RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3434
(83 letters)
>gnl|CDD|215108 PLN00222, PLN00222, tubulin gamma chain; Provisional.
Length = 454
Score = 135 bits (341), Expect = 1e-39
Identities = 57/65 (87%), Positives = 62/65 (95%)
Query: 19 DVVVQPYNSLLTLKRLTLNADCVVVLDNTALNRIACDRLHIENPSFAQINSLVSTIMAVS 78
DVVVQPYNSLLTLKRLTLNADCVVVLDNTALNRIA DRLH+ENP+FAQ NSLVST+M+ S
Sbjct: 180 DVVVQPYNSLLTLKRLTLNADCVVVLDNTALNRIAVDRLHLENPTFAQTNSLVSTVMSAS 239
Query: 79 TSTLR 83
T+TLR
Sbjct: 240 TTTLR 244
>gnl|CDD|100017 cd02188, gamma_tubulin, Gamma-tubulin is a ubiquitous
phylogenetically conserved member of tubulin
superfamily. Gamma is a low abundance protein present
within the cells in both various types of
microtubule-organizing centers and cytoplasmic protein
complexes. Gamma-tubulin recruits the
alpha/beta-tubulin dimers that form the minus ends of
microtubules and is thought to be involved in
microtubule nucleation and capping.
Length = 431
Score = 133 bits (337), Expect = 3e-39
Identities = 55/65 (84%), Positives = 61/65 (93%)
Query: 19 DVVVQPYNSLLTLKRLTLNADCVVVLDNTALNRIACDRLHIENPSFAQINSLVSTIMAVS 78
DVVVQPYNS+LTLKRL LNADCVVVLDNTALNRIA DRLHI+NP+F QINSLVST+M+ S
Sbjct: 178 DVVVQPYNSILTLKRLILNADCVVVLDNTALNRIATDRLHIQNPTFDQINSLVSTVMSAS 237
Query: 79 TSTLR 83
T+TLR
Sbjct: 238 TTTLR 242
>gnl|CDD|227356 COG5023, COG5023, Tubulin [Cytoskeleton].
Length = 443
Score = 100 bits (250), Expect = 9e-27
Identities = 35/65 (53%), Positives = 47/65 (72%)
Query: 19 DVVVQPYNSLLTLKRLTLNADCVVVLDNTALNRIACDRLHIENPSFAQINSLVSTIMAVS 78
DVVV+PYNS+LTL RL N+DC V+DN AL I L I+NPS+ +N L+ST+M+
Sbjct: 177 DVVVEPYNSVLTLHRLLENSDCTFVVDNEALYDICRRNLRIQNPSYDDLNQLISTVMSSV 236
Query: 79 TSTLR 83
T++LR
Sbjct: 237 TTSLR 241
>gnl|CDD|100014 cd00286, Tubulin_FtsZ, Tubulin/FtsZ: Family includes tubulin
alpha-, beta-, gamma-, delta-, and epsilon-tubulins as
well as FtsZ, all of which are involved in polymer
formation. Tubulin is the major component of
microtubules, but also exists as a heterodimer and as a
curved oligomer. Microtubules exist in all eukaryotic
cells and are responsible for many functions, including
cellular transport, cell motility, and mitosis. FtsZ
forms a ring-shaped septum at the site of bacterial cell
division, which is required for constriction of cell
membrane and cell envelope to yield two daughter cells.
FtsZ can polymerize into tubes, sheets, and rings in
vitro and is ubiquitous in eubacteria, archaea, and
chloroplasts.
