKG 349
>gnl|CDD|237381 PRK13419, PRK13419, F0F1 ATP synthase subunit A; Provisional.
Length = 342
Score = 26.6 bits (59), Expect = 6.4
Identities = 9/47 (19%), Positives = 11/47 (23%)
Query: 118 GPAFPFHPALSGPGGHYSGTAHYPYAAAAAAYFHHLGAHHTHGGLTH 164
AF A + + A A A H A H
Sbjct: 19 DAAFASAEAAAEAHHASAAAAAAAPAGEHGAAVHAEAAAHAEQAEGG 65
>gnl|CDD|221480 pfam12238, MSA-2c, Merozoite surface antigen 2c. This family of
proteins is found in eukaryotes. Proteins in this family
are typically between 263 and 318 amino acids in length.
There is a conserved SFT sequence motif. MSA-2 is a
plasma membrane glycoprotein which can be found in
Babesia bovis species.
Length = 201
Score = 26.3 bits (58), Expect = 6.5
Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 4/51 (7%)
Query: 2 TTSASTGTTTMS-SATSAKTPPVRRNRGRSPNTQTPSEDLVPE---SAFTY 48
S+S GT+T S SA +P Q P+ S+FT+
Sbjct: 145 KHSSSQGTSTTRPSDGSATPNTSAPPTPGNPAAQPEKPAETPKGNGSSFTF 195
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 26.7 bits (59), Expect = 6.8
Identities = 13/71 (18%), Positives = 21/71 (29%), Gaps = 6/71 (8%)
Query: 91 RTKWKKQNPGMDVNSPTVPTCPGGSHSGPAFPFHPALSGPGGHYS------GTAHYPYAA 144
+T ++Q + + + SH GP P H P A
Sbjct: 203 QTHRQRQPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMGPPHGPPSRYRPAYEAAPLAP 262
Query: 145 AAAAYFHHLGA 155
A ++Y G
Sbjct: 263 AISSYGPAGGG 273
>gnl|CDD|237323 PRK13263, ureE, urease accessory protein UreE; Provisional.
Length = 206
Score = 26.3 bits (58), Expect = 7.6
Identities = 17/48 (35%), Positives = 20/48 (41%), Gaps = 4/48 (8%)
Query: 122 PFHP-ALSGPGGHYSG---TAHYPYAAAAAAYFHHLGAHHTHGGLTHT 165
PF P A + GGH G T YA A + H G H+H H
Sbjct: 137 PFEPEAGAYGGGHRHGHDATFAEDYALAQQVFHEHHGHSHSHSDHDHD 184
>gnl|CDD|219355 pfam07267, Nucleo_P87, Nucleopolyhedrovirus capsid protein P87.
This family consists of several Nucleopolyhedrovirus
capsid protein P87 sequences. P87 is expressed late in
infection and concentrated in infected cell nuclei.
Length = 606
Score = 26.4 bits (58), Expect = 8.6
Identities = 10/37 (27%), Positives = 12/37 (32%)
Query: 3 TSASTGTTTMSSATSAKTPPVRRNRGRSPNTQTPSED 39
A + S S P +R R R P S D
Sbjct: 336 LFAISSLPDSDSEASDSGPTRKRKRRRVPPLPEYSSD 372
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
0.313 0.126 0.390
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,075,181
Number of extensions: 694157
Number of successful extensions: 587
Number of sequences better than 10.0: 1
Number of HSP's gapped: 578
Number of HSP's successfully gapped: 37
Length of query: 165
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 75
Effective length of database: 6,945,742
Effective search space: 520930650
Effective search space used: 520930650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (24.9 bits)