RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2667
(261 letters)
>gnl|CDD|161920 TIGR00545, lipoyltrans, lipoyltransferase and lipoate-protein
ligase. One member of this group of proteins is bovine
lipoyltransferase, which transfers the lipoyl group from
lipoyl-AMP to the specific Lys of lipoate-dependent
enzymes. However, it does not first activate lipoic acid
with ATP to create lipoyl-AMP and pyrophosphate. Another
member of this group, lipoate-protein ligase A from E.
coli, catalyzes both the activation and the transfer of
lipoate. Homology between the two is full-length, except
for the bovine mitochondrial targeting signal, but is
strongest toward the N-terminus [Protein fate, Protein
modification and repair].
Length = 324
Score = 119 bits (300), Expect = 5e-32
Identities = 66/204 (32%), Positives = 103/204 (50%), Gaps = 43/204 (21%)
Query: 55 VFISQSSNIFTNLALEDWLYKNFDFTNH-HVMLLWRNNPCVVIGRHQNPWQETNLGVLYD 113
+ S S++ + NLALE++L+K F T V+L W+N +VIGR+QN W E NL L +
Sbjct: 3 ILTSPSNDPYFNLALEEYLFKEFPKTQRGKVLLFWQNANTIVIGRNQNTWAEVNLKELEE 62
Query: 114 EGIEIARRNSGGGTVYHDSGNLNVTFFTPRERYNRRNNLEIISRTLEREWNIQTEINTRE 173
+ + + RR SGGG V+HD GN+ +F TP++ N +I TR
Sbjct: 63 DNVNLFRRFSGGGAVFHDLGNICFSFITPKDGKEFEN----------------AKIFTR- 105
Query: 174 DIVYDGKYKVIIPTLISYQTYQEIISRTLEREWNIQTEINTREDIVYDGKYKISGTAAKL 233
+I L S ++ E++ R D+V DG+ KISG+A +
Sbjct: 106 ---------NVIKALNSL---------------GVEAELSGRNDLVVDGR-KISGSAYYI 140
Query: 234 GRPSSYHHCTLLVNVNKSRLSQSL 257
+ +HH TLL + + S+L++ L
Sbjct: 141 TKDRGFHHGTLLFDADLSKLAKYL 164
>gnl|CDD|223173 COG0095, LplA, Lipoate-protein ligase A [Coenzyme metabolism].
Length = 248
Score = 111 bits (280), Expect = 8e-30
Identities = 59/200 (29%), Positives = 89/200 (44%), Gaps = 39/200 (19%)
Query: 58 SQSSNIFTNLALEDWLYKNFDFTNHHVMLLWRNNPCVVIGRHQNPWQETNLGVLYDEGIE 117
+ + NLAL++ L ++ + L W N P VV+GR QN E NL + ++GI
Sbjct: 9 IRDFDPAFNLALDEALLRSL-SEGGTLRLYWWNPPTVVLGRFQNTLPEVNLEYVKEDGIP 67
Query: 118 IARRNSGGGTVYHDSGNLNVTFFTPRERYNRRNNLEIISRTLEREWNIQTEINTREDIVY 177
+ RR SGGG V+HD GNLN + TP E + +Y
Sbjct: 68 VVRRPSGGGAVFHDLGNLNYSVITPDEGG-----------------------LESYETLY 104
Query: 178 DGKYKVIIPTLISYQTYQEIISRTLEREWNIQTEINTREDIVYDGKYKISGTAAKLGRPS 237
+ +I L + +E E R D+V DGK KISG+A + +
Sbjct: 105 KFLLQPVIDALRAL---------GVEG-----AECPGRNDLVVDGK-KISGSAQRRTKGR 149
Query: 238 SYHHCTLLVNVNKSRLSQSL 257
HH TLL++++ L++ L
Sbjct: 150 ILHHGTLLLDIDLELLARVL 169
>gnl|CDD|179655 PRK03822, lplA, lipoate-protein ligase A; Provisional.
