RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12965
(139 letters)
>gnl|CDD|200439 cd11283, ADF_GMF-beta_like, ADF-homology domain of glia maturation
factor beta and related proteins. Actin
depolymerization factor/cofilin-like domains (ADF
domains) are present in a family of essential eukaryotic
actin regulatory proteins. Most of these proteins
enhance the turnover rate of actin and interact with
actin monomers as well as actin filaments. The glia
maturation factor (GMF), however, does not bind actin
but interacts with the Arp2/3 complex (which contains
actin-related proteins, amongst others) and suppresses
Arp2/3 activity, inducing the dissociation of branched
daughter filaments from their mother filaments. This
family includes both mammalian GMF isoforms, GMF-beta
and GMF-gamma. GMF-beta regulates cellular growth,
fission, differentiation and apoptosis. GMF-gamma is
important in myeloid cell development and is an
important regulator for cell migration and polarity in
neutrophils.
Length = 122
Score = 186 bits (474), Expect = 3e-62
Identities = 69/122 (56%), Positives = 99/122 (81%)
Query: 8 DIDDDVKEALKKFRFRKAQSNAALILKVDREKQRICIDDLMEDVSLDELRDILPSHQPRY 67
DI D+VKEALKKFRFRK+++NAALILK+D+EKQ I +D+ +ED+S++EL + LP H PR+
Sbjct: 1 DISDEVKEALKKFRFRKSKANAALILKIDKEKQEIVVDEELEDISIEELAEELPEHSPRF 60
Query: 68 VVYSCRMEHGDGRVSYPMSFIYITPRDAQMALQIMYAGTKLALQQEADLTRVYEVRELEE 127
V+YS +M+H DGR+SYP+ IY +P+ LQ++YAG K L +EA++T+V+E+R+ EE
Sbjct: 61 VLYSYKMKHDDGRISYPLVLIYWSPQGCSPELQMLYAGAKELLVKEAEVTKVFEIRDGEE 120
Query: 128 LT 129
LT
Sbjct: 121 LT 122
>gnl|CDD|214516 smart00102, ADF, Actin depolymerisation factor/cofilin -like
domains. Severs actin filaments and binds to actin
monomers.
Length = 127
Score = 75.0 bits (185), Expect = 2e-18
Identities = 34/127 (26%), Positives = 70/127 (55%), Gaps = 5/127 (3%)
Query: 11 DDVKEALKKFRFRKAQSNAALILKVDREKQRICIDDLM-EDVSLDELRDILPSHQPRYVV 69
+D KEA + + ++ S A+I K+D++ + I ++++ + S DE + LP + RY +
Sbjct: 1 EDCKEAFNELKKKRKHS--AIIFKIDKDNEEIVVEEVGSTEDSYDEFVEELPEDECRYAL 58
Query: 70 YSCRMEHGDGRVSYPMSFIYITPRDAQMALQIMYAGTKLALQQEADLTRVY-EVRELEEL 128
Y + + + S + FI+ +P A + +++YA +K L++E +V + + ++L
Sbjct: 59 YDYKFTTEESKKSKIV-FIFWSPDGAPVKSKMLYASSKDTLKKELGGIQVEVQATDEDDL 117
Query: 129 TEEWLKS 135
EE LK
Sbjct: 118 DEEALKE 124
>gnl|CDD|143992 pfam00241, Cofilin_ADF, Cofilin/tropomyosin-type actin-binding
protein. Severs actin filaments and binds to actin
monomers.
