RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16352
(905 letters)
>gnl|CDD|211386 cd11300, Fut8_like, Alpha 1-6-fucosyltransferase. Alpha
1,6-fucosyltransferase (Fut8) transfers a fucose moiety
from GDP-fucose to the reducing terminal
N-acetylglucosamine of the core structure of Asn-linked
oligosaccharides, in a process termed core fucosylation.
Core fucosylation is essential for the function of
growth factor receptors. O-fucosyltransferase-like
proteins are GDP-fucose dependent enzymes with
similarities to the family 1 glycosyltransferases (GT1).
They are soluble ER proteins that may be proteolytically
cleaved from a membrane-associated preprotein, and are
involved in the O-fucosylation of protein substrates,
the core fucosylation of growth factor receptors, and
other processes.
Length = 328
Score = 510 bits (1315), Expect = e-175
Identities = 193/328 (58%), Positives = 237/328 (72%), Gaps = 5/328 (1%)
Query: 371 DSFDDWRWKESLDLSDLVQRRLEYLQNPPDCRTARKLVCELNKGCGYGCQLHHVVYCFIV 430
D +WR KE LS LVQ+R+ LQNP DC A+KLVC LNKGCG+GCQLHHVVYC IV
Sbjct: 1 DGDSEWRRKELKKLSKLVQKRIHKLQNPKDCSKAKKLVCNLNKGCGFGCQLHHVVYCLIV 60
Query: 431 AYATRRTLILDSKEWSYSRGGWEEVFQPVSKTCTSPEGVSNSGW---PGNNDTQVIYLPI 487
AY T RTLILDSK W YS GGWE+VF P+S+TCT G + + W P N+D QV+ LPI
Sbjct: 61 AYGTNRTLILDSKGWRYSPGGWEKVFLPLSETCTDRSGDNTAVWWWEPTNSDVQVVKLPI 120
Query: 488 IEFINPRPPYLPLAIPEDLEPRLSRLHGDPIVWWIGQFLTFLNNPTPNTREIVAKYGEKI 547
I+ ++ RPP+LPLA+PEDL RL RLHGDP VWWIGQ L +L P P ++ + + +++
Sbjct: 121 IDSLHSRPPFLPLAVPEDLAERLERLHGDPRVWWIGQLLKYLMRPQPWLQDEIDEAKKEL 180
Query: 548 KFQKPIVGIHIRRTDKVDTEAALHPVEEYMTGVEEYYKQLALTQ--TVDVKRVYVATDDA 605
F+ PIVG+HIRRTDK+ TEAA H +EEYM VEE+Y + L +RVY+ATDD
Sbjct: 181 GFKHPIVGVHIRRTDKLGTEAAFHSLEEYMEHVEEWYDKYELRGPSEKVKRRVYLATDDP 240
Query: 606 SVLTEIREKYPQYSVLGDPSIARTASLEHRYLKSSLLGIITDLHYLSNCDHLVCTFSSQI 665
SV E + KYP Y +GDP I+++ASL RY SSL GII D+H LS CD+LVCTFSSQ+
Sbjct: 241 SVFDEAKNKYPNYFFIGDPGISKSASLSTRYSDSSLKGIIIDIHLLSECDYLVCTFSSQV 300
Query: 666 CRTAYEQMNAKFPDASDRYRSLDDIYYF 693
CR AYE M + PDASDR+ SLDDIYY+
Sbjct: 301 CRLAYELMQTRHPDASDRFHSLDDIYYY 328
Score = 385 bits (990), Expect = e-127
Identities = 142/250 (56%), Positives = 176/250 (70%), Gaps = 5/250 (2%)
Query: 115 DSFDDWRWKESLDLSDLVQRRLEYLQNPPDCRTARKLVCELNKGCGYGCQLHHVVYCFIV 174
D +WR KE LS LVQ+R+ LQNP DC A+KLVC LNKGCG+GCQLHHVVYC IV
Sbjct: 1 DGDSEWRRKELKKLSKLVQKRIHKLQNPKDCSKAKKLVCNLNKGCGFGCQLHHVVYCLIV 60
Query: 175 AYATQRTLILDSKEWSYSRGGWEEVFQPVSKTCTSPEGVSNSSW---PGNNDTQVIYLPI 231
AY T RTLILDSK W YS GGWE+VF P+S+TCT G + + W P N+D QV+ LPI
Sbjct: 61 AYGTNRTLILDSKGWRYSPGGWEKVFLPLSETCTDRSGDNTAVWWWEPTNSDVQVVKLPI 120
Query: 232 IEFINPRPPYLPLAIPEDLEPRLSRLHGDPIVWWIGQFLMFLNNPTPNTREIVAKYGEKI 291
I+ ++ RPP+LPLA+PEDL RL RLHGDP VWWIGQ L +L P P ++ + + +++
Sbjct: 121 IDSLHSRPPFLPLAVPEDLAERLERLHGDPRVWWIGQLLKYLMRPQPWLQDEIDEAKKEL 180
Query: 292 KFQKPIVGIHIRRTDKVDTEAALHPVEEYMTGVEEYYKQLALTQ--TVDVKRVYVATDDA 349
F+ PIVG+HIRRTDK+ TEAA H +EEYM VEE+Y + L +RVY+ATDD
Sbjct: 181 GFKHPIVGVHIRRTDKLGTEAAFHSLEEYMEHVEEWYDKYELRGPSEKVKRRVYLATDDP 240
Query: 350 SVLTEIREKS 359
SV E + K
Sbjct: 241 SVFDEAKNKY 250
>gnl|CDD|212726 cd11792, SH3_Fut8, Src homology 3 domain of
Alpha1,6-fucosyltransferase (Fut8). Fut8 catalyzes the
alpha1,6-linkage of a fucose residue from a donor
substrate to N-linked oligosaccharides on glycoproteins
in a process called core fucosylation, which is crucial
for growth factor receptor-mediated biological
functions. Fut8-deficient mice show severe growth
retardation, early death, and a pulmonary emphysema-like
phenotype. Fut8 is also implicated to play roles in
aging and cancer metastasis. It contains an N-terminal
coiled-coil domain, a catalytic domain, and a C-terminal
SH3 domain. The SH3 domain of Fut8 is located in the
lumen and its role in glycosyl transfer is unclear. SH3
domains are protein interaction domains that bind to
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. They play
versatile and diverse roles in the cell including the
regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 55
Score = 97.3 bits (243), Expect = 9e-25
Identities = 30/52 (57%), Positives = 39/52 (75%)
Query: 805 IHIAVLPHTPRHSSEMDLMVGDRISVAGNHWNGYSKGRNLRTDQLALYPTFK 856
+A+ PH PR+ E++L VGD I VAGNHW+GYSKGRN RT + LYP++K
Sbjct: 1 NQVAIYPHKPRNHDEIELRVGDIIGVAGNHWDGYSKGRNRRTGKTGLYPSYK 52
Score = 94.6 bits (236), Expect = 8e-24
Identities = 30/53 (56%), Positives = 38/53 (71%)
Query: 738 IHIAVLPHTPRHSSEMALLVGDRISVAGNHWNGYSKGRNLRTDQLALYPTFKT 790
+A+ PH PR+ E+ L VGD I VAGNHW+GYSKGRN RT + LYP++K
Sbjct: 1 NQVAIYPHKPRNHDEIELRVGDIIGVAGNHWDGYSKGRNRRTGKTGLYPSYKV 53
>gnl|CDD|211389 cd11548, NodZ_like, Alpha 1,6-fucosyltransferase similar to
Bradyrhizobium NodZ. Bradyrhizobium NodZ is an alpha
1,6-fucosyltransferase involved in the biosynthesis of
the nodulation factor, a lipo-chitooligosaccharide
formed by three-to-six beta-1,4-linked
N-acetyl-d-glucosamine (GlcNAc) residues and a fatty
acid acyl group attached to the nitrogen atom at the
non-reducing end. NodZ transfers L-fucose from the
GDP-beta-L-fucose donor to the reducing residue of the
chitin oligosaccharide backbone, before the attachment
of a fatty acid group. O-fucosyltransferase-like
proteins are GDP-fucose dependent enzymes with
similarities to the family 1 glycosyltransferases (GT1).
