RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6178
(912 letters)
>gnl|CDD|219817 pfam08389, Xpo1, Exportin 1-like protein. The sequences featured
in this family are similar to a region close to the
N-terminus of yeast exportin 1 (Xpo1, Crm1). This region
is found just C-terminal to an importin-beta N-terminal
domain (pfam03810) in many members of this family.
Exportin 1 is a nuclear export receptor that interacts
with leucine-rich nuclear export signal (NES) sequences,
and Ran-GTP, and is involved in translocation of
proteins out of the nucleus.
Length = 147
Score = 69.2 bits (170), Expect = 9e-14
Identities = 42/141 (29%), Positives = 63/141 (44%), Gaps = 9/141 (6%)
Query: 104 KNIITQLALALADLALQM--SAWEKPVVYIIEKL-SHKGSILALLEVLTVLPEEV---NV 157
K I +LALALA+LA Q S W ++ L S LL +L VLPEE+ +
Sbjct: 2 KFIRNKLALALAELAKQEWPSNWPTFFPDLVSLLSSSPSGCELLLRILKVLPEEIFDFSR 61
Query: 158 LKLGKNRREEFEEELKAAGPIVIEFLKTCQANCGDNVS-LQTKVLKCFTSW-SSGSL-HD 214
L + RR ++ L++ P ++E L N S L + LKC SW S +
Sbjct: 62 TPLTQQRRNRLKDLLRSQMPQILELLLQILENSVSAHSELLSATLKCLGSWLSWIPIGLI 121
Query: 215 AATDCVSALLPILEYNNNFDA 235
++ L +L + +A
Sbjct: 122 LNDPLLNLLFQLLSDPDLREA 142
>gnl|CDD|197981 smart00913, IBN_N, Importin-beta N-terminal domain. Members of
the importin-beta (karyopherin-beta) family can bind
and transport cargo by themselves, or can form
heterodimers with importin-alpha. As part of a
heterodimer, importin-beta mediates interactions with
the pore complex, while importin-alpha acts as an
adaptor protein to bind the nuclear localisation signal
(NLS) on the cargo through the classical NLS import of
proteins. Importin-beta is a helicoidal molecule
constructed from 19 HEAT repeats. Many nuclear pore
proteins contain FG sequence repeats that can bind to
HEAT repeats within importins.. which is important for
importin-beta mediated transport.
Length = 67
Score = 40.7 bits (96), Expect = 1e-04
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 2/67 (2%)
Query: 29 ASQWLHQLQKSIYAWKIADEMLLHQNELGLEAVYFSAQTMRQKVQNAFFELPSESHVSLR 88
A + L Q QKS W + E+L N +A T++ K+ + LP E ++
Sbjct: 1 AEKQLEQFQKSPGFWLLLLEIL--ANSEDQYVRQLAAITLKNKITRRWSSLPEEEKEEIK 58
Query: 89 DSLIEHL 95
+SL+E L
Sbjct: 59 NSLLELL 65
>gnl|CDD|237554 PRK13909, PRK13909, putative recombination protein RecB;
Provisional.
Length = 910
Score = 33.0 bits (76), Expect = 0.77
Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 7/79 (8%)
Query: 227 LEYNNNFDAVNLNVFTCILSLEEQFHMAVAHEDLEKCMNYCKLFTELAESLLDRIVNESM 286
LE F NL V L+ ++ + DLE +L E + + +
Sbjct: 777 LEMLYAFKIENLEV--LKNLLKNRYGHFLDESDLEDLEKRLELLINNKE-FQALLKDGKL 833
Query: 287 TKQQPFS----IKALDLVL 301
K+Q +K +DL+L
Sbjct: 834 LKEQALLFNGELKQIDLLL 852
>gnl|CDD|235076 PRK02842, PRK02842, light-independent protochlorophyllide reductase
subunit N; Provisional.
