RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12734
(217 letters)
>gnl|CDD|193257 pfam12781, AAA_9, ATP-binding dynein motor region D5. The 380 kDa
motor unit of dynein belongs to the AAA class of
chaperone-like ATPases. The core of the 380 kDa motor
unit contains a concatenated chain of six AAA modules,
of which four correspond to the ATP binding sites with
P-loop signatures described previously, and two are
modules in which the P loop has been lost in evolution.
This particular family is the D5 ATP-binding region of
the motor, but has lost its P-loop.
Length = 228
Score = 55.8 bits (134), Expect = 2e-09
Identities = 22/51 (43%), Positives = 33/51 (64%)
Query: 107 LCDDVMISQWNSEGLPPDELSIQNGILSTRGCHFPLCIDPQTQALKWIRNR 157
L DD ++ WN+EGLP D +S +N + +PL +DPQ Q +KWI+N+
Sbjct: 2 LTDDADVATWNNEGLPSDRMSTENATILGNCERWPLMVDPQLQGIKWIKNK 52
Score = 50.4 bits (120), Expect = 1e-07
Identities = 20/49 (40%), Positives = 31/49 (63%)
Query: 158 EDKNNLKWNSEGLPPDELSIQNGILSTRGCHFPLCIDPQTQALKWIRNR 206
+D + WN+EGLP D +S +N + +PL +DPQ Q +KWI+N+
Sbjct: 4 DDADVATWNNEGLPSDRMSTENATILGNCERWPLMVDPQLQGIKWIKNK 52
>gnl|CDD|193253 pfam12777, MT, Microtubule-binding stalk of dynein motor. the 380
kDa motor unit of dynein belongs to the AAA class of
chaperone-like ATPases. The core of the 380 kDa motor
unit contains a concatenated chain of six AAA modules,
of which four correspond to the ATP binding sites with
P-loop signatures described previously, and two are
modules in which the P loop has been lost in evolution.
This family is the region between D4 and D5 and is the
two predicted alpha-helical coiled coil segments that
form the stalk supporting the ATP-sensitive microtubule
binding component.
Length = 344
Score = 53.9 bits (129), Expect = 1e-08
Identities = 23/85 (27%), Positives = 42/85 (49%)
Query: 2 SKYVGAMTERQKLQEETDIMMRRLEAADKLISGLGREKIRWTADLATLEQNRNQLIGACL 61
+ + A ++ K Q+E + R + A++L+ GL E +RW + + L G L
Sbjct: 256 AAFEKATADKLKCQQEAEATNRTILLANRLVGGLASENVRWAEAVENFKSQEVTLCGDVL 315
Query: 62 LSGAFLCYTSAFTWEFRQQMVYVDW 86
L AF+ Y FT ++R +++ W
Sbjct: 316 LITAFVSYVGYFTKKYRNELMERFW 340
>gnl|CDD|235477 PRK05456, PRK05456, ATP-dependent protease subunit HslV;
Provisional.
Length = 172
Score = 30.0 bits (69), Expect = 0.65
Identities = 14/27 (51%), Positives = 16/27 (59%), Gaps = 8/27 (29%)
Query: 18 TDIMMRRLEA----ADK----LISGLG 36
TD +RRLEA ADK +ISG G
Sbjct: 85 TDRYLRRLEAMLIVADKEHSLIISGNG 111
>gnl|CDD|165727 PLN00160, PLN00160, histone H3; Provisional.
Length = 97
Score = 28.9 bits (64), Expect = 0.67
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 7/67 (10%)
Query: 7 AMTERQKLQEETDIMMRRLEAA---DKLISGLGREKIRW--TADLATLEQNRNQLIGACL 61
A+ E + Q+ TD+++RRL A ++ + RE RW +A LA E L+G L
Sbjct: 7 ALKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVG--L 64
Query: 62 LSGAFLC 68
+ LC
Sbjct: 65 FEDSNLC 71
>gnl|CDD|211862 TIGR03692, ATP_dep_HslV, ATP-dependent protease HslVU, peptidase
subunit. The ATP-dependent protease HslVU, a complex of
hexameric HslU active as a protein-unfolding ATPase and
dodecameric HslV, the catalytic threonine protease
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 171
Score = 29.0 bits (66), Expect = 1.2
Identities = 15/27 (55%), Positives = 16/27 (59%), Gaps = 8/27 (29%)
Query: 18 TDIMMRRLEA----ADK----LISGLG 36
TD +RRLEA ADK LISG G
Sbjct: 84 TDRYLRRLEAMLIVADKETSLLISGTG 110
>gnl|CDD|215507 PLN02939, PLN02939, transferase, transferring glycosyl groups.
Length = 977
Score = 29.9 bits (67), Expect = 1.3
Identities = 18/58 (31%), Positives = 28/58 (48%)
Query: 8 MTERQKLQEETDIMMRRLEAADKLISGLGREKIRWTADLATLEQNRNQLIGACLLSGA 65
+TE++ LQ + +I+ RL D I +EKI LE+ RN+L+ G
Sbjct: 162 LTEKEALQGKINILEMRLSETDARIKLAAQEKIHVEILEEQLEKLRNELLIRGATEGL 219
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 28.9 bits (65), Expect = 2.8
Identities = 10/47 (21%), Positives = 22/47 (46%)
Query: 10 ERQKLQEETDIMMRRLEAADKLISGLGREKIRWTADLATLEQNRNQL 56
KL+ E D ++ +E ++ I + + + T + A L++ L
Sbjct: 323 RLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAELKEELEDL 369
>gnl|CDD|238894 cd01913, protease_HslV, Protease HslV and the ATPase/chaperone HslU
are part of an ATP-dependent proteolytic system that is
the prokaryotic homolog of the proteasome. HslV is a
dimer of hexamers (a dodecamer) that forms a central
proteolytic chamber with active sites on the interior
walls of the cavity. HslV shares significant sequence
and structural similarity with the proteasomal
beta-subunit and both are members of the Ntn-family of
hydrolases. HslV has a nucleophilic threonine residue
at its N-terminus that is exposed after processing of
the propeptide and is directly involved in active site
catalysis.
