RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14432
(189 letters)
>gnl|CDD|181730 PRK09256, PRK09256, hypothetical protein; Provisional.
Length = 138
Score = 105 bits (264), Expect = 2e-29
Identities = 40/91 (43%), Positives = 61/91 (67%), Gaps = 1/91 (1%)
Query: 86 ELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLII 145
EL+ + R+SGPGGQ+VN VST V++RF + A++ L E K++L+ L +R+ KDG ++I
Sbjct: 14 ELEWRFIRASGPGGQNVNKVSTAVELRFDIAASS-LPEFYKERLLALAGHRITKDGVIVI 72
Query: 146 KSDRTRSQQLNLADAMTTLRNMIWKAAKPAP 176
K+ RSQ+ N DA+ L +I +A KP
Sbjct: 73 KAQEFRSQERNREDALERLVALIREALKPPK 103
>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 73.4 bits (181), Expect = 3e-16
Identities = 23/76 (30%), Positives = 34/76 (44%)
Query: 85 EELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLI 144
++L I R+SG GGQHVN + V + L ++ + Q + R G L
Sbjct: 110 DDLRIDTYRASGAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALARKMLKGKLY 169
Query: 145 IKSDRTRSQQLNLADA 160
I + RSQ+ N A
Sbjct: 170 ILAQEKRSQEKNRERA 185
>gnl|CDD|201249 pfam00472, RF-1, RF-1 domain. This domain is found in peptide
chain release factors such as RF-1 and RF-2, and a
number of smaller proteins of unknown function. This
domain contains the peptidyl-tRNA hydrolase activity.
The domain contains a highly conserved motif GGQ, where
the glutamine is thought to coordinate the water that
mediates the hydrolysis.
Length = 114
Score = 63.0 bits (154), Expect = 3e-13
Identities = 24/105 (22%), Positives = 38/105 (36%), Gaps = 26/105 (24%)
Query: 74 PVVIPRFSYITE-ELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIEL 132
P+ I E +L I RSSGPGGQ+VN + V +
Sbjct: 1 PLDEEVEIEIPESDLRIDTFRSSGPGGQNVNKTESAVRLTH------------------- 41
Query: 133 NKNRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMIWKAAKPAPQ 177
+++K RSQ N A+ L+ +++A +
Sbjct: 42 ------LPTGIVVKCQEERSQHKNREKALERLKAKLYEAELQKKR 80
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 44.1 bits (105), Expect = 2e-05
Identities = 18/47 (38%), Positives = 21/47 (44%), Gaps = 12/47 (25%)
Query: 72 VIPVV-------IPRFSYITEELDITYSRSSGPGGQHVNSVSTKVDI 111
V P V I ++L I RSSG GGQHVN + V I
Sbjct: 220 VYPEVDDTIEIEIN-----PKDLRIDTYRSSGAGGQHVNKTDSAVRI 261
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 42.0 bits (100), Expect = 6e-05
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 85 EELDITYSRSSGPGGQHVNSVSTKVDI 111
++L I RSSG GGQHVN+ + V I
Sbjct: 221 KDLRIDTFRSSGAGGQHVNTTDSAVRI 247
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein;
Reviewed.
Length = 200
Score = 40.0 bits (94), Expect = 2e-04
Identities = 19/37 (51%), Positives = 22/37 (59%), Gaps = 4/37 (10%)
Query: 77 IPRFSYITEEL--DITYS--RSSGPGGQHVNSVSTKV 109
I RFS EE +I + RSSGPGGQHVN + V
Sbjct: 95 IGRFSADEEEQSDEIRFETLRSSGPGGQHVNKTDSAV 131
>gnl|CDD|232785 TIGR00020, prfB, peptide chain release factor 2. In many but not
all taxa, there is a conserved real translational
frameshift at a TGA codon. RF-2 helps terminate
translation at TGA codons and can therefore regulate its
own production by readthrough when RF-2 is insufficient.
There is a PFAM model called "RF-1" for the superfamily
of RF-1, RF-2, mitochondrial, RF-H, etc [Protein
synthesis, Translation factors].