They are soluble ER proteins that may be proteolytically
cleaved from a membrane-associated preprotein, and are
involved in the O-fucosylation of protein substrates,
the core fucosylation of growth factor receptors, and
other processes.
Length = 287
Score = 70.1 bits (172), Expect = 5e-13
Identities = 38/148 (25%), Positives = 64/148 (43%), Gaps = 7/148 (4%)
Query: 522 IGQFLTFLNNPTPNTREIVAKYGEKIKFQKPIVGIHIRRTDKVDTEAALHPVEEYMTGVE 581
I +L L P R V K K+ F +P +G+HIR TD + +L + V
Sbjct: 137 IKCYLYRLFTPKQEVRAAVRKLYAKL-FGRPTIGVHIRTTDH---KDSLFIKLSPLHRVV 192
Query: 582 EYYKQLALTQTVDVKRVYVATDDASVLTEIREKYPQYSVLGDPSIARTASLEHRYLKSSL 641
+ ++ + D +++ATD A V E++ +P V L+ +
Sbjct: 193 DALRK-KVALHKDAT-IFLATDSAEVKDELKRLFPDVVVTPKEFPPHGERSASDGLEGAE 250
Query: 642 LGIITDLHYLSNCDHLVCTFSSQICRTA 669
+I D++ L+ CDHL+ + S R A
Sbjct: 251 DALI-DMYLLARCDHLIGSRFSTFSRMA 277
Score = 49.3 bits (118), Expect = 3e-06
Identities = 25/108 (23%), Positives = 44/108 (40%), Gaps = 8/108 (7%)
Query: 266 IGQFLMFLNNPTPNTREIVAKYGEKIKFQKPIVGIHIRRTDKVDTEAALHPVEEYMTGVE 325
I +L L P R V K K+ F +P +G+HIR TD + +L + V
Sbjct: 137 IKCYLYRLFTPKQEVRAAVRKLYAKL-FGRPTIGVHIRTTDH---KDSLFIKLSPLHRVV 192
Query: 326 EYYKQLALTQTVDVKRVYVATDDASVLTEIREK--SLLHVLGILKARD 371
+ ++ + D +++ATD A V E++ ++
Sbjct: 193 DALRK-KVALHKDAT-IFLATDSAEVKDELKRLFPDVVVTPKEFPPHG 238
>gnl|CDD|211383 cd11296, O-FucT_like, GDP-fucose protein O-fucosyltransferase and
related proteins. O-fucosyltransferase-like proteins
are GDP-fucose dependent enzymes with similarities to
the family 1 glycosyltransferases (GT1). They are
soluble ER proteins that may be proteolytically cleaved
from a membrane-associated preprotein, and are involved
in the O-fucosylation of protein substrates, the core
fucosylation of growth factor receptors, and other
processes.
Length = 206
Score = 54.3 bits (131), Expect = 4e-08
Identities = 35/168 (20%), Positives = 62/168 (36%), Gaps = 17/168 (10%)
Query: 520 WWIGQFLTFLNNPTPNTREIVAKYGEKI--KFQKPIVGIHIRRTDKV-----DTEAALHP 572
+G+ L F +P R++ ++ K+ P + +H+RR D +
Sbjct: 43 RLVGKHLRF----SPEIRKLADRFVRKLLGLPGGPYLAVHLRRGDFEVECCHLAKWMGEY 98
Query: 573 VEEYMTGVEEYYKQL-ALTQTVDVKRVYVATDDASVLT---EIREKYPQYSVLGDPSIAR 628
+EE + EE +++ L +K VYVATD+A E+R+ + D +
Sbjct: 99 LEECLLSAEEIAEKIKELMAERKLKVVYVATDEADREELREELRKAGIRVVTKDD--LLE 156
Query: 629 TASLEHRYLKSSLLGIITDLHYLSNCDHLVCTFSSQICRTAYEQMNAK 676
A L + L + D S D + T S +
Sbjct: 157 DAELLELEKLDNYLLSLVDQEICSRADVFIGTGFSTFSSNVALLRRWR 204
Score = 44.3 bits (105), Expect = 8e-05
Identities = 28/122 (22%), Positives = 53/122 (43%), Gaps = 9/122 (7%)
Query: 276 PTPNTREIVAKYGEKI--KFQKPIVGIHIRRTDKV-----DTEAALHPVEEYMTGVEEYY 328
+P R++ ++ K+ P + +H+RR D + +EE + EE
Sbjct: 51 FSPEIRKLADRFVRKLLGLPGGPYLAVHLRRGDFEVECCHLAKWMGEYLEECLLSAEEIA 110
Query: 329 KQL-ALTQTVDVKRVYVATDDASVLTEIREKSLLHVLGILKARDSFDDWRWKESLDLSDL 387
+++ L +K VYVATD+A E+RE+ + ++ D +D E L +
Sbjct: 111 EKIKELMAERKLKVVYVATDEADR-EELREELRKAGIRVVTKDDLLEDAELLELEKLDNY 169
Query: 388 VQ 389
+
Sbjct: 170 LL 171
Score = 35.9 bits (83), Expect = 0.046
Identities = 9/36 (25%), Positives = 15/36 (41%)
Query: 158 GCGYGCQLHHVVYCFIVAYATQRTLILDSKEWSYSR 193
G G+ Q + + ++A RTL+L R
Sbjct: 8 GGGFNNQRNEFLNALLLAILLGRTLVLPLCLACPIR 43
Score = 35.5 bits (82), Expect = 0.081
Identities = 9/36 (25%), Positives = 15/36 (41%)
Query: 414 GCGYGCQLHHVVYCFIVAYATRRTLILDSKEWSYSR 449
G G+ Q + + ++A RTL+L R
Sbjct: 8 GGGFNNQRNEFLNALLLAILLGRTLVLPLCLACPIR 43
>gnl|CDD|212718 cd11784, SH3_SH3RF2_3, Third Src Homology 3 domain of SH3 domain
containing ring finger 2. SH3RF2 is also called POSHER
(POSH-eliminating RING protein) or HEPP1 (heart protein
phosphatase 1-binding protein). It acts as an
anti-apoptotic regulator of the JNK pathway by binding
to and promoting the degradation of SH3RF1 (or POSH), a
scaffold protein that is required for pro-apoptotic JNK
activation. It may also play a role in cardiac functions
together with protein phosphatase 1. SH3RF2 contains an
N-terminal RING finger domain and three SH3 domains.
This model represents the third SH3 domain, located in
the middle, of SH3RF2. SH3 domains are protein
interaction domains that bind to proline-rich ligands
with moderate affinity and selectivity, preferentially
to PxxP motifs. They play versatile and diverse roles in
the cell including the regulation of enzymes, changing
the subcellular localization of signaling pathway
components, and mediating the formation of multiprotein
complex assemblies.
