RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17548
(426 letters)
>gnl|CDD|222441 pfam13898, DUF4205, Domain of unknown function (DUF4205). The
proteins in this family are uncharacterized but often
named FAM188B.
Length = 341
Score = 201 bits (512), Expect = 5e-61
Identities = 91/259 (35%), Positives = 145/259 (55%), Gaps = 12/259 (4%)
Query: 35 WT-QGFQF---SLDEPTALVQYEGGPCAVLAPAQAFILKYIIQNVDP---VNDNWRTIEQ 87
W QGF F S + P LVQ +GGPC VLA QA+ILKY++ P + +
Sbjct: 16 WKKQGFIFSDPSSELPYGLVQNKGGPCGVLAAVQAYILKYLLFGRAPRDCNSGSMLQPSS 75
Query: 88 EDQNKLLVHAVVEMLKQAVDSN--TFHIVYIDATEASSPDYSFDQFHSQIKVQSCSSCDE 145
++ + LV A+ ++L +A ++ T + + + + Y D ++ + + + +E
Sbjct: 76 AERQRALVAALADILWRAGEAKRATVALPCGRSQFSPAGRYKQDNLTEKLMLFTFTKLEE 135
Query: 146 VEQFYNQRIDLLYNR-FGVLLFLYSVLYSKGLARLRLEVSDITEPLIDREFGYGSQSLIN 204
++ F + + G +LFLYS + S+G+ R+R ++ T LI GY +Q L+N
Sbjct: 136 LQAFLYEHLSQFETGGHGCILFLYSAILSRGVERIRSDLDVPTGQLIG-AHGYCTQELVN 194
Query: 205 LMITGRAVNYVFDHV-QDIDGLQLQGINQQSQIGFLTLLEHLRYCEVGSYLKNPINPVWV 263
L++TGRAV+ VF+ V + D L L+GI +S+IGFL+L EH + C+VGSYLK P P+WV
Sbjct: 195 LLLTGRAVSNVFNGVDEGNDNLTLRGILTRSEIGFLSLFEHYQSCQVGSYLKTPRFPIWV 254
Query: 264 LGSETHLTVTFSFEKRLAC 282
+ SE+H +V F L
Sbjct: 255 VCSESHYSVLFCLNPELLS 273
Score = 29.6 bits (67), Expect = 2.9
Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 7/63 (11%)
Query: 360 DMFDIFHYNGLARSNYE-RKVMYRMAHCVLLECNINCLLETN---PMLT-CLQTKWPSIE 414
FD+++Y+GLA + E R + + E + N P L C++TKWP
Sbjct: 279 RRFDLYYYDGLANQDEEIRLTVDTHSA--ADEADHNDQDGVRDLTPPLEHCIRTKWPEAV 336
Query: 415 LSW 417
+ W
Sbjct: 337 IDW 339
>gnl|CDD|238008 cd00051, EFh, EF-hand, calcium binding motif; A diverse superfamily
of calcium sensors and calcium signal modulators; most
examples in this alignment model have 2 active canonical
EF hands. Ca2+ binding induces a conformational change
in the EF-hand motif, leading to the activation or
inactivation of target proteins. EF-hands tend to occur
in pairs or higher copy numbers.
Length = 63
Score = 36.8 bits (86), Expect = 0.001
Identities = 18/60 (30%), Positives = 31/60 (51%)
Query: 289 KARRVFKMFDPDGNNFIASDHLQNLLAKLDLVSDINYVDIMRKKLDPDELGIILLSAFMD 348
+ R F++FD DG+ I++D L+ L L +D M +++D D G I F++
Sbjct: 1 ELREAFRLFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFLE 60
>gnl|CDD|205583 pfam13405, EF_hand_4, EF-hand domain.
Length = 30
Score = 33.3 bits (77), Expect = 0.009
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 289 KARRVFKMFDPDGNNFIASDHLQNLLAKLD 318
+ R FK+FD DG+ +I+++ L+ L L
Sbjct: 1 ELREAFKLFDKDGDGYISAEELRKALRSLG 30
>gnl|CDD|227455 COG5126, FRQ1, Ca2+-binding protein (EF-Hand superfamily) [Signal
transduction mechanisms / Cytoskeleton / Cell division
and chromosome partitioning / General function
prediction only].
