RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14958
(362 letters)
>gnl|CDD|235645 PRK05912, PRK05912, tyrosyl-tRNA synthetase; Validated.
Length = 408
Score = 149 bits (379), Expect = 2e-41
Identities = 52/166 (31%), Positives = 77/166 (46%), Gaps = 33/166 (19%)
Query: 229 DLLVRTPQTVYAGFDPTASSLHIGNLLILINLIHWQRAGHQVIAL------MI------- 275
+ L + P +Y GFDPTA SLH+G+L+ L+ L +Q AGH+ IAL MI
Sbjct: 27 EKLAKEPLRIYLGFDPTAPSLHLGHLVPLLKLRRFQDAGHKPIALIGGFTGMIGDPSGKS 86
Query: 276 --------------------CLSQILWRTCNEEAVVNNMSWYNSINVIDFMNHIARLFRM 315
L + L + +VNN W +N IDF+ + + F +
Sbjct: 87 ETRKLLTREQVAENAETIKEQLFKFLDFEKDGAEIVNNSDWLGKLNAIDFLRDLGKHFTV 146
Query: 316 GDMLKKQSVVTRLESEHGMNYTEFSYQIFQSYDWAHLYKEHNCRFQ 361
ML++ RL G+++TEF Y + Q YD+ L K + C Q
Sbjct: 147 NRMLERDDFKKRLREGQGISFTEFLYPLLQGYDFVALNKRYGCDLQ 192
Score = 90.2 bits (225), Expect = 5e-20
Identities = 43/162 (26%), Positives = 61/162 (37%), Gaps = 49/162 (30%)
Query: 109 IGGATAQVGDPSGKTKDRDKQDLATVQTNTKGIEKNIKTIFRNHEQYFWKDRKDSLKPPI 168
IGG T +GDPSGK++ R V N + I++ + F KD
Sbjct: 72 IGGFTGMIGDPSGKSETRKLLTREQVAENAETIKEQLFKFLD-----FEKDG------AE 120
Query: 169 VVNNMSWYNSINVIDFMNHIARLFRMGDMLKKQSV------------------------- 203
+VNN W +N IDF+ + + F + ML++
Sbjct: 121 IVNNSDWLGKLNAIDFLRDLGKHFTVNRMLERDDFKKRLREGQGISFTEFLYPLLQGYDF 180
Query: 204 -------------GGSDQMGNIKAGHDLISKLYGKTVFDLLV 232
GGSDQ GNI +G DL + GK F L +
Sbjct: 181 VALNKRYGCDLQLGGSDQWGNILSGRDLQRRYGGKPQFGLTM 222
>gnl|CDD|173902 cd00805, TyrRS_core, catalytic core domain of tyrosinyl-tRNA
synthetase. Tyrosinyl-tRNA synthetase (TyrRS) catalytic
core domain. TyrRS is a homodimer which attaches Tyr to
the appropriate tRNA. TyrRS is a class I tRNA
synthetases, so it aminoacylates the 2'-OH of the
nucleotide at the 3' end of the tRNA. The core domain is
based on the Rossman fold and is responsible for the
ATP-dependent formationof the enzyme bound
aminoacyl-adenylate. It contains the class I
characteristic HIGH and KMSKS motifs, which are involved
in ATP binding.