Length = 55
Score = 39.0 bits (91), Expect = 3e-04
Identities = 12/53 (22%), Positives = 28/53 (52%)
Query: 807 IAVLPHTPRHSSEMDLMVGDRISVAGNHWNGYSKGRNLRTDQLALYPTFKSVP 859
+A+ ++ E++L G+ + V G G+ +G +L T ++ ++P+ P
Sbjct: 3 VALHSYSAHRPEELELQKGEGVRVLGKFQEGWLRGLSLVTGRVGIFPSNYVSP 55
Score = 35.1 bits (81), Expect = 0.009
Identities = 11/48 (22%), Positives = 26/48 (54%)
Query: 740 IAVLPHTPRHSSEMALLVGDRISVAGNHWNGYSKGRNLRTDQLALYPT 787
+A+ ++ E+ L G+ + V G G+ +G +L T ++ ++P+
Sbjct: 3 VALHSYSAHRPEELELQKGEGVRVLGKFQEGWLRGLSLVTGRVGIFPS 50
>gnl|CDD|212735 cd11801, SH3_JIP1_like, Src homology 3 domain of JNK-interacting
proteins 1 and 2, and similar domains. JNK-interacting
proteins (JIPs) function as scaffolding proteins for
c-Jun N-terminal kinase (JNK) signaling pathways. They
bind to components of Mitogen-activated protein kinase
(MAPK) pathways such as JNK, MKK, and several MAP3Ks
such as MLK and DLK. There are four JIPs (JIP1-4); all
contain a JNK binding domain. JIP1 and JIP2 also contain
SH3 and Phosphotyrosine-binding (PTB) domains. Both are
highly expressed in the brain and pancreatic beta-cells.
JIP1 functions as an adaptor linking motor to cargo
during axonal transport and also is involved in
regulating insulin secretion. JIP2 form complexes with
fibroblast growth factor homologous factors (FHFs),
which facilitates activation of the p38delta MAPK. The
SH3 domain of JIP1 homodimerizes at the interface
usually involved in proline-rich ligand recognition,
despite the lack of this motif in the domain itself. SH3
domains are protein interaction domains that bind to
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. They play
versatile and diverse roles in the cell including the
regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 55
Score = 38.1 bits (89), Expect = 7e-04
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 6/53 (11%)
Query: 806 HIAVLPHTPRHSSEMDLMVGDRISV---AGNHWNGYSKGRNLRTDQLALYPTF 855
H A+ PRH E++L +GD + V A + W +G NLRT Q ++P
Sbjct: 2 HRALHKFIPRHEDEIELDIGDPVYVEQEADDLW---CEGTNLRTGQRGIFPAA 51
Score = 37.3 bits (87), Expect = 0.002
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 6/53 (11%)
Query: 739 HIAVLPHTPRHSSEMALLVGDRISV---AGNHWNGYSKGRNLRTDQLALYPTF 788
H A+ PRH E+ L +GD + V A + W +G NLRT Q ++P
Sbjct: 2 HRALHKFIPRHEDEIELDIGDPVYVEQEADDLW---CEGTNLRTGQRGIFPAA 51
>gnl|CDD|212717 cd11783, SH3_SH3RF_3, Third Src Homology 3 domain of SH3 domain
containing ring finger 1 (SH3RF1), SH3RF3, and similar
domains. SH3RF1 (or POSH) and SH3RF3 (or POSH2) are
scaffold proteins that function as E3 ubiquitin-protein
ligases. They contain an N-terminal RING finger domain
and four SH3 domains. This model represents the third
SH3 domain, located in the middle of SH3RF1 and SH3RF3,
and similar domains. SH3RF1 plays a role in calcium
homeostasis through the control of the ubiquitin domain
protein Herp. It may also have a role in regulating
death receptor mediated and JNK mediated apoptosis.
SH3RF3 interacts with p21-activated kinase 2 (PAK2) and
GTP-loaded Rac1. It may play a role in regulating JNK
mediated apoptosis in certain conditions. SH3 domains
are protein interaction domains that bind to
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. They play
versatile and diverse roles in the cell including the
regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 55
Score = 38.1 bits (89), Expect = 8e-04
Identities = 16/49 (32%), Positives = 29/49 (59%)
Query: 738 IHIAVLPHTPRHSSEMALLVGDRISVAGNHWNGYSKGRNLRTDQLALYP 786
I++A+ P+ P+ E+ L G+ +V +G+ KG +LRT Q ++P
Sbjct: 1 IYVALYPYKPQKPDELELRKGEMYTVTEKCQDGWFKGTSLRTGQSGVFP 49
Score = 37.0 bits (86), Expect = 0.002
Identities = 16/49 (32%), Positives = 30/49 (61%)
Query: 805 IHIAVLPHTPRHSSEMDLMVGDRISVAGNHWNGYSKGRNLRTDQLALYP 853
I++A+ P+ P+ E++L G+ +V +G+ KG +LRT Q ++P
Sbjct: 1 IYVALYPYKPQKPDELELRKGEMYTVTEKCQDGWFKGTSLRTGQSGVFP 49
>gnl|CDD|211387 cd11301, Fut1_Fut2_like, Alpha-1,2-fucosyltransferase.
Alpha-1,2-fucosyltransferases (Fut1, Fut2) catalyze the
transfer of alpha-L-fucose to the terminal
beta-D-galactose residue of glycoconjugates via an
alpha-1,2-linkage, generating carbohydrate structures
that exhibit H-antigenicity for blood-group
carbohydrates. These structures also act as ligands for
morphogenesis, the adhesion of microbes, and
metastasizing cancer cells. Fut1 is responsible for
producing the H antigen on red blood cells. Fut2 is
expressed in epithelia of secretory tissues, and
individuals termed "secretors" have at least one
functional copy of the gene; they secrete H antigen
which is further processed into A and/or B antigens
depending on the ABO genotype. O-fucosyltransferase-like
proteins are GDP-fucose dependent enzymes with
similarities to the family 1 glycosyltransferases (GT1).
They are soluble ER proteins that may be proteolytically
cleaved from a membrane-associated preprotein, and are
involved in the O-fucosylation of protein substrates,
the core fucosylation of growth factor receptors, and
other processes.
