RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9484
(407 letters)
>gnl|CDD|221325 pfam11934, DUF3452, Domain of unknown function (DUF3452). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria and eukaryotes. This domain
is typically between 124 to 150 amino acids in length.
This domain is found associated with pfam01858,
pfam01857. This domain has a single completely conserved
residue W that may be functionally important.
Length = 138
Score = 120 bits (303), Expect = 5e-33
Identities = 52/146 (35%), Positives = 83/146 (56%), Gaps = 10/146 (6%)
Query: 63 TVPTVNSNRTIEGNLVCLTSLLKHCKMSLNQFLNKCRKWA-DMRKLPDS-FRSKIARLER 120
P V T EGN V LT +L+ CK++L +F K +++ M + ++ F +++ LER
Sbjct: 1 LSPPVGGKGTAEGNGVSLTQILRACKLNLVEFFKKLKQFDVKMDSILENRFGAEVKELER 60
Query: 121 NFAVSKVIFTKYLPMFKEMFKPPDLDELLMHVRHNKKKMIHCTSTKVFEFTWILFVLTKA 180
NF V V++ KY +F+E+F P + C+S+ +F F W+LF+L K
Sbjct: 61 NFVVLSVLYKKYKRIFREIFLEPPEEPPSRSSP--------CSSSDLFRFGWLLFLLAKG 112
Query: 181 EYLDVSNDLVNSFHLLIATCDLIYAN 206
E L + +DLV+S+HLL+ DL+Y N
Sbjct: 113 EALSMFDDLVSSYHLLLCVLDLLYIN 138
>gnl|CDD|202014 pfam01858, RB_A, Retinoblastoma-associated protein A domain. This
domain has the cyclin fold as predicted.
Length = 192
Score = 60.9 bits (148), Expect = 5e-11
Identities = 24/40 (60%), Positives = 31/40 (77%)
Query: 256 VIVRAEASLSRDIVKHLNLTEEQVLDSLAWVSNSPLWKNI 295
+R E LSR++VKHLN EEQ+L+SLAW S+SPLW+ I
Sbjct: 153 SFIRHEGGLSREMVKHLNSIEEQILESLAWKSDSPLWEMI 192
>gnl|CDD|166018 PLN02377, PLN02377, 3-ketoacyl-CoA synthase.
Length = 502
Score = 35.0 bits (80), Expect = 0.065
Identities = 21/84 (25%), Positives = 44/84 (52%), Gaps = 11/84 (13%)
Query: 105 RKLPDSFRS---KIARLERNFAVSKVIFTKYLPMF------KEMFKPPDLDELLMHVRHN 155
R LPD +S K +L ++ +S ++ ++P+ P DL +L +H+++N
Sbjct: 13 RMLPDFLQSVNLKYVKLGYHYLISNLLTLCFIPLIIIISIEASQMNPDDLRQLWIHLQYN 72
Query: 156 KKKMIHCTSTKVFEFTWILFVLTK 179
+I C++ VF T ++++T+
Sbjct: 73 LVSIIICSAFLVFGLT--VYIMTR 94
>gnl|CDD|109440 pfam00382, TFIIB, Transcription factor TFIIB repeat.
Length = 71
Score = 31.9 bits (73), Expect = 0.070
Identities = 13/53 (24%), Positives = 18/53 (33%), Gaps = 1/53 (1%)
Query: 14 QELCMALNIDSTTAKEAWNAYKEMSHHYTLEG-SQLHWLGCSLYVSCRKATVP 65
+ AL + A A K L+G S LY++CR V
Sbjct: 2 KRFADALELPKKVADAANELAKLALDDNLLKGRSPESIAAACLYIACRLEEVK 54
>gnl|CDD|132518 TIGR03478, DMSO_red_II_bet, DMSO reductase family type II enzyme,
iron-sulfur subunit. This model represents the
iron-sulfur subunit, typically called the beta subunit,
of various proteins that also contain a molybdopterin
subunit and a heme b subunit. The group includes two
distinct but very closely related periplasmic proteins
of anaerobic respiration, selenate reductase and
chlorate reductase. Other members of this family include
dimethyl sulphide dehydrogenase and ethylbenzene
dehydrogenase [Energy metabolism, Anaerobic, Energy
metabolism, Electron transport].
