RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17885
(95 letters)
>gnl|CDD|222120 pfam13426, PAS_9, PAS domain.
Length = 101
Score = 33.9 bits (78), Expect = 0.002
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 40 FLLANAQIVDFPIVYCNESFCKISGYNRAEV 70
L+ + D IVY N++ ++ GY R E+
Sbjct: 1 ILVLDP---DGRIVYANDAALRLLGYTREEL 28
>gnl|CDD|237427 PRK13559, PRK13559, hypothetical protein; Provisional.
Length = 361
Score = 34.4 bits (79), Expect = 0.003
Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 11/55 (20%)
Query: 27 YDERQKNGHPDSSFLLANAQ----IV-------DFPIVYCNESFCKISGYNRAEV 70
+D R G F A Q + D PIV N++F ++GY EV
Sbjct: 32 HDPRDFRGASGRLFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEV 86
>gnl|CDD|237426 PRK13558, PRK13558, bacterio-opsin activator; Provisional.
Length = 665
Score = 34.0 bits (78), Expect = 0.006
Identities = 12/29 (41%), Positives = 22/29 (75%)
Query: 42 LANAQIVDFPIVYCNESFCKISGYNRAEV 70
+A+A + D P++Y N++F +I+GY+ EV
Sbjct: 163 IADATLPDEPLIYINDAFERITGYSPDEV 191
>gnl|CDD|219844 pfam08447, PAS_3, PAS fold. The PAS fold corresponds to the
structural domain that has previously been defined as
PAS and PAC motifs. The PAS fold appears in archaea,
eubacteria and eukarya.
Length = 90
Score = 30.4 bits (69), Expect = 0.042
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 52 IVYCNESFCKISGYNRAEVPSDYD 75
I+Y + F +I GY E+ S Y+
Sbjct: 1 IIYWSPRFEEILGYTPEELKSSYE 24
>gnl|CDD|232884 TIGR00229, sensory_box, PAS domain S-box. The PAS domain was
previously described. This sensory box, or S-box domain
occupies the central portion of the PAS domain but is
more widely distributed. It is often tandemly repeated.
Known prosthetic groups bound in the S-box domain
include heme in the oxygen sensor FixL, FAD in the
redox potential sensor NifL, and a 4-hydroxycinnamyl
chromophore in photoactive yellow protein. Proteins
containing the domain often contain other regulatory
domains such as response regulator or sensor histidine
kinase domains. Other S-box proteins include
phytochromes and the aryl hydrocarbon receptor nuclear
translocator [Regulatory functions, Small molecule
interactions].
Length = 124
Score = 30.7 bits (70), Expect = 0.054
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 52 IVYCNESFCKISGYNRAEV 70
I+Y N +F +I GY+ E+
Sbjct: 25 ILYVNPAFEEIFGYSAEEL 43
>gnl|CDD|238075 cd00130, PAS, PAS domain; PAS motifs appear in archaea,
eubacteria and eukarya. Probably the most surprising
identification of a PAS domain was that in EAG-like
K+-channels. PAS domains have been found to bind
ligands, and to act as sensors for light and oxygen in
signal transduction.
Length = 103
Score = 29.9 bits (67), Expect = 0.092
Identities = 9/43 (20%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 49 DFPIVYCNESFCKISGYNRAEVPSDYDIPTYNLLVGSYLQSLY 91
D I+Y N + ++ GY+ E+ +L+ + L
Sbjct: 11 DGRILYANPAAEQLLGYSPEEL---IGKSLLDLIHPEDREELR 50
>gnl|CDD|216228 pfam00989, PAS, PAS fold. The PAS fold corresponds to the
structural domain that has previously been defined as
PAS and PAC motifs. The PAS fold appears in archaea,
eubacteria and eukarya.
Length = 113
Score = 29.7 bits (67), Expect = 0.11
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 52 IVYCNESFCKISGYNRAEV 70
I+Y N + ++ G +R EV
Sbjct: 23 ILYVNAAAEELLGLSREEV 41
>gnl|CDD|214512 smart00091, PAS, PAS domain. PAS motifs appear in archaea,
eubacteria and eukarya. Probably the most surprising
identification of a PAS domain was that in EAG-like
K+-channels.