Length = 265
Score = 41.7 bits (98), Expect = 0.001
Identities = 31/186 (16%), Positives = 56/186 (30%), Gaps = 35/186 (18%)
Query: 493 PRPPYLPLAIPEDLEPRLSRLHGDPIVWWIGQFLTFLNN-------PTPNTREIVAKYGE 545
L R + H + ++ + + E K +
Sbjct: 68 KNLRLLNEDPVLKKLLRENYRHYLGRYYQFWKYFYSIKGEIRQEFKFFEDLEEENNKILK 127
Query: 546 KIKFQ---KPIVGIHIRRTDKVDTEAALHPVEEYMTGVEEYYKQLALT---QTVDVKRVY 599
K+K + V +HIRR D + + Y + Y + A+ + V +
Sbjct: 128 KLKEELKNTNSVSVHIRRGDYLT----NGNAKGYHGICDLEYYKKAIEYIKEKVKNPVFF 183
Query: 600 VATDDASVLTEIREKYPQYSVLGDPSIARTASLEHRYLKSSLLGIITDLHYLSNCDHLVC 659
V +DD + E + +V Y DL+ +S C H++
Sbjct: 184 VFSDDIEWVKENLALTSKENV---------------YFVDGNNSSYEDLYLMSLCKHVII 228
Query: 660 ---TFS 662
TFS
Sbjct: 229 SNSTFS 234
Score = 34.4 bits (79), Expect = 0.23
Identities = 20/125 (16%), Positives = 38/125 (30%), Gaps = 17/125 (13%)
Query: 237 PRPPYLPLAIPEDLEPRLSRLHGDPIVWWIGQFLMFLNN-------PTPNTREIVAKYGE 289
L R + H + ++ + + E K +
Sbjct: 68 KNLRLLNEDPVLKKLLRENYRHYLGRYYQFWKYFYSIKGEIRQEFKFFEDLEEENNKILK 127
Query: 290 KIKFQ---KPIVGIHIRRTDKVDTEAALHPVEEYMTGVEEYYKQLALT---QTVDVKRVY 343
K+K + V +HIRR D + + Y + Y + A+ + V +
Sbjct: 128 KLKEELKNTNSVSVHIRRGDYLT----NGNAKGYHGICDLEYYKKAIEYIKEKVKNPVFF 183
Query: 344 VATDD 348
V +DD
Sbjct: 184 VFSDD 188
>gnl|CDD|212875 cd11942, SH3_JIP2, Src homology 3 domain of JNK-interacting protein
2. JNK-interacting protein 2 (JIP2) is also called
Mitogen-activated protein kinase 8-interacting protein 2
(MAPK8IP2) or Islet-brain-2 (IB2). It is widely
expressed in the brain, where it forms complexes with
fibroblast growth factor homologous factors (FHFs),
which facilitates activation of the p38delta MAPK. JIP2
is enriched in postsynaptic densities and may play a
role in motor and cognitive function. In addition to a
JNK binding domain, JIP2 also contains SH3 and
Phosphotyrosine-binding (PTB) domains. The SH3 domain of
the related protein JIP1 homodimerizes at the interface
usually involved in proline-rich ligand recognition,
despite the lack of this motif in the domain itself. SH3
domains are protein interaction domains that bind to
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. They play
versatile and diverse roles in the cell including the
regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 55
Score = 36.4 bits (84), Expect = 0.003
Identities = 17/50 (34%), Positives = 27/50 (54%)
Query: 806 HIAVLPHTPRHSSEMDLMVGDRISVAGNHWNGYSKGRNLRTDQLALYPTF 855
H AV PRH E++L V D + V + + +G N+RT + ++P F
Sbjct: 2 HRAVFRFIPRHEDELELDVDDPLLVEAEEDDYWYRGYNMRTGERGIFPAF 51
Score = 35.3 bits (81), Expect = 0.008
Identities = 17/50 (34%), Positives = 26/50 (52%)
Query: 739 HIAVLPHTPRHSSEMALLVGDRISVAGNHWNGYSKGRNLRTDQLALYPTF 788
H AV PRH E+ L V D + V + + +G N+RT + ++P F
Sbjct: 2 HRAVFRFIPRHEDELELDVDDPLLVEAEEDDYWYRGYNMRTGERGIFPAF 51
>gnl|CDD|212859 cd11926, SH3_SH3RF1_3, Third Src Homology 3 domain of SH3 domain
containing ring finger 1, an E3 ubiquitin-protein
ligase. SH3RF1 is also called POSH (Plenty of SH3s) or
SH3MD2 (SH3 multiple domains protein 2). It is a
scaffold protein that acts as an E3 ubiquitin-protein
ligase. It plays a role in calcium homeostasis through
the control of the ubiquitin domain protein Herp. It may
also have a role in regulating death receptor mediated
and JNK mediated apoptosis. SH3RF1 also enhances the
ubiquitination of ROMK1 potassium channel resulting in
its increased endocytosis. It contains an N-terminal
RING finger domain and four SH3 domains. This model
represents the third SH3 domain, located in the middle,
of SH3RF1. SH3 domains are protein interaction domains
that bind to proline-rich ligands with moderate affinity
and selectivity, preferentially to PxxP motifs. They
play versatile and diverse roles in the cell including
the regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 55
Score = 34.6 bits (79), Expect = 0.014
Identities = 14/49 (28%), Positives = 30/49 (61%)
Query: 805 IHIAVLPHTPRHSSEMDLMVGDRISVAGNHWNGYSKGRNLRTDQLALYP 853
+++A+ P+TPR E++L G+ V +G+ KG ++ T ++ ++P
Sbjct: 1 VYVAIYPYTPRKEDELELRKGEMFLVFERCQDGWFKGTSMHTSKIGVFP 49
Score = 33.4 bits (76), Expect = 0.039
Identities = 14/49 (28%), Positives = 29/49 (59%)
Query: 738 IHIAVLPHTPRHSSEMALLVGDRISVAGNHWNGYSKGRNLRTDQLALYP 786
+++A+ P+TPR E+ L G+ V +G+ KG ++ T ++ ++P
Sbjct: 1 VYVAIYPYTPRKEDELELRKGEMFLVFERCQDGWFKGTSMHTSKIGVFP 49
>gnl|CDD|212766 cd11832, SH3_Shank, Src homology 3 domain of SH3 and multiple
ankyrin repeat domains (Shank) proteins. Shank proteins
carry scaffolding functions through multiple sites of
protein-protein interaction in its domain architecture,
including ankyrin (ANK) repeats, a long proline rich
region, as well as SH3, PDZ, and SAM domains. They bind
a variety of membrane and cytosolic proteins, and exist
in alternatively spliced isoforms. They are highly
enriched in postsynaptic density (PSD) where they
interact with the cytoskeleton and with postsynaptic
membrane receptors including NMDA and glutamate
receptors. They are crucial in the construction and
organization of the PSD and dendritic spines of
excitatory synapses. There are three members of this
family (Shank1, Shank2, Shank3) which show distinct and
cell-type specific patterns of expression. Shank1 is
brain-specific; Shank2 is found in neurons, glia,
endocrine cells, liver, and kidney; Shank3 is widely
expressed. The SH3 domain of Shank binds GRIP, a
scaffold protein that binds AMPA receptors and Eph
receptors/ligands. SH3 domains are protein interaction
domains that bind to proline-rich ligands with moderate
affinity and selectivity, preferentially to PxxP motifs.
They play versatile and diverse roles in the cell
including the regulation of enzymes, changing the
subcellular localization of signaling pathway
components, and mediating the formation of multiprotein
complex assemblies.
Length = 50
Score = 33.2 bits (76), Expect = 0.032
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 740 IAVLPHTPRHSSEMALLVGDRISV----AGNHWNGYSKGRN 776
IAV ++P+ E++L GDR+ V G W G +GR
Sbjct: 3 IAVKSYSPQEEGEISLHKGDRVKVLSIGEGGFWEGSVRGRT 43
Score = 32.0 bits (73), Expect = 0.098
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 807 IAVLPHTPRHSSEMDLMVGDRISV----AGNHWNGYSKGRN 843
IAV ++P+ E+ L GDR+ V G W G +GR
Sbjct: 3 IAVKSYSPQEEGEISLHKGDRVKVLSIGEGGFWEGSVRGRT 43
>gnl|CDD|212719 cd11785, SH3_SH3RF_C, C-terminal (Fourth) Src Homology 3 domain of
SH3 domain containing ring finger 1 (SH3RF1), SH3RF3,
and similar domains. SH3RF1 (or POSH) and SH3RF3 (or
POSH2) are scaffold proteins that function as E3
ubiquitin-protein ligases. They contain an N-terminal
RING finger domain and four SH3 domains. This model
represents the fourth SH3 domain, located at the
C-terminus of SH3RF1 and SH3RF3, and similar domains.