Length = 269
Score = 120 bits (302), Expect = 9e-32
Identities = 49/153 (32%), Positives = 75/153 (49%), Gaps = 35/153 (22%)
Query: 236 QTVYAGFDPTASSLHIGNLLILINLIHWQRAGHQVIAL------MI-------------C 276
VY GFDPTA SLH+G+L+ L+ L +Q+AGH+VI L MI
Sbjct: 1 LKVYIGFDPTAPSLHLGHLVPLMKLRDFQQAGHEVIVLIGDATAMIGDPSGKSEERKLLD 60
Query: 277 LSQIL-WRTCNEEA--------------VVNNMSWYNSINVIDFMNHIARLFRMGDMLKK 321
L I ++ VNN W S+ +DF+ + + F + ML++
Sbjct: 61 LELIRENAKYYKKQLKAILDFIPPEKAKFVNNSDWLLSLYTLDFLR-LGKHFTVNRMLRR 119
Query: 322 QSVVTRLESEHGMNYTEFSYQIFQSYDWAHLYK 354
+V RLE E G++++EF Y + Q+YD+ +L
Sbjct: 120 DAVKVRLEEEEGISFSEFIYPLLQAYDFVYLDV 152
Score = 93.1 bits (232), Expect = 9e-22
Identities = 47/158 (29%), Positives = 65/158 (41%), Gaps = 45/158 (28%)
Query: 109 IGGATAQVGDPSGKTKDRDKQDLATVQTNTKGIEKNIKTIFRNHEQYFWKDRKDSLKPPI 168
IG ATA +GDPSGK+++R DL ++ N K +K +K I +
Sbjct: 39 IGDATAMIGDPSGKSEERKLLDLELIRENAKYYKKQLKAILDFI----------PPEKAK 88
Query: 169 VVNNMSWYNSINVIDFMNHIARLFRMGDMLKKQSV------------------------- 203
VNN W S+ +DF+ + + F + ML++ +V
Sbjct: 89 FVNNSDWLLSLYTLDFLR-LGKHFTVNRMLRRDAVKVRLEEEEGISFSEFIYPLLQAYDF 147
Query: 204 ---------GGSDQMGNIKAGHDLISKLYGKTVFDLLV 232
GGSDQ GNI G DLI KL K V L
Sbjct: 148 VYLDVDLQLGGSDQRGNITLGRDLIRKLGYKKVVGLTT 185
>gnl|CDD|237360 PRK13354, PRK13354, tyrosyl-tRNA synthetase; Provisional.
Length = 410
Score = 117 bits (296), Expect = 9e-30
Identities = 51/159 (32%), Positives = 83/159 (52%), Gaps = 31/159 (19%)
Query: 234 TPQTVYAGFDPTASSLHIGNLLILINLIHWQRAGHQVIAL------MI------------ 275
P T+Y GFDPTA SLHIG+L+ L+ L +Q AGH+ + L I
Sbjct: 32 KPLTLYLGFDPTAPSLHIGHLVPLMKLKRFQDAGHRPVILIGGFTGKIGDPSGKSKERKL 91
Query: 276 -----------CLSQILWRTCNEE--AVVNNMSWYNSINVIDFMNHIARLFRMGDMLKKQ 322
++ +++ + E +VNN W + +N+IDF+ + F + ML++
Sbjct: 92 LTDEQVQHNAKTYTEQIFKLFDFEKTEIVNNSDWLSKLNLIDFLRDYGKHFTVNRMLERD 151
Query: 323 SVVTRLESEHGMNYTEFSYQIFQSYDWAHLYKEHNCRFQ 361
V +RLE E G+++TEF Y + Q+YD+ HL ++ + Q
Sbjct: 152 DVKSRLEREQGISFTEFFYPLLQAYDFVHLNRKEDVDLQ 190
Score = 82.3 bits (204), Expect = 2e-17
Identities = 46/160 (28%), Positives = 65/160 (40%), Gaps = 51/160 (31%)
Query: 109 IGGATAQVGDPSGKTKDRDKQDLATVQTNTKGIEKNIKTIFRNHEQYFWKDRKDSLKPPI 168
IGG T ++GDPSGK+K+R VQ N K + I +F D + +
Sbjct: 72 IGGFTGKIGDPSGKSKERKLLTDEQVQHNAKTYTEQIFKLF---------DFEKT----E 118
Query: 169 VVNNMSWYNSINVIDFMNHIARLFRMGDMLKKQSV------------------------- 203
+VNN W + +N+IDF+ + F + ML++ V
Sbjct: 119 IVNNSDWLSKLNLIDFLRDYGKHFTVNRMLERDDVKSRLEREQGISFTEFFYPLLQAYDF 178
Query: 204 -------------GGSDQMGNIKAGHDLISKLYGKTVFDL 230
