RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14372
(210 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 = 39.3 bits (92), Expect = 3e-04
Identities = 26/90 (28%), Positives = 38/90 (42%), Gaps = 8/90 (8%)
Query: 42 VSTPEIRIPWGCGIVGYVAESGEPVNIPDAYLVSTPQIRIPWGC-GIVCYLAESGEPVNI 100
+ T IR P G+ G VAE+G P+NIPD + G+ +L P+
Sbjct: 45 LPTLGIRFPLDEGLAGRVAETGRPLNIPDVEADPLFAEDLLGRYQGVRSFL---AVPLVA 101
Query: 101 PD---AYL-LINKFDDLAFSKNDENFVEAY 126
L L NK F++ DE ++A
Sbjct: 102 DGELVGVLALHNKKSPRPFTEEDEELLQAL 131
Score = 30.0 bits (68), Expect = 0.45
Identities = 11/30 (36%), Positives = 15/30 (50%)
Query: 11 SYLLYSIPWGCGIVCYLAESGEPVNIPDAY 40
L P G+ +AE+G P+NIPD
Sbjct: 46 PTLGIRFPLDEGLAGRVAETGRPLNIPDVE 75
>gnl|CDD|224867 COG1956, COG1956, GAF domain-containing protein [Signal
transduction mechanisms].
Length = 163
Score = 33.8 bits (78), Expect = 0.028
Identities = 24/68 (35%), Positives = 32/68 (47%), Gaps = 9/68 (13%)
Query: 7 LSRASYLLY----SIPWGCGIVCYLAESGEPVNIPDAYLVSTPEIRIPWGCGIVGYVAES 62
L+ AS LL + W G YL E E V P + +RIP+G G+ G A +
Sbjct: 37 LANASALLKERLPDVNW-VGF--YLLEGDELVLGP--FQGKVACVRIPFGKGVCGTAAAT 91
Query: 63 GEPVNIPD 70
GE V + D
Sbjct: 92 GETVRVDD 99
>gnl|CDD|226133 COG3605, PtsP, Signal transduction protein containing GAF and PtsI
domains [Signal transduction mechanisms].
Length = 756
Score = 32.0 bits (73), Expect = 0.23
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 11/50 (22%)
Query: 47 IRIPWGCGIVGYVAESGEPVNIPDAYLVSTPQIRIPWGCGIVCYLAESGE 96
+++ +G G+VG V S EP+N+ DA S P + YL E+GE
Sbjct: 66 VQLAFGEGLVGLVGRSAEPLNLADA--QSHPSFK---------YLPETGE 104
>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 = 29.1 bits (65), Expect = 0.85
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 21 CGIVCYLAESGEPVNIPDAYLVSTP--EIRIPWGCGIVGYVAESGEPVNIPDAY 72
C I+ A+ + L P R+P G GIVG V G P+ +PD
Sbjct: 22 CAILLADADGLLLYLVAGDGLSDIPLAARRLPLGGGIVGEVIAGGRPIVVPDVQ 75
>gnl|CDD|132534 TIGR03495, phage_LysB, phage lysis regulatory protein, LysB family.
Members of this protein family are phage lysis
regulatory protein, including the well-studied protein
LysB (lysis protein B) of Enterobacteria phage P2. For
members of this family, genes are found in phage or in
prophage regions of bacterial genomes, typically near a
phage lysozyme or phage holin.
Length = 135
Score = 28.5 bits (64), Expect = 1.2
Identities = 20/79 (25%), Positives = 30/79 (37%), Gaps = 9/79 (11%)
Query: 129 AVIAMAKQSVTLDVLSYHASASLEDAQRLRSNNSSLIVPMAKQSVTLDVLSYHASASLED 188
V + QS L +A A LE A R+ + + A ++ L VL A + E
Sbjct: 10 LVAGLGWQSQRLR----NARADLERANRVLKAQQAEL---ASKANQLIVLLALAKRNEEA 62
Query: 189 AQRLRRT--NKTKEEQNRE 205
+LR+ RE
Sbjct: 63 QAQLRQQLAQARALLAQRE 81
>gnl|CDD|182937 PRK11061, PRK11061, fused phosphoenolpyruvate-protein
phosphotransferase PtsP/GAF domain; Provisional.
Length = 748
Score = 29.2 bits (66), Expect = 1.6
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 47 IRIPWGCGIVGYVAESGEPVNIPDA 71
+ + + GIVG V EP+N+ DA
Sbjct: 66 VTLAFDEGIVGLVGRLAEPINLADA 90
>gnl|CDD|219783 pfam08297, U3_snoRNA_assoc, U3 snoRNA associated. This family of
proteins is associated with U3 snoRNA. U3 snoRNA is
required for nucleolar processing of pre-18S ribosomal
RNA.