Length = 160
Score = 33.8 bits (78), Expect = 0.074
Identities = 17/82 (20%), Positives = 36/82 (43%), Gaps = 10/82 (12%)
Query: 291 RRVFKMFDPDGNNFIASDHLQNLLAKL------DLVSDI-NYVDIMRKKLDPDELGIILL 343
+ F++FD D + I + L +L L ++ + +D + +D E + ++
Sbjct: 23 KEAFQLFDRDSDGLIDRNELGKILRSLGFNPSEAEINKLFEEIDAGNETVDFPEF-LTVM 81
Query: 344 SAFMDEFFGDPEKPPPDMFDIF 365
S + GD E+ + F +F
Sbjct: 82 SVKLKR--GDKEEELREAFKLF 101
>gnl|CDD|185504 PTZ00184, PTZ00184, calmodulin; Provisional.
Length = 149
Score = 33.2 bits (76), Expect = 0.12
Identities = 20/61 (32%), Positives = 32/61 (52%)
Query: 286 SADKARRVFKMFDPDGNNFIASDHLQNLLAKLDLVSDINYVDIMRKKLDPDELGIILLSA 345
S ++ + FK+FD DGN FI++ L++++ L VD M ++ D D G I
Sbjct: 82 SEEEIKEAFKVFDRDGNGFISAAELRHVMTNLGEKLTDEEVDEMIREADVDGDGQINYEE 141
Query: 346 F 346
F
Sbjct: 142 F 142
>gnl|CDD|191473 pfam06214, SLAM, Signaling lymphocytic activation molecule (SLAM)
protein. This family consists of several mammalian
signaling lymphocytic activation molecule (SLAM)
proteins. Optimal T cell activation and expansion
require engagement of the TCR plus co-stimulatory
signals delivered through accessory molecules. SLAM, a
70-kDa co-stimulatory molecule belonging to the Ig
superfamily, is defined as a human cell surface molecule
that mediates CD28-independent proliferation of human T
cells and IFN-gamma production by human Th1 and Th2
clones. SLAM has also been recognised as a receptor for
measles virus.
Length = 126
Score = 31.3 bits (71), Expect = 0.29
Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 3/60 (5%)
Query: 80 DNWRTIEQEDQNKLL---VHAVVEMLKQAVDSNTFHIVYIDATEASSPDYSFDQFHSQIK 136
+ E NK + +H +V M + +S IV +D +E SP Y D + ++
Sbjct: 42 SVLLPLTSERINKSMNKSIHILVTMAESPGNSVKKKIVSLDLSEGGSPRYLEDGYKFHLE 101
>gnl|CDD|163554 TIGR03842, F420_CPS_4043, F420-dependent oxidoreductase, CPS_4043
family. This model represents a family of putative
F420-dependent oxidoreductases, fairly closely related
to 5,10-methylenetetrahydromethanopterin reductase (mer,
TIGR03555), both within the bacterial luciferase-like
monoxygenase (LLM) family. A fairly deep split (to about
40 % sequence identity) in the present family separates
a strictly Actinobacterial clade from an
alpha/beta/gamma-proteobacterial clade, in which the
member is often the only apparent F420-dependent LLM
family member. The specific function, and whether
Actinobacterial and Proteobacterial clades differ in
function, are unknown [Unknown function, Enzymes of
unknown specificity].
Length = 330
Score = 32.4 bits (74), Expect = 0.46
Identities = 22/84 (26%), Positives = 34/84 (40%), Gaps = 3/84 (3%)
Query: 210 RAVNYVFDHVQDIDGLQLQGINQQSQIGFLTLLEHLRYCEVGSYLKNPINPVWVLGSETH 269
+A + FD+V D L Q+ + + +L R VG + NP+ W + +
Sbjct: 21 QAERHGFDYVWTFDSHILW---QEPFVIYSQILAATRNMVVGPMVTNPLTRDWTVTASLF 77
Query: 270 LTVTFSFEKRLACLESSADKARRV 293
T+ F R C D A RV
Sbjct: 78 ATLNEMFGNRTVCGIGRGDSAVRV 101
>gnl|CDD|200946 pfam00036, efhand, EF hand. The EF-hands can be divided into two
classes: signaling proteins and buffering/transport
proteins. The first group is the largest and includes
the most well-known members of the family such as
calmodulin, troponin C and S100B. These proteins
typically undergo a calcium-dependent conformational
change which opens a target binding site. The latter
group is represented by calbindin D9k and do not undergo
calcium dependent conformational changes.
Length = 29
Score = 28.6 bits (65), Expect = 0.49
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 289 KARRVFKMFDPDGNNFIASDHLQNLLAKL 317
+ + FK FD DG+ I+ + + LL KL
Sbjct: 1 ELKEAFKEFDKDGDGKISFEEFKELLKKL 29
>gnl|CDD|234385 TIGR03897, lanti_2_LanM, type 2 lantibiotic biosynthesis protein
LanM. Members of this family are known generally as
LanM, a multifunctional enzyme of lantibiotic
biosynthesis. This catalysis by LanM distinguishes the
type 2 lantibiotics, such as mersacidin, cinnamycin, and
lichenicidin, from LanBC-produced type 1 lantibiotics
such as nisin and subtilin. The N-terminal domain
contains regions associated with Ser and Thr
dehydration. The C-terminal region contains a pfam05147
domain, which catalyzes the formation of the lanthionine
bridge [Cellular processes, Toxin production and
resistance].