Length = 338
Score = 112 bits (282), Expect = 3e-29
Identities = 60/201 (29%), Positives = 94/201 (46%), Gaps = 42/201 (20%)
Query: 57 ISQSSNIFTNLALEDWLYKNFDFTNHHVMLLWRNNPCVVIGRHQNPWQETNLGVLYDEGI 116
IS S + + NLA+E+ +++ V+ LWRN VVIGR QNPW+E N + ++ +
Sbjct: 8 ISDSYDPWFNLAVEECIFRQMP-ATQRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNV 66
Query: 117 EIARRNSGGGTVYHDSGNLNVTFFTPRERYNRRNNLEIISRTLEREWNIQTEINTREDIV 176
+ARR+SGGG V+HD GN TF + Y++ + I+ L + E + R D+V
Sbjct: 67 RLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNALNS-LGVSAEASGRNDLV 125
Query: 177 YDGKYKVIIPTLISYQTYQEIISRTLEREWNIQTEINTREDIVYDGKYKISGTAAKLGRP 236
+ T +G K+SG+A + +
Sbjct: 126 -----------------------------------VKTA-----EGDRKVSGSAYRETKD 145
Query: 237 SSYHHCTLLVNVNKSRLSQSL 257
+HH TLL+N + SRL+ L
Sbjct: 146 RGFHHGTLLLNADLSRLANYL 166
>gnl|CDD|172552 PRK14061, PRK14061, unknown domain/lipoate-protein ligase A fusion
protein; Provisional.
Length = 562
Score = 100 bits (249), Expect = 6e-24
Identities = 69/239 (28%), Positives = 109/239 (45%), Gaps = 44/239 (18%)
Query: 22 PKLLPSSGVATSRFYSSKPRAPVHNDETKIQKSV--FISQSSNIFTNLALEDWLYKNFDF 79
P LL +S S K P+ + + ++ IS S + + NLA+E+ +++
Sbjct: 195 PFLLTASKPVPEEEESEKKECPITTRKEIVMSTLRLLISDSYDPWFNLAVEECIFRQMPA 254
Query: 80 TNHHVMLLWRNNPCVVIGRHQNPWQETNLGVLYDEGIEIARRNSGGGTVYHDSGNLNVTF 139
T V+ LWRN VVIGR QNPW+E N + ++ + +ARR+SGGG V+HD GN TF
Sbjct: 255 T-QRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNVRLARRSSGGGAVFHDLGNTCFTF 313
Query: 140 FTPRERYNRRNNLEIISRTLEREWNIQTEINTREDIVYDGKYKVIIPTLISYQTYQEIIS 199
+ Y++ + I+ L + E + R D+V
Sbjct: 314 MAGKPEYDKTISTSIVLNALN-ALGVSAEASGRNDLV----------------------- 349
Query: 200 RTLEREWNIQTEINTREDIVYDGKYKISGTAAKLGRPSSYHHCTLLVNVNKSRLSQSLH 258
+ T E G K+SG+A + + +HH TLL+N + SRL+ L+
Sbjct: 350 ------------VKTAE-----GDRKVSGSAYRETKDRGFHHGTLLLNADLSRLANYLN 391
>gnl|CDD|217367 pfam03099, BPL_LplA_LipB, Biotin/lipoate A/B protein ligase family.
This family includes biotin protein ligase,
lipoate-protein ligase A and B. Biotin is covalently
attached at the active site of certain enzymes that
transfer carbon dioxide from bicarbonate to organic
acids to form cellular metabolites. Biotin protein
ligase (BPL) is the enzyme responsible for attaching
biotin to a specific lysine at the active site of biotin
enzymes. Each organism probably has only one BPL. Biotin
attachment is a two step reaction that results in the
formation of an amide linkage between the carboxyl group
of biotin and the epsilon-amino group of the modified
lysine. Lipoate-protein ligase A (LPLA) catalyzes the
formation of an amide linkage between lipoic acid and a
specific lysine residue in lipoate dependent enzymes.
The unusual biosynthesis pathway of lipoic acid is
mechanistically intertwined with attachment of the
cofactor.
