RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7062
(148 letters)
>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
proteins that cover a wide variety of functions
including adaptor/regulatory modules in signal
transduction, pre-mRNA processing and cytoskeleton
assembly; typically contains a GH dipeptide 11-24
residues from its N-terminus and the WD dipeptide at its
C-terminus and is 40 residues long, hence the name WD40;
between GH and WD lies a conserved core; serves as a
stable propeller-like platform to which proteins can
bind either stably or reversibly; forms a propeller-like
structure with several blades where each blade is
composed of a four-stranded anti-parallel b-sheet;
instances with few detectable copies are hypothesized to
form larger structures by dimerization; each WD40
sequence repeat forms the first three strands of one
blade and the last strand in the next blade; the last
C-terminal WD40 repeat completes the blade structure of
the first WD40 repeat to create the closed ring
propeller-structure; residues on the top and bottom
surface of the propeller are proposed to coordinate
interactions with other proteins and/or small ligands; 7
copies of the repeat are present in this alignment.
Length = 289
Score = 41.2 bits (97), Expect = 5e-05
Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 10/81 (12%)
Query: 37 IRMYDFGSNNPNPVINCEGVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLCFIQQ--- 93
IR++D V G + V V F DG+ + + D ++WD+
Sbjct: 75 IRLWD--LETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLR 132
Query: 94 -----VNALRITPDKQLLASA 109
VN++ +PD +AS+
Sbjct: 133 GHTDWVNSVAFSPDGTFVASS 153
Score = 41.2 bits (97), Expect = 6e-05
Identities = 23/84 (27%), Positives = 34/84 (40%), Gaps = 10/84 (11%)
Query: 36 HIRMYDFGSNNPNPVINCEGVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLCFIQQ-- 93
I+++D + + G V V F DG + +G ED R+WDL Q
Sbjct: 200 TIKLWDL--STGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTL 257
Query: 94 ------VNALRITPDKQLLASAEE 111
V +L +PD + LAS
Sbjct: 258 SGHTNSVTSLAWSPDGKRLASGSA 281
Score = 40.4 bits (95), Expect = 1e-04
Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 10/81 (12%)
Query: 37 IRMYDFGSNNPNPVINCEGVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLS--------L 88
I+++D V G + V V F DG+ + + D ++WDLS
Sbjct: 159 IKLWDL--RTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLR 216
Query: 89 CFIQQVNALRITPDKQLLASA 109
VN++ +PD LLAS
Sbjct: 217 GHENGVNSVAFSPDGYLLASG 237
Score = 40.0 bits (94), Expect = 1e-04
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 27 MVAALGGYQHIRMYDFGSNNPNPVINCEGVSKNVVEVGFQEDGKWMFTGGEDCRARIWD 85
++A+ IR++D + + G + +V + + DGK + +G D RIWD
Sbjct: 233 LLASGSEDGTIRVWDLRTGECVQTL--SGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 36.9 bits (86), Expect = 0.001
Identities = 18/81 (22%), Positives = 37/81 (45%), Gaps = 10/81 (12%)
Query: 37 IRMYDFGSNNPNPVINCEGVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLC------- 89
I+++D + +G + V +V DG ++ +G D R+WDL
Sbjct: 33 IKVWDL--ETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLETGECVRTLT 90
Query: 90 -FIQQVNALRITPDKQLLASA 109
V+++ +PD ++L+S+
Sbjct: 91 GHTSYVSSVAFSPDGRILSSS 111
Score = 36.9 bits (86), Expect = 0.002
Identities = 15/53 (28%), Positives = 20/53 (37%), Gaps = 8/53 (15%)
Query: 65 FQEDGKWMFTGGEDCRARIWDLSLCF--------IQQVNALRITPDKQLLASA 109
F DGK + TG D ++WDL V + + D LAS
Sbjct: 17 FSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASG 69
Score = 35.8 bits (83), Expect = 0.005
Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 10/81 (12%)
Query: 37 IRMYDFGSNNPNPVINCEGVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLC------- 89
I+++D + G + V V F DG ++ + +D ++WDL
Sbjct: 117 IKVWDV--ETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLT 174
Query: 90 -FIQQVNALRITPDKQLLASA 109
+VN++ +PD + L S+
Sbjct: 175 GHTGEVNSVAFSPDGEKLLSS 195
