RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 028426
(209 letters)
>gnl|CDD|223173 COG0095, LplA, Lipoate-protein ligase A [Coenzyme metabolism].
Length = 248
Score = 74.7 bits (184), Expect = 2e-16
Identities = 43/186 (23%), Positives = 73/186 (39%), Gaps = 19/186 (10%)
Query: 16 RDQVPVMKRFTGGGTVVVDKGTVFVTLICNKDDVPGVQPFPRSIMSWSGLLYNQVFK--- 72
D +PV++R +GGG V D G + ++I + S + L V
Sbjct: 63 EDGIPVVRRPSGGGAVFHDLGNLNYSVITPDEG------GLESYETLYKFLLQPVIDALR 116
Query: 73 --GIADFQLR-ENDYVFGNRKFGGNAQSITKNRWIHHTSFLWDYAEGNMA-FLKQPARAP 128
G+ + ND V +K G+AQ TK R +HH + L D +A L+ P
Sbjct: 117 ALGVEGAECPGRNDLVVDGKKISGSAQRRTKGRILHHGTLLLDIDLELLARVLRVPKEKI 176
Query: 129 EYRMERGHTEFICRMNEYLPRT--DFIEKTTEAVETYFSVKNVNLEATEEPCGAEFVPST 186
+ + + E + + E L + +F+E EA V+ E E +
Sbjct: 177 KSKGIKSVRERVANLEELLKISVEEFLEALLEAFFKVLGVE----LEEYELTPEELELAE 232
Query: 187 RLLSKQ 192
+L ++
Sbjct: 233 KLAEEK 238
>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 = 54.7 bits (132), Expect = 5e-10
Identities = 20/101 (19%), Positives = 32/101 (31%), Gaps = 7/101 (6%)
Query: 19 VPVMKRFTGGGTVVVD-KGTVFVTLICNKDDVPGVQPFPRSIMSWSG------LLYNQVF 71
V V +R TGG V G + +L+ + + + L
Sbjct: 22 VVVARRQTGGRRVWHSPGGNLAYSLLLLPELKSFKPSDLPAYVLLLVLAVLEALGPKAGI 81
Query: 72 KGIADFQLRENDYVFGNRKFGGNAQSITKNRWIHHTSFLWD 112
GI ND + +K G Q I + +HH +
Sbjct: 82 PGIWVRIKWPNDLLVNGKKIAGILQEIRRGGTLHHGTLGIG 122
>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 = 52.1 bits (125), Expect = 4e-08
Identities = 45/157 (28%), Positives = 72/157 (45%), Gaps = 17/157 (10%)
Query: 17 DQVPVMKRFTGGGTVVVDKGTVFVTLICNKD--DVPGVQPFPRSIMSWSGLLYNQVFKGI 74
D V + +RF+GGG V D G + + I KD + + F R+++ N + G+
Sbjct: 63 DNVNLFRRFSGGGAVFHDLGNICFSFITPKDGKEFENAKIFTRNVIKA----LNSL--GV 116
Query: 75 -ADFQLRENDYVFGNRKFGGNAQSITKNRWIHHTSFLWDYAEGNMAFLKQPARAPEYRME 133
A+ R ND V RK G+A ITK+R HH + L+D +A + ++E
Sbjct: 117 EAELSGR-NDLVVDGRKISGSAYYITKDRGFHHGTLLFDADLSKLAKYLNVDKT---KIE 172
Query: 134 -RGHTEFICR---MNEYLPRTDFIEKTTEAVETYFSV 166
+G T R + EYLP + E + +F+
Sbjct: 173 SKGITSVRSRVVNVKEYLPNITTEQFLEEMTQAFFTY 209
>gnl|CDD|172552 PRK14061, PRK14061, unknown domain/lipoate-protein ligase A fusion
protein; Provisional.
Length = 562
Score = 34.3 bits (78), Expect = 0.037
Identities = 45/165 (27%), Positives = 68/165 (41%), Gaps = 18/165 (10%)
Query: 17 DQVPVMKRFTGGGTVVVDKGTVFVTLICNKDDVPGVQPFPRSIMSWSGLLYNQVFKGIAD 76
D V + +R +GGG V D G T + K P +S S +L G++
Sbjct: 288 DNVRLARRSSGGGAVFHDLGNTCFTFMAGK-------PEYDKTISTSIVLNALNALGVSA 340
Query: 77 FQLRENDYVF----GNRKFGGNAQSITKNRWIHHTSFLWDYAEGNMAFLKQPARAPEYRM 132
ND V G+RK G+A TK+R HH + L + +A P + +
Sbjct: 341 EASGRNDLVVKTAEGDRKVSGSAYRETKDRGFHHGTLLLNADLSRLANYLNPDK--KKLA 398
Query: 133 ERGHTEFICR---MNEYLPRTDFIEKTTEAV-ETYFSVKNVNLEA 173
+G T R + E LP E+ EA+ E +F+ +EA
Sbjct: 399 AKGITSVRSRVTNLTELLPGIPH-EQVCEAITEAFFAHYGERVEA 442
>gnl|CDD|179655 PRK03822, lplA, lipoate-protein ligase A; Provisional.
