RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7545
(235 letters)
>gnl|CDD|100024 cd06060, misato, Human Misato shows similarity with Tubulin/FtsZ
family of GTPases and is localized to the the outer
membrane of mitochondria. It has a role in mitochondrial
fusion and in mitochondrial distribution and morphology.
Mutations in its Drosophila homolog (misato) lead to
irregular chromosome segregation during mitosis.
Deletion of the budding yeast homolog DML1 is lethal and
unregulate expression of DML1 leads to mitochondrial
dispersion and abnormalities in cell morphology. The
Misato/DML1 protein family is conserved from yeast to
human, but its exact function is still unknown.
Length = 493
Score = 184 bits (470), Expect = 8e-56
Identities = 78/172 (45%), Positives = 106/172 (61%), Gaps = 7/172 (4%)
Query: 33 KNYQLEESVKYWSDFMRTRYHPKSFNLIQEYQHENSSQPFDCYLQGGEVWKSELMTEDWT 92
K Y LE SV WSD++ R HP+S N+I +Y H+ +SQPF+ + QG +W+ E E++
Sbjct: 79 KVYNLEASVNVWSDYLYARLHPRSINVINQYNHDGTSQPFEVFGQGESLWQDESFQEEFE 138
Query: 93 DKVRSFVEECDCLQGFQILSDATGGFGGLCASSLQHLKDEYSTKSCLVFPVIPPQTLES- 151
D++R +VEECD LQGFQ+L D GF G+ A L+HL+DEY S L+FP +PP
Sbjct: 139 DRLRFYVEECDYLQGFQVLCDLHDGFSGVGAKCLEHLQDEYGKAS-LLFPGLPPVIPPDA 197
Query: 152 ----NFKLRNVNTALFFASLSELSDVFSPLSISSDCWNQTETYRKFPYMEYN 199
N R +NTAL A LSE S +F PLS+S W + R FPY+ Y+
Sbjct: 198 SSDKNSI-RVLNTALGLAQLSEHSSLFVPLSLSGTLWRKPGPPRTFPYLNYD 248
>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 = 66.7 bits (163), Expect = 6e-13
Identities = 42/158 (26%), Positives = 58/158 (36%), Gaps = 23/158 (14%)
Query: 37 LEESVKYWSDFMRTRYHPKSFNLIQEYQHENSSQPFDCYLQGGEVWKS------ELMTED 90
E V + R F + Q H + G W E E+
Sbjct: 27 TEPGVIDETLSGPYRLL---FCIGQLITHGGGA---------GNNWAFGHETAGEEYQEE 74
Query: 91 WTDKVRSFVEECDCLQGFQILSDATGGFG-GLCASSLQHLKDEYSTKSCLVFPVIPPQTL 149
D +R EECD LQGF I GG G GL + LKDEY + + F ++P
Sbjct: 75 ILDIIRKEAEECDSLQGFFITHSLGGGTGSGLGPVLAERLKDEYPKRLKITFSILPGPD- 133
Query: 150 ESNFKLRNVNTALFFASLSELSDVFSPLSISSDCWNQT 187
E +R N+ L +L+E SD I ++
Sbjct: 134 EGV-IVRPYNSILTLHTLTEHSDCLVV--IDNEALFDI 168
>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 = 55.4 bits (134), Expect = 4e-09
Identities = 32/82 (39%), Positives = 40/82 (48%), Gaps = 2/82 (2%)
Query: 93 DKVRSFVEECDCLQGFQILSDATGGFG-GLCASSLQHLKDEYSTKSCLVFPVIPPQTLES 151
D++R VE+CD LQGFQI GG G GL + L+ L DEY F + P S
Sbjct: 77 DRIRKQVEKCDSLQGFQITHSLGGGTGSGLGSLLLELLSDEYPKILINTFSIFPSPQGSS 136
Query: 152 NFKLRNVNTALFFASLSELSDV 173
N + N+ L L E SD
Sbjct: 137 NV-VEPYNSILSLNHLLENSDS 157
>gnl|CDD|227356 COG5023, COG5023, Tubulin [Cytoskeleton].