GG+DQ GNI G DL KL G+ F L
Sbjct: 179 VHLNRKEDVDLQIGGTDQWGNILMGRDLQRKLEGEEQFGL 218
>gnl|CDD|223240 COG0162, TyrS, Tyrosyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 401
Score = 111 bits (281), Expect = 1e-27
Identities = 53/161 (32%), Positives = 78/161 (48%), Gaps = 38/161 (23%)
Query: 229 DLLVRTPQTVYAGFDPTASSLHIGNLLILINLIHWQRAGHQVIAL------MI------- 275
LL P VY GFDPTA SLH+G+L+ L+ L +Q AGH+ I L MI
Sbjct: 26 KLLEEGPLRVYIGFDPTAPSLHLGHLVPLMKLRRFQDAGHKPIVLIGDATAMIGDPSGKS 85
Query: 276 --------------------CLSQIL-WRTCNEEAVVNNMSWYNSINVIDFMNHIARLFR 314
L + L + VNN W +N +DF+ + + F
Sbjct: 86 EERKLLTRETVLENAETIKKQLGKFLDNKAE----FVNNSDWLKKLNYLDFLRDVGKHFS 141
Query: 315 MGDMLKKQSVVTRLESEHGMNYTEFSYQIFQSYDWAHLYKE 355
+ ML++ V RLE E G+++TEF+Y + Q+YD+ +L K+
Sbjct: 142 VNRMLRRDDVKKRLEREQGISFTEFNYPLLQAYDFVYLNKD 182
Score = 77.7 bits (192), Expect = 9e-16
Identities = 45/154 (29%), Positives = 61/154 (39%), Gaps = 48/154 (31%)
Query: 109 IGGATAQVGDPSGKTKDRDKQDLATVQTNTKGIEKNIKTIFRNHEQYFWKDRKDSLKPPI 168
IG ATA +GDPSGK+++R TV N + I+K + N
Sbjct: 71 IGDATAMIGDPSGKSEERKLLTRETVLENAETIKKQLGKFLDNKA--------------E 116
Query: 169 VVNNMSWYNSINVIDFMNHIARLFRMGDMLKKQSV------------------------- 203
VNN W +N +DF+ + + F + ML++ V
Sbjct: 117 FVNNSDWLKKLNYLDFLRDVGKHFSVNRMLRRDDVKKRLEREQGISFTEFNYPLLQAYDF 176
Query: 204 ---------GGSDQMGNIKAGHDLISKLYGKTVF 228
GGSDQ GNI AG DLI +L K V
Sbjct: 177 VYLNKDLQLGGSDQWGNILAGRDLIRRLGQKKVV 210
>gnl|CDD|216003 pfam00579, tRNA-synt_1b, tRNA synthetases class I (W and Y).
Length = 291
Score = 97.0 bits (242), Expect = 5e-23
Identities = 40/149 (26%), Positives = 64/149 (42%), Gaps = 28/149 (18%)
Query: 235 PQTVYAGFDPTASSLHIGNLLILINLIHWQRAGHQVIALMICL-------SQILWRTCNE 287
P VY GFDPT LH+G L+ L+ L+ +Q+AGH+V L+ L S+ R
Sbjct: 5 PLRVYTGFDPTGP-LHLGYLVPLMKLVQFQQAGHEVFFLIGDLTAIIGDPSKSEERKLLS 63
Query: 288 EA--------------------VVNNMSWYNSINVIDFMNHIARLFRMGDMLKKQSVVTR 327
+VNN W + + + + F + ML+ + V R
Sbjct: 64 REEVLENAKAQLACGLDPEKSEIVNNSDWLEHLELAWLLRDLGNHFSLNRMLQFKDVKKR 123
Query: 328 LESEHGMNYTEFSYQIFQSYDWAHLYKEH 356
L+ G++ EF+Y + Q+ D L +
Sbjct: 124 LKQNPGISLGEFTYPLLQAADILLLKADL 152
Score = 43.8 bits (104), Expect = 7e-05
Identities = 34/163 (20%), Positives = 52/163 (31%), Gaps = 56/163 (34%)
Query: 109 IGGATAQVGDPSGKTKDRDKQDLATVQTNTKG-IEKNIKTIFRNHEQYFWKDRKDSLKPP 167
IG TA +GDPS K+++R V N K + + +
Sbjct: 43 IGDLTAIIGDPS-KSEERKLLSREEVLENAKAQLACGLD-----------------PEKS 84
Query: 168 IVVNNMSWYNSINVIDFMNHIARLFRMGDMLKKQSV------------------------ 203
+VNN W + + + + F + ML+ + V
