RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8476
(421 letters)
>gnl|CDD|214500 smart00065, GAF, Domain present in phytochromes and cGMP-specific
phosphodiesterases. Mutations within these domains in
PDE6B result in autosomal recessive inheritance of
retinitis pigmentosa.
Length = 149
Score = 66.6 bits (163), Expect = 3e-13
Identities = 28/93 (30%), Positives = 47/93 (50%), Gaps = 4/93 (4%)
Query: 289 IAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLIN 348
+A VA TG+ LNI DV + + ++ R L +P+ + ++GV L N
Sbjct: 58 LAGRVAETGRPLNIPDVE---ADPLFAEDLLGRYQGVRSFLAVPLVADGE-LVGVLALHN 113
Query: 349 KVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYE 381
K + +PFT+ D + +A A + + N Q+YE
Sbjct: 114 KKSPRPFTEEDEELLQALANQLAIALANAQLYE 146
Score = 50.1 bits (120), Expect = 2e-07
Identities = 35/175 (20%), Positives = 59/175 (33%), Gaps = 57/175 (32%)
Query: 55 NLECLVTKIMTEARDLLKCERCAVFLLKSETSEASHLERILERPGRVISERKPLCRRESN 114
+LE L+ I+ E R LL +R ++L+ E E +L ++
Sbjct: 1 DLEELLQTILEELRQLLGADRVLIYLV----DENDRGELVLV---------------AAD 41
Query: 115 NVDIEDILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQ 174
+ + + P D +A VA TG+
Sbjct: 42 GLTLPTLGIRFPLDEGLA----------------------------------GRVAETGR 67
Query: 175 ILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKISER 229
LNI DV + + ++ R L +P+ + ++GV L NK S R
Sbjct: 68 PLNIPDVE---ADPLFAEDLLGRYQGVRSFLAVPLVADGE-LVGVLALHNKKSPR 118
>gnl|CDD|216590 pfam01590, GAF, GAF domain. This domain is present in
cGMP-specific phosphodiesterases, adenylyl and guanylyl
cyclases, phytochromes, FhlA and NifA. Adenylyl and
guanylyl cyclases catalyze ATP and GTP to the second
messengers cAMP and cGMP, respectively, these products
up-regulating catalytic activity by binding to the
regulatory GAF domain(s). The opposite hydrolysis
reaction is catalyzed by phosphodiesterase.
cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes
the conversion of guanosine 3',5'-cyclic phosphate to
guanosine 5'-phosphate. Here too, cGMP regulates
catalytic activity by GAF-domain binding. Phytochromes
are regulatory photoreceptors in plants and bacteria
which exist in two thermally-stable states that are
reversibly inter-convertible by light: the Pr state
absorbs maximally in the red region of the spectrum,
while the Pfr state absorbs maximally in the far-red
region. This domain is also found in FhlA (formate
hydrogen lyase transcriptional activator) and NifA, a
transcriptional activator which is required for
activation of most Nif operons which are directly
involved in nitrogen fixation. NifA interacts with
sigma-54.
Length = 143
Score = 46.8 bits (111), Expect = 2e-06
Identities = 20/89 (22%), Positives = 37/89 (41%), Gaps = 4/89 (4%)
Query: 288 TIAKYVASTGQILNIGDVPSWMR--EEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQ 345
I V + G+ + + DV R + D R L +P+ G + +IGV
Sbjct: 57 GIVGEVIAGGRPIVVPDVQDDPRFSDLTALASDFLRGLGIRSCLAVPLKGGGE-LIGVLV 115
Query: 346 LINKVTRQPFTDCDVSIFEAFAIFCGLGI 374
L + R FT+ ++ + +A A + +
Sbjct: 116 LHSTSPRA-FTEEELELLQALADQVAIAL 143
Score = 40.2 bits (94), Expect = 4e-04
Identities = 32/173 (18%), Positives = 54/173 (31%), Gaps = 56/173 (32%)
Query: 55 NLECLVTKIMTEARDLLKCERCAVFLLKSETSEASHLERILERPGRVISERKPLCRRESN 114
+LE L+ I+ E R+LL +RCA+ L ++
Sbjct: 1 DLEELLQTILEELRELLGADRCAILLADADGLL--------------------------- 33
Query: 115 NVDIEDILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQ 174
+ + D +A + GG GE V + G+
Sbjct: 34 ---LYLVAGDGLSDIPLAARRLPLGGGIVGE-----------------------VIAGGR 67
Query: 175 ILNIGDVPSWMR--EEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINK 225
+ + DV R + D R L +P+ G + +IGV L +
Sbjct: 68 PIVVPDVQDDPRFSDLTALASDFLRGLGIRSCLAVPLKGGGE-LIGVLVLHST 119
>gnl|CDD|225113 COG2203, FhlA, FOG: GAF domain [Signal transduction mechanisms].