Length = 364
Score = 38.2 bits (89), Expect = 0.002
Identities = 14/28 (50%), Positives = 17/28 (60%)
Query: 84 TEELDITYSRSSGPGGQHVNSVSTKVDI 111
E+L I R+SG GGQHVN + V I
Sbjct: 234 PEDLRIDTYRASGAGGQHVNKTDSAVRI 261
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 37.6 bits (88), Expect = 0.002
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 85 EELDITYSRSSGPGGQHVNSVSTKVDI 111
++L I RSSG GGQHVN+ + V I
Sbjct: 223 KDLRIDTFRSSGAGGQHVNTTDSAVRI 249
>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model
describes peptide chain release factor 1 (PrfA, RF-1),
and excludes the related peptide chain release factor 2
(PrfB, RF-2). RF-1 helps recognize and terminate
translation at UAA and UAG stop codons. The
mitochondrial release factors are prfA-like, although
not included above the trusted cutoff for this model.
RF-1 does not have a translational frameshift [Protein
synthesis, Translation factors].
Length = 360
Score = 37.0 bits (86), Expect = 0.003
Identities = 14/27 (51%), Positives = 17/27 (62%)
Query: 85 EELDITYSRSSGPGGQHVNSVSTKVDI 111
+L I RSSG GGQHVN+ + V I
Sbjct: 221 ADLRIDTFRSSGAGGQHVNTTDSAVRI 247
>gnl|CDD|213768 TIGR03072, release_prfH, putative peptide chain release factor H.
Members of this protein family are bacterial proteins
homologous to peptide chain release factors 1 (RF-1,
product of the prfA gene), and 2 (RF-2, product of the
prfB gene). The member from Escherichia coli K-12,
designated prfH, appears to be a pseudogene. This class
I release factor is always found as the downstream gene
of a two-gene operon [Protein synthesis, Translation
factors].
Length = 200
Score = 36.3 bits (84), Expect = 0.004
Identities = 14/28 (50%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 84 TEELDITYS--RSSGPGGQHVNSVSTKV 109
E +I + RSSGPGGQHVN + V
Sbjct: 103 ATEDEIRFETLRSSGPGGQHVNKTESAV 130
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional.
Length = 326
Score = 33.6 bits (76), Expect = 0.047
Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 6/42 (14%)
Query: 76 VIPRFS------YITEELDITYSRSSGPGGQHVNSVSTKVDI 111
V+P F+ TE+L I R+SG GGQHVN+ + V I
Sbjct: 182 VVPEFNDEVEIEVRTEDLKIDTYRASGAGGQHVNTTDSAVRI 223
>gnl|CDD|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional.
Length = 339
Score = 32.5 bits (74), Expect = 0.094
Identities = 19/43 (44%), Positives = 23/43 (53%), Gaps = 4/43 (9%)
Query: 72 VIPVVIPRFSYITEELDI---TYSRSSGPGGQHVNSVSTKVDI 111
V PV+ E D+ TY RSSG GGQHVN+ + V I
Sbjct: 184 VYPVIDDNIEVDVNESDVRIDTY-RSSGAGGQHVNTTDSAVRI 225
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
Length = 325
Score = 31.3 bits (71), Expect = 0.25
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 85 EELDITYSRSSGPGGQHVNSVSTKVDI 111
E+L I R+ G GGQHVN + V I
Sbjct: 196 EDLKIDTYRAGGAGGQHVNKTESAVRI 222
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional.
Length = 313
Score = 29.2 bits (65), Expect = 1.2
Identities = 12/19 (63%), Positives = 13/19 (68%)
Query: 93 RSSGPGGQHVNSVSTKVDI 111
RSSG GGQHVN + V I
Sbjct: 184 RSSGAGGQHVNKTESAVRI 202
>gnl|CDD|218297 pfam04864, Alliinase_C, Allinase. Allicin is a thiosulphinate that
gives rise to dithiines, allyl sulphides and ajoenes,
the three groups of active compounds in Allium species.
Allicin is synthesised from sulfoxide cysteine
derivatives by alliinase (EC:4.4.1.4), whose C-S lyase
activity cleaves C(beta)-S(gamma) bonds. It is thought
that this enzyme forms part of a primitive plant defence
system.
Length = 362
Score = 28.5 bits (64), Expect = 2.3
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 3/42 (7%)
Query: 112 RFKVNAANWLNEDVKKQLIELNKNRLNKDGYL---IIKSDRT 150
+++ NAA ++N D IEL + N DG L +I +
Sbjct: 122 KWEGNAAAYVNTDNPGPFIELVTSPNNPDGTLREAVIDGSKA 163
>gnl|CDD|178298 PLN02695, PLN02695, GDP-D-mannose-3',5'-epimerase.
