RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12707
(245 letters)
>gnl|CDD|225427 COG2872, COG2872, Predicted metal-dependent hydrolases related to
alanyl-tRNA synthetase HxxxH domain [General function
prediction only].
Length = 241
Score = 151 bits (384), Expect = 2e-45
Identities = 83/232 (35%), Positives = 120/232 (51%), Gaps = 29/232 (12%)
Query: 11 LKEYKSKVVSCKRNETRPTEYHVRMEDTIFFPTGGGQHCDKGTLGGVE----VVDVYRDG 66
LKE+++ VV + NE + ++ TIF+PTGGGQ D GTL V DV +DG
Sbjct: 12 LKEFEATVVDVEDNE-------IVLDRTIFYPTGGGQPGDTGTLIWAGGEYVVEDVTKDG 64
Query: 67 DEAVHVV--NKEFQVGELLDMKIDWAHRLDQTQQHTGQHLLSAVIDKMFGYDTESWNCGS 124
+E VHV+ + + +VG+ + +KIDW R + HT HLLSAV+ K++G T + G
Sbjct: 65 EEIVHVLAEHAKLKVGDKVKLKIDWERRYRHMRMHTALHLLSAVLYKVYGALTTGFEIGE 124
Query: 125 DVCDVELATKDKDLTEADIAAIEQECNNKIRQGVKVWASEY-------QPGDPALKTAHT 177
D ++ D + TE +I +E N +++ + V PG LK
Sbjct: 125 DYARIDF---DGEDTEDEIEEVEALANELVKENLPVIIYFIPREEAEKLPGLVKLKN--- 178
Query: 178 RGLPKDHKGSIRIVHIDGIDNNMCCGTHVDNISQLQSIKLLKTTRAQKSKSL 229
+P D +G IRIV I ID C GTHV N ++ IK+LKT + K K
Sbjct: 179 -KVPPDVEGKIRIVEIGDIDVQPCGGTHVKNTGEIGEIKILKTEK--KGKGN 227
>gnl|CDD|237551 PRK13902, alaS, alanyl-tRNA synthetase; Provisional.
Length = 900
Score = 112 bits (282), Expect = 3e-28
Identities = 71/237 (29%), Positives = 104/237 (43%), Gaps = 46/237 (19%)
Query: 11 LKEYKSKVVSCKRNETRPTEYHVRMEDTIFFPTGGGQHCDKGTL----GGVEVVDVYRDG 66
++E+++KV+ N +V ++ T F+P GGGQ D G L G +VVDV + G
Sbjct: 507 MREFEAKVLGVIDN-------YVVLDQTAFYPEGGGQPADTGVLIVDGKGYKVVDVQKVG 559
Query: 67 DEAVHVVNKEF-QVGELLDMKIDWAHRLDQTQQHTGQHLLSAVIDKMFGYDTESWNCGSD 125
VHV+ E + G+ + +IDW R + HT H++ A K+ G W G+
Sbjct: 560 GVIVHVLEGEPPKKGDEVRGEIDWERRYRLMRHHTATHIILAAARKVLG--DHVWQAGAQ 617
Query: 126 VCDVELATKD----KDLTEADIAAIEQECNNKIRQGVKVWASE--------------YQP 167
V+ A D K +T ++ IE+ N + + V YQ
Sbjct: 618 K-TVDKARLDITHYKRITREEVKEIERLANEIVMENRPVKVEWMDRNEAEQKYGFRLYQG 676
Query: 168 GDPALKTAHTRGLPKDHKGSIRIVHIDGIDNNMCCGTHVDNISQLQSIKLLKTTRAQ 224
G P KT IR+V I D C GTHV N ++ IK+LKT R Q
Sbjct: 677 GVPPGKT-------------IRVVEIGDWDVEACGGTHVSNTGEIGPIKILKTERIQ 720
>gnl|CDD|234309 TIGR03683, A-tRNA_syn_arch, alanyl-tRNA synthetase. This family of
alanyl-tRNA synthetases is limited to the archaea, and
is a subset of those sequences identified by the model
pfam07973 covering the second additional domain (SAD) of
alanyl and threonyl tRNA synthetases.