Length = 127
Score = 62.8 bits (153), Expect = 1e-13
Identities = 31/127 (24%), Positives = 64/127 (50%), Gaps = 5/127 (3%)
Query: 11 DDVKEALKKFRFRKAQSNAALILKVDREKQRICIDDLME-DVSLDELRDILPSHQPRYVV 69
D++K + + + RK + +I K+D++K +I ++ + + S DE + LP + RY V
Sbjct: 1 DNLKASFNELKKRK--KHNYIIFKIDKDKDQIVVEQVGDTGDSYDEFVEELPERECRYAV 58
Query: 70 YSCRMEHGDGRVSYPMSFIYITPRDAQMALQIMYAGTKLALQQEADLTRVY-EVRELEEL 128
Y + S + + P A + +++YA +K AL++ +V + + ++L
Sbjct: 59 YDVEYTTDGSKKSKIVFVSWS-PDGAPVKSKMLYASSKDALKRALGGIQVEVQATDADDL 117
Query: 129 TEEWLKS 135
+EE L
Sbjct: 118 SEEELLE 124
>gnl|CDD|200440 cd11284, ADF_Twf-C_like, C-terminal ADF domain of twinfilin and
related proteins. Actin depolymerization
factor/cofilin-like domains (ADF domains) are present in
a family of essential eukaryotic actin regulatory
proteins. Twinfilin contains two ADF domains, and
inhibits the assembly of actin filaments by strongly
interacting with monomeric ADP-actin (ADP-G-actin) in a
1:1 stochiometry (with it's C-terminal ADF domain,
Twf-C) and inhibiting the actin monomer's nucleotide
exchange. Mammalian twinfilin may also cap the barbed
ends of F-actin filaments and prevent further assembly
(or disassembly), in a process which requires both ADF
domains. The N-terminal ADF domain (Twf-N) binds G-actin
with a lower affinity than Twf-C; Twf-C can also bind
F-actin. During capping, Twf-N may interact with the
terminal actin subunit, and Twf-C may bind between two
adjacent subunits at the side of the filament.
Length = 132
Score = 56.1 bits (136), Expect = 4e-11
Identities = 32/134 (23%), Positives = 59/134 (44%), Gaps = 14/134 (10%)
Query: 8 DIDDDVKEALKKFRFRKAQSNAALILKVDREKQRICIDDLMEDVSLDELRDILPSHQPRY 67
+ ++ K+AL + + + L +D E + I + D+L ++PS PRY
Sbjct: 6 PVSEEAKDALSEL---ASGGVNLVQLSIDLENETIELVSSSSISIPDDLSSLIPSDHPRY 62
Query: 68 VVYSCRMEHGDGRVSYPMSFIYITPRDAQMALQIMYAGTKLALQQEA------DLTRVYE 121
Y R H FIY P +++ +++YA +K L A ++ + E
Sbjct: 63 HFY--RYPHTYLSSVV---FIYSCPSGSKVKERMLYASSKSGLLNHAEDEGKIEIDKKIE 117
Query: 122 VRELEELTEEWLKS 135
+ + +ELTE +L
Sbjct: 118 IGDPDELTESFLSD 131
>gnl|CDD|200442 cd11286, ADF_cofilin_like, Cofilin, Destrin, and related actin
depolymerizing factors. Actin depolymerization
factor/cofilin-like domains (ADF domains) are present in
a family of essential eukaryotic actin regulatory
proteins. These proteins enhance the turnover rate of
actin, and interact with actin monomers (G-actin) as
well as actin filaments (F-actin), typically with a
preference for ADP-G-actin subunits. The basic function
of cofilin is to promote disassembly of aged actin
filaments. Vertebrates have three isoforms of cofilin:
cofilin-1 (Cfl1, non-muscle cofilin), cofilin-2 (muscle
cofilin), and ADF (destrin). When bound to actin
monomers, cofilins inhibit their spontaneous exchange of
nucleotides. The cooperative binding to (aged)
ADP-F-actin induces a local change in the actin filament
structure and further promotes aging.
Length = 133
Score = 51.8 bits (125), Expect = 2e-09
Identities = 35/127 (27%), Positives = 65/127 (51%), Gaps = 8/127 (6%)
Query: 9 IDDDVKEALKKFRFRKAQSNAALILKVDREKQRICIDDLME-DVSLDELRDILPSHQPRY 67
+ D+ A + + +K + +I K+ +K+ I ++ + E D S D+ + LP ++ RY
Sbjct: 5 VSDECITAFNELKLKK--KHKYIIFKISDDKKEIVVEKVGERDASYDDFLEKLPENECRY 62
Query: 68 VVYSCRMEHGDGRVSYPMSFIYITPRDAQMALQIMYAGTKLALQQEADLTRVY---EVRE 124
VY E DG + FI P A + +++YA +K AL+++ L + + +
Sbjct: 63 AVYDFEYETKDGGKRSKLVFISWCPDTAPIKSKMLYASSKDALKKK--LNGIKKEIQATD 120
Query: 125 LEELTEE 131
L EL+EE
Sbjct: 121 LSELSEE 127
>gnl|CDD|200435 cd00013, ADF_gelsolin, Actin depolymerization factor/cofilin- and
gelsolin-like domains. Actin depolymerization
factor/cofilin-like domains are present in a family of
essential eukaryotic actin regulatory proteins; these
proteins enhance the turnover rate of actin and interact
with actin monomers as well as actin filaments.