Length = 427
Score = 32.2 bits (74), Expect = 1.2
Identities = 27/94 (28%), Positives = 42/94 (44%), Gaps = 12/94 (12%)
Query: 669 IVVLYSKHPHSSFLYLGSILVDEYATSHCVSGLLDMVQAFLPPTY--AILQEEDGLKNHP 726
+V L+ K + FL +GS +H + V F P + AIL+E D L
Sbjct: 26 VVWLHRKIQDAFFLVVGS-----RTCAHLLQSAAG-VMIFAEPRFGTAILEEGD-LAGLA 78
Query: 727 DTVDDLFRLCTRFLQRAP---IAFLTSSFISSVM 757
D ++L R+ ++R P + FL S S V+
Sbjct: 79 DANEELDRVVEELIKRRPNISVLFLVGSCPSEVI 112
>gnl|CDD|239868 cd04403, RhoGAP_ARHGAP27_15_12_9, RhoGAP_ARHGAP27_15_12_9:
GTPase-activator protein (GAP) domain for Rho-like
GTPases found in ARHGAP27 (also called CAMGAP1),
ARHGAP15, 12 and 9-like proteins; This subgroup of
ARHGAPs are multidomain proteins that contain RhoGAP,
PH, SH3 and WW domains. Most members that are studied
show GAP activity towards Rac1, some additionally show
activity towards Cdc42. Small GTPases cluster into
distinct families, and all act as molecular switches,
active in their GTP-bound form but inactive when
GDP-bound. The Rho family of GTPases activates effectors
involved in a wide variety of developmental processes,
including regulation of cytoskeleton formation, cell
proliferation and the JNK signaling pathway. GTPases
generally have a low intrinsic GTPase hydrolytic
activity but there are family-specific groups of GAPs
that enhance the rate of GTP hydrolysis by several
orders of magnitude.
Length = 187
Score = 31.2 bits (71), Expect = 1.8
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 59 EAVYFSAQTMR-QKVQNAFFELPSESHVSLRDSLIEHLCRTNDTSGKNIITQLALAL 114
A+ S R V++ LP +H +L+ L HLCR + KN +T LA+
Sbjct: 99 AAIKLSDYEQRVSAVKDLIKSLPKPNHDTLK-MLFRHLCRVIEHGEKNRMTTQNLAI 154
>gnl|CDD|217743 pfam03810, IBN_N, Importin-beta N-terminal domain.
Length = 71
Score = 29.1 bits (66), Expect = 1.9
Identities = 14/70 (20%), Positives = 28/70 (40%), Gaps = 4/70 (5%)
Query: 29 ASQWLHQLQKSI-YAWKIADEMLLHQNELGLEAVYFSAQTMRQKVQNAF--FELPSESHV 85
A + L Q +K W + +L L+ +A ++ + + LP E
Sbjct: 1 AEKQLEQFEKQDPGFWSKLLQ-ILSDTSSDLQVRQLAALYLKNLITRHWNQLSLPPEEKE 59
Query: 86 SLRDSLIEHL 95
+R++L+ L
Sbjct: 60 QIRNNLLNLL 69
>gnl|CDD|238937 cd01979, Pchlide_reductase_N, Pchlide_reductase_N: N protein of the
NB protein complex of Protochlorophyllide
(Pchlide)_reductase. Pchlide reductase catalyzes the
reductive formation of chlorophyllide (chlide) from
protochlorophyllide (pchlide) during biosynthesis of
chlorophylls and bacteriochlorophylls. This group
contains both the light-independent Pchlide reductase
(DPOR) and light-dependent Pchlide reductase (LPOR).
Angiosperms contain only LPOR, cyanobacteria, algae and
gymnosperms contain both DPOR and LPOR, primitive
anoxygenic photosynthetic bacteria contain only DPOR. NB
is structurally similar to the FeMo protein of
nitrogenase, forming an N2B2 heterotetramer. N and B are
homologous to the FeMo alpha and beta subunits
respectively. Also in common with nitrogenase in vitro
DPOR activity requires ATP hydrolysis and dithoionite or
ferredoxin as electron donor. The NB protein complex may
serve as a catalytic site for Pchlide reduction similar
to MoFe for nitrogen reduction.
Length = 396
Score = 31.6 bits (72), Expect = 1.9
Identities = 24/94 (25%), Positives = 40/94 (42%), Gaps = 11/94 (11%)
Query: 669 IVVLYSKHPHSSFLYLGSILVDEYATSHCVSGLLDMVQAFLPPTY--AILQEEDGLKNHP 726
+ LY K S FL +G+ +H + L V F P + A L+E D L
Sbjct: 17 VAWLYQKIEDSFFLVVGT-----KTCAHFLQNALG-VMIFAEPRFAMAELEEGD-LSALL 69
Query: 727 DTVDDLFRLCTRFLQRAP--IAFLTSSFISSVMQ 758
+ +L R+ T+ + + FL S + V++
Sbjct: 70 NDYAELDRVVTQIKRDRNPSVIFLIGSCTTEVIK 103
>gnl|CDD|218726 pfam05742, NRDE, NRDE protein. In eukaryotes this family is
predicted to play a role in protein secretion and Golgi
organisation. In plants this family includes Solanum
habrochaites Cwp, which is involved in water
permeability in the cuticles of fruit. Mouse T10 has
been found to be expressed during early embryogenesis in
mice. This protein contains a conserved NRDE motif.