Length = 931
Score = 31.9 bits (73), Expect = 0.87
Identities = 21/62 (33%), Positives = 28/62 (45%), Gaps = 21/62 (33%)
Query: 125 DYSFDQFHSQIKVQSCSSCDEVEQFYNQRIDLLYNRFGVLLFLYSVLYSKGLARLRLEVS 184
DY + +F I+ + C S +EVE+F Y R GVLL L LY L +
Sbjct: 204 DYGWMEF---IEHEPCESEEEVERF--------YQRAGVLLAL---LYL-------LNGT 242
Query: 185 DI 186
D
Sbjct: 243 DF 244
>gnl|CDD|197492 smart00054, EFh, EF-hand, calcium binding motif. EF-hands are
calcium-binding motifs that occur at least in pairs.
Links between disease states and genes encoding
EF-hands, particularly the S100 subclass, are emerging.
Each motif consists of a 12 residue loop flanked on
either side by a 12 residue alpha-helix. EF-hands
undergo a conformational change unpon binding calcium
ions.
Length = 29
Score = 27.7 bits (63), Expect = 0.95
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 291 RRVFKMFDPDGNNFIASDHLQNLLAKL 317
+ F++FD DG+ I + ++LL L
Sbjct: 3 KEAFRLFDKDGDGKIDFEEFKDLLKAL 29
>gnl|CDD|235516 PRK05582, PRK05582, DNA topoisomerase I; Validated.
Length = 650
Score = 31.3 bits (72), Expect = 1.1
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 317 LDLVSDINYVDIMRKKLDPDELGIILLSAFMDEFFGD 353
+ + YV + +K+L P ELG I+ ++EFF D
Sbjct: 479 ISTIQKRGYVKLEKKRLVPTELGEIVNE-LLEEFFPD 514
>gnl|CDD|221507 pfam12281, DUF3620, Protein of unknown function (DUF3620). This
family of proteins is found in bacteria. Proteins in
this family are typically between 281 and 358 amino
acids in length. There are two completely conserved
residues (G and P) that may be functionally important.
Length = 216
Score = 30.8 bits (70), Expect = 1.1
Identities = 12/69 (17%), Positives = 27/69 (39%), Gaps = 4/69 (5%)
Query: 40 QFSLDEP--TALVQYEGGPCAVLAPA-QAFIL-KYIIQNVDPVNDNWRTIEQEDQNKLLV 95
+ L++P ++ G P V P + F + K I+ + + + +Q L++
Sbjct: 136 DWLLNDPVRAVVLDRSGRPVRVQVPDPERFAVHKLIVSQRRDGDPRAKRRKDLEQAALVI 195
Query: 96 HAVVEMLKQ 104
+ E
Sbjct: 196 ELLAERRPH 204
>gnl|CDD|176513 cd08571, GDPD_SHV3_plant, Glycerophosphodiester phosphodiesterase
domain of glycerophosphodiester phosphodiesterase-like
protein SHV3 and SHV3-like proteins. This subfamily
corresponds to the glycerophosphodiester
phosphodiesterase (GDPD) domain present in
glycerophosphodiester phosphodiesterase (GP-GDE)-like
protein SHV3 and SHV3-like proteins (SVLs), which may
play an important role in cell wall organization. The
prototype of this family is a
glycosylphosphatidylinositol (GPI) anchored protein SHV3
encoded by shaven3 (shv3) gene from Arabidopsis
thaliana. Members in this family show sequence homology
to bacterial GP-GDEs (EC 3.1.4.46) that catalyze the
hydrolysis of various glycerophosphodiesters, and
produce sn-glycerol-3-phosphate (G3P) and the
corresponding alcohols. Both, SHV3 and SVLs, have two
tandemly repeated GDPD domains whose biochemical
functions remain unclear. The residues essential for
interactions with the substrates and calcium ions in
bacterial GP-GDEs are not conserved in SHV3 and SVLs,
which suggests that the function of GDPD domains in
these proteins might be distinct from those in typical
bacterial GP-GDEs. In addition, the two tandem repeats
show low sequence similarity to each other, suggesting
they have different biochemical function. Most members
of this family are Arabidopsis-specific gene products.
To date, SHV3 orthologues are only found in
Physcomitrella patens.