Length = 67
Score = 28.9 bits (65), Expect = 0.12
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 49 DFPIVYCNESFCKISGYNRAEV 70
D I+Y N + ++ GY+ E+
Sbjct: 20 DGRILYANPAAEELLGYSPEEL 41
>gnl|CDD|237425 PRK13557, PRK13557, histidine kinase; Provisional.
Length = 540
Score = 29.6 bits (67), Expect = 0.17
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 49 DFPIVYCNESFCKISGYNRAEV 70
D PIV+ N +F +++GY E+
Sbjct: 52 DNPIVFANRAFLEMTGYAAEEI 73
>gnl|CDD|221967 pfam13188, PAS_8, PAS domain.
Length = 64
Score = 27.5 bits (61), Expect = 0.32
Identities = 8/39 (20%), Positives = 14/39 (35%)
Query: 52 IVYCNESFCKISGYNRAEVPSDYDIPTYNLLVGSYLQSL 90
I+Y N + ++ GY + L L+ L
Sbjct: 22 ILYANPAALELLGYELLGELLGELLDDLEALAEEALELL 60
>gnl|CDD|225112 COG2202, AtoS, FOG: PAS/PAC domain [Signal transduction
mechanisms].
Length = 232
Score = 28.7 bits (62), Expect = 0.38
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 49 DFPIVYCNESFCKISGYNRAEV 70
D I+Y N + ++ GY+ E
Sbjct: 131 DGRILYANPAAEELLGYSPEEE 152
>gnl|CDD|106506 PRK13560, PRK13560, hypothetical protein; Provisional.
Length = 807
Score = 26.9 bits (59), Expect = 1.8
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 4/35 (11%)
Query: 36 PDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEV 70
D +F D + CN++ C G+ R E+
Sbjct: 214 ADPAFWKDE----DAKVFGCNDAACLACGFRREEI 244
>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis). This
nucleolar family of proteins are involved in 60S
ribosomal biogenesis. They are specifically involved in
the processing beyond the 27S stage of 25S rRNA
maturation. This family contains sequences that bear
similarity to the glioma tumour suppressor candidate
region gene 2 protein (p60). This protein has been
found to interact with herpes simplex type 1 regulatory
proteins.
Length = 387
Score = 26.6 bits (59), Expect = 1.8
Identities = 7/15 (46%), Positives = 9/15 (60%), Gaps = 1/15 (6%)
Query: 6 NKRGWRKNT-APEVE 19
K+ WRKN +VE
Sbjct: 4 GKKAWRKNIDITDVE 18
>gnl|CDD|188475 TIGR03960, rSAM_fuse_unch, radical SAM family uncharacterized
protein. This model describes a radical SAM protein, or
protein region, regularly found paired with or fused to
a region described by TIGR03936. PSI-BLAST analysis of
TIGR03936 suggests a relationship to the tRNA
pseudouridine synthase TruA, suggesting that this system
may act in RNA modification [Unknown function, Enzymes
of unknown specificity].
Length = 605
Score = 26.5 bits (59), Expect = 2.2
Identities = 18/54 (33%), Positives = 22/54 (40%), Gaps = 19/54 (35%)
Query: 27 YDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSDYDIPTYN 80
Y + +K G FL A+I P VY VPS YD+ TYN
Sbjct: 172 YKKAKKEGGTREEFLERAAKI---PGVY---------------VPSLYDV-TYN 206
>gnl|CDD|227361 COG5028, COG5028, Vesicle coat complex COPII, subunit SEC24/subunit
SFB2/subunit SFB3 [Intracellular trafficking and
secretion].
Length = 861
Score = 26.3 bits (58), Expect = 3.2
Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 2/53 (3%)
Query: 38 SSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSDYDIPTYNLLVGSYLQSL 90
S+ L A + P++ + K S + PSD I N L L+ L
Sbjct: 654 STQLPLPANLKLLPLLM--LALLKSSAFRSGSTPSDIRISALNRLTSLPLKQL 704
>gnl|CDD|182797 PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase;
Provisional.