Length = 267
Score = 30.0 bits (68), Expect = 4.7
Identities = 13/48 (27%), Positives = 21/48 (43%)
Query: 74 NAFFELPSESHVSLRDSLIEHLCRTNDTSGKNIITQLALALADLALQM 121
N+ + P R L E L +++ S + II QL LA+ +
Sbjct: 153 NSLLDTPWPKVRVGRKLLEERLEASDELSVETIIQQLLEILANTSAFA 200
>gnl|CDD|202161 pfam02214, K_tetra, K+ channel tetramerisation domain. The
N-terminal, cytoplasmic tetramerisation domain (T1) of
voltage-gated K+ channels encodes molecular determinants
for subfamily-specific assembly of alpha-subunits into
functional tetrameric channels. It is distantly related
to the BTB/POZ domain pfam00651.
Length = 92
Score = 28.3 bits (64), Expect = 5.0
Identities = 10/23 (43%), Positives = 11/23 (47%), Gaps = 5/23 (21%)
Query: 472 IDKHPHTLETILNFL-----LHC 489
D+ P ETILNF LH
Sbjct: 44 FDRSPKHFETILNFYRTGGKLHR 66
>gnl|CDD|149958 pfam09088, MIF4G_like, MIF4G like. Members of this family are
involved in mediating U snRNA export from the nucleus.
They adopt a highly helical structure, wherein the
polypeptide chain forms a right-handed solenoid. At the
tertiary level, the domain is composed of a superhelical
arrangement of successive antiparallel pairs of helices.
Length = 189
Score = 28.9 bits (65), Expect = 8.0
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 8/50 (16%)
Query: 426 SVAKNVLPEENDVVPK--VVEAIL----HLPPSTHIAVRYTSLLLLGELC 469
SV K + P E+ + +VE IL LP + + Y SLL+ ELC
Sbjct: 51 SVDKLLDPPESTWKLEDVIVETILGELFQLPTPPYKPIYYHSLLI--ELC 98
>gnl|CDD|222728 pfam14390, DUF4420, Domain of unknown function (DUF4420). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria and archaea.
Proteins in this family are typically between 310 and
334 amino acids in length.
Length = 305
Score = 29.2 bits (66), Expect = 9.0
Identities = 14/55 (25%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 572 LCELIEKQIKPEKNKK---SDPVIWLDRLAAIFKHTSPRIMSEPHPCQGVITELW 623
LCE + ++I+ ++ + S V L++ + ++ + +SE QG+I EL
Sbjct: 93 LCEDLIERIEDAEDPRDLLSAVVERLEKWQELLRNKGRKGLSE-EEQQGLIGELL 146
>gnl|CDD|151993 pfam11557, DUF3233, Protein of unknown function (DUF3233). This is
a bacterial family of uncharacterized proteins.
Length = 327
Score = 29.3 bits (66), Expect = 9.0
Identities = 29/122 (23%), Positives = 48/122 (39%), Gaps = 19/122 (15%)
Query: 9 TVYAVVHTLYLNPNKTEKEKASQWLHQLQKSIYAWKIADEMLLHQN----ELGLEAVYFS 64
TVY + +T L+ S+W H+LQ + D++ L + + + VY +
Sbjct: 82 TVYTLPYTFALSEEG------SEWSHELQVRLSYVHTEDDLSLLDDSSISDSIKDEVYGA 135
Query: 65 AQTMRQKVQNAFFELPSESHVSLRDSLIEHLCRTNDTSGKN--IITQLALALADLALQMS 122
A R K Q E + +L + HL +T N + + L L + S
Sbjct: 136 AIEYRYKYQ--LTE-----NWTLSVGIGAHLMHYRNTYTYNSDVSKSYSSILDGLLVNTS 188
Query: 123 AW 124
AW
Sbjct: 189 AW 190
>gnl|CDD|192367 pfam09758, FPL, Uncharacterized conserved protein. This entry
represents an N-terminal region of approximately 150
residues of a family of proteins of unknown function. It
contains a highly conserved FPL motif.
Length = 149
Score = 28.3 bits (64), Expect = 9.1
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 9/52 (17%)
Query: 465 LGELCE---WIDKHPHTL------ETILNFLLHCLQQPGLASVTANALQSIS 507
L E+ E W DK+ + I++ L L + V LQ++S
Sbjct: 1 LREIAEYLIWGDKNDDDFFDYFLEKNIMSTFLRILTNLTPSEVKIQILQTVS 52
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
0.321 0.134 0.398
Gapped
Lambda K H
0.267 0.0764 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 45,554,288
Number of extensions: 4471722
Number of successful extensions: 3964
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3957
Number of HSP's successfully gapped: 22
Length of query: 912
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 806
Effective length of database: 6,236,078
Effective search space: 5026278868
Effective search space used: 5026278868
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 (21.9 bits)
S2: 64 (28.4 bits)