Length = 328
Score = 87.1 bits (216), Expect = 3e-22
Identities = 32/66 (48%), Positives = 46/66 (69%)
Query: 18 HDVVVQPYNSLLTLKRLTLNADCVVVLDNTALNRIACDRLHIENPSFAQINSLVSTIMAV 77
V+V+PYNS+LTL LT ++DC+VV+DN AL I LHI+ P+F IN L++T ++
Sbjct: 134 EGVIVRPYNSILTLHTLTEHSDCLVVIDNEALFDICPRPLHIDKPTFDHINELLATALSS 193
Query: 78 STSTLR 83
T+ LR
Sbjct: 194 LTTPLR 199
>gnl|CDD|100023 cd06059, Tubulin, The tubulin superfamily includes five distinct
families, the alpha-, beta-, gamma-, delta-, and
epsilon-tubulins and a sixth family (zeta-tubulin) which
is present only in kinetoplastid protozoa. The alpha-
and beta-tubulins are the major components of
microtubules, while gamma-tubulin plays a major role in
the nucleation of microtubule assembly. The delta- and
epsilon-tubulins are widespread but unlike the alpha,
beta, and gamma-tubulins they are not ubiquitous among
eukaryotes. The alpha/beta-tubulin heterodimer is the
structural subunit of microtubules. The alpha- and
beta-tubulins share 40% amino-acid sequence identity,
exist in several isotype forms, and undergo a variety of
posttranslational modifications. The structures of
alpha- and beta-tubulin are basically identical: each
monomer is formed by a core of two beta-sheets
surrounded by alpha-helices. The monomer structure is
very compact, but can be divided into three regions
based on function: the amino-terminal nucleotide-binding
region, an intermediate taxol-binding region and the
carboxy-terminal region which probably constitutes the
binding surface for motor proteins. Also included in
this group is the mitochondrial Misato/DML1 protein
family, involved in mitochondrial fusion and in
mitochondrial distribution and morphology.
Length = 382
Score = 75.8 bits (187), Expect = 5e-18
Identities = 27/65 (41%), Positives = 44/65 (67%)
Query: 19 DVVVQPYNSLLTLKRLTLNADCVVVLDNTALNRIACDRLHIENPSFAQINSLVSTIMAVS 78
VV+PYNS+L+L L N+D V++ DN AL I +L I+ PSF +N++++ I++
Sbjct: 136 SNVVEPYNSILSLNHLLENSDSVILFDNEALYNILTRQLDIDEPSFDDLNNIIAQIISSI 195
Query: 79 TSTLR 83
T++LR
Sbjct: 196 TASLR 200
>gnl|CDD|214867 smart00864, Tubulin, Tubulin/FtsZ family, GTPase domain. This
domain is found in all tubulin chains, as well as the
bacterial FtsZ family of proteins. These proteins are
involved in polymer formation. Tubulin is the major
component of microtubules, while FtsZ is the
polymer-forming protein of bacterial cell division, it
is part of a ring in the middle of the dividing cell
that is required for constriction of cell membrane and
cell envelope to yield two daughter cells. FtsZ and
tubulin are GTPases, this entry is the GTPase domain.
FtsZ can polymerise into tubes, sheets, and rings in
vitro and is ubiquitous in bacteria and archaea.
Length = 192
Score = 71.7 bits (177), Expect = 2e-17
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 19 DVVVQPYNSLLTLKRLTLNADCVVVLDNTALNRIACDRLHIENPSFAQINSLVSTIMAVS 78
+ VV+PYN+ L L+ L + D ++V+DN AL I C R P+F N L++ ++
Sbjct: 126 EGVVRPYNAELGLEELREHVDSLIVIDNDALLDI-CGRKLPLRPAFKDANDLLAQAVSGI 184
Query: 79 TSTLR 83
T +R
Sbjct: 185 TDLIR 189
>gnl|CDD|100016 cd02187, beta_tubulin, The tubulin superfamily includes five
distinct families, the alpha-, beta-, gamma-, delta-,
and epsilon-tubulins and a sixth family (zeta-tubulin)
which is present only in kinetoplastid protozoa. The
alpha- and beta-tubulins are the major components of
microtubules, while gamma-tubulin plays a major role in
the nucleation of microtubule assembly. The delta- and
epsilon-tubulins are widespread but unlike the alpha,
beta, and gamma-tubulins they are not ubiquitous among
eukaryotes. The alpha/beta-tubulin heterodimer is the
structural subunit of microtubules. The alpha- and
beta-tubulins share 40% amino-acid sequence identity,
exist in several isotype forms, and undergo a variety of
posttranslational modifications. The structures of
alpha- and beta-tubulin are basically identical: each
monomer is formed by a core of two beta-sheets
surrounded by alpha-helices. The monomer structure is
very compact, but can be divided into three regions
based on function: the amino-terminal nucleotide-binding
region, an intermediate taxol-binding region and the
carboxy-terminal region which probably constitutes the
binding surface for motor proteins.