Length = 902
Score = 112 bits (281), Expect = 4e-28
Identities = 71/236 (30%), Positives = 105/236 (44%), Gaps = 46/236 (19%)
Query: 12 KEYKSKVVSCKRNETRPTEYHVRMEDTIFFPTGGGQHCDKGTL----GGVEVVDVYRDGD 67
+E+++KV+ N +V ++ T F+P GGGQ D G L G VVDV + G
Sbjct: 512 REFEAKVLGVFDN-------YVVLDQTAFYPEGGGQPADTGYLITNGGEYRVVDVQKVGG 564
Query: 68 EAVHVVNKE-FQVGELLDMKIDWAHRLDQTQQHTGQHLLSAVIDKMFGYDTESWNCGSDV 126
VH V+ E + G+ + +IDW RL + HT H+L A ++ G W G+
Sbjct: 565 VIVHKVDGEGIKEGDEVKGEIDWERRLRLMRHHTATHVLLAAARRVLG--RHVWQAGAQK 622
Query: 127 CDVELATKD----KDLTEADIAAIEQECNNKIRQGVKVW--------ASE------YQPG 168
D + A D K ++E +I IE+ N + + V A + YQ G
Sbjct: 623 -DTDKARLDITHYKRISEEEIKEIERLANRIVMENRPVSVKWMDRNEAEQKYGFRLYQGG 681
Query: 169 DPALKTAHTRGLPKDHKGSIRIVHIDGIDNNMCCGTHVDNISQLQSIKLLKTTRAQ 224
P + IR+V I+ D C GTH N ++ IK+LKT R Q
Sbjct: 682 VPPGRE-------------IRVVEIEDWDVQACGGTHCRNTGEIGPIKILKTERIQ 724
>gnl|CDD|223092 COG0013, AlaS, Alanyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 879
Score = 98.9 bits (247), Expect = 1e-23
Identities = 61/215 (28%), Positives = 89/215 (41%), Gaps = 31/215 (14%)
Query: 30 EYHVRMEDTIFFPTGGGQHCDKGTL-----GGVEVVDVYRDGDEA-VHVV---NKEFQVG 80
E +V ++ T F+ GGQ D G + G EV DV + G+ VH + E +VG
Sbjct: 489 EVYVVLDQTPFYAESGGQVGDTGYIFGDGGGRFEVTDVQKVGNGVIVHKGKVESGELKVG 548
Query: 81 ELLDMKIDWAHRLDQTQQHTGQHLLSAVIDKMFGYDTESWNCGSDVCDVELATKD----K 136
+ + ++D R + HT HLL A + K+ G W GS V D E D K
Sbjct: 549 DEVTAEVDEERRRRLMRNHTATHLLHAALRKVLG--DHVWQAGSLV-DPEKLRFDFSHYK 605
Query: 137 DLTEADIAAIEQECNNKIRQGVKVWASEYQPGDPALKTAHTRGL-------PKDHKGSIR 189
LT ++ IE+ N IR+ + V E L A +G D +R
Sbjct: 606 ALTAEELKEIERLVNEIIRENLPVKTEE-----MDLDEAKAKGAMALFGEKYGDE---VR 657
Query: 190 IVHIDGIDNNMCCGTHVDNISQLQSIKLLKTTRAQ 224
+V I +C GTHV N + K++
Sbjct: 658 VVEIGDFSVELCGGTHVSNTGDIGLFKIISEEGIA 692
>gnl|CDD|232931 TIGR00344, alaS, alanine--tRNA ligase. The model describes
alanine--tRNA ligase. This enzyme catalyzes the reaction
(tRNAala + L-alanine + ATP = L-alanyl-tRNAala +
pyrophosphate + AMP) [Protein synthesis, tRNA
aminoacylation].
