RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7075
(135 letters)
>gnl|CDD|216028 pfam00621, RhoGEF, RhoGEF domain. Guanine nucleotide exchange
factor for Rho/Rac/Cdc42-like GTPases Also called
Dbl-homologous (DH) domain. It appears that pfam00169
domains invariably occur C-terminal to RhoGEF/DH
domains.
Length = 179
Score = 72.6 bits (179), Expect = 4e-17
Identities = 39/103 (37%), Positives = 54/103 (52%), Gaps = 2/103 (1%)
Query: 5 LCRQVFEKPLKESKILTREEHGQIFVNWKEIIVCNHMFLRALRVRRDMSSKGDIRMIGDI 64
+ +VF KPL+ES IL+ EE IF N +EI+ + FL L R + DI+ IGDI
Sbjct: 18 ILVEVFLKPLRESPILSEEEIKTIFSNIEEILELHQEFLEELEER--LEEWPDIQRIGDI 75
Query: 65 LCEHLPRMTAYVRFCSCQLSAAALLQKLTDQSPEFKTISKKCR 107
+ P Y +CS A LL+KL ++P F K+C
Sbjct: 76 FLKFAPFFKVYSTYCSNYPRALELLKKLRKKNPRFAKFLKECE 118
>gnl|CDD|238091 cd00160, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous
(DH) domain. It appears that PH domains invariably occur
C-terminal to RhoGEF/DH domains.
Length = 181
Score = 67.7 bits (166), Expect = 4e-15
Identities = 43/134 (32%), Positives = 62/134 (46%), Gaps = 6/134 (4%)
Query: 5 LCRQVFEKPL-KESKILTREEHGQIFVNWKEIIVCNHMFLRALRVRRDMSSKGDIRMIGD 63
L +VF KPL KE L+ EE +F N +EI + +FL++L R + K IGD
Sbjct: 21 LLVEVFLKPLDKELLPLSPEEVELLFGNIEEIYEFHRIFLKSLEERVEEWDK-SGPRIGD 79
Query: 64 ILCEHLPRMTAYVRFCSCQLSAAALLQKLTDQSPEFKTISKKCRWISRIFLLETETISP- 122
+ + P Y +CS A LL+KL + F+ +K LE+ + P
Sbjct: 80 VFLKLAPFFKIYSEYCSNHPDALELLKKLKKFNKFFQEFLEKAESECGRLKLESLLLKPV 139
Query: 123 --LLKLISPLLKEI 134
L K LLKE+
Sbjct: 140 QRLTKYPL-LLKEL 152
>gnl|CDD|214619 smart00325, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases. Guanine nucleotide exchange
factor for Rho/Rac/Cdc42-like GTPases Also called
Dbl-homologous (DH) domain. It appears that PH domains
invariably occur C-terminal to RhoGEF/DH domains.
Improved coverage.
Length = 180
Score = 59.6 bits (145), Expect = 4e-12
Identities = 33/103 (32%), Positives = 49/103 (47%), Gaps = 3/103 (2%)
Query: 5 LCRQVFEKPL-KESKILTREEHGQIFVNWKEIIVCNHMFLRALRVRRDMSSKGDIRMIGD 63
L +VF KPL KE K+L+ E +F N +EI + FL L R + + IGD
Sbjct: 18 LLVEVFLKPLKKELKLLSPNELETLFGNIEEIYEFHRDFLDELEERIEEWD-DSVERIGD 76
Query: 64 ILCEHLPRMTAYVRFCSCQLSAAALLQKLTDQSPEFKTISKKC 106
+ + Y +CS A LL+KL ++P F+ K+
Sbjct: 77 VFLKLEEFFKIYSEYCSNHPDALELLKKL-KKNPRFQKFLKEI 118
>gnl|CDD|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases [Signal transduction
mechanisms].