Length = 425
Score = 66.1 bits (162), Expect = 2e-14
Identities = 26/65 (40%), Positives = 40/65 (61%)
Query: 19 DVVVQPYNSLLTLKRLTLNADCVVVLDNTALNRIACDRLHIENPSFAQINSLVSTIMAVS 78
D VV+PYN+ L++ +L N+D +DN AL I L + NP++ +N LVS +M+
Sbjct: 176 DTVVEPYNATLSVHQLVENSDETFCIDNEALYDICFRTLKLTNPTYGDLNHLVSAVMSGI 235
Query: 79 TSTLR 83
T+ LR
Sbjct: 236 TTCLR 240
>gnl|CDD|240228 PTZ00010, PTZ00010, tubulin beta chain; Provisional.
Length = 445
Score = 63.3 bits (154), Expect = 2e-13
Identities = 26/65 (40%), Positives = 39/65 (60%)
Query: 19 DVVVQPYNSLLTLKRLTLNADCVVVLDNTALNRIACDRLHIENPSFAQINSLVSTIMAVS 78
D VV+PYN+ L++ +L NAD + +DN AL I L + P++ +N LVS +M+
Sbjct: 177 DTVVEPYNATLSVHQLVENADESMCIDNEALYDICFRTLKLTTPTYGDLNHLVSAVMSGV 236
Query: 79 TSTLR 83
T LR
Sbjct: 237 TCCLR 241
>gnl|CDD|100015 cd02186, alpha_tubulin, The tubulin superfamily includes five
distinct families, the alpha-, beta-, gamma-, delta-,
and epsilon-tubulins and a sixth family (zeta-tubulin)
which is present only in kinetoplastid protozoa. The
alpha- and beta-tubulins are the major components of
microtubules, while gamma-tubulin plays a major role in
the nucleation of microtubule assembly. The delta- and
epsilon-tubulins are widespread but unlike the alpha,
beta, and gamma-tubulins they are not ubiquitous among
eukaryotes. The alpha/beta-tubulin heterodimer is the
structural subunit of microtubules. The alpha- and
beta-tubulins share 40% amino-acid sequence identity,
exist in several isotype forms, and undergo a variety of
posttranslational modifications. The structures of
alpha- and beta-tubulin are basically identical: each
monomer is formed by a core of two beta-sheets
surrounded by alpha-helices. The monomer structure is
very compact, but can be divided into three regions
based on function: the amino-terminal nucleotide-binding
region, an intermediate taxol-binding region and the
carboxy-terminal region which probably constitutes the
binding surface for motor proteins.
Length = 434
Score = 61.9 bits (151), Expect = 5e-13
Identities = 24/63 (38%), Positives = 41/63 (65%)
Query: 21 VVQPYNSLLTLKRLTLNADCVVVLDNTALNRIACDRLHIENPSFAQINSLVSTIMAVSTS 80
VV+PYNS+LT L ++DC ++DN A+ I L IE P++ +N L++ +++ T+
Sbjct: 180 VVEPYNSVLTTHSLLEHSDCSFMVDNEAIYDICRRNLDIERPTYTNLNRLIAQVVSSITA 239
Query: 81 TLR 83
+LR
Sbjct: 240 SLR 242
>gnl|CDD|215107 PLN00220, PLN00220, tubulin beta chain; Provisional.