Sbjct: 85 EIVNNSDWLEHLELAWLLRDLGNHFSLNRMLQFKDVKKRLKQNPGISLGEFTYPLLQAAD 144
Query: 204 ----------GGSDQMGNIKAGHDLI---SKLYGKTVFDLLVR 233
GGSDQ G+I+ G DL +K K L
Sbjct: 145 ILLLKADLQPGGSDQWGHIELGRDLARRFNKKVFKKPVGLTNP 187
>gnl|CDD|232889 TIGR00234, tyrS, tyrosyl-tRNA synthetase. This tyrosyl-tRNA
synthetase model starts picking up tryptophanyl-tRNA
synthetases at scores of 0 and below. The proteins found
by this model have a deep split between two groups. One
group contains bacterial and organellar eukaryotic
examples. The other contains archaeal and cytosolic
eukaryotic examples [Protein synthesis, tRNA
aminoacylation].
Length = 377
Score = 91.3 bits (227), Expect = 1e-20
Identities = 46/156 (29%), Positives = 74/156 (47%), Gaps = 33/156 (21%)
Query: 231 LVRTPQTVYAGFDPTASSLHIGNLLILINLIHWQRAGHQVIAL-------------MICL 277
L+ +Y GFDPTA SLH+G+L+ L+ L +Q+AGH+VI L
Sbjct: 26 LLERKIKLYVGFDPTAPSLHLGHLVPLLKLRDFQQAGHEVIVLLGDATALIGDPSGKSEE 85
Query: 278 SQILWRTCNEEAV------------------VNNMSWYNSINVIDFMNHIARLFRMGDML 319
++L R +E VNN W +N IDF+ + ++F + ML
Sbjct: 86 RKLLTREEVQENAENIKKQIARFLDFEKAKFVNNSEWLLKLNYIDFIRDLGKIFSVNRML 145
Query: 320 KKQSVVTRLESEHGMNYTEFSYQIFQSYDWAHLYKE 355
++ + +RLE +EF Y + Q+YD+ +L +
Sbjct: 146 RRDAFSSRLERGIS--LSEFIYPLLQAYDFVYLNVD 179
Score = 74.0 bits (182), Expect = 1e-14
Identities = 46/172 (26%), Positives = 65/172 (37%), Gaps = 49/172 (28%)
Query: 93 DLQDMFLTTKELSNGKIGGATAQVGDPSGKTKDRDKQDLATVQTNTKGIEKNIKTIFRNH 152
D Q L +G ATA +GDPSGK+++R VQ N + I+K I
Sbjct: 57 DFQQAGHEVIVL----LGDATALIGDPSGKSEERKLLTREEVQENAENIKKQIARFLDF- 111
Query: 153 EQYFWKDRKDSLKPPIVVNNMSWYNSINVIDFMNHIARLFRMGDMLKKQS---------- 202
+ VNN W +N IDF+ + ++F + ML++ +
Sbjct: 112 ------------EKAKFVNNSEWLLKLNYIDFIRDLGKIFSVNRMLRRDAFSSRLERGIS 159
Query: 203 ----------------------VGGSDQMGNIKAGHDLISKLYGKTVFDLLV 232
+GGSDQ GNI G DLI + F L V
Sbjct: 160 LSEFIYPLLQAYDFVYLNVDLQIGGSDQWGNILKGRDLIRRNLPSLGFGLTV 211
>gnl|CDD|173893 cd00395, Tyr_Trp_RS_core, catalytic core domain of tyrosinyl-tRNA
and tryptophanyl-tRNA synthetase. Tyrosinyl-tRNA
synthetase (TyrRS)/Tryptophanyl-tRNA synthetase (TrpRS)
catalytic core domain. These enzymes attach Tyr or Trp,
respectively, to the appropriate tRNA. These class I
enzymes are homodimers, which aminoacylate the 2'-OH of
the nucleotide at the 3' of the appropriate tRNA. The
core domain is based on the Rossman fold and is
responsible for the ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. It contains the class
I characteristic HIGH and KMSKS motifs, which are
involved in ATP binding.
