RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4041
(162 letters)
>gnl|CDD|224817 COG1905, NuoE, NADH:ubiquinone oxidoreductase 24 kD subunit [Energy
production and conversion].
Length = 160
Score = 29.9 bits (68), Expect = 0.37
Identities = 15/57 (26%), Positives = 21/57 (36%), Gaps = 14/57 (24%)
Query: 90 LEAVSKFLDIAGSKVDYRRYGEALFDILIAGGLLGKTLDPTTRAGVMVCRICKTTAC 146
+E ++ L I ++V YG A F T G R+C TAC
Sbjct: 46 IEEIADMLGIPRARV----YGVATF----------YTQFFLKPVGRHHIRVCTGTAC 88
>gnl|CDD|200454 cd11315, AmyAc_bac1_AmyA, Alpha amylase catalytic domain found in
bacterial Alpha-amylases (also called
1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC
3.2.1.1) catalyzes the hydrolysis of alpha-(1,4)
glycosidic linkages of glycogen, starch, related
polysaccharides, and some oligosaccharides. This group
includes Firmicutes, Proteobacteria, Actinobacteria, and
Cyanobacteria. The Alpha-amylase family comprises the
largest family of glycoside hydrolases (GH), with the
majority of enzymes acting on starch, glycogen, and
related oligo- and polysaccharides. These proteins
catalyze the transformation of alpha-1,4 and alpha-1,6
glucosidic linkages with retention of the anomeric
center. The protein is described as having 3 domains: A,
B, C. A is a (beta/alpha) 8-barrel; B is a loop between
the beta 3 strand and alpha 3 helix of A; C is the
C-terminal extension characterized by a Greek key. The
majority of the enzymes have an active site cleft found
between domains A and B where a triad of catalytic
residues (Asp, Glu and Asp) performs catalysis. Other
members of this family have lost the catalytic activity
as in the case of the human 4F2hc, or only have 2
residues that serve as the catalytic nucleophile and the
acid/base, such as Thermus A4 beta-galactosidase with 2
Glu residues (GH42) and human alpha-galactosidase with 2
Asp residues (GH31). The family members are quite
extensive and include: alpha amylase,
maltosyltransferase, cyclodextrin glycotransferase,
maltogenic amylase, neopullulanase, isoamylase,
1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 352
Score = 28.4 bits (64), Expect = 1.6
Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 2/48 (4%)
Query: 83 LNAAGTDLEAVSKFLDIAGSKVDYRRYGEALFDILIAGGLLGKTLDPT 130
L G+ + +L + G V YG L L L G +LDP
Sbjct: 210 LQDGGSRDSDYASYLSLGG--VTASAYGFPLRGALKNAFLFGGSLDPA 255
>gnl|CDD|184624 PRK14327, PRK14327, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 509
Score = 28.1 bits (63), Expect = 2.0
Identities = 24/74 (32%), Positives = 31/74 (41%), Gaps = 18/74 (24%)
Query: 29 VVIMYQVGEDKFVSYCMNQKTEKPVLSGQRIKTRKR------DEKEKYDPAGFRDYILSG 82
V IMY G DKF +YC+ T R K R R E G+++ L G
Sbjct: 216 VNIMY--GCDKFCTYCIVPYT--------RGKERSRRPEDIIQEVRHLARQGYKEITLLG 265
Query: 83 --LNAAGTDLEAVS 94
+NA G D E +
Sbjct: 266 QNVNAYGKDFEDIE 279
>gnl|CDD|226607 COG4122, COG4122, Predicted O-methyltransferase [General function
prediction only].
Length = 219
Score = 27.7 bits (62), Expect = 2.9
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 10/46 (21%)
Query: 96 FLDIAGSKVDYRRYGEALFDILIAGGLL--------GKTLDPTTRA 133
F+D K DY Y E +L GGL+ G+ DP+ R
Sbjct: 137 FIDAD--KADYPEYLERALPLLRPGGLIVADNVLFGGRVADPSIRD 180
>gnl|CDD|132773 cd06863, PX_Atg24p, The phosphoinositide binding Phox Homology
domain of yeast Atg24p, an autophagic degradation
protein. The PX domain is a phosphoinositide (PI)
binding module present in many proteins with diverse
functions. The yeast Atg24p is a sorting nexin (SNX)
which is involved in membrane fusion events at the
vacuolar surface during pexophagy. This is facilitated
via binding of Atg24p to phosphatidylinositol
3-phosphate (PI3P) through its PX domain. SNXs make up
the largest group among PX domain containing proteins.
They are involved in regulating membrane traffic and
protein sorting in the endosomal system. The PX domain
of SNXs binds PIs and targets the protein to
PI-enriched membranes. SNXs differ from each other in
PI-binding specificity and affinity, and the presence
of other protein-protein interaction domains, which
help determine subcellular localization and specific
function in the endocytic pathway.
Length = 118
Score = 26.9 bits (60), Expect = 3.2
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 36 GEDKFVSYCMNQKTEKPVLSGQRIKTRKR 64
D ++SY + KT P S + K R+R
Sbjct: 15 SSDTYISYLITTKTNLPSFSRKEFKVRRR 43
>gnl|CDD|218849 pfam05997, Nop52, Nucleolar protein,Nop52. Nop52 believed to be
involved in the generation of 28S rRNA.
Length = 210
Score = 26.8 bits (60), Expect = 4.2
Identities = 7/9 (77%), Positives = 7/9 (77%)
Query: 21 MWMCDKPEV 29
MWM DKP V
Sbjct: 51 MWMSDKPLV 59
>gnl|CDD|226544 COG4058, McrA, Methyl coenzyme M reductase, alpha subunit
[Coenzyme metabolism].