Length = 447
Score = 62.1 bits (151), Expect = 5e-13
Identities = 29/65 (44%), Positives = 39/65 (60%)
Query: 19 DVVVQPYNSLLTLKRLTLNADCVVVLDNTALNRIACDRLHIENPSFAQINSLVSTIMAVS 78
D VV+PYN+ L++ +L NAD +VLDN AL I L + PSF +N L+S M+
Sbjct: 177 DTVVEPYNATLSVHQLVENADECMVLDNEALYDICFRTLKLTTPSFGDLNHLISATMSGV 236
Query: 79 TSTLR 83
T LR
Sbjct: 237 TCCLR 241
>gnl|CDD|177802 PLN00221, PLN00221, tubulin alpha chain; Provisional.
Length = 450
Score = 57.9 bits (140), Expect = 1e-11
Identities = 25/63 (39%), Positives = 40/63 (63%)
Query: 21 VVQPYNSLLTLKRLTLNADCVVVLDNTALNRIACDRLHIENPSFAQINSLVSTIMAVSTS 80
VV+PYNS+L+ L + D V+LDN A+ I L IE P++ +N L+S +++ T+
Sbjct: 181 VVEPYNSVLSTHSLLEHTDVAVLLDNEAIYDICRRSLDIERPTYTNLNRLISQVISSLTA 240
Query: 81 TLR 83
+LR
Sbjct: 241 SLR 243
>gnl|CDD|100018 cd02189, delta_tubulin, The tubulin superfamily includes five
distinct families, the alpha-, beta-, gamma-, delta-,
and epsilon-tubulins and a sixth family (zeta-tubulin)
which is present only in kinetoplastid protozoa. The
alpha- and beta-tubulins are the major components of
microtubules, while gamma-tubulin plays a major role in
the nucleation of microtubule assembly. The delta- and
epsilon-tubulins are widespread but unlike the alpha,
beta, and gamma-tubulins they are not ubiquitous among
eukaryotes. Delta-tubulin plays an essential role in
forming the triplet microtubules of centrioles and basal
bodies.
Length = 446
Score = 57.3 bits (139), Expect = 2e-11
Identities = 19/57 (33%), Positives = 38/57 (66%)
Query: 20 VVVQPYNSLLTLKRLTLNADCVVVLDNTALNRIACDRLHIENPSFAQINSLVSTIMA 76
V+VQ YN++LTL L ++D +++L+N ++RI +++N S + IN +++ +A
Sbjct: 173 VIVQNYNTVLTLAHLYESSDAIILLENDDIHRICSKLRNLKNVSLSDINKVIAHQLA 229
>gnl|CDD|185562 PTZ00335, PTZ00335, tubulin alpha chain; Provisional.
Length = 448
Score = 57.0 bits (138), Expect = 3e-11
Identities = 24/63 (38%), Positives = 40/63 (63%)
Query: 21 VVQPYNSLLTLKRLTLNADCVVVLDNTALNRIACDRLHIENPSFAQINSLVSTIMAVSTS 80
VV+PYNS+L+ L + D V+LDN A+ I L IE P++ +N L++ +++ T+
Sbjct: 181 VVEPYNSVLSTHSLLEHTDVAVMLDNEAIYDICRRNLDIERPTYTNLNRLIAQVISSLTA 240
Query: 81 TLR 83
+LR
Sbjct: 241 SLR 243
>gnl|CDD|215710 pfam00091, Tubulin, Tubulin/FtsZ family, GTPase domain. This
family includes the tubulin alpha, beta and gamma
chains, as well as the bacterial FtsZ family of
proteins. Members of this family are involved in polymer
formation. FtsZ is the polymer-forming protein of
bacterial cell division. It is part of a ring in the
middle of the dividing cell that is required for
constriction of cell membrane and cell envelope to yield
two daughter cells. FtsZ and tubulin are GTPases. FtsZ
can polymerise into tubes, sheets, and rings in vitro
and is ubiquitous in eubacteria and archaea. Tubulin is
the major component of microtubules.