SH3RF1 plays a role in calcium homeostasis through the
control of the ubiquitin domain protein Herp. It may
also have a role in regulating death receptor mediated
and JNK mediated apoptosis. SH3RF3 interacts with
p21-activated kinase 2 (PAK2) and GTP-loaded Rac1. It
may play a role in regulating JNK mediated apoptosis in
certain conditions. SH3 domains are protein interaction
domains that bind to proline-rich ligands with moderate
affinity and selectivity, preferentially to PxxP motifs.
They play versatile and diverse roles in the cell
including the regulation of enzymes, changing the
subcellular localization of signaling pathway
components, and mediating the formation of multiprotein
complex assemblies.
Length = 55
Score = 32.8 bits (75), Expect = 0.053
Identities = 14/46 (30%), Positives = 26/46 (56%)
Query: 808 AVLPHTPRHSSEMDLMVGDRISVAGNHWNGYSKGRNLRTDQLALYP 853
++P+ P+ +E++L GD + V +G+ KG RT + L+P
Sbjct: 4 VIVPYPPQSEAELELKEGDIVFVHKKREDGWFKGTLQRTGKTGLFP 49
Score = 31.7 bits (72), Expect = 0.16
Identities = 14/46 (30%), Positives = 25/46 (54%)
Query: 741 AVLPHTPRHSSEMALLVGDRISVAGNHWNGYSKGRNLRTDQLALYP 786
++P+ P+ +E+ L GD + V +G+ KG RT + L+P
Sbjct: 4 VIVPYPPQSEAELELKEGDIVFVHKKREDGWFKGTLQRTGKTGLFP 49
>gnl|CDD|212917 cd11984, SH3_Shank3, Src homology 3 domain of SH3 and multiple
ankyrin repeat domains protein 3. Shank3, also called
ProSAP2 (Proline-rich synapse-associated protein 2), is
widely expressed. It plays a role in the formation of
dendritic spines and synapses. Haploinsufficiency of the
Shank3 gene causes the 22q13 deletion/Phelan-McDermid
syndrome, and variants of Shank3 have been implicated in
autism spectrum disorder, schizophrenia, and
intellectual disability. Shank proteins carry
scaffolding functions through multiple sites of
protein-protein interaction in its domain architecture,
including ankyrin (ANK) repeats, a long proline rich
region, as well as SH3, PDZ, and SAM domains. The SH3
domain of Shank binds GRIP, a scaffold protein that
binds AMPA receptors and Eph receptors/ligands. SH3
domains are protein interaction domains that bind to
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. They play
versatile and diverse roles in the cell including the
regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 52
Score = 32.6 bits (74), Expect = 0.061
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 804 RIHIAVLPHTPRHSSEMDLMVGDRISV----AGNHWNGYSKGRN 843
R IAV ++P+ E+ L G+R+ V G W G KGR
Sbjct: 1 RTFIAVKAYSPQGEGEIQLNRGERVKVLSIGEGGFWEGTVKGRT 44
Score = 32.2 bits (73), Expect = 0.096
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 737 RIHIAVLPHTPRHSSEMALLVGDRISV----AGNHWNGYSKGRN 776
R IAV ++P+ E+ L G+R+ V G W G KGR
Sbjct: 1 RTFIAVKAYSPQGEGEIQLNRGERVKVLSIGEGGFWEGTVKGRT 44
>gnl|CDD|214620 smart00326, SH3, Src homology 3 domains. Src homology 3 (SH3)
domains bind to target proteins through sequences
containing proline and hydrophobic amino acids.
Pro-containing polypeptides may bind to SH3 domains in 2
different binding orientations.
Length = 56
Score = 32.1 bits (74), Expect = 0.11
Identities = 12/43 (27%), Positives = 19/43 (44%)
Query: 803 RRIHIAVLPHTPRHSSEMDLMVGDRISVAGNHWNGYSKGRNLR 845
A+ +T + E+ GD I+V +G+ KGR R
Sbjct: 2 GPQVRALYDYTAQDPDELSFKKGDIITVLEKSDDGWWKGRLGR 44
Score = 31.4 bits (72), Expect = 0.16
Identities = 12/43 (27%), Positives = 20/43 (46%)
Query: 736 SRIHIAVLPHTPRHSSEMALLVGDRISVAGNHWNGYSKGRNLR 778
A+ +T + E++ GD I+V +G+ KGR R
Sbjct: 2 GPQVRALYDYTAQDPDELSFKKGDIITVLEKSDDGWWKGRLGR 44
>gnl|CDD|226183 COG3657, COG3657, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 100
Score = 32.7 bits (75), Expect = 0.17
Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 13/61 (21%)
Query: 110 TLKARDSFDDWRWKESLDLSDL-----VQRRLEYLQ--NPPDCRTARKLVCEL--NKGCG 160
TLK D+F +W K L D + RL+ L N D + + V EL + G G
Sbjct: 5 TLKGTDTFSEWLKK----LKDRRAKAKIAARLDRLALGNFGDVKPVGEGVSELRIDHGPG 60
Query: 161 Y 161
Y
Sbjct: 61 Y 61
Score = 31.2 bits (71), Expect = 0.64
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 13/60 (21%)
Query: 367 LKARDSFDDWRWKESLDLSDL-----VQRRLEYLQ--NPPDCRTARKLVCEL--NKGCGY 417
LK D+F +W K L D + RL+ L N D + + V EL + G GY
Sbjct: 6 LKGTDTFSEWLKK----LKDRRAKAKIAARLDRLALGNFGDVKPVGEGVSELRIDHGPGY 61
>gnl|CDD|212876 cd11943, SH3_JIP1, Src homology 3 domain of JNK-interacting protein
1. JNK-interacting protein 1 (JIP1) is also called
Islet-brain 1 (IB1) or Mitogen-activated protein kinase
8-interacting protein 1 (MAPK8IP1). It is highly
expressed in neurons, where it functions as an adaptor
linking motor to cargo during axonal transport. It also
affects microtubule dynamics in neurons. JIP1 is also
found in pancreatic beta-cells, where it is involved in
regulating insulin secretion. In addition to a JNK
binding domain, JIP1 also contains SH3 and
Phosphotyrosine-binding (PTB) domains. Its SH3 domain
homodimerizes at the interface usually involved in
proline-rich ligand recognition, despite the lack of
this motif in the domain itself. SH3 domains are protein
interaction domains that bind to proline-rich ligands
with moderate affinity and selectivity, preferentially
to PxxP motifs. They play versatile and diverse roles in
the cell including the regulation of enzymes, changing
the subcellular localization of signaling pathway
components, and mediating the formation of multiprotein
complex assemblies.