Length = 338
Score = 29.7 bits (67), Expect = 1.1
Identities = 29/101 (28%), Positives = 47/101 (46%), Gaps = 13/101 (12%)
Query: 17 DQVPVMKRFTGGGTVVVDKGTVFVTLICNKDDVPGVQPFPRSIMSWSGLLYNQVFK-GIA 75
D V + +R +GGG V D G T + K P + ++I + ++ N + G++
Sbjct: 64 DNVRLARRSSGGGAVFHDLGNTCFTFMAGK---PE---YDKTIST--SIVLNALNSLGVS 115
Query: 76 DFQLRENDYVF----GNRKFGGNAQSITKNRWIHHTSFLWD 112
ND V G+RK G+A TK+R HH + L +
Sbjct: 116 AEASGRNDLVVKTAEGDRKVSGSAYRETKDRGFHHGTLLLN 156
>gnl|CDD|191441 pfam06073, DUF934, Bacterial protein of unknown function
(DUF934). This family consists of several bacterial
proteins of unknown function. One of the members of
this family, BMEI1764, is thought to be an
oxidoreductase.
Length = 110
Score = 28.3 bits (64), Expect = 1.3
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 7 ELLEIGSVLRDQVPVMKR 24
EL +G VLRDQ+ M R
Sbjct: 51 ELRAVGDVLRDQLFFMLR 68
>gnl|CDD|226272 COG3749, COG3749, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 167
Score = 27.7 bits (62), Expect = 3.0
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 7 ELLEIGSVLRDQVPVMKR 24
EL +G VL DQ+P M R
Sbjct: 106 ELRAVGDVLIDQLPFMLR 123
>gnl|CDD|216646 pfam01681, C6, C6 domain. This domain of unknown function is
found in a C. elegans protein. It is presumed to be an
extracellular domain. The C6 domain contains six
conserved cysteine residues in most copies of the
domain. However some copies of the domain are missing
cysteine residues 1 and 3 suggesting that these form a
disulphide bridge.
Length = 92
Score = 26.6 bits (59), Expect = 3.7
Identities = 13/27 (48%), Positives = 15/27 (55%)
Query: 21 VMKRFTGGGTVVVDKGTVFVTLICNKD 47
VM GGG + GTV +TL CN D
Sbjct: 50 VMLLNNGGGPLESGVGTVNITLTCNSD 76
>gnl|CDD|236163 PRK08140, PRK08140, enoyl-CoA hydratase; Provisional.
Length = 262
Score = 27.6 bits (62), Expect = 4.3
Identities = 11/20 (55%), Positives = 14/20 (70%), Gaps = 2/20 (10%)
Query: 112 DYAEGNMAFLKQPARAPEYR 131
DYAEG AFL++ RAP +
Sbjct: 243 DYAEGVSAFLEK--RAPRFT 260
>gnl|CDD|200537 cd11276, Sema_plexin_B2, The Sema domain, a protein interacting
module, of Plexin B2. Plexin B2 serves as the receptor
of Sema4C and Sema4G. By signaling the effect of Sema4C
and Sema4G, the plexin B2 receptor plays important roles
in neural tube closure and cerebellar granule cell
development. Mice lacking Plexin B2 demonstrated defects
in closure of the neural tube and disorganization of the
embryonic brain. In developing kidney, Sema4C-Plexin B2
signaling modulates ureteric branching. Plexin B2 is
expressed both in the pretubular aggregates and the
ureteric epithelium in the developing kidney. Deletion
of Plexin B2 results in renal hypoplasia and occasional
double ureters. The Sema domain is located at the
N-terminus and contains four disulfide bonds formed by
eight conserved cysteine residues. It serves as a
ligand-recognition and -binding module.
Length = 449
Score = 27.4 bits (61), Expect = 5.3
Identities = 9/21 (42%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 177 PCGAEFVPSTRLLSKQELEEA 197
PCG+E +P L S+ EL
Sbjct: 346 PCGSEHLPYP-LGSRDELALT 365
>gnl|CDD|240245 PTZ00050, PTZ00050, 3-oxoacyl-acyl carrier protein synthase;
Provisional.
Length = 421
Score = 27.3 bits (61), Expect = 6.7
Identities = 11/51 (21%), Positives = 18/51 (35%), Gaps = 9/51 (17%)
Query: 159 AVETYFSVK---------NVNLEATEEPCGAEFVPSTRLLSKQELEEALGT 200
AVE+ ++ +NLE + C V Q ++ L T
Sbjct: 355 AVESIVTILSLYEQIIPPTINLENPDAECDLNLVQGKTAHPLQSIDAVLST 405
>gnl|CDD|233894 TIGR02492, flgK_ends, flagellar hook-associated protein FlgK. The
flagellar hook-associated protein FlgK of bacterial
flagella has conserved N- and C-terminal domains. The
central region is highly variable in length and
sequence, and often contains substantial runs of
low-complexity sequence. This model is built from an
alignment of FlgK sequences with the central region
excised. Note that several other proteins of the
flagellar apparatus also are homologous in the N- and
C-terminal regions to FlgK, but are excluded from this
model [Cellular processes, Chemotaxis and motility].
Length = 324
Score = 26.9 bits (60), Expect = 9.3
Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 1 MLRKPSELLEIGSVLRDQVPVMKRFTGGGTVVVDKGTVFVTLICNKDDV 49
+L++ S+L+ I SV ++ + +TG G V+VD +
Sbjct: 202 LLKELSQLIGI-SVSENENGTVNVYTGSGQVLVDGARTVTGSSTSPLTA 249
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
0.320 0.137 0.413
Gapped
Lambda K H
0.267 0.0807 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,907,823
Number of extensions: 1004402
Number of successful extensions: 732
Number of sequences better than 10.0: 1
Number of HSP's gapped: 727
Number of HSP's successfully gapped: 15
Length of query: 209
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 116
Effective length of database: 6,812,680
Effective search space: 790270880
Effective search space used: 790270880
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: 57 (25.6 bits)