Length = 97
Score = 44.0 bits (104), Expect = 1e-06
Identities = 23/99 (23%), Positives = 40/99 (40%), Gaps = 3/99 (3%)
Query: 29 AALILKVDREKQRICIDDLMEDVSLDELRDILPSHQPRYVVYSCRMEHGDGRVSYPMSFI 88
++ KVD +K+ I + DE + LP PRY Y + H FI
Sbjct: 1 DWVLFKVDAKKEEIVVGSTGAGFL-DEFLEELPEDDPRYAFYRFKYPH-SDDKRSKFVFI 58
Query: 89 YITPRDAQMALQIMYAGTKLALQQEA-DLTRVYEVRELE 126
P + +++YA K L++ L ++R+ +
Sbjct: 59 SWIPDGVSIKQKMVYATNKQTLKEALFGLAVPVQIRDGD 97
>gnl|CDD|239908 cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs8_sc7: Rrp5
Homo sapiens S1 repeat 8 (hs8) and Saccharomyces
cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a
trans-acting factor important for biogenesis of both
the 40S and 60S eukaryotic ribosomal subunits. Rrp5
has two distinct regions, an N-terminal region
containing tandemly repeated S1 RNA-binding domains (12
S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in
H. sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of
A0-A2. This CD includes H. sapiens S1 repeat 8 and S.
cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but
not in prokaryotes or archaea.
Length = 83
Score = 31.0 bits (71), Expect = 0.048
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 9 IDDDVKEALKKFRFRKAQSNAALILKVDREKQRI 42
I D+ F F+K QS A + VD EKQR
Sbjct: 47 ISDEFVTDPS-FGFKKGQSVTAKVTSVDEEKQRF 79
>gnl|CDD|178755 PLN03216, PLN03216, actin depolymerizing factor; Provisional.
Length = 141
Score = 29.5 bits (66), Expect = 0.37
Identities = 23/108 (21%), Positives = 53/108 (49%), Gaps = 3/108 (2%)
Query: 9 IDDDVKEALKKFRFRKAQSNAALILKVDREKQRICIDDL-MEDVSLDELRDILPSHQPRY 67
+ D+ K + + +++K ++ K+D + +++ +D + S D+L LP+ RY
Sbjct: 12 VTDECKNSFMEMKWKKVHR--YIVFKIDEKSRKVTVDKVGGPGESYDDLAASLPTDDCRY 69
Query: 68 VVYSCRMEHGDGRVSYPMSFIYITPRDAQMALQIMYAGTKLALQQEAD 115
V+ D + FI +P +++ +++YA +K L++ D
Sbjct: 70 AVFDFDFVTVDNCRKSKIFFIAWSPEASRIRAKMLYATSKDGLRRVLD 117
>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal
structure and biogenesis].
Length = 541
Score = 29.6 bits (67), Expect = 0.52
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 8 DIDDDVKEALKKFRFRKAQSNAALILKVDREKQRI 42
D+ D + +++K A +L VD+EK+RI
Sbjct: 395 DLSWDRPG-EEAEKYKKGDEVEAKVLAVDKEKERI 428
>gnl|CDD|240195 cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: Ribosomal
protein S1 (RPS1) domain. RPS1 is a component of the
small ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria,
the tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain. While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains
have been identified in plants and humans, however
these lack the N-terminal HMBPP reductase domain. This
CD includes S1 repeat 5 (ec5) of the Escherichia coli
RPS1. Autoantibodies to double-stranded DNA from
patients with systemic lupus erythematosus cross-react
with the human RPS1 homolog.
Length = 69
Score = 27.8 bits (62), Expect = 0.66
Identities = 9/30 (30%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 13 VKEALKKFRFRKAQSNAALILKVDREKQRI 42
V+ + ++ K Q A++L +D E++RI
Sbjct: 39 VRHPSEIYK--KGQEVEAVVLNIDVERERI 66
>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 565
Score = 29.4 bits (67), Expect = 0.69
Identities = 15/37 (40%), Positives = 23/37 (62%), Gaps = 4/37 (10%)
Query: 8 DI--DDDVKEALKKFRFRKAQSNAALILKVDREKQRI 42
DI D +EA++ ++ K A++LKVD EK+RI
Sbjct: 405 DISWDKKGEEAVELYK--KGDEVEAVVLKVDVEKERI 439
>gnl|CDD|215621 PLN03188, PLN03188, kinesin-12 family protein; Provisional.