Length = 55
Score = 31.5 bits (71), Expect = 0.17
Identities = 15/53 (28%), Positives = 27/53 (50%)
Query: 806 HIAVLPHTPRHSSEMDLMVGDRISVAGNHWNGYSKGRNLRTDQLALYPTFKSV 858
H AV PRH E++L V D + V + + + N+RT ++P + ++
Sbjct: 2 HRAVFRFVPRHPDELELEVDDPLLVEVQAEDYWYEAYNMRTGARGIFPAYYAI 54
Score = 29.2 bits (65), Expect = 0.98
Identities = 15/50 (30%), Positives = 24/50 (48%)
Query: 739 HIAVLPHTPRHSSEMALLVGDRISVAGNHWNGYSKGRNLRTDQLALYPTF 788
H AV PRH E+ L V D + V + + + N+RT ++P +
Sbjct: 2 HRAVFRFVPRHPDELELEVDDPLLVEVQAEDYWYEAYNMRTGARGIFPAY 51
>gnl|CDD|212714 cd11780, SH3_Sorbs_3, Third (or C-terminal) Src Homology 3 domain
of Sorbin and SH3 domain containing (Sorbs) proteins and
similar domains. This family, also called the vinexin
family, is composed predominantly of adaptor proteins
containing one sorbin homology (SoHo) and three SH3
domains. Members include the third SH3 domains of Sorbs1
(or ponsin), Sorbs2 (or ArgBP2), Vinexin (or Sorbs3),
and similar domains. They are involved in the regulation
of cytoskeletal organization, cell adhesion, and growth
factor signaling. Members of this family bind multiple
partners including signaling molecules like c-Abl,
c-Arg, Sos, and c-Cbl, as well as cytoskeletal molecules
such as vinculin and afadin. They may have overlapping
functions. SH3 domains are protein interaction domains
that bind to proline-rich ligands with moderate affinity
and selectivity, preferentially to PxxP motifs. They
play versatile and diverse roles in the cell including
the regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 55
Score = 31.1 bits (71), Expect = 0.19
Identities = 13/46 (28%), Positives = 24/46 (52%)
Query: 808 AVLPHTPRHSSEMDLMVGDRISVAGNHWNGYSKGRNLRTDQLALYP 853
A+ +TP++ E++L GD + V +G+ G + RT +P
Sbjct: 4 ALYSYTPQNEDELELREGDIVYVMEKCDDGWFVGTSERTGLFGTFP 49
>gnl|CDD|212819 cd11886, SH3_BOI, Src Homology 3 domain of fungal BOI-like
proteins. This subfamily includes the Saccharomyces
cerevisiae proteins BOI1 and BOI2, and similar proteins.
They contain an N-terminal SH3 domain, a Sterile alpha
motif (SAM), and a Pleckstrin homology (PH) domain at
the C-terminus. BOI1 and BOI2 interact with the SH3
domain of Bem1p, a protein involved in bud formation.
They promote polarized cell growth and participates in
the NoCut signaling pathway, which is involved in the
control of cytokinesis. SH3 domains bind to proline-rich
ligands with moderate affinity and selectivity,
preferentially to PxxP motifs; they play a role in the
regulation of enzymes by intramolecular interactions,
changing the subcellular localization of signal pathway
components and mediate multiprotein complex assemblies.
Length = 55
Score = 30.8 bits (70), Expect = 0.27
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 815 RHSSEMDLMVGDRISVAGN---HWNGYSKGRNLRTDQLALYP 853
R E+ L GD+I + + +G+ GRNLRT + L+P
Sbjct: 11 RSEDELTLKPGDKIELIEDDEEFGDGWYLGRNLRTGETGLFP 52
Score = 29.6 bits (67), Expect = 0.68
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 748 RHSSEMALLVGDRISVAGN---HWNGYSKGRNLRTDQLALYP 786
R E+ L GD+I + + +G+ GRNLRT + L+P
Sbjct: 11 RSEDELTLKPGDKIELIEDDEEFGDGWYLGRNLRTGETGLFP 52
>gnl|CDD|212725 cd11791, SH3_UBASH3, Src homology 3 domain of Ubiquitin-associated
and SH3 domain-containing proteins, also called TULA (T
cell Ubiquitin LigAnd) family of proteins. UBASH3 or
TULA proteins are also referred to as Suppressor of T
cell receptor Signaling (STS) proteins. They contain an
N-terminal UBA domain, a central SH3 domain, and a
C-terminal histidine phosphatase domain. They bind c-Cbl
through the SH3 domain and to ubiquitin via UBA. In some
vertebrates, there are two TULA family proteins, called
UBASH3A (also called TULA or STS-2) and UBASH3B (also
called TULA-2 or STS-1), which show partly overlapping
as well as distinct functions. UBASH3B is widely
expressed while UBASH3A is only found in lymphoid cells.
UBASH3A facilitates apoptosis induced in T cells through
its interaction with the apoptosis-inducing factor AIF.
UBASH3B is an active phosphatase while UBASH3A is not.
SH3 domains are protein interaction domains that bind to
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. They play
versatile and diverse roles in the cell including the
regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 59
Score = 30.7 bits (70), Expect = 0.31
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 4/53 (7%)
Query: 738 IHIAVLPHTPRHSSEMALLVGDRISVAGNHWN----GYSKGRNLRTDQLALYP 786
+ + P+TP+ E+ L+ GD I V+ + G+ +G + T L P
Sbjct: 1 VLRVLYPYTPQEEDELELVPGDYIYVSPEELDSSSDGWVEGTSWLTGCSGLLP 53
Score = 30.3 bits (69), Expect = 0.48
Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 805 IHIAVLPHTPRHSSEMDLMVGDRISVAGNHWN----GYSKGRNLRTDQLALYP 853
+ + P+TP+ E++L+ GD I V+ + G+ +G + T L P
Sbjct: 1 VLRVLYPYTPQEEDELELVPGDYIYVSPEELDSSSDGWVEGTSWLTGCSGLLP 53
>gnl|CDD|212916 cd11983, SH3_Shank2, Src homology 3 domain of SH3 and multiple
ankyrin repeat domains protein 2. Shank2, also called
ProSAP1 (Proline-rich synapse-associated protein 1) or
CortBP1 (Cortactin-binding protein 1), is found in
neurons, glia, endocrine cells, liver, and kidney. It
plays a role in regulating dendritic spine volume and
branching and postsynaptic clustering. Mutations in the
Shank2 gene are associated with autism spectrum disorder
and mental retardation. Shank proteins carry scaffolding
functions through multiple sites of protein-protein
interaction in its domain architecture, including
ankyrin (ANK) repeats, a long proline rich region, as
well as SH3, PDZ, and SAM domains. The SH3 domain of
Shank binds GRIP, a scaffold protein that binds AMPA
receptors and Eph receptors/ligands. SH3 domains are
protein interaction domains that bind to proline-rich
ligands with moderate affinity and selectivity,
preferentially to PxxP motifs. They play versatile and
diverse roles in the cell including the regulation of
enzymes, changing the subcellular localization of
signaling pathway components, and mediating the
formation of multiprotein complex assemblies.
Length = 52
Score = 29.5 bits (66), Expect = 0.70
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 4/42 (9%)
Query: 737 RIHIAVLPHTPRHSSEMALLVGDRISV----AGNHWNGYSKG 774
R + V + P+ E+ L GDR+ V G W G ++G
Sbjct: 1 RHFVVVKSYQPQVEGEIPLHKGDRVKVLSIGEGGFWEGSARG 42
Score = 29.5 bits (66), Expect = 0.86
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 4/42 (9%)
Query: 804 RIHIAVLPHTPRHSSEMDLMVGDRISV----AGNHWNGYSKG 841
R + V + P+ E+ L GDR+ V G W G ++G
Sbjct: 1 RHFVVVKSYQPQVEGEIPLHKGDRVKVLSIGEGGFWEGSARG 42
>gnl|CDD|212858 cd11925, SH3_SH3RF3_3, Third Src Homology 3 domain of SH3 domain
containing ring finger 3, an E3 ubiquitin-protein
ligase. SH3RF3 is also called POSH2 (Plenty of SH3s 2)
or SH3MD4 (SH3 multiple domains protein 4). It is a
scaffold protein with E3 ubiquitin-protein ligase
activity. It was identified in the screen for
interacting partners of p21-activated kinase 2 (PAK2).