Length = 553
Score = 27.1 bits (60), Expect = 5.2
Identities = 11/47 (23%), Positives = 19/47 (40%), Gaps = 4/47 (8%)
Query: 37 EDKFVSYCMNQKTEKPVLSGQRIKTRKRD----EKEKYDPAGFRDYI 79
++KF + T+ V G R RK++ K+ + G Y
Sbjct: 14 KEKFEEDPEEKYTKFYVFGGWRQSARKQEFVKAAKKIAEKRGIPFYN 60
>gnl|CDD|235557 PRK05682, flgE, flagellar hook protein FlgE; Validated.
Length = 407
Score = 26.7 bits (60), Expect = 5.6
Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 4/46 (8%)
Query: 80 LSGLNAAGTDLEAVSKFLDIAGSK-VDYRRYGEALFDILIAGGLLG 124
+SGLNAA L+ + +IA + ++ A F L A
Sbjct: 7 VSGLNAASNRLDVIGN--NIANANTTGFKS-SRAEFADLYANSAGT 49
>gnl|CDD|187773 cd09642, Cas8c_I-C, CRISPR/Cas system-associated protein Cas8c.
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;
Large proteins, some contain Zn-finger domain; signature
gene for I-C subtype; also known as Csd1 family.
Length = 574
Score = 26.6 bits (59), Expect = 6.5
Identities = 15/80 (18%), Positives = 27/80 (33%), Gaps = 4/80 (5%)
Query: 56 GQRIKTRKRDEKEKYDPAGFRDYILSGLNAAGTDLEAVSKFLDIAGSKVDYRRYGE--AL 113
+RI+ +E Y L+ N G + ++ LD + Y G A+
Sbjct: 415 LRRIRADVAYREEWYKRLALLKACLNRQNRRGKKKKELTVALDKTNTNRAY-LLGRLLAV 473
Query: 114 FDILIAGGLLGKTLDPTTRA 133
+ + L L+ T
Sbjct: 474 LE-KLQERALPGELNATIAD 492
>gnl|CDD|191464 pfam06166, DUF979, Protein of unknown function (DUF979). This
family consists of several putative bacterial membrane
proteins. The function of this family is unclear.
Length = 308
Score = 26.4 bits (59), Expect = 7.4
Identities = 21/60 (35%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 78 YILSGLNAAGTDLEAVSKFLDIAGSKVDYRRYGEALFDILIAGGLLGKTLDPTTRAGVMV 137
YIL GL T AV D + + +R+G ALF L+A L P GV+V
Sbjct: 5 YILIGLVLLVT---AVLSLRD----RTNPKRFGTALFWGLLALTFLFGDYLPAVVVGVLV 57
>gnl|CDD|213617 TIGR01417, PTS_I_fam, phosphoenolpyruvate-protein
phosphotransferase. This model recognizes a distinct
clade of phophoenolpyruvate (PEP)-dependent enzymes.
Most members are known or deduced to function as the
phosphoenolpyruvate-protein phosphotransferase (or
enzyme I) of PTS sugar transport systems. However, some
species with both a member of this family and a homolog
of the phosphocarrier protein HPr lack a IIC component
able to serve as a permease. An HPr homolog designated
NPr has been implicated in the regulation of nitrogen
assimilation, which demonstrates that not all
phosphotransferase system components are associated
directly with PTS transport.
Length = 565
Score = 26.7 bits (59), Expect = 7.6
Identities = 13/38 (34%), Positives = 16/38 (42%)
Query: 17 TTVLMWMCDKPEVVIMYQVGEDKFVSYCMNQKTEKPVL 54
TVL M +V +G DK + Y K E P L
Sbjct: 317 KTVLEAMESDAVIVRTLDIGGDKELPYLNFPKEENPFL 354
>gnl|CDD|132422 TIGR03379, glycerol3P_GlpC, glycerol-3-phosphate dehydrogenase,
anaerobic, C subunit. Members of this protein family
are the membrane-anchoring, non-catalytic C subunit,
product of the glpC gene, of a three-subunit,
FAD-dependent, anaerobic glycerol-3-phosphate
dehydrogenase. GlpC lasks classical hydrophobic
transmembrane helices; Cole, et al suggest interaction
with the membrane may involve amphipathic helices. GlcC
has conserved Cys-containing motifs suggestive of
iron-sulfur binding. This complex is found mostly in
Escherichia coli and closely related species [Energy
metabolism, Anaerobic].
Length = 397
Score = 26.3 bits (58), Expect = 8.4
Identities = 24/90 (26%), Positives = 36/90 (40%), Gaps = 20/90 (22%)
Query: 38 DKFVSYCMNQK-TEKPVLSGQRI-----KTRKRDEKEKYDPAGFRDYILSGLNAAG---- 87
D+ + YC N K E S +I + R + +K+K + RD++LS + G
Sbjct: 48 DEALKYCTNCKRCEVACPSDVKIGDIIARARNKYQKKKPNIKKLRDFVLSHTDLMGSIST 107
Query: 88 ---------TDLEAVSKFLDIAGSKVDYRR 108
T L+ V K LD V R
Sbjct: 108 PFAPIVNAITGLKPVKKLLDKT-LGVSKHR 136
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 0.137 0.410
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,120,701
Number of extensions: 741141
Number of successful extensions: 574
Number of sequences better than 10.0: 1
Number of HSP's gapped: 574
Number of HSP's successfully gapped: 20
Length of query: 162
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 73
Effective length of database: 6,990,096
Effective search space: 510277008
Effective search space used: 510277008
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: 55 (24.9 bits)