Length = 210
Score = 55.4 bits (134), Expect = 5e-11
Identities = 21/47 (44%), Positives = 34/47 (72%)
Query: 18 HDVVVQPYNSLLTLKRLTLNADCVVVLDNTALNRIACDRLHIENPSF 64
+ VV+PYN++L LK L ++D V+V+DN AL I ++L I++P+F
Sbjct: 162 SEGVVRPYNAILGLKELIEHSDSVIVIDNDALLEICDNQLDIKSPAF 208
>gnl|CDD|240395 PTZ00387, PTZ00387, epsilon tubulin; Provisional.
Length = 465
Score = 47.8 bits (114), Expect = 5e-08
Identities = 23/64 (35%), Positives = 30/64 (46%), Gaps = 19/64 (29%)
Query: 9 LGSDIIEILH-------------------DVVVQPYNSLLTLKRLTLNADCVVVLDNTAL 49
LG+ I+ +L DV+ PYNS L+ L +ADCV+ LDN AL
Sbjct: 148 LGTRILGMLEDEFPHVFRFCPVVFPSAVDDVITSPYNSFFALRELIEHADCVLPLDNDAL 207
Query: 50 NRIA 53
IA
Sbjct: 208 ANIA 211
>gnl|CDD|100019 cd02190, epsilon_tubulin, The tubulin superfamily includes five
distinct families, the alpha-, beta-, gamma-, delta-,
and epsilon-tubulins and a sixth family (zeta-tubulin)
which is present only in kinetoplastid protozoa. The
epsilon-tubulins which are widespread but not ubiquitous
among eukaryotes play a role in basal body/centriole
morphogenesis.
Length = 379
Score = 45.0 bits (107), Expect = 4e-07
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 12/65 (18%)
Query: 19 DVVVQPYNSLLTLKRLTLNADCVVVLDNTALNRIACDRLHIENPSFAQINSLVSTIMAVS 78
DV+ PYNS+L L+ L +ADCV+ ++N AL F +NS+V+ ++
Sbjct: 145 DVITSPYNSVLALRELIEHADCVLPIENQAL------------VPFDAMNSIVANLLLNL 192
Query: 79 TSTLR 83
TS++R
Sbjct: 193 TSSMR 197
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 26.4 bits (59), Expect = 1.6
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 38 ADCVVVLDNTALNRIACDRLHI 59
+DCV++L N L I
Sbjct: 193 SDCVIILRNRLEGEKRTRTLRI 214
>gnl|CDD|226849 COG4425, COG4425, Predicted membrane protein [Function unknown].
Length = 588
Score = 26.3 bits (58), Expect = 2.0
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 41 VVVLDNTALNRIACDR-LHIENPSFAQINSLV 71
VVL T LN + LH + SFAQ+N+L+
Sbjct: 204 AVVLTWTLLNGVLLKFALHFADSSFAQVNALM 235
>gnl|CDD|225512 COG2964, COG2964, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 220
Score = 25.7 bits (57), Expect = 2.9
Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 8/68 (11%)
Query: 3 SVYFDTLGSDIIEILHDVVVQPYNSLLTLKRLTLNADCVVVLDNT-------ALNRIACD 55
SV F + D++ L + +Q N+ L N + V L A+N +A
Sbjct: 141 SVNFASSVEDLVAQLLEWTIQEVNADRLLSNNAKNREIVKALYEKGIFNLKDAINIVAD- 199
Query: 56 RLHIENPS 63
RL I +
Sbjct: 200 RLGISRHT 207
>gnl|CDD|227321 COG4988, CydD, ABC-type transport system involved in cytochrome bd
biosynthesis, ATPase and permease components [Energy
production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 559
Score = 25.7 bits (57), Expect = 3.3
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 34 LTLNADCVVVLDNTALNRIAC-DRLHIENPSFAQ 66
+AD +VVLDN L + L + +A
Sbjct: 517 DAADADRIVVLDNGRLVEQGTHEELSEKQGLYAN 550
>gnl|CDD|233763 TIGR02175, PorC_KorC, 2-oxoacid:acceptor oxidoreductase, gamma
subunit, pyruvate/2-ketoisovalerate family. A number
of anaerobic and microaerophilic species lack pyruvate
dehydrogenase and have instead a four subunit,
oxygen-sensitive pyruvate oxidoreductase, with either
ferredoxins or flavodoxins (H. pylori) used as the
acceptor. Several related four-subunit enzymes may
exist in the same species. This model describes the
gamma subunit. In Pyrococcus furious, enzymes active on
pyruvate and 2-ketoisovalerate share a common gamma
subunit.