Length = 321
Score = 31.7 bits (72), Expect = 0.60
Identities = 11/41 (26%), Positives = 14/41 (34%), Gaps = 8/41 (19%)
Query: 360 ETAPG--------SSGPGLDDLSPAPAPGGAPPEVDFGIDF 392
ET PG G G PG P +D+G +
Sbjct: 42 ETYPGKGYPRNWERKGGGFKRGGKLKQPGIIPTLIDYGDPW 82
>gnl|CDD|131920 TIGR02873, spore_ylxY, probable sporulation protein, polysaccharide
deacetylase family. Members of this protein family are
most closely related to TIGR02764, a subset of
polysaccharide deacetylase family proteins found in a
species if and only if the species forms endospores like
those of Bacillus subtilis or Clostridium tetani. This
family is likewise restricted to spore-formers, but is
not universal among them in having sequences with
full-length matches to the model [Energy metabolism,
Biosynthesis and degradation of polysaccharides,
Cellular processes, Sporulation and germination].
Length = 268
Score = 31.0 bits (70), Expect = 0.85
Identities = 23/61 (37%), Positives = 30/61 (49%), Gaps = 15/61 (24%)
Query: 333 NKMYEEYILSVGDFDERIFLPKFQSFDETAPGSSGPGLDDLSPAPAPGGAP--PEVDFGI 390
NKM +E G FDE++ + FDE +P LDDL P+P G P P V I
Sbjct: 45 NKMKQE-----GRFDEKLLV-----FDEVSPSVH---LDDLPPSPIYRGHPEKPMVALLI 91
Query: 391 D 391
+
Sbjct: 92 N 92
>gnl|CDD|217305 pfam02970, TBCA, Tubulin binding cofactor A.
Length = 91
Score = 28.4 bits (64), Expect = 2.1
Identities = 7/32 (21%), Positives = 17/32 (53%)
Query: 295 IEDSGQEIPGCEQKLRGNIEDLSAILEPENFD 326
++++ +P C+++L+ + DL LE
Sbjct: 50 LKETEMMLPDCKRRLQKAVADLEEYLEEYEEG 81
>gnl|CDD|212486 cd06168, LSMD1, LSM domain containing 1. The eukaryotic Sm and
Sm-like (LSm) proteins associate with RNA to form the
core domain of the ribonucleoprotein particles involved
in a variety of RNA processing events including
pre-mRNA splicing, telomere replication, and mRNA
degradation. Members of this family share a highly
conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet. LSMD1 proteins have a single Sm-like domain
structure. Sm-like proteins exist in archaea as well as
prokaryotes, forming heptameric and hexameric ring
structures similar to those found in eukaryotes.
Length = 73
Score = 27.5 bits (62), Expect = 2.7
Identities = 9/31 (29%), Positives = 12/31 (38%), Gaps = 8/31 (25%)
Query: 50 WLGCSLYVSCRKATVPTVNSNRTIEGNLVCL 80
LG +L V T+ R + G VC
Sbjct: 7 LLGRTLRV--------TLTDGRVLVGTFVCT 29
>gnl|CDD|218745 pfam05783, DLIC, Dynein light intermediate chain (DLIC). This
family consists of several eukaryotic dynein light
intermediate chain proteins. The light intermediate
chains (LICs) of cytoplasmic dynein consist of multiple
isoforms, which undergo post-translational modification
to produce a large number of species. DLIC1 is known to
be involved in assembly, organisation, and function of
centrosomes and mitotic spindles when bound to
pericentrin. DLIC2 is a subunit of cytoplasmic dynein 2
that may play a role in maintaining Golgi organisation
by binding cytoplasmic dynein 2 to its Golgi-associated
cargo.
Length = 490
Score = 29.0 bits (65), Expect = 4.5
Identities = 16/37 (43%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 347 DERIFLPKFQSFDETAPGSSGPGLDDLSPAPAPGGAP 383
DE++FL K QS P + G++ SPA +PGG+P
Sbjct: 349 DEQVFLMKQQSLLAKQPATPTRGVE--SPARSPGGSP 383
>gnl|CDD|224476 COG1560, HtrB, Lauroyl/myristoyl acyltransferase [Cell envelope
biogenesis, outer membrane].