Length = 851
Score = 81.7 bits (202), Expect = 1e-17
Identities = 53/207 (25%), Positives = 85/207 (41%), Gaps = 15/207 (7%)
Query: 30 EYHVRMEDTIFFPTGGGQHCDKGTL----GGVEVVDVYRDGDEAVH---VVNKEFQVGEL 82
+V ++ T F+ GGQ D G L G VVDV + H V +VG+
Sbjct: 484 SVYVILDQTPFYAESGGQIGDTGYLIANDGKFRVVDVQKPNGVVFHFGEVEGGSLKVGDK 543
Query: 83 LDMKIDWAHRLDQTQQHTGQHLLSAVIDKMFGYDTESWNCGSDVCDVELATKD----KDL 138
+ ID RL + H+ HLL A + K+ G W GS V V+ D + L
Sbjct: 544 VIAVIDEKRRLRIMRNHSATHLLHAALQKVLG--NHVWQAGSLV-SVKKLRFDFSHYRAL 600
Query: 139 TEADIAAIEQECNNKIRQGVKVWASEYQPGDPALKTAHTRGLPKDHKGSIRIVHIDGIDN 198
T ++ IE N +I + + + D A + + +R+V + +
Sbjct: 601 TREELEKIEDLVNEQILANIPI-KVIFMDLDEAKAKGAFALFGEKYGEKVRVVSVGDVSV 659
Query: 199 NMCCGTHVDNISQLQSIKLLKTTRAQK 225
+C GTHV N ++ K++K +
Sbjct: 660 ELCGGTHVRNTGEIGLFKIVKESGIAA 686
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 66.6 bits (164), Expect = 1e-12
Identities = 51/204 (25%), Positives = 80/204 (39%), Gaps = 37/204 (18%)
Query: 38 TIFFPTGGGQHCDKGTLGG---VEVVDVYRDGDEA-VH---VVNKEFQVGELLDMKIDWA 90
T F+ GGQ D G + EV D + + VH V E +VG+ + ++D
Sbjct: 485 TPFYAESGGQVGDTGVIEDGGVFEVTDTQKPPNGLIVHRGKVEEGELKVGDEVTAEVDEE 544
Query: 91 HRLDQTQQHTGQHLLSAVIDKMFGYDTESWNCGSDVCDVELATKD----KDLTEADIAAI 146
R + H+ HLL A + ++ G GS V + D + LT ++ I
Sbjct: 545 RRRAIARNHSATHLLHAALREVLGEHVT--QAGSLV-APDRLRFDFSHFEALTPEELRKI 601
Query: 147 EQECNNKIRQGVKVWASEYQPGDPALKTAHTRGLPKDHKGSI-----------RIVHIDG 195
E N KIR+ + V +E + A K G++ R+V I
Sbjct: 602 EDLVNEKIRENLPV-ETEEMSIEEAKK-----------MGAMALFGEKYGDEVRVVSIGD 649
Query: 196 IDNNMCCGTHVDNISQLQSIKLLK 219
+C GTHV N + K++
Sbjct: 650 FSIELCGGTHVSNTGDIGLFKIVS 673
>gnl|CDD|215487 PLN02900, PLN02900, alanyl-tRNA synthetase.