Length = 370
Score = 27.1 bits (60), Expect = 5.7
Identities = 11/24 (45%), Positives = 18/24 (75%)
Query: 2 NTILSFHKLISNQRNVVKRFYKSS 25
NT++SF+ L + + N VKRF+ +S
Sbjct: 113 NTMISFNMLEAARINGVKRFFYAS 136
>gnl|CDD|236834 PRK11067, PRK11067, outer membrane protein assembly factor YaeT;
Provisional.
Length = 803
Score = 27.3 bits (61), Expect = 5.9
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 4/23 (17%)
Query: 120 WLNEDVKKQLIELNKNRLNKDGY 142
WL D L+E K RLN+ G+
Sbjct: 376 WLGSD----LVEQGKERLNRLGF 394
>gnl|CDD|216673 pfam01739, CheR, CheR methyltransferase, SAM binding domain. CheR
proteins are part of the chemotaxis signaling mechanism
in bacteria. CheR methylates the chemotaxis receptor at
specific glutamate residues. CheR is an
S-adenosylmethionine- dependent methyltransferase - the
C-terminal domain (this one) binds SAM.
Length = 194
Score = 26.8 bits (60), Expect = 6.7
Identities = 8/42 (19%), Positives = 19/42 (45%)
Query: 104 SVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLII 145
D+ F N + +E+ +++++ + L GYL +
Sbjct: 130 PPLGDFDVIFCRNVLIYFDEETQRKILNRFASALKPGGYLFL 171
>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi. This family includes
the fifth essential DNA polymerase in yeast EC:2.7.7.7.
Pol5p is localised exclusively to the nucleolus and
binds near or at the enhancer region of rRNA-encoding
DNA repeating units.
Length = 784
Score = 26.8 bits (59), Expect = 8.8
Identities = 11/77 (14%), Positives = 18/77 (23%), Gaps = 5/77 (6%)
Query: 94 SSGPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQ 153
SS V +V K + + L E +G + +
Sbjct: 149 SSSEKVLSVFLSYKRVLRNEKSLPVLLEKTENIRSLCE-----SFLEGDSLSSTQVDAHL 203
Query: 154 QLNLADAMTTLRNMIWK 170
NL + W
Sbjct: 204 AGNLLLLLKQKLPASWI 220
>gnl|CDD|99811 cd06215, FNR_iron_sulfur_binding_1, Iron-sulfur binding ferredoxin
reductase (FNR) proteins combine the FAD and NAD(P)
binding regions of FNR with an iron-sulfur binding
cluster domain. Ferredoxin-NADP+ (oxido)reductase is an
FAD-containing enzyme that catalyzes the reversible
electron transfer between NADP(H) and electron carrier
proteins such as ferredoxin and flavodoxin. Isoforms of
these flavoproteins (i.e. having a non-covalently bound
FAD as a prosthetic group) are present in chloroplasts,
mitochondria, and bacteria in which they participate in
a wide variety of redox metabolic pathways. The
C-terminal portion of the FAD/NAD binding domain
contains most of the NADP(H) binding residues and the
N-terminal sub-domain interacts non-covalently with the
isoalloxazine rings of the flavin molecule which lies
largely in a large gap betweed the two domains. In this
ferredoxin like sub-group, the FAD/NAD sub-domains is
typically fused to a C-terminal iron-sulfur binding
domain. Iron-sulfur proteins play an important role in
electron transfer processes and in various enzymatic
reactions. The family includes plant and algal
ferredoxins which act as electron carriers in
photosynthesis and ferredoxins which participate in
redox chains from bacteria to mammals. Ferredoxin
reductase first accepts one electron from reduced
ferredoxin to form a flavin semiquinone intermediate.
The enzyme then accepts a second electron to form FADH2
which then transfers two electrons and a proton to NADP+
to form NADPH.
Length = 231
Score = 26.4 bits (59), Expect = 9.0
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 9/52 (17%)
Query: 82 YITEELDI-------TYSRSSGPGGQHVNSVSTKVDIRFKVNAANWLNEDVK 126
++T EL+I Y+ SS P S++ K V +NWL++++K
Sbjct: 33 FLTLELEIDGETVYRAYTLSSSPSRPDSLSITVKRVPGGLV--SNWLHDNLK 82
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
0.317 0.134 0.380
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,475,509
Number of extensions: 860244
Number of successful extensions: 736
Number of sequences better than 10.0: 1
Number of HSP's gapped: 735
Number of HSP's successfully gapped: 29
Length of query: 189
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 98
Effective length of database: 6,901,388
Effective search space: 676336024
Effective search space used: 676336024
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: 56 (25.3 bits)