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 39.7 bits (91), Expect = 2e-04
Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 11/83 (13%)
Query: 37 IRMYDFGSNNPNPVINCEGVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLCFIQ---- 92
IR++D S++ + + G S +V+ V F DGK + +G D R+WDL +
Sbjct: 265 IRLWDLRSSS-SLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLT 323
Query: 93 ------QVNALRITPDKQLLASA 109
V++L +PD LL S
Sbjct: 324 LKGHEGPVSSLSFSPDGSLLVSG 346
Score = 37.0 bits (84), Expect = 0.002
Identities = 23/82 (28%), Positives = 34/82 (41%), Gaps = 11/82 (13%)
Query: 37 IRMYDFGSNNPNPVINCEGVSKNVVEVGFQEDGKWMFTGGEDCRARIWDLSLCFI----- 91
IR++D + G S +VV F DG + +G D R+WDL
Sbjct: 223 IRLWDLSTGKLLRST-LSGHSDSVVSS-FSPDGSLLASGSSDGTIRLWDLRSSSSLLRTL 280
Query: 92 ----QQVNALRITPDKQLLASA 109
V ++ +PD +LLAS
Sbjct: 281 SGHSSSVLSVAFSPDGKLLASG 302
Score = 33.9 bits (76), Expect = 0.019
Identities = 28/105 (26%), Positives = 46/105 (43%), Gaps = 11/105 (10%)
Query: 13 GQISTVFDSKHLVEMVAALGGYQHIRMYDFGSNNPNPVINCEGVSKNVVEVGFQEDGKWM 72
G +S++ S +V+ IR++D + P + NV+ V F DG+ +
Sbjct: 329 GPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKP---LKTLEGHSNVLSVSFSPDGRVV 385
Query: 73 FTGGEDCRARIWDLSL--------CFIQQVNALRITPDKQLLASA 109
+G D R+WDLS +V +L +PD + LAS
Sbjct: 386 SSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASG 430
Score = 31.2 bits (69), Expect = 0.18
Identities = 23/92 (25%), Positives = 42/92 (45%), Gaps = 7/92 (7%)
Query: 21 SKHLVEMVAALGGYQH-IRMYDFGSNNPNPVINCEGVSKNVVEVGFQEDGKWMFTGGEDC 79
S V + G +R++D + + + N +G + V + F DGK + +G D
Sbjct: 377 SFSPDGRVVSSGSTDGTVRLWDL--STGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDN 434
Query: 80 RARIWDLSLCFIQQVNALRITPDKQLLASAEE 111
R+WDL + ++ +PD ++LAS
Sbjct: 435 TIRLWDLK----TSLKSVSFSPDGKVLASKSS 462
>gnl|CDD|197651 smart00320, WD40, WD40 repeats. Note that these repeats are
permuted with respect to the structural repeats
(blades) of the beta propeller domain.
Length = 40
Score = 33.1 bits (76), Expect = 0.004
Identities = 11/40 (27%), Positives = 21/40 (52%)
Query: 46 NPNPVINCEGVSKNVVEVGFQEDGKWMFTGGEDCRARIWD 85
+ + +G + V V F DGK++ +G +D ++WD
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 32.7 bits (75), Expect = 0.005
Identities = 11/38 (28%), Positives = 18/38 (47%)
Query: 48 NPVINCEGVSKNVVEVGFQEDGKWMFTGGEDCRARIWD 85
+ +G + V V F DG + +G +D R+WD
Sbjct: 2 KLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
>gnl|CDD|188126 TIGR01283, nifE, nitrogenase molybdenum-iron cofactor biosynthesis
protein NifE. This protein is part of the NifEN complex
involved in biosynthesis of the molybdenum-iron cofactor
used by the homologous NifDK complex of nitrogenase. In
a few species, the protein is found as a NifEN fusion
protein [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other, Central intermediary metabolism,
Nitrogen fixation].
Length = 453
Score = 29.6 bits (67), Expect = 0.56
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 102 DKQLLASAEELSCCYCGAAVFVYNSCYPA 130
+K+L + E+ Y AVFVY++C PA
Sbjct: 103 EKKLFHAIREIVERYHPPAVFVYSTCVPA 131
>gnl|CDD|238930 cd01968, Nitrogenase_NifE_I, Nitrogenase_NifE_I: a subgroup of the
NifE subunit of the NifEN complex: NifE forms an
alpha2beta2 tetramer with NifN. NifE and NifN are
structurally homologous to nitrogenase MoFe protein
alpha and beta subunits respectively. NifEN
participates in the synthesis of the iron-molybdenum
cofactor (FeMoco) of the MoFe protein. NifB-co (an iron
and sulfur containing precursor of the FeMoco) from NifB
is transferred to the NifEN complex where it is further
processed to FeMoco. The NifEN bound precursor of FeMoco
has been identified as a molybdenum-free, iron- and
sulfur- containing analog of FeMoco. It has been
suggested that this NifEN bound precursor also acts as a
cofactor precursor in nitrogenase systems which require
a cofactor other than FeMoco: i.e. iron-vanadium
cofactor (FeVco) or iron only cofactor (FeFeco).