Length = 936
Score = 62.3 bits (152), Expect = 4e-11
Identities = 57/212 (26%), Positives = 89/212 (41%), Gaps = 36/212 (16%)
Query: 30 EYHVRMEDTIFFPTGGGQHCDKGTLGG-----VEVVDVYRDGDEAVH---VVNKEFQVGE 81
E + ++ T F+ GGQ D G L G VEV DV + G +H V VG+
Sbjct: 521 EVGIVLDKTSFYAESGGQIGDTGVLEGSGGAVVEVSDVQKAGGFVLHIGTVTEGSVSVGD 580
Query: 82 LLDMKIDWAHRLDQTQQHTGQHLLSAVIDKMFGYDTESWNCGSDVCDVELA---TKDKDL 138
+ K+D+ R HT HLL++ + ++ G + GS V +L + K +
Sbjct: 581 AVTCKVDYDRRRRIAPNHTATHLLNSALKEVLGDHVD--QKGSLVAFEKLRFDFSHGKPM 638
Query: 139 TEADIAAIEQECNNKIRQGVKVWASEYQPGDPALKTAHTRGLPKDHKGSI---------- 188
T ++ +E N I + V A E L A K G
Sbjct: 639 TPEELREVESLVNEWIGDALPVEAKEM-----PLADA------KRINGLRAVFGEKYPDP 687
Query: 189 -RIVHIDGIDN-NMCCGTHVDNISQLQSIKLL 218
R+V + G+ + +C GTHV N ++ ++ KLL
Sbjct: 688 VRVVSVGGVYSMELCGGTHVSNTAEAEAFKLL 719
>gnl|CDD|197931 smart00863, tRNA_SAD, Threonyl and Alanyl tRNA synthetase second
additional domain. The catalytically active form of
threonyl/alanyl tRNA synthetase is a dimer. Within the
tRNA synthetase class II dimer, the bound tRNA interacts
with both monomers making specific interactions with the
catalytic domain, the C-terminal domain, and this SAD
domain (the second additional domain). The second
additional domain is comprised of a pair of
perpendicularly orientated antiparallel beta sheets, of
four and three strands, respectively, that surround a
central alpha helix that forms the core of the domain.
Length = 43
Score = 52.4 bits (127), Expect = 1e-09
Identities = 12/38 (31%), Positives = 20/38 (52%)
Query: 188 IRIVHIDGIDNNMCCGTHVDNISQLQSIKLLKTTRAQK 225
+R+V I +C GTHV N ++ + K+L + A
Sbjct: 1 VRVVSIGDFSVELCGGTHVPNTGEIGAFKILSVSGAYW 38
>gnl|CDD|219676 pfam07973, tRNA_SAD, Threonyl and Alanyl tRNA synthetase second
additional domain. The catalytically active from of
threonyl/alanyl tRNA synthetase is a dimer. Within the
tRNA synthetase class II dimer, the bound tRNA interacts
with both monomers making specific interactions with the
catalytic domain, the C-terminal domain, and this domain
(the second additional domain). The second additional
domain is comprised of a pair of perpendicularly
orientated antiparallel beta sheets, of four and three
strands, respectively, that surround a central alpha
helix that forms the core of the domain.
Length = 44
Score = 50.9 bits (123), Expect = 4e-09
Identities = 14/38 (36%), Positives = 22/38 (57%)
Query: 188 IRIVHIDGIDNNMCCGTHVDNISQLQSIKLLKTTRAQK 225
+R+V I D ++C GTHV N ++ + K+LK K
Sbjct: 1 VRVVRIGDFDVDLCGGTHVPNTGEIGAFKILKGDSKNK 38
>gnl|CDD|178546 PLN02961, PLN02961, alanine-tRNA ligase.
Length = 223
Score = 43.5 bits (103), Expect = 3e-05
Identities = 55/211 (26%), Positives = 78/211 (36%), Gaps = 46/211 (21%)
Query: 38 TIFFPTGGGQHCDKGTLGGVE------VVDVYRDGDEAVHV---------VNKEFQVGEL 82
TIF P GGGQ D G + V DV R H F+ G+
Sbjct: 10 TIFHPQGGGQPSDTGRIVISGGDTKFSVQDVRRKDGVVYHYGVFEGSNPESASPFEAGDE 69
Query: 83 LDMKIDWAHRLDQTQQHTGQHLLSAVIDKMFGYDTESWNCG------------SDVCDVE 130
+ + +D + R ++ H+ HLL + G D VE
Sbjct: 70 VTVTVDESRRKLHSRLHSAGHLLDVCMA----------RVGLGPLEPGKGYHFPDGPFVE 119
Query: 131 LATK-DKDLTEADIAAIEQECNNKIRQGVKVWASEYQPGDPALKTAHTRGLP----KDHK 185
K + ++ +E E N I +G KV A+ P D A LP KD
Sbjct: 120 YKGKIPQGELDSKQDELEAEANELIAEGGKVSAAVL-PYDEA-AELCGGSLPDYIAKD-- 175
Query: 186 GSIRIVHIDGIDNNMCCGTHVDNISQLQSIK 216
+ RIV I C GTHV ++S++ S+K
Sbjct: 176 STPRIVKIGDSPGCPCGGTHVADVSEITSVK 206
>gnl|CDD|216484 pfam01411, tRNA-synt_2c, tRNA synthetases class II (A). Other tRNA
synthetase sub-families are too dissimilar to be
included. This family includes only alanyl-tRNA
synthetases.