Length = 273
Score = 85.0 bits (210), Expect = 6e-19
Identities = 45/159 (28%), Positives = 68/159 (42%), Gaps = 36/159 (22%)
Query: 237 TVYAGFDPTASSLHIGNLLILINLIHWQRAGHQVIALMICLSQIL--------WRTCNEE 288
T+Y G DPTA SLHIG+L+ L+ +Q AGH+ I L+ + I+ RT N+
Sbjct: 1 TLYCGIDPTADSLHIGHLIGLLTFRRFQHAGHRPIFLIGGQTGIIGDPSGKKSERTLNDP 60
Query: 289 --------------------------AVVNNMSWYNSINVIDFMNHIARLFRMGDMLKKQ 322
+ NN W + I F+ + + + M +K
Sbjct: 61 EEVRQNIRRIAAQYLAVGIFEDPTQATLFNNSDWPGPLAHIQFLRDLGKHVYVNYMERKT 120
Query: 323 SVVTRLESEHGMNYTEFSYQIFQSYDWAHLYKEHNCRFQ 361
S +R SE G++ TEF+Y Q+ D+ L C Q
Sbjct: 121 SFQSR--SEEGISATEFTYPPLQAADFLLLNTTEGCDIQ 157
Score = 60.4 bits (146), Expect = 2e-10
Identities = 38/172 (22%), Positives = 53/172 (30%), Gaps = 48/172 (27%)
Query: 109 IGGATAQVGDPSGKTKDRDKQDLATVQTNTKGIEKNIKTIFRNHEQYFWKDRKDSLKPPI 168
IGG T +GDPSGK +R D V+ N + I + +
Sbjct: 38 IGGQTGIIGDPSGKKSERTLNDPEEVRQNIRRIAAQYLAVG--------IFEDPT--QAT 87
Query: 169 VVNNMSWYNSINVIDFMNHIARLFRMGDMLKKQSV------------------------- 203
+ NN W + I F+ + + + M +K S
Sbjct: 88 LFNNSDWPGPLAHIQFLRDLGKHVYVNYMERKTSFQSRSEEGISATEFTYPPLQAADFLL 147
Query: 204 -----------GGSDQMGNIKAGHDLISKLYGKTVFDLLVRTPQTVYAGFDP 244
GGSDQ GNI G +L + G T T V P
Sbjct: 148 LNTTEGCDIQPGGSDQWGNITLGRELARRFNGFT--IAEGLTIPLVTKLDGP 197
>gnl|CDD|173901 cd00802, class_I_aaRS_core, catalytic core domain of class I amino
acyl-tRNA synthetase. Class I amino acyl-tRNA
synthetase (aaRS) catalytic core domain. These enzymes
are mostly monomers which aminoacylate the 2'-OH of the
nucleotide at the 3' of the appropriate tRNA. The core
domain is based on the Rossman fold and is responsible
for the ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding.
Length = 143
Score = 29.8 bits (67), Expect = 1.0
Identities = 12/43 (27%), Positives = 20/43 (46%)
Query: 185 MNHIARLFRMGDMLKKQSVGGSDQMGNIKAGHDLISKLYGKTV 227
A + + +GGSDQ+G+I+ G +L+ K G
Sbjct: 80 FLQAADFLLLYETECDIHLGGSDQLGHIELGLELLKKAGGPAR 122
>gnl|CDD|238397 cd00774, GlyRS-like_core, Glycyl-tRNA synthetase (GlyRS)-like class
II core catalytic domain. GlyRS functions as a homodimer
in eukaryotes, archaea and some bacteria and as a
heterotetramer in the remainder of prokaryotes. It is
responsible for the attachment of glycine to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP binding and hydrolysis.