Length = 1320
Score = 28.0 bits (62), Expect = 2.0
Identities = 25/56 (44%), Positives = 33/56 (58%), Gaps = 10/56 (17%)
Query: 11 DDVKEALKKFRFRKAQSN-----AALI--LKVDREKQRICIDDLMEDVSLD-ELRD 58
DDVK+A + R A+S AA I LKV+REK+R + D E+ SL +LRD
Sbjct: 1138 DDVKKAAARAGVRGAESKFINALAAEISALKVEREKERRYLRD--ENKSLQAQLRD 1191
>gnl|CDD|240114 cd04801, CBS_pair_M50_like, This cd contains two tandem repeats
of the cystathionine beta-synthase (CBS pair) domains
in association with the metalloprotease peptidase M50.
CBS is a small domain originally identified in
cystathionine beta-synthase and subsequently found in a
wide range of different proteins. CBS domains usually
come in tandem repeats, which associate to form a
so-called Bateman domain or a CBS pair which is
reflected in this model. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains. It has been proposed that
the CBS domain may play a regulatory role, although its
exact function is unknown.
Length = 114
Score = 26.8 bits (60), Expect = 2.1
Identities = 14/59 (23%), Positives = 20/59 (33%), Gaps = 9/59 (15%)
Query: 49 EDVSLDELRD--ILPSHQPRYVVYSCRMEHGDGRVS------YPMSFIYITPRDAQMAL 99
++L E +L S+Q R+VV G +S P S T M
Sbjct: 8 AHLTLREFVREYVLGSNQRRFVVVD-NEGRYVGIISLADLRAIPTSQWAQTTVIQVMTP 65
>gnl|CDD|240213 cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12: Rrp5 is a
trans-acting factor important for biogenesis of both
the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has
two distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of
A0-A2. This CD includes S. cerevisiae S1 repeat 12
(sc12). Rrp5 is found in eukaryotes but not in
prokaryotes or archaea.
Length = 77
Score = 26.5 bits (59), Expect = 2.2
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 10 DDDVKEALKKFRFRKAQSNAALILKVDREKQRI 42
D+ V +A K FR A +LK+D EK+RI
Sbjct: 38 DNRVADASK--LFRVGDKVRAKVLKIDAEKKRI 68
>gnl|CDD|201444 pfam00788, RA, Ras association (RalGDS/AF-6) domain. RasGTP
effectors (in cases of AF6, canoe and RalGDS); putative
RasGTP effectors in other cases. Recent evidence (not
yet in MEDLINE) shows that some RA domains do NOT bind
RasGTP. Predicted structure similar to that determined,
and that of the RasGTP-binding domain of Raf kinase.
Length = 87
Score = 26.5 bits (59), Expect = 2.4
Identities = 11/57 (19%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 13 VKEALKKFRFRKAQSNAALILKVDREKQRICIDDLMEDVSLDELRDILPSHQPRYVV 69
++ ALKKF + L++ ++R+ DD + L + R+++
Sbjct: 29 IRAALKKFGLADDPEDYVLVVLERGGEERVLPDD---EKPLQIQLQLPGDASSRFLL 82
>gnl|CDD|237077 PRK12364, PRK12364, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 842
Score = 27.4 bits (61), Expect = 3.3
Identities = 12/65 (18%), Positives = 27/65 (41%), Gaps = 1/65 (1%)
Query: 3 PVKVCDIDDDVKEALKKFRFRKAQSNAALILKVDREKQRICIDDLMEDVSLDELRDILPS 62
V V +I D V++ L + + L + R ++R + +++ D + +L
Sbjct: 58 NVSVEEIQDLVEKTLMEHGHYAEVKSYIL-YRAQRTEKRKAREQIIKFFDDDTVLGVLKE 116
Query: 63 HQPRY 67
Q +
Sbjct: 117 IQKDF 121
>gnl|CDD|218244 pfam04754, Transposase_31, Putative transposase, YhgA-like. This
family of putative transposases includes the YhgA
sequence from Escherichia coli and several prokaryotic
homologues.