Length = 551
Score = 36.1 bits (84), Expect = 0.013
Identities = 18/60 (30%), Positives = 25/60 (41%), Gaps = 7/60 (11%)
Query: 38 TIFFPTGGGQHCDKGTL----GGVEVVDVYRDGDEAVHVVNKE---FQVGELLDMKIDWA 90
T F+ GGQ D G + G V DV + G VH E +VG+ + +D
Sbjct: 491 TPFYAESGGQIGDTGYIIGEGGEFRVTDVQKYGGVVVHKGKLESGSLKVGDTVIAVVDED 550
>gnl|CDD|234962 PRK01584, PRK01584, alanyl-tRNA synthetase; Provisional.
Length = 594
Score = 35.9 bits (83), Expect = 0.016
Identities = 30/132 (22%), Positives = 58/132 (43%), Gaps = 6/132 (4%)
Query: 91 HRLDQTQQHTGQHLLSAVIDKMFGYDTESWNCGSDVCDVELA---TKDKDLTEADIAAIE 147
H + T+ HT HLL + + G GS++ L + + +T+ +I +E
Sbjct: 449 HSYETTKLHTATHLLHKALRLVLGDHVRQK--GSNITAERLRFDFSHPEKMTDDEIKKVE 506
Query: 148 QECNNKIRQGVKVWASEYQPGDPALKTAHTRGLPKDHKGSIRIVHIDGIDNNMCCGTHVD 207
N +I+ + V E + A + + ++ +++ IDG +C G HV+
Sbjct: 507 DIVNLQIKNDLSV-KKEVMSLEEAREKGAMALFGEKYEDIVKVYEIDGFSKEVCGGPHVE 565
Query: 208 NISQLQSIKLLK 219
N +L + K+ K
Sbjct: 566 NTGELGTFKIQK 577
>gnl|CDD|234752 PRK00413, thrS, threonyl-tRNA synthetase; Reviewed.
Length = 638
Score = 31.6 bits (73), Expect = 0.36
Identities = 27/124 (21%), Positives = 50/124 (40%), Gaps = 31/124 (25%)
Query: 108 VIDKMFGYDTESWNCGSDVCDVELATKDKDLTEADIAAIEQECNNKIRQGVKVWASEYQP 167
VI+ F YD + ++ T D+ AIE+E I++ +
Sbjct: 97 VIENGFYYDFDR---------------ERPFTPEDLEAIEKEMKEIIKENYPIEREVV-S 140
Query: 168 GDPALKTAHTRG----------LPKDHKGSIRI-VHIDGIDNNMCCGTHVDNISQLQSIK 216
+ A++ RG +P+D I + + +D +C G HV + ++++ K
Sbjct: 141 REEAIELFKDRGEPYKVELIEEIPED--EEISLYRQGEFVD--LCRGPHVPSTGKIKAFK 196
Query: 217 LLKT 220
LLK
Sbjct: 197 LLKV 200
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 31.8 bits (72), Expect = 0.36
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 111 KMFGYDTESWNCGSDVCDVELATKDKDLTEADIAAIEQECN-NKIRQGVKVWASE 164
++F T S DV ELA + T ADI A+ +E +R+ + A E
Sbjct: 629 EIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRESIGSPAKE 683
>gnl|CDD|232967 TIGR00418, thrS, threonyl-tRNA synthetase. This model represents
the threonyl-tRNA synthetase found in most organisms.