Length = 177
Score = 25.0 bits (55), Expect = 4.1
Identities = 8/26 (30%), Positives = 11/26 (42%)
Query: 29 LTLKRLTLNADCVVVLDNTALNRIAC 54
+ + D VVVLD T L +
Sbjct: 58 IRVHSQIYEPDYVVVLDPTLLKTVNV 83
>gnl|CDD|183334 PRK11836, PRK11836, deubiquitinase; Provisional.
Length = 403
Score = 25.4 bits (55), Expect = 4.7
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 6 FDTLGSDIIEILHDVVVQPYNSLLTLKRLTLNA 38
+D G + +IL+ +V P N L++ RL NA
Sbjct: 57 YDKFGKEAEDILYHIVRNPTNETLSIIRLIKNA 89
>gnl|CDD|176390 cd01795, USP48_C, USP ubiquitin-specific protease. The USP
(ubiquitin-specific protease) family is one of at least
seven deubiquitylating enzyme (DUB) families capable of
deconjugating ubiquitin and ubiquitin-like adducts.
While the USP's have a conserved catalytic core domain,
they differ in their domain architectures. This
subfamily, which includes USP31, and USP48, has a
carboxy-terminal ubiquitin-like domain in addition to a
DUSP (domain of ubiquitin-specific proteases) domain,.
Length = 107
Score = 24.7 bits (53), Expect = 5.5
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 8 TLGSDIIEILHDVVVQPYNSLLTLKRLTLNADCVVV 43
TL I+I+H V P++ L++ L+ DC +
Sbjct: 26 TLKELKIQIMHAFSVAPFDQNLSIDGKILSDDCATL 61
>gnl|CDD|219153 pfam06733, DEAD_2, DEAD_2. This represents a conserved region
within a number of RAD3-like DNA-binding helicases that
are seemingly ubiquitous - members include proteins of
eukaryotic, bacterial and archaeal origin. RAD3 is
involved in nucleotide excision repair, and forms part
of the transcription factor TFIIH in yeast.
Length = 168
Score = 24.6 bits (54), Expect = 6.4
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 19 DVVVQPYNSLL---TLKRLTLN-ADCVVVLD 45
D+++ PYN LL + L +N + +V+ D
Sbjct: 116 DIIILPYNYLLDPKIRESLKINLKNSIVIFD 146
>gnl|CDD|237273 PRK13018, PRK13018, cell division protein FtsZ; Provisional.
Length = 378
Score = 24.6 bits (54), Expect = 8.2
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 31 LKRLTLNADCVVVLDNTALNRIA 53
++RL AD V+V+DN L I
Sbjct: 168 IERLREAADTVIVIDNNRLLDIV 190
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 0.135 0.373
Gapped
Lambda K H
0.267 0.0842 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,956,140
Number of extensions: 307580
Number of successful extensions: 277
Number of sequences better than 10.0: 1
Number of HSP's gapped: 276
Number of HSP's successfully gapped: 29
Length of query: 83
Length of database: 10,937,602
Length adjustment: 52
Effective length of query: 31
Effective length of database: 8,631,194
Effective search space: 267567014
Effective search space used: 267567014
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 (24.0 bits)