Length = 175
Score = 40.0 bits (93), Expect = 8e-04
Identities = 12/93 (12%), Positives = 34/93 (36%), Gaps = 5/93 (5%)
Query: 292 YVASTGQILNIGDVPSWMREEVCNDEDEESDF-TTRCILCMPIFNGQKTVIGVAQLINKV 350
G+ + + D+ + D R L +P+ + + + + +
Sbjct: 83 IALREGRPVVVEDILQ---DPRFRDNPLVLLEPPIRSYLGVPLIAQGELLGLLC-VHDSE 138
Query: 351 TRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENA 383
R+ +++ ++ + E A + I ++YE
Sbjct: 139 PRRQWSEEELELLEELAEQVAIAIERARLYEEL 171
>gnl|CDD|222174 pfam13492, GAF_3, GAF domain.
Length = 129
Score = 30.9 bits (70), Expect = 0.49
Identities = 11/55 (20%), Positives = 24/55 (43%), Gaps = 2/55 (3%)
Query: 59 LVTKIMTEARDLLKCERCAVFLLKSETSEASHLERIL--ERPGRVISERKPLCRR 111
L+ +++ ++L +R A++LL + E + R + E PL +
Sbjct: 5 LLERLLELLAEILGADRAALYLLDEDGLELRLVAGSGGEPRLSESLPEDSPLAQW 59
>gnl|CDD|234396 TIGR03919, T7SS_EccB, type VII secretion protein EccB,
Actinobacterial. This model represents the
transmembrane protein EccB of the actinobacterial flavor
of type VII secretion systems. Species such as
Mycobacterium tuberculosis have several instances of
this system per genome, designated EccB1, EccB2, etc.
This model does not identify functionally related
proteins in the Firmicutes such as Staphylococcus aureus
and Bacillus anthracis [Protein fate, Protein and
peptide secretion and trafficking].
Length = 456
Score = 30.7 bits (70), Expect = 1.5
Identities = 14/56 (25%), Positives = 19/56 (33%)
Query: 126 PEDPSIAFSTVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDV 181
PE P +A + G PG L P +V + YV + I V
Sbjct: 230 PEGPPLAAPAIPGAGAPGPVLLGGLPVGSVVRVSTAGGGAQYYVVLADGLQPITPV 285
Score = 30.7 bits (70), Expect = 1.5
Identities = 14/56 (25%), Positives = 19/56 (33%)
Query: 250 PEDPSIAFSTVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDV 305
PE P +A + G PG L P +V + YV + I V
Sbjct: 230 PEGPPLAAPAIPGAGAPGPVLLGGLPVGSVVRVSTAGGGAQYYVVLADGLQPITPV 285
>gnl|CDD|143427 cd07109, ALDH_AAS00426, Uncharacterized Saccharopolyspora spinosa
aldehyde dehydrogenase (AAS00426)-like.
Uncharacterized aldehyde dehydrogenase of
Saccharopolyspora spinosa (AAS00426) and other similar
sequences, are present in this CD.
Length = 454
Score = 30.3 bits (69), Expect = 2.3
Identities = 16/38 (42%), Positives = 24/38 (63%), Gaps = 4/38 (10%)
Query: 36 FERNQILLKLARSIF---EEQSNLECLVT-KIMTEARD 69
ER ++LL++AR I +E + LE L T K +T+AR
Sbjct: 42 AERGRLLLRIARLIREHADELARLESLDTGKPLTQARA 79
>gnl|CDD|187886 cd09756, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily
protein Cas5. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas5 is a RAMP superfamily protein; Subunit of the
Cascade complex.