This protein is a class II tRNA synthetase, and is
recognized by the pfam model tRNA-synt_2b. Note that B.
subtilis has closely related isozymes thrS and thrZ. The
N-terminal regions are quite dissimilar between archaeal
and eubacterial forms, while some eukaryotic forms are
missing sequence there altogether. [Protein synthesis,
tRNA aminoacylation].
Length = 563
Score = 30.8 bits (70), Expect = 0.73
Identities = 32/161 (19%), Positives = 55/161 (34%), Gaps = 30/161 (18%)
Query: 99 HTGQHLLSAVIDKMFGYDTESWNCG-----SDVCDVELATKDKDLTEADIAAIEQECNNK 153
H+ HLL+ Y G D EL D+ T+ D+ IE++
Sbjct: 2 HSIAHLLA--EALKQLYPDVKLAIGPVVEDGFYYDFEL---DRSFTQEDLEKIEKDMKEI 56
Query: 154 IRQGVKV------WASE---YQPGDPALKTAHTRGLPKDHKGSIRIVHIDGIDNNMCCGT 204
++ V ++ +P K +P K + +D +C G
Sbjct: 57 AKKNYPVAKLSVSLEEALEAFKVLEP-YKLELLDEIPNGVKRTPYGWGKAFVD--LCKGP 113
Query: 205 HVDNISQLQSIKLLKTTRAQKSKSLCIYLYLLGRRLMIQEL 245
H+ N S +++ KL K A Y + M+Q +
Sbjct: 114 HLPNTSFIKAFKLEKVAGA--------YWRGDSKNKMLQRI 146
>gnl|CDD|220663 pfam10266, Strumpellin, Hereditary spastic paraplegia protein
strumpellin. This is a family of proteins conserved
from plants to humans, in which two closely situated
point mutations in the human protein lead to the
condition of hereditary spastic paraplegia. Strumpellin
contains one known domain called a spectrin repeat that
consists of three alpha-helices of a characteristic
length wrapped in a left-handed coiled coil. The
spectrin proteins have multiple copies of this repeat,
which can then form multimers in the cell. Spectrin
associates with the cell membrane via spectrin repeats
in the ankyrin protein. The spectrin repeat is a
structural platform for cytoskeletal protein assemblies.
Length = 1077
Score = 29.6 bits (67), Expect = 1.8
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 146 IEQECNNKIRQGVKVWASEYQ 166
+E ECN +++ V W SEYQ
Sbjct: 755 VEMECNAFLKKKVYEWQSEYQ 775
>gnl|CDD|233007 TIGR00522, dph5, diphthine synthase. Alternate name: diphthamide
biosynthesis S-adenosylmethionine-dependent
methyltransferase. This protein participates in the
modification of a specific His of elongation factor 2 of
eukarotes and Archaea to diphthamide. The protein was
characterized in Saccharomyces cerevisiae and designated
DPH5 [Protein fate, Protein modification and repair].
Length = 257
Score = 27.9 bits (62), Expect = 4.3
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 4/53 (7%)
Query: 167 PGDPALKTAHTRGLPKDHKGSI--RIVHIDGIDNNMC--CGTHVDNISQLQSI 215
GDP + T HT + + I RI+H I + +C G + + +I
Sbjct: 83 AGDPMVATTHTDLKLEAKRKGIETRIIHGASISSAVCGLTGLQLYKFGKTATI 135
>gnl|CDD|175985 cd04018, C2C_Ferlin, C2 domain third repeat in Ferlin. Ferlins are
involved in vesicle fusion events. Ferlins and other
proteins, such as Synaptotagmins, are implicated in
facilitating the fusion process when cell membranes fuse
together. There are six known human Ferlins: Dysferlin
(Fer1L1), Otoferlin (Fer1L2), Myoferlin (Fer1L3),
Fer1L4, Fer1L5, and Fer1L6. Defects in these genes can
lead to a wide range of diseases including muscular
dystrophy (dysferlin), deafness (otoferlin), and
infertility (fer-1, fertilization factor-1).