Length = 171
Score = 27.9 bits (63), Expect = 3.2
Identities = 15/27 (55%), Positives = 16/27 (59%), Gaps = 8/27 (29%)
Query: 18 TDIMMRRLEA----ADK----LISGLG 36
TD +RRLEA ADK LISG G
Sbjct: 84 TDRYLRRLEAMLIVADKEHTLLISGNG 110
>gnl|CDD|215082 PLN00161, PLN00161, histone H3; Provisional.
Length = 135
Score = 26.9 bits (59), Expect = 4.9
Identities = 18/56 (32%), Positives = 33/56 (58%), Gaps = 5/56 (8%)
Query: 7 AMTERQKLQEETDIMMRRLEAA---DKLISGLGREKIRWTAD--LATLEQNRNQLI 57
A+ E +K Q+ T++++R+L A ++ + + RE RWTA+ LA E + L+
Sbjct: 41 ALREIRKYQKSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLV 96
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 27.8 bits (62), Expect = 5.1
Identities = 13/48 (27%), Positives = 20/48 (41%)
Query: 9 TERQKLQEETDIMMRRLEAADKLISGLGREKIRWTADLATLEQNRNQL 56
E L+EE + + RLE ++ + L E L LE+ L
Sbjct: 723 RELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESL 770
>gnl|CDD|199906 cd10318, RGL11, Rhamnogalacturonan lyase of the polysaccharide
lyase family 11. The rhamnogalacturonan lyase of the
polysaccharide lyase family 11 (RGL11) cleaves glycoside
bonds in polygalacturonan as well as RG
(rhamnogalacturonan) type-I through a beta-elimination
reaction. Functionally characterized members of this
family, YesW and YesX from Bacillus subtilis, cleave
glycoside bonds between rhamnose and galacturonic acid
residues in the RG-I region of plant cell wall pectin.
YesW and YesX work synergistically, with YesW cleaving
the glycoside bond of the RG chain endolytically, and
YesX converting the resultant oligosaccharides through
an exotype reaction. This domain is sometimes found in
architectures with non-catalytic carbohydrate-binding
modules (CBMs). There are two types of RG lyases, which
both cleave the alpha-1,4 bonds of the RG-I main chain
through a beta-elimination reaction, but belong to two
structurally unrelated polysaccharide lyase (PL)
families, 4 and 11.
Length = 564
Score = 27.6 bits (62), Expect = 5.3
Identities = 13/35 (37%), Positives = 17/35 (48%)
Query: 103 LEKELCDDVMISQWNSEGLPPDELSIQNGILSTRG 137
L +EL D I +WN E D L +G+ S G
Sbjct: 460 LLRELLDGTTIDKWNWENEKSDRLLTASGVTSNNG 494
>gnl|CDD|217458 pfam03256, APC10, Anaphase-promoting complex, subunit 10 (APC10).
Length = 175
Score = 27.0 bits (60), Expect = 6.4
Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 6/64 (9%)
Query: 70 TSAFTWEFRQQMVYVDWQSNITKLSIPIVSDFRL----EKELCDDVMISQWNSEGLPPDE 125
+F Q + I L++ +S + + L DD + + W S+G P
Sbjct: 6 PPSFGDP--SQRELAGFMREIGGLAVWSLSSCKHGNGVDHLLRDDNLDTYWQSDGSQPHL 63
Query: 126 LSIQ 129
++IQ
Sbjct: 64 VNIQ 67
>gnl|CDD|237526 PRK13837, PRK13837, two-component VirA-like sensor kinase;
Provisional.
Length = 828
Score = 27.7 bits (62), Expect = 6.5
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 5 VGAMTERQKLQEETDIMMRRLEAADKL 31
+ ER++L+ E D + RRLE A +L
Sbjct: 421 LAHAIERRRLETERDALERRLEHARRL 447
>gnl|CDD|213755 TIGR02977, phageshock_pspA, phage shock protein A. Members of this
family are the phage shock protein PspA, from the phage
shock operon. This is a narrower family than the set of
PspA and its homologs, sometimes several in a genome, as
described by pfam04012. PspA appears to maintain the
protonmotive force under stress conditions that include
overexpression of certain phage secretins, heat shock,
ethanol, and protein export defects [Cellular processes,
Adaptations to atypical conditions].
Length = 219
Score = 26.5 bits (59), Expect = 10.0
Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 7/46 (15%)
Query: 6 GAMTERQKLQEETDIMMRRLEAADKLISGLGREKIRWTADLATLEQ 51
A+ E+QK QE + + R L A ++ ++ + D+A L+
Sbjct: 89 AALIEKQKAQELAEALERELAAVEETLA-------KLQEDIAKLQA 127
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 0.135 0.422
Gapped
Lambda K H
0.267 0.0565 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,021,888
Number of extensions: 994339
Number of successful extensions: 831
Number of sequences better than 10.0: 1
Number of HSP's gapped: 831
Number of HSP's successfully gapped: 27
Length of query: 217
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 124
Effective length of database: 6,812,680
Effective search space: 844772320
Effective search space used: 844772320
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 (26.1 bits)