Length = 87
Score = 27.0 bits (60), Expect = 2.8
Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 14/58 (24%)
Query: 117 KNDENFVEAYEKAVIAMAKQSVTLDVLSYHASASLEDAQRLRSNNSSLIVPMAKQSVT 174
KN F++ EK + K VT+ VLS NNS + P A++ +
Sbjct: 34 KNKLRFLKKLEKRPKDVKKGPVTVRVLS--------------DNNSRKLPPKAEKKIV 77
>gnl|CDD|216344 pfam01175, Urocanase, Urocanase.
Length = 545
Score = 28.7 bits (65), Expect = 2.8
Identities = 12/64 (18%), Positives = 28/64 (43%), Gaps = 16/64 (25%)
Query: 121 NFVEAYEKAVIAMAKQSVTLDVLSYHASA------------SLEDAQRLRSNNSSLIVPM 168
N + + + ++ + D+++ SA +LE+A LR ++ V +
Sbjct: 232 NAADVLPE----LVRRGIRPDLVTDQTSAHDPLNGYLPAGYTLEEAAELRKSDPEEFVKL 287
Query: 169 AKQS 172
A++S
Sbjct: 288 ARES 291
>gnl|CDD|237222 PRK12837, PRK12837, 3-ketosteroid-delta-1-dehydrogenase;
Provisional.
Length = 513
Score = 28.3 bits (63), Expect = 3.5
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 91 LAESGEPVNIPDAYLL--INKFDDLAFSKNDENFV---EAYEKAVIAMAKQSVTLDVLSY 145
L E + +P L + +F+ A + DE+F EAY++A A V +D +
Sbjct: 378 LEELAAKIGVPADALTATVARFNGFAAAGVDEDFGRGDEAYDRAFSGGASPLVPIDTPPF 437
Query: 146 HASA 149
HA+A
Sbjct: 438 HAAA 441
>gnl|CDD|188365 TIGR03675, arCOG00543, arCOG00543 universal archaeal
KH-domain/beta-lactamase-domain protein. This family of
proteins is universal in the archaea and consistsof an
N-terminal type-1 KH-domain (pfam00013) a central
beta-lactamase-domain (pfam00753) with a C-terminal
motif associated with RNA metabolism (pfam07521).
KH-domains are associated with RNA-binding, so taken
together, this protein is a likely metal-dependent
RNAase. This family was defined in as arCOG01782.
Length = 630
Score = 28.4 bits (64), Expect = 3.5
Identities = 14/37 (37%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 39 AYLVSTPEIRIPWGCGI-VGYVAESGEP-VNIPDAYL 73
A L+STPE R+ CG+ VG ++ P +++P+ L
Sbjct: 190 ALLLSTPESRVLLDCGVNVGADGDNAYPYLDVPEFQL 226
>gnl|CDD|240364 PTZ00332, PTZ00332, paraflagellar rod protein; Provisional.
Length = 589
Score = 28.0 bits (62), Expect = 3.7
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 16/69 (23%)
Query: 144 SYHASASLEDAQRLRSNNSSLIVPMAKQSVTLDVLSYHAS---ASLEDAQRLRR--TNKT 198
+ ++ ++DA+R KQ D+ H + A LEDA+ ++R TNK
Sbjct: 258 ANQETSQMKDAKR-----------RLKQRCETDLKHIHDAIQKADLEDAEAMKRYATNKE 306
Query: 199 KEEQNREEN 207
K E+ EN
Sbjct: 307 KSERFIREN 315
>gnl|CDD|227661 COG5366, COG5366, Protein involved in propagation of M2 dsRNA
satellite of L-A virus [General function prediction
only].
Length = 531
Score = 28.0 bits (62), Expect = 4.2
Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 2/59 (3%)
Query: 103 AYLLINKFDDLAFSKNDENFVEAYEKAVIAMAKQSVTLDVLSYHASASLEDAQRLRSNN 161
AYL+ + AF +D ++ ++ ++ M+ S + +H LE L S+
Sbjct: 157 AYLMSAETCSYAFGPSDILLLDGVDRIILDMSFGSDKPPLDVFHVPRFLE--MFLLSSR 213
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
0.316 0.132 0.391
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: 10,545,928
Number of extensions: 982682
Number of successful extensions: 933
Number of sequences better than 10.0: 1
Number of HSP's gapped: 931
Number of HSP's successfully gapped: 22
Length of query: 210
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 117
Effective length of database: 6,812,680
Effective search space: 797083560
Effective search space used: 797083560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.8 bits)