Structurally they have 6 tandem C2 domains, designated
as (C2A-C2F) and a single C-terminal transmembrane
domain, though there is a new study that disputes this
and claims that there are actually 7 tandem C2 domains
with another C2 domain inserted between C2D and C2E.
In a subset of them (Dysferlin, Myoferlin, and Fer1)
there is an additional conserved domain called DysF. C2
domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions. This cd contains the third C2
repeat, C2C, and has a type-II topology.
Length = 151
Score = 27.2 bits (61), Expect = 5.8
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 188 IRIVHIDGIDNNMCCGTHVDNISQ 211
I+I D + N+ GTH ++S+
Sbjct: 80 IQIRDWDRVGNDDVIGTHFIDLSK 103
>gnl|CDD|128904 smart00657, RPOL4c, DNA-directed RNA-polymerase II subunit.
Length = 118
Score = 26.5 bits (59), Expect = 6.8
Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 2/58 (3%)
Query: 91 HRLDQTQQHTGQHLLSAVIDKMFGYDTE--SWNCGSDVCDVELATKDKDLTEADIAAI 146
+ + Q LS V+ K Y ++ + V V K K L + +IA +
Sbjct: 20 LKRQSKESEEEQQPLSTVMKKTLKYLSKFARFKNREIVRAVRTLLKSKKLHKFEIAQL 77
>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5
(SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich
splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an
important role in both, constitutive and alternative,
splicing of many pre-mRNAs. It can shuttle between the
nucleus and cytoplasm. SRSF5 regulates both alternative
splicing and basal splicing. It is the only SR protein
efficiently selected from nuclear extracts (NE) by the
splicing enhancer (ESE) and essential for enhancer
activation. SRSF6 preferentially interacts with a
number of purine-rich splicing enhancers (ESEs) to
activate splicing of the ESE-containing exon. It is the
only protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types
of RNA sites. Members in this family contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 25.4 bits (56), Expect = 7.7
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 8/60 (13%)
Query: 31 YHVRMEDTIFFPTGGGQHCD---KGTLGGVEVVDVYRDGDEAVHVVNKEFQVGELLDMKI 87
Y R D F G G+ + K G VE D RD D+AV+ +N + EL ++
Sbjct: 9 YRARERDVERFFKGYGRIREINLKNGFGFVEFED-PRDADDAVYELNGK----ELCGERV 63
>gnl|CDD|234864 PRK00915, PRK00915, 2-isopropylmalate synthase; Validated.
Length = 513
Score = 27.4 bits (62), Expect = 9.0
Identities = 23/105 (21%), Positives = 43/105 (40%), Gaps = 26/105 (24%)
Query: 99 HTGQHLLSAVIDKM--FGYDTESWNCGSDVCDV-----ELATKDKDLTEADIAAI-EQEC 150
H+G+H A ++ GY ++ ELA K K++ + D+ A+ E E
Sbjct: 331 HSGRH---AFKHRLEELGYKLSD----EELDKAFERFKELADKKKEVFDEDLEALVEDET 383
Query: 151 NNKIRQGVKVWASEYQPGDPALKTAHTRGLPKDHKGSIRIVHIDG 195
+ + K+ + + Q G TA ++++ IDG
Sbjct: 384 QQEEPEHYKLESLQVQSGSSGTPTA-----------TVKLRDIDG 417
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 0.135 0.414
Gapped
Lambda K H
0.267 0.0906 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,031,606
Number of extensions: 1091716
Number of successful extensions: 843
Number of sequences better than 10.0: 1
Number of HSP's gapped: 823
Number of HSP's successfully gapped: 25
Length of query: 245
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 151
Effective length of database: 6,768,326
Effective search space: 1022017226
Effective search space used: 1022017226
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: 58 (25.8 bits)