RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5676
(96 letters)
>gnl|CDD|203236 pfam05347, Complex1_LYR, Complex 1 protein (LYR family).
Proteins in this family have been identified as a
component of the higher eukaryotic NADH complex. In
Saccharomyces cerevisiae, the Isd11 protein has been
shown to play a role in Fe/S cluster biogenesis in
mitochondria. We have named this family LYR after a
highly conserved tripeptide motif close to the
N-terminus of these proteins.
Length = 59
Score = 39.9 bits (94), Expect = 5e-06
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 22 RQVQSLYKRAVRNLEAYHSDIVDLRIEAVLLRARFDKHKDEKDLVKIRALLAEGEKEL 79
++V SLY++ +R + +R F K+K+ D KI ALL EG+K+L
Sbjct: 1 KEVLSLYRQLLREARKFPDYNAREYFRR-RIRDEFRKNKNLTDPEKIEALLKEGKKQL 57
>gnl|CDD|221996 pfam13232, Complex1_LYR_1, Complex1_LYR-like. This is a family
of proteins carrying the LYR motif of family
Complex1_LYR, pfam05347, likely to be involved in Fe-S
cluster biogenesis in mitochondria.
Length = 61
Score = 39.1 bits (92), Expect = 1e-05
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 22 RQVQSLYKRAVRNLEAYHSDIVDLRIEAV-LLRARFDKHKDEKDLVKIRALLAEGEKEL 79
++V SLY++ +R A + R +R F K+KD D KI LL EG+K+L
Sbjct: 1 KEVLSLYRQLLR--AARKFPDYNFREYIRRRIRDEFRKNKDLTDPEKIEKLLKEGKKQL 57
>gnl|CDD|221290 pfam11885, DUF3405, Protein of unknown function (DUF3405). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are typically between 636 to 810
amino acids in length.
Length = 483
Score = 26.2 bits (58), Expect = 2.7
Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 6/42 (14%)
Query: 49 AVLLRARFDKHKDEKDLVKIRALLAE------GEKELFETTH 84
AV++RA E D++ +R+L++E GE ++ H
Sbjct: 94 AVVIRAWHGYKWTENDILNLRSLISELSLRSGGEYDVHLLVH 135
>gnl|CDD|238668 cd01372, KISc_KIF4, Kinesin motor domain, KIF4-like subfamily.
Members of this group seem to perform a variety of
functions, and have been implicated in neuronal
organelle transport and chromosome segregation during
mitosis. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In most kinesins, the
motor domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
Kinesin motor domains hydrolyze ATP at a rate of about
80 per second, and move along the microtubule at a speed
of about 6400 Angstroms per second. To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 341
Score = 26.1 bits (58), Expect = 3.0
Identities = 14/60 (23%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 9 RAIQIPFELPTHRRQVQSLYKRAVRNLEAYHSDIVDLRIEAVLLRARFDKHKDEKDLVKI 68
RAIQ F+ ++ + ++ V LE Y+ ++ DL + ++ +D K + I
Sbjct: 109 RAIQHIFKK-IDEKKDEPDFQLKVSFLELYNEEVRDLLSPSTSEKSPIQIREDSKGNIII 167
>gnl|CDD|178029 PLN02407, PLN02407, diphosphomevalonate decarboxylase.
Length = 343
Score = 25.9 bits (57), Expect = 3.1
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 10/48 (20%)
Query: 52 LRARFDKHKDEKDLVKIRALLAEGEKELFETTH---PSPIKFPTSPGL 96
+RAR +DE+ +KI K+ +E H S FPT+ GL
Sbjct: 80 IRARATDVEDEEKGIKIT-------KKDWEKLHVHIASYNNFPTAAGL 120
>gnl|CDD|217526 pfam03385, DUF288, Protein of unknown function, DUF288.
Length = 390
Score = 25.9 bits (57), Expect = 4.1
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 9 RAIQIPFELPTHRRQVQSLYKRAVRNLEAYHSDIVD 44
R + + FEL + +RA + L Y DIV+
Sbjct: 137 RRMHLEFELVDPNKTEDESIQRAEQKLN-YFGDIVN 171
>gnl|CDD|212119 cd10808, YdjC, Escherichia coli YdjC-like family of proteins.
Uncharacterized subfamily of YdjC-like family of
proteins. Included in this subfamily is the
uncharacterized Escherichia coli protein YdjC (also
known as ChbG), encoded by the chb
(N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel
operon, which encodes enzymes involved in growth on an
N,N'-diacetylchitobiose carbon source. The molecular
function of this subfamily is unclear.
Length = 259
Score = 25.7 bits (57), Expect = 4.2
Identities = 25/94 (26%), Positives = 31/94 (32%), Gaps = 27/94 (28%)
Query: 9 RAIQIPFELPTHRRQVQSLYKRAVRNLEAYHSDIVDLRIEAVLLRARFDKHK-------- 60
A++IP E P R +S +R V L + A RAR +
Sbjct: 151 PAVRIPDEPPFFARLAKSGLRRRAG---------VGLSVLAARARARLRRLGLSTPDGFW 201
Query: 61 --------DEKDLVKIRALLAEGEKELFETTHPS 86
DE L I L EG EL HP
Sbjct: 202 GIVAGGALDEATLRAILDRLPEGVTEL--MCHPG 233
>gnl|CDD|233479 TIGR01578, MiaB-like-B, MiaB-like tRNA modifying enzyme,
archaeal-type. This clade of sequences is closely
related to MiaB, a modifier of isopentenylated
adenosine-37 of certain eukaryotic and bacterial tRNAs
(see TIGR01574). Sequence alignments suggest that this
equivalog performs the same chemical transformation as
MiaB, perhaps on a different (or differently modified)
tRNA base substrate. This clade is a member of a
subfamily (TIGR00089) and spans the archaea and
eukaryotes. The only archaeal miaB-like genes are in
this clade, while eukaryotes have sequences described by
This model as well as ones falling within the scope of
the MiaB equivalog model [Protein synthesis, tRNA and
rRNA base modification].
Length = 420
Score = 25.5 bits (56), Expect = 4.4
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 53 RARFDKHKDEKDLVKIRALLAEGEKELFET 82
R + + EK + K R L+AEG KE++ T
Sbjct: 156 RGKLASYPPEKIVEKARQLVAEGCKEIWIT 185
>gnl|CDD|151215 pfam10730, DUF2521, Protein of unknown function (DUF2521).
Family of unknown function specific to Bacillus.
Length = 147
Score = 24.6 bits (54), Expect = 7.8
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 43 VDLRIEAVLLRARFDK---HKDEKDLVKIRALLAEGEKELFET 82
+D IEA LL R+ + + + + K R E EKEL +T
Sbjct: 58 IDFAIEAYLLGGRYGRFGYYGEPAEDAKKRC--EEEEKELTDT 98
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
0.323 0.138 0.390
Gapped
Lambda K H
0.267 0.0798 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,111,759
Number of extensions: 442459
Number of successful extensions: 494
Number of sequences better than 10.0: 1
Number of HSP's gapped: 492
Number of HSP's successfully gapped: 37
Length of query: 96
Length of database: 10,937,602
Length adjustment: 63
Effective length of query: 33
Effective length of database: 8,143,300
Effective search space: 268728900
Effective search space used: 268728900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.1 bits)