Length = 443
Score = 53.2 bits (128), Expect = 3e-08
Identities = 32/88 (36%), Positives = 45/88 (51%), Gaps = 4/88 (4%)
Query: 87 MTEDWTDKVRSFVEECDCLQGFQILSDATGGFG-GLCASSLQHLKDEYSTKSCLVFPVIP 145
+ +D D +R + CD LQGF +L GG G GL + L+ L++EY K L F V P
Sbjct: 112 IIDDVMDMIRREADGCDGLQGFLLLHSLGGGTGSGLGSLLLERLREEYPKKIKLTFSVFP 171
Query: 146 -PQTLESNFKLRNVNTALFFASLSELSD 172
P+ S+ + N+ L L E SD
Sbjct: 172 APKV--SDVVVEPYNSVLTLHRLLENSD 197
>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 = 49.6 bits (119), Expect = 4e-07
Identities = 30/83 (36%), Positives = 39/83 (46%), Gaps = 4/83 (4%)
Query: 93 DKVRSFVEECDCLQGFQILSDATGGFG-GLCASSLQHLKDEYSTKSCLVFPVIP-PQTLE 150
D++R + C LQGF I GG G G + L+ L +Y KS L F V P PQ
Sbjct: 119 DRIRKLADNCTGLQGFLIFHSFGGGTGSGFGSLLLERLSVDYGKKSKLEFTVYPSPQVST 178
Query: 151 SNFKLRNVNTALFFASLSELSDV 173
+ + N+ L SL E SD
Sbjct: 179 AVVE--PYNSVLTTHSLLEHSDC 199
>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 = 49.2 bits (118), Expect = 5e-07
Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 93 DKVRSFVEECDCLQGFQILSDATGGFG-GLCASSLQHLKDEYSTKSCLVFPVIP 145
D VR E CDCLQGFQ+ GG G G+ + +++EY + F V P
Sbjct: 117 DVVRKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMATFSVFP 170
>gnl|CDD|185562 PTZ00335, PTZ00335, tubulin alpha chain; Provisional.
Length = 448
Score = 48.6 bits (116), Expect = 1e-06
Identities = 29/83 (34%), Positives = 41/83 (49%), Gaps = 4/83 (4%)
Query: 93 DKVRSFVEECDCLQGFQILSDATGGFG-GLCASSLQHLKDEYSTKSCLVFPVIP-PQTLE 150
D++R + C LQGF + GG G GL + L+ L +Y KS L F + P PQ
Sbjct: 120 DRIRKLADNCTGLQGFLVFHAVGGGTGSGLGSLLLERLSVDYGKKSKLGFTIYPSPQVST 179
Query: 151 SNFKLRNVNTALFFASLSELSDV 173
+ + N+ L SL E +DV
Sbjct: 180 AVVE--PYNSVLSTHSLLEHTDV 200
>gnl|CDD|215107 PLN00220, PLN00220, tubulin beta chain; Provisional.
Length = 447
Score = 47.1 bits (112), Expect = 3e-06
Identities = 27/72 (37%), Positives = 36/72 (50%), Gaps = 7/72 (9%)
Query: 75 YLQGGEVWKSELMTEDWTDKVRSFVEECDCLQGFQILSDATGGFG-GLCASSLQHLKDEY 133
Y +G E+ S L D VR E CDCLQGFQ+ GG G G+ + +++EY
Sbjct: 106 YTEGAELIDSVL------DVVRKEAENCDCLQGFQVCHSLGGGTGSGMGTLLISKIREEY 159
Query: 134 STKSCLVFPVIP 145
+ L F V P
Sbjct: 160 PDRMMLTFSVFP 171
>gnl|CDD|240228 PTZ00010, PTZ00010, tubulin beta chain; Provisional.