Length = 1175
Score = 36.0 bits (83), Expect = 0.003
Identities = 24/97 (24%), Positives = 43/97 (44%), Gaps = 6/97 (6%)
Query: 7 RQVFEKPLKESKILTREEHGQ----IFVNWKEIIVCNHMFLRALRVRRDMSSKGDIRMIG 62
R + KPL+ES I+ +F N EI N L+AL R+ + I
Sbjct: 507 RDTWIKPLEESNIIPENARRNFIKHVFANINEIYAVNSKLLKALTNRQ--CLSPIVNGIA 564
Query: 63 DILCEHLPRMTAYVRFCSCQLSAAALLQKLTDQSPEF 99
DI +++P+ ++++ + Q A ++ +P F
Sbjct: 565 DIFLDYVPKFEPFIKYGASQPYAKYEFEREKSVNPNF 601
>gnl|CDD|217257 pfam02867, Ribonuc_red_lgC, Ribonucleotide reductase, barrel
domain.
Length = 516
Score = 29.4 bits (67), Expect = 0.55
Identities = 27/107 (25%), Positives = 39/107 (36%), Gaps = 32/107 (29%)
Query: 34 EIIVCNHMFLRALR------VRRDMSSKGDIRMIGDILCEHLPR--------MTAYVRFC 79
E +V N LR LR ++ +++ G ++ I +I E ++
Sbjct: 412 EFLVVNPYLLRDLRELWSEEMKNELAYNGSVQPIPEIPEEIKALYKTAFDIDPKGHID-- 469
Query: 80 SCQLSAAALLQKLTDQSPEFKTISKKCRWISRIFLLETETISPLLKL 126
AA Q DQS ISK +FL E T S L L
Sbjct: 470 -----MAAARQPFVDQS-----ISKT------LFLPEDATASDLKSL 500
>gnl|CDD|218169 pfam04604, L_biotic_typeA, Type-A lantibiotic. Lantibiotics are
antibiotic peptides distinguished by the presence of the
rare thioether amino acids lanthionine and/or
methyl-lanthionine. They are produced by Gram-positive
bacteria as gene-encoded precursor peptides and undergo
post-translational modification to generate the mature
peptide. Based on their structural and functional
features lantibiotics are currently divided into two
major groups: the flexible amphiphilic type-A and the
rather rigid and globular type-B. Type-A lantibiotics
act primarily by pore formation in the bacterial
membrane by a mechanism involving the interaction with
specific docking molecules such as the membrane
precursor lipid II.
Length = 50
Score = 27.0 bits (60), Expect = 0.73
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 10/44 (22%)
Query: 82 QLSAAALLQKLTDQSPE----------FKTISKKCRWISRIFLL 115
Q A LQ+++++ + KTIS +CR S F+
Sbjct: 4 QTEALNSLQEVSEEELDQILGGKGSGVIKTISHECRMNSWQFVF 47
>gnl|CDD|226272 COG3749, COG3749, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 167
Score = 28.1 bits (63), Expect = 0.93
Identities = 14/58 (24%), Positives = 28/58 (48%), Gaps = 7/58 (12%)
Query: 44 RALRVRRDMSSKGDIRMIGDILCEHLPRMTAYVR--FCSCQLSAAALLQKLTDQSPEF 99
LR R + +G++R +GD+L + LP M +R F + + +++L +
Sbjct: 95 ELLRSR--LGFQGELRAVGDVLIDQLPFM---LRCGFDAFAVRNDVAIERLLEGLGGI 147
>gnl|CDD|191441 pfam06073, DUF934, Bacterial protein of unknown function
(DUF934). This family consists of several bacterial
proteins of unknown function. One of the members of
this family, BMEI1764, is thought to be an
oxidoreductase.
Length = 110
Score = 27.5 bits (62), Expect = 1.1
Identities = 19/58 (32%), Positives = 26/58 (44%), Gaps = 7/58 (12%)
Query: 44 RALRVRRDMSSKGDIRMIGDILCEHLPRMTAYVR--FCSCQLSAAALLQKLTDQSPEF 99
R LR R KG++R +GD+L + L M +R F S L A L+ F
Sbjct: 40 RLLRERYGY--KGELRAVGDVLRDQLFFM---LRCGFDSFALRADKDLEDALKALDRF 92
>gnl|CDD|236324 PRK08652, PRK08652, acetylornithine deacetylase; Provisional.