This alignment contains only sequences from the GlyRS
form which homodimerizes. The heterotetramer glyQ is in
a different family of class II aaRS. Class II assignment
is based upon its structure and the presence of three
characteristic sequence motifs. This domain is also
found at the N-terminus of the accessory subunit of
mitochondrial polymerase gamma (Pol gamma b). Pol gamma
b stimulates processive DNA synthesis and is functional
as a homodimer, which can associate with the catalytic
subunit Pol gamma alpha to form a heterotrimer. Despite
significant both structural and sequence similarity with
GlyRS, Pol gamma b lacks conservation of several class
II functional residues.
Length = 254
Score = 30.3 bits (69), Expect = 1.3
Identities = 24/90 (26%), Positives = 35/90 (38%), Gaps = 22/90 (24%)
Query: 50 YKLSPCGHLLAENIKKEWVRSCVLRREE----------PAFLYS-QQGDCENETDL---- 94
Y P G L NIK W +S VL E+ P ++ G E+ +L
Sbjct: 25 YDYGPLGVELKNNIKSAWRKSFVLEEEDMLEIDSPIITPELMFKTSIGPVESGGNLGYLR 84
Query: 95 ----QDMFLTTK---ELSNGKIGGATAQVG 117
Q +F+ K E + K+ AQ+G
Sbjct: 85 PETAQGIFVNFKNLLEFNRRKLPFGVAQIG 114
>gnl|CDD|173903 cd00806, TrpRS_core, catalytic core domain of tryptophanyl-tRNA
synthetase. Tryptophanyl-tRNA synthetase (TrpRS)
catalytic core domain. TrpRS is a homodimer which
attaches Tyr to the appropriate tRNA. TrpRS is a class I
tRNA synthetases, so it aminoacylates the 2'-OH of the
nucleotide at the 3' end of the tRNA. The core domain is
based on the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains class I characteristic
HIGH and KMSKS motifs, which are involved in ATP
binding.
Length = 280
Score = 30.2 bits (69), Expect = 1.5
Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 237 TVYAGFDPTASSLHIGNLL-ILINLIHWQRAGHQVIALMICLSQILWRTCNEEAVVNN 293
V +G P+ SLH+G+ L + Q AG+++ + L + + + E + N
Sbjct: 1 RVLSGIQPS-GSLHLGHYLGAFRFWVWLQEAGYELFFFIADLHALTVKQLDPEELRQN 57
>gnl|CDD|241419 cd13265, PH_evt, Evectin Pleckstrin homology (PH) domain. There
are 2 members of the evectin family (also called
pleckstrin homology domain containing, family B): evt-1
(also called PLEKHB1) and evt-2 (also called PLEKHB2).
evt-1 is specific to the nervous system, where it is
expressed in photoreceptors and myelinating glia. evt-2
is widely expressed in both neural and nonneural
tissues. Evectins possess a single N-terminal PH domain
and a C-terminal hydrophobic region. evt-1 is thought to
function as a mediator of post-Golgi trafficking in
cells that produce large membrane-rich organelles. It is
a candidate gene for the inherited human retinopathy
autosomal dominant familial exudative vitreoretinopathy
and a susceptibility gene for multiple sclerosis. evt-2
is essential for retrograde endosomal membrane transport
from the plasma membrane (PM) to the Golgi. Two membrane
trafficking pathways pass through recycling endosomes: a
recycling pathway and a retrograde pathway that links
the PM to the Golgi/ER. Its PH domain that is unique in
that it specifically recognizes phosphatidylserine (PS),
but not polyphosphoinositides. PS is an anionic
phospholipid class in eukaryotic biomembranes, is highly
enriched in the PM, and plays key roles in various
physiological processes such as the coagulation cascade,
recruitment and activation of signaling molecules, and
clearance of apoptotic cells. PH domains are only found
in eukaryotes. They share little sequence conservation,
but all have a common fold, which is electrostatically
polarized. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 108
Score = 28.8 bits (65), Expect = 1.6
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 63 IKKEWV--RSCVLRREEPAF--LYSQQGDC----ENETDLQDMFLTTKELSNGKIGGATA 114
+K W+ +S +L+R + + LYS E+ D++ E N ++G
Sbjct: 4 VKSGWLLRQSTILKRWKKNWFVLYSDGELSYYEDESRRDVEGRINMPIECRNIRVGLECR 63
Query: 115 QVGDPSGKTKD 125
V P G+++D
Sbjct: 64 DVQPPEGRSRD 74
>gnl|CDD|180188 PRK05664, PRK05664, threonine-phosphate decarboxylase; Reviewed.