Length = 445
Score = 45.5 bits (108), Expect = 9e-06
Identities = 28/72 (38%), Positives = 36/72 (50%), Gaps = 7/72 (9%)
Query: 75 YLQGGEVWKSELMTEDWTDKVRSFVEECDCLQGFQILSDATGGFG-GLCASSLQHLKDEY 133
Y +G E+ S L D VR E CDCLQGFQI GG G G+ + L++EY
Sbjct: 106 YTEGAELIDSVL------DVVRKEAESCDCLQGFQITHSLGGGTGSGMGTLLISKLREEY 159
Query: 134 STKSCLVFPVIP 145
+ + F V P
Sbjct: 160 PDRIMMTFSVFP 171
>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 = 45.4 bits (108), Expect = 9e-06
Identities = 22/55 (40%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 92 TDKVRSFVEECDCLQGFQILSDATGGFG-GLCASSLQHLKDEYSTKSCLVFPVIP 145
+K+R E+CD LQ F IL GG G GL L+ L DE+ V V P
Sbjct: 86 LEKIRKAAEKCDSLQSFFILHSLGGGTGSGLGTYVLELLADEFPEVYRFVTSVYP 140
>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 = 44.2 bits (105), Expect = 2e-05
Identities = 27/82 (32%), Positives = 37/82 (45%), Gaps = 5/82 (6%)
Query: 93 DKVRSFVEECDCLQGFQILSDATGGFG-GLCASSLQHLKDEYSTKSCLVFPVIPPQTLES 151
+++R +E+CD L GF I + GG G G + LK+ Y + V V P T E
Sbjct: 107 EEIRKELEKCDGLDGFFITAGLGGGTGSGAAPVIAEILKELY--GALTVAVVTFPFTSEG 164
Query: 152 NFKLRNVNTALFFASLSELSDV 173
+R N L L E SD
Sbjct: 165 --VVRPYNAILGLKELIEHSDS 184
>gnl|CDD|177802 PLN00221, PLN00221, tubulin alpha chain; Provisional.
Length = 450
Score = 42.1 bits (99), Expect = 1e-04
Identities = 31/83 (37%), Positives = 42/83 (50%), Gaps = 4/83 (4%)
Query: 93 DKVRSFVEECDCLQGFQILSDATGGFG-GLCASSLQHLKDEYSTKSCLVFPVIP-PQTLE 150
D++R + C LQGF + + GG G GL + L+ L +Y KS L F V P PQ
Sbjct: 120 DRIRKLADNCTGLQGFLVFNAVGGGTGSGLGSLLLERLSVDYGKKSKLGFTVYPSPQV-- 177
Query: 151 SNFKLRNVNTALFFASLSELSDV 173
S + N+ L SL E +DV
Sbjct: 178 STAVVEPYNSVLSTHSLLEHTDV 200
>gnl|CDD|240395 PTZ00387, PTZ00387, epsilon tubulin; Provisional.
Length = 465
Score = 41.6 bits (98), Expect = 2e-04
Identities = 28/94 (29%), Positives = 41/94 (43%), Gaps = 9/94 (9%)
Query: 89 EDWTDKVRSFVEECDCLQGFQILSDATGGFG-GLCASSLQHLKDEYS---TKSCLVFPVI 144
+ ++ VR VE+CD LQ F ++ GG G GL L L+DE+ +VFP
Sbjct: 115 DSISESVRRQVEQCDSLQSFFLMHSLGGGTGSGLGTRILGMLEDEFPHVFRFCPVVFPSA 174
Query: 145 PPQTLESNFKLRNVNTALFFASLSELSDVFSPLS 178
+ S + N+ L E +D PL
Sbjct: 175 VDDVITSPY-----NSFFALRELIEHADCVLPLD 203
>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 = 40.4 bits (95), Expect = 5e-04
Identities = 34/85 (40%), Positives = 43/85 (50%), Gaps = 3/85 (3%)
Query: 89 EDWTDKVRSFVEECDCLQGFQILSDATGGFG-GLCASSLQHLKDEYSTKSCLVFPVIPPQ 147
ED D +R VE+CD +GF +L GG G GL + + L+DEY L V P
Sbjct: 110 EDILDLIRKEVEKCDSFEGFLVLHSLAGGTGSGLGSRVTELLRDEYPESLLLNIVVWPYT 169
Query: 148 TLESNFKLRNVNTALFFASLSELSD 172
T E ++N NT L A L E SD
Sbjct: 170 TGEV--IVQNYNTVLTLAHLYESSD 192
>gnl|CDD|215108 PLN00222, PLN00222, tubulin gamma chain; Provisional.