Length = 743
Score = 25.9 bits (57), Expect = 3.8
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 19 ELVRRTYMYDERQKNGHPDSSFLL 42
E + T+ Y +Q GHPD+S LL
Sbjct: 33 ERLAETWAYCLQQTQGHPDASLLL 56
>gnl|CDD|239846 cd04381, RhoGap_RalBP1, RhoGap_RalBP1: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain
present in RalBP1 proteins, also known as RLIP, RLIP76
or cytocentrin. RalBP1 plays an important role in
endocytosis during interphase. During mitosis, RalBP1
transiently associates with the centromere and has been
shown to play an essential role in the proper assembly
of the mitotic apparatus. RalBP1 is an effector of the
Ral GTPase which itself is an effector of Ras. RalBP1
contains a RhoGAP domain, which shows weak activity
towards Rac1 and Cdc42, but not towards Ral, and a Ral
effector domain binding motif. 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 = 182
Score = 25.5 bits (56), Expect = 4.3
Identities = 26/107 (24%), Positives = 37/107 (34%), Gaps = 45/107 (42%)
Query: 15 APEVELVRRTYMYDERQKNGHPDSSFLLANAQIVDFPIVY-------------CNESFCK 61
A V R+ +D +D P+V+ C E K
Sbjct: 3 ASLSLAVERSRCHDG------------------IDLPLVFRECIDYVEKHGMKC-EGIYK 43
Query: 62 ISG-----------YNRAEVP--SDYDIPTYNLLVGSYLQSLYLPLI 95
+SG YNR E P +Y+ PT L+ YL+ L PL+
Sbjct: 44 VSGIKSKVDELKAAYNRRESPNLEEYEPPTVASLLKQYLRELPEPLL 90
>gnl|CDD|238898 cd01917, ACS_2, Acetyl-CoA synthase (ACS), also known as
acetyl-CoA decarbonylase, is found in acetogenic and
methanogenic organisms and is responsible for the
synthesis and breakdown of acetyl-CoA. ACS forms a
heterotetramer with carbon monoxide dehydrogenase
(CODH) consisting of two ACS and two CODH subunits.
CODH reduces carbon dioxide to carbon monoxide and ACS
then synthesizes acetyl-CoA from carbon monoxide, CoA,
and a methyl group donated by another protein (CoFeSP).
ACS has three structural domains, an N-terminal
rossman fold domain with a helical region at its
N-terminus which interacts with CODH, and two alpha +
beta fold domains. A Ni-Fe-S center referred to as the
A-cluster is located in the C-terminal domain. A large
cavity exists between the three domains which may bind
CoA.
Length = 287
Score = 25.2 bits (55), Expect = 5.7
Identities = 9/39 (23%), Positives = 17/39 (43%), Gaps = 8/39 (20%)
Query: 17 EVELVRRTYMYDERQKNGHPDSSFLLANAQIVDFPIVYC 55
E+ L + Y G+PD+++ L P++ C
Sbjct: 14 EILLNKAILEYGPDHPVGYPDTAYNL--------PVIRC 44
>gnl|CDD|227746 COG5459, COG5459, Predicted rRNA methylase [Translation, ribosomal
structure and biogenesis].
Length = 484
Score = 25.3 bits (55), Expect = 5.9
Identities = 7/33 (21%), Positives = 10/33 (30%)
Query: 3 EMGNKRGWRKNTAPEVELVRRTYMYDERQKNGH 35
E G G+ + L+ DE H
Sbjct: 225 ERGTPAGFERILRARQILLAPGNFPDEFNYFAH 257
>gnl|CDD|206583 pfam14416, PMR5N, PMR5 N terminal Domain. The plant family with
PMR5, ESK1, TBL3 etc have a N-terminal C rich predicted
sugar binding domain followed by the PC-Esterase (acyl
esterase) domain.
Length = 55
Score = 23.4 bits (51), Expect = 9.5
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 31 QKNGHPDSSFL 41
QKNG PDS +L
Sbjct: 35 QKNGRPDSDYL 45
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
0.319 0.137 0.420
Gapped
Lambda K H
0.267 0.0686 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,850,598
Number of extensions: 381366
Number of successful extensions: 248
Number of sequences better than 10.0: 1
Number of HSP's gapped: 248
Number of HSP's successfully gapped: 22
Length of query: 95
Length of database: 10,937,602
Length adjustment: 62
Effective length of query: 33
Effective length of database: 8,187,654
Effective search space: 270192582
Effective search space used: 270192582
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 (21.7 bits)
S2: 53 (24.3 bits)