Length = 330
Score = 29.2 bits (66), Expect = 3.4
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 262 HWQRAGHQVIAL 273
W+RAGHQV L
Sbjct: 102 AWRRAGHQVREL 113
>gnl|CDD|223500 COG0423, GRS1, Glycyl-tRNA synthetase (class II) [Translation,
ribosomal structure and biogenesis].
Length = 558
Score = 29.3 bits (66), Expect = 3.5
Identities = 18/53 (33%), Positives = 21/53 (39%), Gaps = 16/53 (30%)
Query: 24 SEIFGLKYFLSPLLSRGSASTQGISRYKLSPCGHLLAENIKKEWVRSCVLRRE 76
SEI+G G A Y P G L NIK+ W +S V RE
Sbjct: 23 SEIYG-----------GLAGF-----YDYGPLGVELKNNIKEAWRKSFVTERE 59
>gnl|CDD|232888 TIGR00233, trpS, tryptophanyl-tRNA synthetase. This model
represents tryptophanyl-tRNA synthetase. Some members of
the family have a pfam00458 domain amino-terminal to the
region described by this model [Protein synthesis, tRNA
aminoacylation].
Length = 327
Score = 29.2 bits (66), Expect = 3.5
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 235 PQTVYAGFDPTASSLHIGNLLILINLIHWQRAGHQVIALMICLSQILWRTCNEEAV 290
V G P+ +H+G+ L I Q+ G ++ + L I + + +A+
Sbjct: 2 KFRVLTGIQPS-GKMHLGHYLGAIQTKWLQQFGVELFICIADLHAITVKQTDPDAL 56
>gnl|CDD|235240 PRK04173, PRK04173, glycyl-tRNA synthetase; Provisional.
Length = 456
Score = 28.9 bits (66), Expect = 4.3
Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 16/54 (29%)
Query: 24 SEIFGLKYFLSPLLSRGSASTQGISRYKLSPCGHLLAENIKKEWVRSCVLRREE 77
SEI+G G A + P G L NIK+ W +S V RE+
Sbjct: 21 SEIYG-----------GLAGF-----WDYGPLGVELKNNIKRAWWKSFVQERED 58
>gnl|CDD|192184 pfam08932, DUF1914, Domain of unknown function (DUF1914). This
domain has no known function. It is found in a various
putative receptor proteins from Lactococcus
bacteriophages.
Length = 114
Score = 27.5 bits (61), Expect = 4.4
Identities = 18/89 (20%), Positives = 37/89 (41%), Gaps = 8/89 (8%)
Query: 168 IVVNNMSWYNSINVIDFMNHIARLFRMGDMLKKQSVGG-----SDQMGNIKAGHDLISKL 222
I +N++S S+++ + + L+K+++ S + NI +G
Sbjct: 1 ISINSISLKGSLDIPTQTLTVQTGNGLTGQLQKKNMDLVIYRFSGSITNINSGAIFP--- 57
Query: 223 YGKTVFDLLVRTPQTVYAGFDPTASSLHI 251
+ F + PQ++ F T +S HI
Sbjct: 58 WVTFPFRAIPNVPQSLVGHFAGTGNSFHI 86
>gnl|CDD|234739 PRK00376, lspA, lipoprotein signal peptidase; Reviewed.