Length = 302
Score = 30.3 bits (69), Expect = 1.8
Identities = 16/42 (38%), Positives = 19/42 (45%), Gaps = 5/42 (11%)
Query: 87 QEDQNKLLVHAVVEMLKQAVDSNTFHIVYIDATEASSPDYSF 128
E + L V AV+ L +A T VYI SSPD S
Sbjct: 144 AEHKGLLSVDAVLTSLSKAGYDQTAKKVYI-----SSPDSSV 180
>gnl|CDD|240534 cd13129, MATE_epsE_like, Multidrug and toxic compound extrusion
family and similar proteins. This model represents a
subfamily of the multidrug and toxic compound extrusion
(MATE)-like proteins, including Ralstonia solanaceraum
GMI1000 epsE, which may be involved in exporting
exopolysaccharide EPS I, a virulence factor. Proteins
from the MATE family are involved in exporting
metabolites across the cell membrane and are often
responsible for multidrug resistance (MDR).
Length = 411
Score = 30.5 bits (69), Expect = 1.9
Identities = 10/44 (22%), Positives = 20/44 (45%)
Query: 166 FLYSVLYSKGLARLRLEVSDITEPLIDREFGYGSQSLINLMITG 209
L+ + S L + + S I L +E+G + S+ +L +
Sbjct: 299 LLFGLGLSLPLGCVFILASQIFAWLYGKEYGSAAASMRSLAVAA 342
>gnl|CDD|222234 pfam13575, DUF4135, Domain of unknown function (DUF4135). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria and archaea, and is
approximately 380 amino acids in length. The family is
found in association with pfam05147. This domain may be
involved in synthesis of a lantibiotic compound.
Length = 369
Score = 30.3 bits (69), Expect = 1.9
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 11/47 (23%)
Query: 125 DYSFDQFHSQIKVQSCSSCDEVEQFYNQRIDLLYNRFGVLLFLYSVL 171
DY +++F I+ + C+S +EV++F Y R G LL L +L
Sbjct: 113 DYGWEEF---IEHKPCASEEEVKRF--------YRRAGALLALLYLL 148
>gnl|CDD|226440 COG3930, COG3930, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 434
Score = 30.2 bits (68), Expect = 2.3
Identities = 18/74 (24%), Positives = 29/74 (39%), Gaps = 5/74 (6%)
Query: 191 IDREFGYGSQSLINLMITGRAV-NYVFDHVQDIDGLQLQGINQQS---QIGFLTLLEHLR 246
I + Y +I + + + V DH++D QL G QQ Q+ L
Sbjct: 96 IAPQLLY-RPLVIQIEERKCKLYSMVIDHLEDPVLYQLYGEKQQELDLQLTMLFSAGDRT 154
Query: 247 YCEVGSYLKNPINP 260
+ + G L +NP
Sbjct: 155 FADFGLALYGYVNP 168
>gnl|CDD|223813 COG0742, COG0742, N6-adenine-specific methylase [DNA replication,
recombination, and repair].
Length = 187
Score = 29.1 bits (66), Expect = 2.7
Identities = 10/50 (20%), Positives = 23/50 (46%), Gaps = 7/50 (14%)
Query: 68 LKYIIQNVDPVNDNWRTIEQEDQNKLLVHAVVEMLKQAVDSNTFHIVYID 117
+K + +N+ + E + ++L + + LKQ F +V++D
Sbjct: 79 VKILKENLK-------ALGLEGEARVLRNDALRALKQLGTREPFDLVFLD 121
>gnl|CDD|235648 PRK05932, PRK05932, RNA polymerase factor sigma-54; Reviewed.
Length = 455
Score = 29.4 bits (67), Expect = 4.0
Identities = 11/80 (13%), Positives = 26/80 (32%), Gaps = 19/80 (23%)
Query: 278 KRLACLESSADKARRVFKMFDPDG--------------NNFIASDHLQNLLAK----LDL 319
+ L + + + FDP G + L + LDL
Sbjct: 146 ESLGVELDEVEAVLKRIQSFDPAGVGARDLQECLLLQLEQLDDTPRLDEAMEIISDHLDL 205
Query: 320 VSDINYVDIMRK-KLDPDEL 338
++ ++ + +K + ++L
Sbjct: 206 LARRDFRTLAKKLGVKEEDL 225
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
0.322 0.138 0.418
Gapped
Lambda K H
0.267 0.0689 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,042,574
Number of extensions: 2170832
Number of successful extensions: 1733
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1726
Number of HSP's successfully gapped: 29
Length of query: 426
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 326
Effective length of database: 6,502,202
Effective search space: 2119717852
Effective search space used: 2119717852
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: 60 (27.0 bits)