Length = 135
Score = 28.3 bits (64), Expect = 3.8
Identities = 17/66 (25%), Positives = 21/66 (31%), Gaps = 10/66 (15%)
Query: 77 AVFLLKSETSEASHLERI---LERPGRVIS-ERK------PLCRRESNNVDIEDILAHTP 126
AVF + LE + L P + RK PL D+ LA P
Sbjct: 68 AVFTVALTEGAPPLLEELAAALRSPVFPLYLGRKSCPPARPLFLGLFEAADLLAALAALP 127
Query: 127 EDPSIA 132
S A
Sbjct: 128 WQASRA 133
>gnl|CDD|212567 cd11694, DHR2_DOCK_D, Dock Homology Region 2, a GEF domain, of
Class D Dedicator of Cytokinesis proteins. DOCK
proteins are atypical guanine nucleotide exchange
factors (GEFs) that lack the conventional Dbl homology
(DH) domain. As GEFs, they activate small GTPases by
exchanging bound GDP for free GTP. They are divided
into four classes (A-D) based on sequence similarity
and domain architecture; class D, also called the
Zizimin subfamily, includes Dock9, 10 and 11. Class D
Docks are specific GEFs for Cdc42. Dock9 plays
important roles in spine formation and dendritic
growth. Dock10 and Dock11 are preferentially expressed
in lymphocytes. All DOCKs contain two homology domains:
the DHR-1 (Dock homology region-1), also called CZH1
(CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2
(also called CZH2 or Docker). The DHR-1 domain binds
phosphatidylinositol-3,4,5-triphosphate. This alignment
model represents the DHR-2 domain of class D DOCKs,
which contains the catalytic GEF activity for Cdc42.
Class D DOCKs also contain a Pleckstrin homology (PH)
domain at the N-terminus.
Length = 376
Score = 28.8 bits (65), Expect = 6.0
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 7/53 (13%)
Query: 8 RNQVFQRYLTFCGIGIQNAQLFEMSILEFERNQILLKLARSIFEEQSNLECLV 60
R + L C G+ A+ +E + E L KL I+E++ + E L
Sbjct: 40 RKDLLLELLEACVEGLWKAERYE-LLGE------LYKLIIPIYEKRRDFEQLA 85
>gnl|CDD|223051 PHA03336, PHA03336, uncharacterized protein; Provisional.
Length = 462
Score = 28.4 bits (63), Expect = 8.0
Identities = 21/89 (23%), Positives = 30/89 (33%), Gaps = 20/89 (22%)
Query: 134 STVFELGGPGGEALVKSPGNTVCNTHSRLATI-------------------AKYVASTGQ 174
+TV L G G + NTV N R+ T+ K+V +
Sbjct: 54 NTVLRLHGSPGFFIHVKHVNTVYNRQQRVRTVRKGVMPHKTIQNSTVRRATNKFVTDKKK 113
Query: 175 ILNIGDVPSWMREEVCNDEDEESDFTTRC 203
I + V S R E E S++T
Sbjct: 114 IFTVDGVKS-TRIEFTTAEHRSSNYTANA 141
Score = 28.4 bits (63), Expect = 8.0
Identities = 21/89 (23%), Positives = 30/89 (33%), Gaps = 20/89 (22%)
Query: 258 STVFELGGPGGEALVKSPGNTVCNTHSRLATI-------------------AKYVASTGQ 298
+TV L G G + NTV N R+ T+ K+V +
Sbjct: 54 NTVLRLHGSPGFFIHVKHVNTVYNRQQRVRTVRKGVMPHKTIQNSTVRRATNKFVTDKKK 113
Query: 299 ILNIGDVPSWMREEVCNDEDEESDFTTRC 327
I + V S R E E S++T
Sbjct: 114 IFTVDGVKS-TRIEFTTAEHRSSNYTANA 141
>gnl|CDD|223394 COG0317, SpoT, Guanosine polyphosphate
pyrophosphohydrolases/synthetases [Signal transduction
mechanisms / Transcription].
Length = 701
Score = 28.4 bits (64), Expect = 8.0
Identities = 14/68 (20%), Positives = 31/68 (45%), Gaps = 8/68 (11%)
Query: 30 EMSILEFERNQILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETSEAS 89
++ I ++R+ +L +++ + E+ N V + T + ++ A E +
Sbjct: 629 DIEIRAYDRSGLLRDVSQVLANEKIN----VLGVNTRSDK----DQFATMQFTIEVKNLN 680
Query: 90 HLERILER 97
HL R+L R
Sbjct: 681 HLGRVLAR 688
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 0.136 0.403
Gapped
Lambda K H
0.267 0.0694 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,108,313
Number of extensions: 2018632
Number of successful extensions: 1415
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1410
Number of HSP's successfully gapped: 20
Length of query: 421
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 322
Effective length of database: 6,546,556
Effective search space: 2107991032
Effective search space used: 2107991032
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: 60 (27.0 bits)