Length = 454
Score = 37.1 bits (86), Expect = 0.005
Identities = 34/130 (26%), Positives = 55/130 (42%), Gaps = 11/130 (8%)
Query: 54 PKSFNLIQEYQHENSSQPFDCYLQ-----GGEVWKS-----ELMTEDWTDKVRSFVEECD 103
P+ N IQ ++ N + ++ G W S E + ED D + + D
Sbjct: 71 PRVINGIQNSEYRNLYNHENIFVSDHGGGAGNNWASGYHQGEQVEEDIMDMIDREADGSD 130
Query: 104 CLQGFQILSDATGGFG-GLCASSLQHLKDEYSTKSCLVFPVIPPQTLESNFKLRNVNTAL 162
L+GF + GG G G+ + L+ L D YS K + V P Q S+ ++ N+ L
Sbjct: 131 SLEGFVLCHSIAGGTGSGMGSYLLEALNDRYSKKLVQTYSVFPNQMETSDVVVQPYNSLL 190
Query: 163 FFASLSELSD 172
L+ +D
Sbjct: 191 TLKRLTLNAD 200
>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 = 31.8 bits (73), Expect = 0.30
Identities = 28/99 (28%), Positives = 44/99 (44%), Gaps = 7/99 (7%)
Query: 75 YLQGGEVWKSELMTEDWTDKVRSFVEECDCLQGFQILSDATGGFG-GLCASSLQHLKDEY 133
Y QG EV + E++ D + + D L+GF + GG G G+ + L+ L D Y
Sbjct: 106 YSQGEEV-QEEIL-----DIIDREADGSDSLEGFVLCHSIAGGTGSGMGSYLLERLNDRY 159
Query: 134 STKSCLVFPVIPPQTLESNFKLRNVNTALFFASLSELSD 172
K + V P Q S+ ++ N+ L L +D
Sbjct: 160 PKKLIQTYSVFPNQDESSDVVVQPYNSILTLKRLILNAD 198
>gnl|CDD|132988 cd06657, STKc_PAK4, Catalytic domain of the Protein
Serine/Threonine Kinase, p21-activated kinase 4.
Serine/threonine kinases (STKs), p21-activated kinase
(PAK) 4, catalytic (c) domain. STKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
PAK subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. PAKs are Rho family
GTPase-regulated kinases that serve as important
mediators in the function of Cdc42 (cell division cycle
42) and Rac. PAKs from higher eukaryotes are classified
into two groups (I and II), according to their
biochemical and structural features. PAK4 belongs to
group II. Group II PAKs contain a PBD (p21-binding
domain) and a C-terminal catalytic domain, but do not
harbor an AID (autoinhibitory domain) or SH3 binding
sites. PAK4 regulates cell morphology and cytoskeletal
organization. It is essential for embryonic viability
and proper neural development. Mice lacking PAK4 die
due to defects in the fetal heart. In addition, their
spinal cord motor neurons showed failure to
differentiate and migrate. PAK4 also plays a role in
cell survival and tumorigenesis. It is overexpressed in
many primary tumors including colon, esophageal, and
mammary tumors. PAK4 has also been implicated in viral
and bacterial infection pathways.
Length = 292
Score = 30.8 bits (69), Expect = 0.48
Identities = 10/24 (41%), Positives = 18/24 (75%)
Query: 59 LIQEYQHENSSQPFDCYLQGGEVW 82
++++YQHEN + ++ YL G E+W
Sbjct: 70 IMRDYQHENVVEMYNSYLVGDELW 93
>gnl|CDD|232890 TIGR00235, udk, uridine kinase. Model contains a number of
longer eukaryotic proteins and starts bringing in
phosphoribulokinase hits at scores of 160 and below
[Purines, pyrimidines, nucleosides, and nucleotides,
Salvage of nucleosides and nucleotides].
Length = 207
Score = 28.9 bits (65), Expect = 1.7
Identities = 11/42 (26%), Positives = 18/42 (42%), Gaps = 6/42 (14%)
Query: 24 PFDCYLQDCKNYQLEESVKYWSDFMRTRYHPKSFNLIQEYQH 65
D Y +D + ++ E K D HP +F+ Y+H
Sbjct: 39 SQDNYYKDQSHLEMAERKKTNFD------HPDAFDNDLLYEH 74
>gnl|CDD|106187 PRK13225, PRK13225, phosphoglycolate phosphatase; Provisional.
Length = 273
Score = 28.9 bits (64), Expect = 2.4
Identities = 25/70 (35%), Positives = 35/70 (50%), Gaps = 11/70 (15%)
Query: 82 WKSELMTEDWTDKVRSFVEECDCLQGFQILSDATGGFGGLCASSLQHLKDEYSTKSCLVF 141
WK+ + D VE+ L+GF +TGG G S L LK +ST++ VF
Sbjct: 6 WKAFIARLSAIDPCGKAVEK---LRGF-----STGGIKG--GSFLHRLKG-FSTRNPQVF 54
Query: 142 PVIPPQTLES 151
P PQTL++
Sbjct: 55 PQSYPQTLQA 64
>gnl|CDD|173728 cd06614, STKc_PAK, Catalytic domain of the Protein
Serine/Threonine Kinase, p21-activated kinase.