Length = 124
Score = 79.8 bits (197), Expect = 5e-19
Identities = 34/156 (21%), Positives = 57/156 (36%), Gaps = 34/156 (21%)
Query: 96 IGRHQNPWQ-ETNLGVLYDEGIEIARRNSGGGTVYHDS-GNLNVTFFTPRERYNRRNNLE 153
+GR Q + E NL L + G+ +ARR +GG V+H GNL + E +
Sbjct: 1 LGRRQKSTKEEVNLEGLEEGGVVVARRQTGGRRVWHSPGGNLAYSLLLLPELKS------ 54
Query: 154 IISRTLEREWNIQTEINTREDIVYDGKYKVIIPTLISYQTYQEIISRTLEREWNIQTEIN 213
+ L+ + + + I I
Sbjct: 55 -----------------------FKPSDLPAYVLLLVLAVLEALGPKA--GIPGIWVRIK 89
Query: 214 TREDIVYDGKYKISGTAAKLGRPSSYHHCTLLVNVN 249
D++ +GK KI+G ++ R + HH TL + +N
Sbjct: 90 WPNDLLVNGK-KIAGILQEIRRGGTLHHGTLGIGIN 124
>gnl|CDD|221343 pfam11962, Peptidase_G2, Peptidase_G2, IMC autoproteolytic cleavage
domain. This domain is found at the very C-terminus of
bacteriophage parallel beta-helical tailspike proteins.
It carries the enzymic residues that induce
autoproteolytic cleavage to bring about maturation of
the folding process of the helix in a chaperone-like
manner. The domain thus mediates the assembly of a large
tailspike protein and then releases itself after
maturation. These C-terminal regions that
autoproteolytically release themselves after maturation
are exchangeable between functionally unrelated
N-terminal proteins and have been identified in a number
of bacteriophage tailspike proteins.
Length = 222
Score = 29.2 bits (66), Expect = 1.5
Identities = 18/78 (23%), Positives = 29/78 (37%), Gaps = 15/78 (19%)
Query: 91 NPCVVIGRHQNPWQETNLGVLYDEGIEIARRNSGGGTVYHDSGNLNVTFF---TPRERYN 147
V++G WQ+ L ++ GG +Y + + + P+E +
Sbjct: 98 TAGVILGSASFHWQDRYL------------KDEFGGRIYEEVTDEDGNVETVKEPKENPD 145
Query: 148 RRNNLEIISRTLEREWNI 165
NLE I R EWN
Sbjct: 146 YDPNLEYIPREERPEWNP 163
>gnl|CDD|107356 cd06361, PBP1_GPC6A_like, Ligand-binding domain of the promiscuous
L-alpha-amino acid receptor GPRC6A which is a
broad-spectrum amino acid-sensing receptor. This family
includes the ligand-binding domain of the promiscuous
L-alpha-amino acid receptor GPRC6A which is a
broad-spectrum amino acid-sensing receptor, and its fish
homolog, the 5.24 chemoreceptor. GPRC6A is a member of
the family C of G-protein-coupled receptors that
transduce extracellular signals into G-protein
activation and ultimately into cellular responses.
Length = 403
Score = 28.7 bits (64), Expect = 3.4
Identities = 23/95 (24%), Positives = 39/95 (41%), Gaps = 7/95 (7%)
Query: 153 EIISRTLEREWNIQTEINTREDIVYDGKYKVIIPTLISYQT---YQEIISRTLEREWNIQ 209
EI+ +L + I T E I+ + K VI+ + + + I R + + W
Sbjct: 207 EILPASLSDNTKLNRIIRTTEKIIEENKVNVIVVFARQFHVFLLFNKAIERNINKVWIAS 266
Query: 210 TEINTREDIVYDGKY----KISGTAAKLGRPSSYH 240
+T + I+ D K+ G K G SS+H
Sbjct: 267 DNWSTAKKILTDPNVKKIGKVVGFTFKSGNISSFH 301
>gnl|CDD|200459 cd11320, AmyAc_AmyMalt_CGTase_like, Alpha amylase catalytic domain
found in maltogenic amylases, cyclodextrin
glycosyltransferase, and related proteins. Enzymes such
as amylases, cyclomaltodextrinase (CDase), and
cyclodextrin glycosyltransferase (CGTase) degrade starch
to smaller oligosaccharides by hydrolyzing the
alpha-D-(1,4) linkages between glucose residues. In the
case of CGTases, an additional cyclization reaction is
catalyzed yielding mixtures of cyclic oligosaccharides
which are referred to as alpha-, beta-, or
gamma-cyclodextrins (CDs), consisting of six, seven, or
eight glucose residues, respectively. CGTases are
characterized depending on the major product of the
cyclization reaction. Besides having similar catalytic
site residues, amylases and CGTases contain carbohydrate
binding domains that are distant from the active site
and are implicated in attaching the enzyme to raw starch
granules and in guiding the amylose chain into the
active site. The maltogenic alpha-amylase from Bacillus
is a five-domain structure, unlike most alpha-amylases,
but similar to that of cyclodextrin glycosyltransferase.