It may play a role in regulating JNK mediated apoptosis
in certain conditions. It also interacts with GTP-loaded
Rac1. SH3RF3 is highly homologous to SH3RF1; it also
contains an N-terminal RING finger domain and four SH3
domains. This model represents the third SH3 domain,
located in the middle, of SH3RF3. SH3 domains are
protein interaction domains that bind to proline-rich
ligands with moderate affinity and selectivity,
preferentially to PxxP motifs. They play versatile and
diverse roles in the cell including the regulation of
enzymes, changing the subcellular localization of
signaling pathway components, and mediating the
formation of multiprotein complex assemblies.
Length = 57
Score = 29.6 bits (66), Expect = 0.78
Identities = 14/49 (28%), Positives = 28/49 (57%)
Query: 805 IHIAVLPHTPRHSSEMDLMVGDRISVAGNHWNGYSKGRNLRTDQLALYP 853
I++A+ + P+ + E++L G+ V +G+ KG +LRT ++P
Sbjct: 2 IYLALYAYKPQKNDELELRKGEMYRVIEKCQDGWFKGTSLRTGVSGVFP 50
>gnl|CDD|212690 cd00174, SH3, Src Homology 3 domain superfamily. Src Homology 3
(SH3) domains are protein interaction domains that bind
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. Thus, they
are referred to as proline-recognition domains (PRDs).
SH3 domains are less selective and show more diverse
specificity compared to other PRDs. They have been shown
to bind peptide sequences that lack the PxxP motif;
examples include the PxxDY motif of Eps8 and the
RKxxYxxY sequence in SKAP55. SH3 domain containing
proteins play versatile and diverse roles in the cell,
including the regulation of enzymes, changing the
subcellular localization of signaling pathway
components, and mediating the formation of multiprotein
complex assemblies, among others. Many members of this
superfamily are adaptor proteins that associate with a
number of protein partners, facilitating complex
formation and signal transduction.
Length = 51
Score = 28.6 bits (65), Expect = 1.5
Identities = 8/39 (20%), Positives = 17/39 (43%)
Query: 740 IAVLPHTPRHSSEMALLVGDRISVAGNHWNGYSKGRNLR 778
A+ + + E++ GD I+V +G+ +G
Sbjct: 3 RALYDYEAQDDDELSFKKGDIITVLEKDDDGWWEGELNG 41
Score = 28.6 bits (65), Expect = 1.6
Identities = 8/39 (20%), Positives = 16/39 (41%)
Query: 807 IAVLPHTPRHSSEMDLMVGDRISVAGNHWNGYSKGRNLR 845
A+ + + E+ GD I+V +G+ +G
Sbjct: 3 RALYDYEAQDDDELSFKKGDIITVLEKDDDGWWEGELNG 41
>gnl|CDD|144876 pfam01442, Apolipoprotein, Apolipoprotein A1/A4/E domain. These
proteins contain several 22 residue repeats which form a
pair of alpha helices. This family includes:
Apolipoprotein A-I. Apolipoprotein A-IV. Apolipoprotein
E.
Length = 191
Score = 30.7 bits (70), Expect = 2.1
Identities = 24/105 (22%), Positives = 43/105 (40%), Gaps = 14/105 (13%)
Query: 10 RKRVSKDVQELWYYVSSELTQFRTELVNKTPQLAGGPNIQYELARKRVSKDVQELWYYVS 69
R+SK+ + L + +L R L P L EL + +V ++++EL ++
Sbjct: 29 WARLSKETEALREELQKDLEDVRARL---QPYLD-------EL-KAKVGQNLEELRQRLA 77
Query: 70 SELTQFRTELVNKTPQLAGKLDRIIAETAEHKRSLLHVLDTLKAR 114
+ R L +L KL E + L ++ L+AR
Sbjct: 78 PYAEELRKRLNRDAEELRRKLAPYA---EELRDRLRQNVEALRAR 119
>gnl|CDD|236872 PRK11183, PRK11183, D-lactate dehydrogenase; Provisional.
Length = 564
Score = 31.0 bits (71), Expect = 3.0
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 13/41 (31%)
Query: 343 YVATDDASVLTEIREKSLLHVLGILKA---------RDSFD 374
Y+ T+D +VLTEIR H+L K RD+FD
Sbjct: 273 YIGTNDPAVLTEIRR----HILANFKNLPVAGEYMHRDAFD 309
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 30.6 bits (69), Expect = 4.3
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 6/53 (11%)
Query: 596 KRVYVAT----DDASVLTEIREKYP--QYSVLGDPSIARTASLEHRYLKSSLL 642
++V+VA D ++L ++E+Y + + DP+I A+L HRY+ L
Sbjct: 334 QKVFVAEPSVEDTIAILRGLKERYELHHHVQITDPAIVAAATLSHRYIADRQL 386
>gnl|CDD|214617 smart00323, RasGAP, GTPase-activator protein for Ras-like GTPases.
All alpha-helical domain that accelerates the GTPase
activity of Ras, thereby "switching" it into an "off"
position. Improved domain limits from structure.
Length = 344
Score = 30.4 bits (69), Expect = 4.3
Identities = 22/123 (17%), Positives = 37/123 (30%), Gaps = 30/123 (24%)
Query: 569 ALHPVEEYMTGVEEYYKQLALTQTVDVKRVYVATDDASVLTEIREKYPQYSVLGDPSIAR 628
A +E YM V Y L + ++ +K + DP+
Sbjct: 99 ATKSMEVYMKLVGNQYLHTTLKPVLK-----------KIVES--KKSCEV----DPAKLE 141
Query: 629 TASLEHR------YLKSSLLGIITDLHYLSNCDHLVCTFSSQICRTAYEQMNAKFPDASD 682
LE Y++ II + + IC+ + +FPDA
Sbjct: 142 GEDLETNLENLLQYVERLFDAIINSSDR---LPYGLR----DICKQLRQAAEKRFPDADV 194
Query: 683 RYR 685
Y+
Sbjct: 195 IYK 197
>gnl|CDD|219499 pfam07653, SH3_2, Variant SH3 domain. SH3 (Src homology 3) domains
are often indicative of a protein involved in signal
transduction related to cytoskeletal organisation. First
described in the Src cytoplasmic tyrosine kinase. The
structure is a partly opened beta barrel.
Length = 53
Score = 27.4 bits (62), Expect = 4.4
Identities = 9/35 (25%), Positives = 14/35 (40%), Gaps = 4/35 (11%)
Query: 745 HTPRHSSEMALLVGDRISV----AGNHWNGYSKGR 775
+ +E++L GD + V W G GR
Sbjct: 8 YVATDPNELSLKKGDVVKVLDKDDNGWWEGERGGR 42
>gnl|CDD|187660 cd08957, WbmH_like_SDR_e, Bordetella bronchiseptica enzymes WbmH
and WbmG-like, extended (e) SDRs. Bordetella
bronchiseptica enzymes WbmH and WbmG, and related
proteins. This subgroup exhibits the active site tetrad
and NAD-binding motif of the extended SDR family. It has
been proposed that the active site in Bordetella WbmG
and WbmH cannot function as an epimerase, and that it
plays a role in O-antigen synthesis pathway from
UDP-2,3-diacetamido-2,3-dideoxy-l-galacturonic acid.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 307
Score = 30.2 bits (68), Expect = 5.2
Identities = 19/66 (28%), Positives = 28/66 (42%), Gaps = 6/66 (9%)
Query: 337 VDVKRVYVATDDASVLT-----EIREKSLLHVLGI-LKARDSFDDWRWKESLDLSDLVQR 390
V +K ++ A +A L E+ E V I L +F D+ WKE LS+ V
Sbjct: 231 VSIKELFDAVVEALDLPLRPEVEVVELGPDDVPSILLDPSRTFQDFGWKEFTPLSETVSA 290
Query: 391 RLEYLQ 396
L +
Sbjct: 291 ALAWYD 296
>gnl|CDD|206732 cd04169, RF3, Release Factor 3 (RF3) protein involved in the
terminal step of translocation in bacteria. Peptide
chain release factor 3 (RF3) is a protein involved in
the termination step of translation in bacteria.