Serine/threonine kinases (STKs), p21-activated kinase
(PAK) subfamily, catalytic (c) domain. STKs catalyze
the transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
PAK subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. PAKs are Rho family
GTPase-regulated kinases that serve as important
mediators in the function of Cdc42 (cell division cycle
42) and Rac. PAKs are implicated in the regulation of
many cellular processes including growth factor
receptor-mediated proliferation, cell polarity, cell
motility, cell death and survival, and actin
cytoskeleton organization. PAK deregulation is
associated with tumor development. PAKs from higher
eukaryotes are classified into two groups (I and II),
according to their biochemical and structural features.
Group I PAKs contain a PBD (p21-binding domain)
overlapping with an AID (autoinhibitory domain), a
C-terminal catalytic domain, SH3 binding sites and a
non-classical SH3 binding site for PIX (PAK-interacting
exchange factor). Group II PAKs contain a PBD and a
catalytic domain, but lack other motifs found in group
I PAKs. Since group II PAKs do not contain an obvious
AID, they may be regulated differently from group I
PAKs. Group I PAKs interact with the SH3 containing
proteins Nck, Grb2 and PIX; no such binding has been
demonstrated for group II PAKs.
Length = 286
Score = 28.7 bits (65), Expect = 2.5
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 59 LIQEYQHENSSQPFDCYLQGGEVWKS-ELM 87
++++ +H N +D YL G E+W E M
Sbjct: 68 IMKDCKHPNIVDYYDSYLVGDELWVVMEYM 97
>gnl|CDD|219567 pfam07775, PaRep2b, PaRep2b protein. This is a family of proteins,
expressed in the crenarchaeon Pyrobaculum aerophilum,
whose members are variable in length and level of
conservation. The presence of numerous frameshifts and
internal stop codons in multiple alignments are thought
to indicate that most family members are no longer
functional.
Length = 510
Score = 28.7 bits (64), Expect = 3.2
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 8/31 (25%)
Query: 79 GEVWKSELMTE--------DWTDKVRSFVEE 101
G W+ +L T+ +W + VR+FVEE
Sbjct: 139 GGKWRVQLTTDGITAIRHDEWLNAVRAFVEE 169
>gnl|CDD|224732 COG1819, COG1819, Glycosyl transferases, related to
UDP-glucuronosyltransferase [Carbohydrate transport and
metabolism / Signal transduction mechanisms].
Length = 406
Score = 28.5 bits (64), Expect = 3.3
Identities = 7/34 (20%), Positives = 12/34 (35%)
Query: 197 EYNVRECIMKELNNSAYLECLNRTKESLNPIIGC 230
E +R + + L + +Y R E G
Sbjct: 355 EERLRAAVNEVLADDSYRRAAERLAEEFKEEDGP 388
>gnl|CDD|226470 COG3961, COG3961, Pyruvate decarboxylase and related thiamine
pyrophosphate-requiring enzymes [Carbohydrate transport
and metabolism / Coenzyme metabolism / General function
prediction only].
Length = 557
Score = 28.4 bits (64), Expect = 3.9
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 2/29 (6%)
Query: 92 TDKVRSFVEECDCLQGF-QILSD-ATGGF 118
+VR VE D + +L+D TGGF
Sbjct: 267 EPEVREAVESADLILTIGVLLTDFNTGGF 295
>gnl|CDD|132979 cd06648, STKc_PAK_II, Catalytic domain of the Protein
Serine/Threonine Kinase, Group II p21-activated kinase.
Serine/threonine kinases (STKs), p21-activated kinase
(PAK) subfamily, Group II, catalytic (c) domain. STKs
catalyze the transfer of the gamma-phosphoryl group
from ATP to serine/threonine residues on protein
substrates. The PAK subfamily is part of a larger
superfamily that includes the catalytic domains of
other protein STKs, protein tyrosine kinases, RIO
kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. PAKs are Rho
family GTPase-regulated kinases that serve as important
mediators in the function of Cdc42 (cell division cycle
42) and Rac. PAKs from higher eukaryotes are classified
into two groups (I and II), according to their
biochemical and structural features. Group II PAKs,
also called non-conventional PAKs, include PAK4, PAK5,
and PAK6. Group II PAKs contain PBD (p21-binding
domain) and catalytic domains, but lack other motifs
found in group I PAKs, such as an AID (autoinhibitory
domain) and SH3 binding sites. Since group II PAKs do
not contain an obvious AID, they may be regulated
differently from group I PAKs. While group I PAKs
interact with the SH3 containing proteins Nck, Grb2 and
PIX, no such binding has been demonstrated for group II
PAKs. Some known substrates of group II PAKs are also
substrates of group I PAKs such as Raf, BAD, LIMK and
GEFH1. Unique group II substrates include MARK/Par-1
and PDZ-RhoGEF. Group II PAKs play important roles in
filopodia formation, neuron extension, cytoskeletal
organization, and cell survival.