Length = 203
Score = 26.8 bits (60), Expect = 3.9
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 16/53 (30%)
Query: 59 ILPSHQPRY--VVYSCRMEHGDGRVSYPMSFIYI------TPRDAQMALQIMY 103
I + RY ++YS + + GDG +IY+ TP D MA +++
Sbjct: 46 IEEDLRERYSDLLYSVKTKGGDG-------YIYLLIEHQSTP-DKWMAFRLLR 90
>gnl|CDD|234300 TIGR03662, Chlor_Arch_YYY, Chlor_Arch_YYY domain. Members of this
highly hydrophobic probable integral membrane family
belong to two classes. In one, a single copy of the
region modeled by This model represents essentially the
full length of a strongly hydrophobic protein of about
700 to 900 residues (variable because of long inserts in
some). The domain architecture of the other class
consists of an additional N-terminal region, two copies
of the region represented by this model, and three to
four repeats of TPR, or tetratricopeptide repeat. The
unusual species range includes several Archaea, several
Chloroflexi, and Clostridium phytofermentans. An unusual
motif YYYxG is present, and we suggest the name
Chlor_Arch_YYY protein. The function is unknown.
Length = 723
Score = 27.0 bits (60), Expect = 4.0
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 5/42 (11%)
Query: 83 YPMSFIYITPRDAQMALQIMYAGTKLALQQEADLTRVYEVRE 124
Y + ++Y+ P + Q Y + AL+ DL V+E
Sbjct: 680 YGVDYVYVGPLERQR-----YGLSTDALEDLGDLEPVFEQGS 716
>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM1 of Nop4p (also known as
Nop77p), encoded by YPL043W from Saccharomyces
cerevisiae. It is an essential nucleolar protein
involved in processing and maturation of 27S pre-rRNA
and biogenesis of 60S ribosomal subunits. Nop4p has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 79
Score = 25.6 bits (56), Expect = 4.3
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 11 DDVKEALKKFRFRKAQSNAALILKVDREKQR 41
+D +EAL K + +K IL++D ++R
Sbjct: 52 EDAQEALAKLKNKKLHGR---ILRLDIAERR 79
>gnl|CDD|240513 cd06089, KOW_RPL26, KOW motif of Ribosomal Protein L26. RPL26
and its bacterial paralogs RPL24 have a KOW motif at
their N terminal. KOW domain is known as an RNA-binding
motif that is shared so far among some families of
ribosomal proteins, the essential bacterial
transcriptional elongation factor NusG, the eukaryotic
chromatin elongation factor Spt5, the higher eukaryotic
KIN17 proteins and Mtr4. RPL26 makes a very minor
contributions to the biogenesis, structure, and
function of 60s ribosomal subunits. However, RPL24 is
essential to generate the first intermediate during 50s
ribosomal subunits assembly. RPL26 have an
extra-ribosomal function to enhances p53 translation
after DNA damage.
Length = 65
Score = 25.2 bits (56), Expect = 4.5
Identities = 7/16 (43%), Positives = 13/16 (81%)
Query: 32 ILKVDREKQRICIDDL 47
+LKVDR+K R+ ++ +
Sbjct: 18 VLKVDRKKNRVIVEGV 33
>gnl|CDD|223503 COG0426, FpaA, Uncharacterized flavoproteins [Energy production and
conversion].
Length = 388
Score = 26.5 bits (59), Expect = 5.0
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 15/61 (24%)
Query: 8 DIDDDVKEAL---KKFRFRKAQSNAALILKVDREKQRICIDDLMEDVSLDELRDILPSHQ 64
D+D++E L +K+ NA L+L ++ + L ++ I PSH
Sbjct: 176 RFDEDIEELLPDMRKYYANLMAPNARLVLWA------------LKKIKLLKIEMIAPSHG 223
Query: 65 P 65
P
Sbjct: 224 P 224
>gnl|CDD|226288 COG3765, WzzB, Chain length determinant protein [Cell envelope
biogenesis, outer membrane].