Length = 347
Score = 28.6 bits (64), Expect = 1.1
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 1/68 (1%)
Query: 67 EHLPRMTAYVRFCSCQLSAAALLQKLTDQSPEFKTISKKCRWISRIFLLETETISPLLKL 126
E L ++ ++ +Q++ SPE+ +I CR + + +L
Sbjct: 184 EMLEKLKELLKALGKYFDPHIGIQEIIGGSPEY-SIPALCRLRLDARIPPEVEVEDVLDE 242
Query: 127 ISPLLKEI 134
I P+L E
Sbjct: 243 IDPILDEY 250
>gnl|CDD|227546 COG5221, DOP1, Dopey and related predicted leucine zipper
transcription factors [Transcription].
Length = 1618
Score = 27.2 bits (60), Expect = 3.5
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 2/40 (5%)
Query: 92 LTDQSPEFKTISKKCRWISRIFLLETETISPLLKLISPLL 131
D+SP T WIS + L P K+++ L
Sbjct: 710 HDDRSPRAGTREMI--WISSLNKLSGIGRVPNRKVLTENL 747
>gnl|CDD|240521 cd13394, Syo1_like, Fungal symportin 1 (syo1) and similar proteins.
This family of eukaryotic proteins includes
Saccharomyces cerevisiae Ydl063c and Chaetomium
thermophilum Syo1, which mediate the co-import of two
ribosomal proteins, Rpl5 and Rpl11 (which both interact
with 5S rRNA) into the nucleus. Import precedes their
association with rRNA and subsequent ribosome assembly
in the nucleolus. The primary structure of syo1 is a
mixture of Armadillo- (ARM, N-terminal part of syo1) and
HEAT-repeats (C-terminal part of syo1).
Length = 597
Score = 26.1 bits (58), Expect = 6.4
Identities = 10/48 (20%), Positives = 19/48 (39%), Gaps = 1/48 (2%)
Query: 80 SCQLSAAALLQKLTDQSPEF-KTISKKCRWISRIFLLETETISPLLKL 126
S +A L L++ +PEF +S + + + + S L
Sbjct: 205 SLFNAALQCLYTLSEDNPEFIDKLSSDPEILGNLLDIVSSDPSSSNIL 252
>gnl|CDD|185485 PTZ00156, PTZ00156, 60S ribosomal protein L11; Provisional.
Length = 172
Score = 25.8 bits (57), Expect = 6.8
Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 4/29 (13%)
Query: 85 AAALLQKLTDQSPEFKTISKKCRWISRIF 113
AA +L++LT Q P F K R+ R F
Sbjct: 32 AAKVLEQLTGQKPVF----SKARYTVRSF 56
>gnl|CDD|213261 cd03294, ABC_Pro_Gly_Betaine, ATP-binding cassette domain of the
osmoprotectant proline/glycine betaine uptake system.
This family comprises the glycine betaine/L-proline ATP
binding subunit in bacteria and its equivalents in
archaea. This transport system belong to the larger
ATP-Binding Cassette (ABC) transporter superfamily. The
characteristic feature of these transporters is the
obligatory coupling of ATP hydrolysis to substrate
translocation. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 269
Score = 26.1 bits (58), Expect = 7.2
Identities = 8/29 (27%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 25 HGQIFVNWKEIIVCNHMFLRALRVRRDMS 53
G++ ++ ++I + LR LR R+ +S
Sbjct: 78 SGKVLIDGQDIAAMSRKELRELR-RKKIS 105
>gnl|CDD|226643 COG4175, ProV, ABC-type proline/glycine betaine transport system,
ATPase component [Amino acid transport and metabolism].
Length = 386
Score = 25.8 bits (57), Expect = 8.3
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 25 HGQIFVNWKEIIVCNHMFLRALRVRRDMS 53
G+I V+ K+I + LR LR R+ +S
Sbjct: 82 RGEILVDGKDIAKLSAAELRELR-RKKIS 109
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
0.328 0.139 0.420
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,853,557
Number of extensions: 601137
Number of successful extensions: 614
Number of sequences better than 10.0: 1
Number of HSP's gapped: 610
Number of HSP's successfully gapped: 23
Length of query: 135
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 48
Effective length of database: 7,078,804
Effective search space: 339782592
Effective search space used: 339782592
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.2 bits)