Length = 285
Score = 28.2 bits (63), Expect = 4.0
Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 3/29 (10%)
Query: 57 FN---LIQEYQHENSSQPFDCYLQGGEVW 82
FN ++++YQH N + + YL G E+W
Sbjct: 64 FNEVVIMRDYQHPNIVEMYSSYLVGDELW 92
>gnl|CDD|132989 cd06658, STKc_PAK5, Catalytic domain of the Protein
Serine/Threonine Kinase, p21-activated kinase 5.
Serine/threonine kinases (STKs), p21-activated kinase
(PAK) 5, catalytic (c) domain. STKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
PAK subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. PAKs are Rho family
GTPase-regulated kinases that serve as important
mediators in the function of Cdc42 (cell division cycle
42) and Rac. PAKs from higher eukaryotes are classified
into two groups (I and II), according to their
biochemical and structural features. PAK5 belongs to
group II. Group II PAKs contain a PBD (p21-binding
domain) and a C-terminal catalytic domain, but do not
harbor an AID (autoinhibitory domain) or SH3 binding
sites. PAK5 is mainly expressed in the brain. It is not
required for viability, but together with PAK6, it is
required for normal levels of locomotion and activity,
and for learning and memory. PAK5 cooperates with Inca
(induced in neural crest by AP2) in the regulation of
cell adhesion and cytoskeletal organization in the
embryo and in neural crest cells during craniofacial
development. PAK5 may also play a role in controlling
the signaling of Raf-1, an effector of Ras, at the
mitochondria.
Length = 292
Score = 27.3 bits (60), Expect = 7.5
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 59 LIQEYQHENSSQPFDCYLQGGEVW 82
++++Y HEN ++ YL G E+W
Sbjct: 72 IMRDYHHENVVDMYNSYLVGDELW 95
>gnl|CDD|132966 cd06635, STKc_TAO1, Catalytic domain of the Protein
Serine/Threonine Kinase, Thousand-and-one amino acids 1.
Serine/threonine kinases (STKs), thousand-and-one amino
acids 1 (TAO1) subfamily, catalytic (c) domain. STKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine/threonine residues on protein substrates.
The TAO subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. TAO proteins possess mitogen-activated protein
kinase (MAPK) kinase kinase (MAPKKK or MAP3K or MKKK)
activity. MAPK signaling cascades are important in
mediating cellular responses to extracellular signals.
TAO1 is sometimes referred to as prostate-derived
sterile 20-like kinase 2 (PSK2). TAO1 activates the p38
MAPK through direct interaction with and activation of
MEK3. TAO1 is highly expressed in the brain and may play
a role in neuronal apoptosis. TAO1 interacts with the
checkpoint proteins BubR1 and Mad2, and plays an
important role in regulating mitotic progression, which
is required for both chromosome congression and
checkpoint-induced anaphase delay. TAO1 may play a role
in protecting genomic stability.
Length = 317
Score = 27.0 bits (59), Expect = 9.4
Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 6/49 (12%)
Query: 34 NYQLEESVKYWSDFMRTRYHPKSFNLIQEYQHENSSQPFDCYLQGGEVW 82
+Y ++S + W D + K +Q +H NS + CYL+ W
Sbjct: 59 SYSGKQSNEKWQDII------KEVKFLQRIKHPNSIEYKGCYLREHTAW 101
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 0.134 0.423
Gapped
Lambda K H
0.267 0.0616 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,263,819
Number of extensions: 974577
Number of successful extensions: 823
Number of sequences better than 10.0: 1
Number of HSP's gapped: 815
Number of HSP's successfully gapped: 31
Length of query: 235
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 141
Effective length of database: 6,768,326
Effective search space: 954333966
Effective search space used: 954333966
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 (26.0 bits)