Termination occurs when class I release factors (RF1 or
RF2) recognize the stop codon at the A-site of the
ribosome and activate the release of the nascent
polypeptide. The class II release factor RF3 then
initiates the release of the class I RF from the
ribosome. RF3 binds to the RF/ribosome complex in the
inactive (GDP-bound) state. GDP/GTP exchange occurs,
followed by the release of the class I RF. Subsequent
hydrolysis of GTP to GDP triggers the release of RF3
from the ribosome. RF3 also enhances the efficiency of
class I RFs at less preferred stop codons and at stop
codons in weak contexts.
Length = 268
Score = 29.9 bits (68), Expect = 5.3
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 229 LPIIEFINP--RPPYLPLAIPEDLEPRLSRLHGDPIVWWIG 267
+PII FIN R PL + +++E L + P+ W IG
Sbjct: 124 IPIITFINKLDREGRDPLELLDEIENELG-IDCAPMTWPIG 163
Score = 29.9 bits (68), Expect = 5.3
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 485 LPIIEFINP--RPPYLPLAIPEDLEPRLSRLHGDPIVWWIG 523
+PII FIN R PL + +++E L + P+ W IG
Sbjct: 124 IPIITFINKLDREGRDPLELLDEIENELG-IDCAPMTWPIG 163
>gnl|CDD|233488 TIGR01599, PYST-A, Plasmodium yoelii subtelomeric family PYST-A.
This model represents a paralogous family of Plasmodium
yoelii genes preferentially located in the subtelomeric
regions of the chromosomes. Members of this family are
expressed in both the Sporozoite and Gametozoite life
stages. A single high-scoring gene was identified in the
complete genome of P. falciparum as well as a single
gene from P. chaboudi from GenBank which were included
in the seed. There are no obvious homologs to these
genes in any non-Plasmodium organism. These observations
suggest an expansion of this family in yoelii from a
common Plasmodium ancestor gene (present in a single
copy in falciparum).
Length = 208
Score = 29.3 bits (66), Expect = 7.1
Identities = 19/100 (19%), Positives = 34/100 (34%), Gaps = 19/100 (19%)
Query: 656 HLVCTFSSQICRTAYEQMNA------KFPDASDRYRSLDDIYYFGVPTATIWC--ICRTA 707
HLVCT +I R A E M + + Y +Y P +T++ T
Sbjct: 5 HLVCTDPKEIKR-AEEIMEEAELRLKRHAINKNDYN----LYSTPNPDSTVYYKKDHNTI 59
Query: 708 YEQMNAKFPDAS------DRYRSLDDIYYFGGQLSRIHIA 741
+++ D + +D FG + + +
Sbjct: 60 IGKIHLTIQDPNKYDAIIKTLWDFNDNKKFGRKFIKGKVV 99
>gnl|CDD|225504 COG2956, COG2956, Predicted N-acetylglucosaminyl transferase
[Carbohydrate transport and metabolism].
Length = 389
Score = 29.7 bits (67), Expect = 7.2
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 13/51 (25%)
Query: 118 DDWRWKESLD-LSDLVQRRLEYLQNPPDCRTARKLVCELNKGCGYGCQLHH 167
++ R KESLD L D+V + L+ P R CG+ +
Sbjct: 330 EEGRAKESLDLLRDMVGEQ---LRRKPRYRCQN---------CGFTAHTLY 368
Score = 29.7 bits (67), Expect = 7.2
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 13/51 (25%)
Query: 374 DDWRWKESLD-LSDLVQRRLEYLQNPPDCRTARKLVCELNKGCGYGCQLHH 423
++ R KESLD L D+V + L+ P R CG+ +
Sbjct: 330 EEGRAKESLDLLRDMVGEQ---LRRKPRYRCQN---------CGFTAHTLY 368
>gnl|CDD|203331 pfam05830, NodZ, Nodulation protein Z (NodZ). The nodulation genes
of Rhizobia are regulated by the nodD gene product in
response to host-produced flavonoids and appear to
encode enzymes involved in the production of a
lipo-chitose signal molecule required for infection and
nodule formation. NodZ is required for the addition of a
2-O-methylfucose residue to the terminal reducing
N-acetylglucosamine of the nodulation signal. This
substitution is essential for the biological activity of
this molecule. Mutations in nodZ result in defective
nodulation. nodZ represents a unique nodulation gene
that is not under the control of NodD and yet is
essential for the synthesis of an active nodulation
signal.
Length = 322
Score = 29.8 bits (67), Expect = 7.6
Identities = 38/145 (26%), Positives = 60/145 (41%), Gaps = 29/145 (20%)
Query: 531 NPTPNTR-EIVAKYGEKIKFQKPIVGIHIRRTDK----------VDTEAALHPVEEYMTG 579
P P + I A Y E I+G+H+R + D E ALH V T
Sbjct: 148 KPRPEIQARIDAIYQEHFL-GYSIIGVHVRHGNGEDIMDHAPYWADPELALHQV---CTA 203
Query: 580 VEEYYKQLALTQTVDVKRVYVATDDASVLTEIREKYPQYSVLGDPSIARTASLEHRYLKS 639
+ E K L + V RV++ TD A VL ++ +P + A A H S
Sbjct: 204 IREA-KALPHPRPV---RVFLCTDSAQVLDQVSGVFPDLFAIPKRFQADQAGPLH----S 255
Query: 640 SLLGI------ITDLHYLSNCDHLV 658
+ LG+ + +++ L+ CD ++
Sbjct: 256 AALGVEGGFSALVEMYLLARCDTVI 280
>gnl|CDD|182701 PRK10754, PRK10754, quinone oxidoreductase, NADPH-dependent;
Provisional.
Length = 327
Score = 29.3 bits (66), Expect = 9.5
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 6/59 (10%)
Query: 754 ALLVGDRISVAGNHWNGYSKGRNLRTDQLALYP---TFKTSADSF---PAFAYIFRRIH 806
+ VGDR+ A + YS N+ D+ A+ P +F+ +A SF Y+ R+ +
Sbjct: 78 HIKVGDRVVYAQSALGAYSSVHNVPADKAAILPDAISFEQAAASFLKGLTVYYLLRKTY 136
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
0.320 0.137 0.426
Gapped
Lambda K H
0.267 0.0813 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 47,151,636
Number of extensions: 4708255
Number of successful extensions: 3776
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3761
Number of HSP's successfully gapped: 65
Length of query: 905
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 799
Effective length of database: 6,236,078
Effective search space: 4982626322
Effective search space used: 4982626322
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: 64 (28.3 bits)