In addition to the A, B, and C domains, they have a
domain D and a starch-binding domain E. Maltogenic
amylase is an endo-acting amylase that has activity on
cyclodextrins, terminally modified linear maltodextrins,
and amylose. 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 = 389
Score = 28.4 bits (64), Expect = 4.0
Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 5/64 (7%)
Query: 90 NNPCVVIG---RHQNPWQETNLGVLYDEGIEIARRNSGGGTVYHDSGNLNVTFFTPRERY 146
N V+I H +P G LYD G + + +H N + ++ RE+
Sbjct: 116 NGIKVIIDFVPNHSSPADYAEDGALYDNGTLVGDYPNDDNGWFH--HNGGIDDWSDREQV 173
Query: 147 NRRN 150
+N
Sbjct: 174 RYKN 177
>gnl|CDD|217752 pfam03833, PolC_DP2, DNA polymerase II large subunit DP2.
Length = 852
Score = 27.8 bits (62), Expect = 7.8
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 126 GTVYHDSGNLNVTFFTPRE 144
GT+ D +L +T F P E
Sbjct: 717 GTIRFDMTDLPITHFRPAE 735
>gnl|CDD|219020 pfam06422, PDR_CDR, CDR ABC transporter. Corresponds to a region
of the PDR/CDR subgroup of ABC transporters comprising
extracellular loop 3, transmembrane segment 6 and
linker region.
Length = 102
Score = 26.0 bits (58), Expect = 8.3
Identities = 7/21 (33%), Positives = 14/21 (66%), Gaps = 3/21 (14%)
Query: 70 EDWLYKNFDFTNHHVMLLWRN 90
+D+L +++ ++ H LWRN
Sbjct: 34 DDYLEESYGYSYSH---LWRN 51
>gnl|CDD|232935 TIGR00354, polC, DNA polymerase, archaeal type II, large subunit.
This model represents the large subunit, DP2, of a two
subunit novel Archaeal replicative DNA polymerase first
characterized for Pyrococcus furiosus. Structure of DP2
appears to be organized as a ~950 residue component
separated from a ~300 residue component by a ~150
residue intein. The other subunit, DP1, has sequence
similarity to the eukaryotic DNA polymerase delta small
subunit [DNA metabolism, DNA replication, recombination,
and repair].
Length = 1095
Score = 27.5 bits (61), Expect = 9.3
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 126 GTVYHDSGNLNVTFFTPRE 144
GT D+ +L +T F P E
Sbjct: 711 GTARFDATDLPITHFKPAE 729
>gnl|CDD|227650 COG5346, COG5346, Predicted membrane protein [Function unknown].
Length = 136
Score = 26.4 bits (58), Expect = 10.0
Identities = 10/39 (25%), Positives = 16/39 (41%)
Query: 166 QTEINTREDIVYDGKYKVIIPTLISYQTYQEIISRTLER 204
N ++ Y K++ I+P Y I TL+R
Sbjct: 19 TFSSNEPDNNFYRKKFEHILPPPDLLSQYNSIYPNTLQR 57
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
0.319 0.134 0.405
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,171,686
Number of extensions: 1235268
Number of successful extensions: 956
Number of sequences better than 10.0: 1
Number of HSP's gapped: 951
Number of HSP's successfully gapped: 29
Length of query: 261
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 166
Effective length of database: 6,723,972
Effective search space: 1116179352
Effective search space used: 1116179352
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 (21.8 bits)
S2: 58 (26.2 bits)