Length = 160
Score = 28.2 bits (64), Expect = 4.8
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 168 IVVNNMSWYNSINVIDFMN 186
+V+ N S+ VI F N
Sbjct: 28 LVLQNFELGESVPVIPFFN 46
Score = 27.8 bits (63), Expect = 5.9
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 9/40 (22%)
Query: 270 VIALMICLSQI--LWRTCNEEAVVNNMSWYNSINVIDFMN 307
+ L+I L Q+ V+ N S+ VI F N
Sbjct: 14 LAVLVIILDQLSKYL-------VLQNFELGESVPVIPFFN 46
>gnl|CDD|222164 pfam13480, Acetyltransf_6, Acetyltransferase (GNAT) domain. This
family contains proteins with N-acetyltransferase
functions.
Length = 144
Score = 27.6 bits (62), Expect = 6.2
Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 6/57 (10%)
Query: 224 GKTV-FDLLVRTPQTVYA---GFDPTASSLHIGNLLILINLIHWQRA-GHQVIALMI 275
G+ V L +R +Y G+DP + L G LL+ LI G +V
Sbjct: 82 GEPVAAVLGLRDGGRLYYYLGGYDPEFARLSPGLLLLW-ELIEDAAEEGVRVFDFGR 137
>gnl|CDD|185001 PRK15041, PRK15041, methyl-accepting chemotaxis protein I;
Provisional.
Length = 554
Score = 28.4 bits (63), Expect = 6.6
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 15/76 (19%)
Query: 181 VIDFMNHIARLFRMGDMLKKQSVGGSDQMGNIKAGHDLISKLYGKTVFDLLVRTPQTVYA 240
+ID + HIA GD++K V GS++MG + + + + G+ L+RT V
Sbjct: 225 LIDSIRHIAG----GDLVKPIEVDGSNEMGQLA---ESLRHMQGE-----LMRTVGDVRN 272
Query: 241 GFDPT---ASSLHIGN 253
G + AS + GN
Sbjct: 273 GANAIYSGASEIATGN 288
>gnl|CDD|238141 cd00229, SGNH_hydrolase, SGNH_hydrolase, or GDSL_hydrolase, is a
diverse family of lipases and esterases. The tertiary
fold of the enzyme is substantially different from that
of the alpha/beta hydrolase family and unique among all
known hydrolases; its active site closely resembles the
typical Ser-His-Asp(Glu) triad from other serine
hydrolases, but may lack the carboxlic acid.
Length = 187
Score = 27.8 bits (61), Expect = 8.1
Identities = 31/178 (17%), Positives = 51/178 (28%), Gaps = 17/178 (9%)
Query: 113 TAQVGDPSGKTKDRDKQDLATVQTNTKGIEKNI----KTIFRNHEQYFWKDRKDSLKPPI 168
TA G SG T L + N+ T + + KP +
Sbjct: 9 TAGYGASSGSTFYSLLLYLLLLAGGPGVEVINLGVSGATTADALRRLGLRLALLKDKPDL 68
Query: 169 VV----NNMSWYNSINVIDFMNHIARLFRMGDMLKKQS------VGGSDQMGNIKAGHDL 218
V+ N ID A L + D L++++ + +
Sbjct: 69 VIIELGTNDLGRGGDTSID--EFKANLEELLDALRERAPGAKVILITPPPPPPREGLLGR 126
Query: 219 ISKLYGKTVFDLLVRTPQTVYAGF-DPTASSLHIGNLLILINLIHWQRAGHQVIALMI 275
Y + + + P D A L + IH AGH++IA +
Sbjct: 127 ALPRYNEAIKAVAAENPAPSGVDLVDLAALLGDEDKSLYSPDGIHPNPAGHKLIAEAL 184
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 0.135 0.410
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,951,128
Number of extensions: 1687541
Number of successful extensions: 1227
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1215
Number of HSP's successfully gapped: 44
Length of query: 362
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 264
Effective length of database: 6,590,910
Effective search space: 1740000240
Effective search space used: 1740000240
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 (26.8 bits)