Length = 347
Score = 26.3 bits (58), Expect = 5.8
Identities = 27/120 (22%), Positives = 47/120 (39%), Gaps = 14/120 (11%)
Query: 8 DIDDDVKEALKKF--RFRKAQSNAALILKVDREKQRICIDDLMEDVSLDELRDILPSHQP 65
D EA +F +F + S L+ D KQ++ + ++ LD L + +
Sbjct: 87 REAPDRSEAYSEFIKQFSSSDSLREFWLQTDYYKQKLTGESKIDAALLDRLINNI----- 141
Query: 66 RYVVYSCRMEHGDGRVSYPMSFIYITPRDAQMALQ--IMYAGTKLALQQEADLTRVYEVR 123
S + D + +SF T DAQ L+ I + K+A + +L +R
Sbjct: 142 -----SFKPGGFDLATNLTVSFTAETAEDAQDLLRGYIAFVSQKVAQELLDNLKDAIALR 196
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 26.3 bits (58), Expect = 7.4
Identities = 10/25 (40%), Positives = 19/25 (76%)
Query: 34 KVDREKQRICIDDLMEDVSLDELRD 58
+V +E++ + +D++ME V LD L+D
Sbjct: 985 EVSKEEKMMFVDEVMELVELDNLKD 1009
>gnl|CDD|223020 PHA03246, PHA03246, large tegument protein UL36; Provisional.
Length = 3095
Score = 26.1 bits (57), Expect = 7.8
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 116 LTRVYEVRELEELTEEWLK 134
LT+V E +EL+ T EWLK
Sbjct: 1730 LTKVEETKELDTQTVEWLK 1748
>gnl|CDD|239986 cd04613, CBS_pair_SpoIVFB_EriC_assoc2, This cd contains two
tandem repeats of the cystathionine beta-synthase (CBS
pair) domains in association with either the SpoIVFB
domain (sporulation protein, stage IV cell wall
formation, F locus, promoter-distal B) or the chloride
channel protein EriC. SpoIVFB is one of 4 proteins
involved in endospore formation; the others are SpoIVFA
(sporulation protein, stage IV cell wall formation, F
locus, promoter-proximal A), BofA (bypass-of-forespore
A ), and SpoIVB (sporulation protein, stage IV cell
wall formation, B locus). SpoIVFB is negatively
regulated by SpoIVFA and BofA and activated by SpoIVB.
It is thought that SpoIVFB, SpoIVFA, and BofA are
located in the mother-cell membrane that surrounds the
forespore and that SpoIVB is secreted from the
forespore into the space between the two where it
activates SpoIVFB. EriC is involved in inorganic ion
transport and metabolism. CBS is a small domain
originally identified in cystathionine beta-synthase
and subsequently found in a wide range of different
proteins. CBS domains usually come in tandem repeats,
which associate to form a so-called Bateman domain or a
CBS pair which is reflected in this model. The
interface between the two CBS domains forms a cleft
that is a potential ligand binding site. The CBS pair
coexists with a variety of other functional domains.
It has been proposed that the CBS domain may play a
regulatory role, although its exact function is
unknown.
Length = 114
Score = 25.2 bits (56), Expect = 8.7
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 3 PVKVCDIDDDVKEALKKF 20
P V +D +++ALKKF
Sbjct: 67 PPVVVYPEDSLEDALKKF 84
>gnl|CDD|143322 cd07698, IgC_MHC_I_alpha3, Class I major histocompatibility
complex (MHC) alpha chain immunoglobulin domain.
IgC_MHC_I_alpha3; Immunoglobulin (Ig) domain of major
histocompatibility complex (MHC) class I alpha chain.
Class I MHC proteins bind antigenic peptide fragments
and present them to CD8+ T lymphocytes. Class I
molecules consist of a transmembrane alpha chain and a
small chain called the beta2 microglobulin. The alpha
chain contains three extracellular domains, two of
which fold together to form the peptide-binding cleft
(alpha1 and alpha2), and one which has an Ig fold
(alpha3). Peptide binding to class I molecules occurs
in the endoplasmic reticulum (ER) and involves both
chaperones and dedicated factors to assist in peptide
loading. Class I MHC molecules are expressed on most
nucleated cells.
Length = 93
Score = 24.9 bits (55), Expect = 9.0
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 16/46 (34%)
Query: 46 DLMEDVSLDELRDILPSH----QPRYVV---------YSCRMEHGD 78
D ++DV E +ILP+ Q + YSCR+EH
Sbjct: 41 DSVDDV---ESGEILPNGDGTYQLWVTLEVPPEDKARYSCRVEHSG 83
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.136 0.394
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,304,304
Number of extensions: 661129
Number of successful extensions: 885
Number of sequences better than 10.0: 1
Number of HSP's gapped: 876
Number of HSP's successfully gapped: 56
Length of query: 139
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 52
Effective length of database: 7,078,804
Effective search space: 368097808
Effective search space used: 368097808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.5 bits)