Length = 410
Score = 28.8 bits (65), Expect = 0.90
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 102 DKQLLASAEELSCCYCGAAVFVYNSCYPA 130
+K+L + E+ Y AVFVY++C A
Sbjct: 71 EKKLYKAILEIIERYHPKAVFVYSTCVVA 99
>gnl|CDD|148150 pfam06372, Gemin6, Gemin6 protein. This family consists of
several mammalian Gemin6 proteins. The exact function
of Gemin6 is unknown but it has been found to form part
of the pfam06003 complex. The SMN complex plays a key
role in the biogenesis of spliceosomal small nuclear
ribonucleoproteins (snRNPs) and other ribonucleoprotein
particles.
Length = 169
Score = 27.4 bits (60), Expect = 2.5
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 50 VINCEGVSKNVVEVGFQEDGKWMFTG 75
+ + VS N++ F EDG +G
Sbjct: 34 LFCTDPVSANIILSNFLEDGALSNSG 59
>gnl|CDD|172952 PRK14477, PRK14477, bifunctional nitrogenase molybdenum-cofactor
biosynthesis protein NifE/NifN; Provisional.
Length = 917
Score = 27.4 bits (61), Expect = 3.7
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 102 DKQLLASAEELSCCYCGAAVFVYNSCYPA 130
+K+L + EL+ Y AVFVY +C A
Sbjct: 97 EKKLYRAILELAERYQPKAVFVYATCVTA 125
>gnl|CDD|188123 TIGR01265, tyr_nico_aTase, tyrosine/nicotianamine family
aminotransferase. This subfamily of pyridoxal
phosphate-dependent enzymes includes known examples of
both tyrosine aminotransferase from animals and
nicotianamine aminotransferase from barley.
Length = 403
Score = 26.9 bits (60), Expect = 4.2
Identities = 15/62 (24%), Positives = 20/62 (32%), Gaps = 20/62 (32%)
Query: 18 VFDSKHLVEMVA------------------ALGGYQHIRMYDFGSNNPNPVINCEGVSKN 59
VF HL ++ G I M F S P V++ G+SK
Sbjct: 185 VFSRDHLQKIAEVAEKLGIPIIADEIYGHMVFGDAPFIPMASFASIVP--VLSLGGISKR 242
Query: 60 VV 61
V
Sbjct: 243 WV 244
>gnl|CDD|206204 pfam14034, Spore_YtrH, Sporulation protein YtrH. This family of
proteins is involved in sporulation. It may contribute
to the formation and stability of the thick
peptidoglycan layer between the two membranes of the
spore, known as the cortex. In Bacillus subtilis its
expression is regulated by sigma-E.
Length = 102
Score = 26.0 bits (58), Expect = 5.2
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 11/43 (25%)
Query: 2 VAALGGILTAF---------GQISTVFDSKHLVEMVAALGGYQ 35
VAA+GG F G++ + K L+ +++A G
Sbjct: 49 VAAIGGTFDTFRSLERGLFEGELRDLI--KQLLYILSAFLGAH 89
>gnl|CDD|218187 pfam04637, Herpes_pp85, Herpesvirus phosphoprotein 85 (HHV6-7
U14/HCMV UL25). This family includes UL25 proteins from
HCMV, as well as U14 proteins from HHV 6 and HHV7. These
85 kD phosphoproteins appear to act as structural
antigens, but their precise function is otherwise
unknown.
Length = 502
Score = 26.6 bits (59), Expect = 5.2
Identities = 9/29 (31%), Positives = 11/29 (37%)
Query: 117 CGAAVFVYNSCYPAAVVASNTLVKPQVTR 145
C V + NS P LV PQ+
Sbjct: 28 CLGQVALLNSGLPMPPYTLEALVDPQIKN 56
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
0.322 0.136 0.421
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,392,908
Number of extensions: 649572
Number of successful extensions: 501
Number of sequences better than 10.0: 1
Number of HSP's gapped: 496
Number of HSP's successfully gapped: 24
Length of query: 148
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 60
Effective length of database: 7,034,450
Effective search space: 422067000
Effective search space used: 422067000
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: 54 (24.6 bits)