Length = 308
Score = 28.8 bits (65), Expect = 5.1
Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 4/45 (8%)
Query: 121 NFAVSKVIFTKYLPMFKEMFKP---PDLDELLMHVR-HNKKKMIH 161
N+ + + P M++P P LD L+ R +++
Sbjct: 134 NWELGGRALAQQGPKVTAMYRPPKNPLLDWLITRGRERFGGRLLP 178
>gnl|CDD|202488 pfam02964, MeMO_Hyd_G, Methane monooxygenase, hydrolase gamma
chain.
Length = 161
Score = 27.9 bits (62), Expect = 7.0
Identities = 14/71 (19%), Positives = 29/71 (40%), Gaps = 5/71 (7%)
Query: 73 IEGNLVCLTSLLKHCKMSLNQFLNKCRKWADMRKLPDSFRSKIARLERNFAVSKVIFTKY 132
IE + ++LK K ++ + K D + ++ +K+ A K +
Sbjct: 51 IERKIEEKLAVLKTEKFNVADLITKATTGEDAAAVEATWVAKM-----KAAADKYEAERI 105
Query: 133 LPMFKEMFKPP 143
F++ +KPP
Sbjct: 106 HIEFRQAYKPP 116
>gnl|CDD|187718 cd08649, FMT_core_NRPS_like, N-terminal formyl transferase
catalytic core domain of NRPS_like proteins, one of the
proteins involved in the synthesis of Oxazolomycin.
This family represents the N-terminal formyl transferase
catalytic core domain present in a subgroup of
non-ribosomal peptide synthetases. In Streptomyces albus
a member of this family has been shown to be involved in
the synthesis of oxazolomycin (OZM). OZM is a hybrid
peptide-polyketide antibiotic and exhibits potent
antitumor and antiviral activities. It is a multi-domain
protein consisting of a formyl transferase domain, a
Flavin-utilizing monoxygenase domain, a LuxE domain
functioning as an acyl protein synthetase and a
pp-binding domain, which may function as an acyl
carrier. It shows sequence similarity with other
peptide-polyketide biosynthesis proteins.
Length = 166
Score = 27.6 bits (62), Expect = 7.3
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 312 NIEDLSAILEPENFDYNFKVVN 333
E L +L E FD+ F +VN
Sbjct: 49 PGEALEELLSDEPFDWLFSIVN 70
>gnl|CDD|226717 COG4267, COG4267, Predicted membrane protein [Function unknown].
Length = 467
Score = 28.5 bits (64), Expect = 7.7
Identities = 20/87 (22%), Positives = 39/87 (44%), Gaps = 3/87 (3%)
Query: 122 FAVSKVIFTKYLPMFKEMFKPPDLDELLMHVRHNKKKMIHCTSTKVFEFTWILFVLTKAE 181
F +S + T + +KE ++ L + +N KKMI + E + + +
Sbjct: 287 FLIS--LETDFQENYKEYYQAIRGGGTLREIENNLKKMILTLRQGILEIMELQMLASLLC 344
Query: 182 YLDVSNDLVNSFHLLIATCDLIYANVI 208
+L +++ L+ F L DL Y +V+
Sbjct: 345 FL-LADALLLWFGLSEYYLDLFYVDVL 370
>gnl|CDD|214641 smart00385, CYCLIN, domain present in cyclins, TFIIB and
Retinoblastoma. A helical domain present in cyclins
and TFIIB (twice) and Retinoblastoma (once). A protein
recognition domain functioning in cell-cycle and
transcription control.
Length = 83
Score = 26.4 bits (59), Expect = 8.9
Identities = 11/48 (22%), Positives = 19/48 (39%), Gaps = 1/48 (2%)
Query: 14 QELCMALNIDSTTAKEAWNAYKEMSHHYTLEGSQLHWLG-CSLYVSCR 60
+ +C ALN+D T A N Y + +LY++ +
Sbjct: 4 RRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASK 51
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
0.321 0.137 0.424
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,772,527
Number of extensions: 1993013
Number of successful extensions: 1655
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1652
Number of HSP's successfully gapped: 18
Length of query: 407
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 308
Effective length of database: 6,546,556
Effective search space: 2016339248
Effective search space used: 2016339248
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: 60 (26.8 bits)