RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1870
(264 letters)
>gnl|CDD|238393 cd00770, SerRS_core, Seryl-tRNA synthetase (SerRS) class II core
catalytic domain. SerRS is responsible for the
attachment of serine to the 3' OH group of ribose of the
appropriate tRNA. This domain It is primarily
responsible for ATP-dependent formation of the enzyme
bound aminoacyl-adenylate. Class II assignment is based
upon its structure and the presence of three
characteristic sequence motifs in the core domain. SerRS
synthetase is a homodimer.
Length = 297
Score = 279 bits (715), Expect = 3e-94
Identities = 93/209 (44%), Positives = 133/209 (63%), Gaps = 10/209 (4%)
Query: 19 GERSQIYHLEPNYYGNGWCLSGTAEMGIARYLMNQTLPESQLPKQIAAMSKCYRAEI-SV 77
Q+Y +E L TAE+ +A ++ L E +LP + A S C+R E S
Sbjct: 93 KFDEQLYKVEGEDL----YLIATAEVPLAALHRDEILEEEELPLKYAGYSPCFRKEAGSA 148
Query: 78 VADEKGVYRVHCFTKIEMFGVTLPEDSEKQLEQFLQFEESLFGELGIHTRTLNMGANELG 137
D +G++RVH F K+E F T PE+S ++LE+ + E + ELG+ R +N+ +LG
Sbjct: 149 GRDTRGLFRVHQFEKVEQFVFTKPEESWEELEELISNAEEILQELGLPYRVVNICTGDLG 208
Query: 138 AQAYKKYDVEAWMPGRKHWGELSSCSDCTDYQARRLNIR---TEDGK--FAHTLNGTACA 192
A KKYD+EAWMPG+ + E+SSCS+CTD+QARRLNIR +DGK + HTLNGTA A
Sbjct: 209 FAAAKKYDIEAWMPGQGKYREISSCSNCTDFQARRLNIRYRDKKDGKKQYVHTLNGTALA 268
Query: 193 IPRLLMALVETHQNQDGTVNIPECLQPFM 221
PR ++A++E +Q +DG+V IPE L+P+M
Sbjct: 269 TPRTIVAILENYQTEDGSVVIPEVLRPYM 297
>gnl|CDD|235461 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 243 bits (623), Expect = 9e-79
Identities = 83/213 (38%), Positives = 123/213 (57%), Gaps = 12/213 (5%)
Query: 23 QIYHLE-PNYYGNGWCLSGTAEMGIARYLMNQTLPESQLPKQIAAMSKCYRAEI-SVVAD 80
+Y +E + Y L TAE+ + ++ L E +LP + A S C+R+E S D
Sbjct: 216 DLYKIEDDDLY-----LIPTAEVPLTNLHRDEILDEEELPLKYTAYSPCFRSEAGSAGRD 270
Query: 81 EKGVYRVHCFTKIEMFGVTLPEDSEKQLEQFLQFEESLFGELGIHTRTLNMGANELGAQA 140
+G+ RVH F K+E+ T PEDS +LE+ E + +L + R + + +LG A
Sbjct: 271 TRGLIRVHQFDKVELVKFTKPEDSYAELEELTANAEEILQKLELPYRVVLLCTGDLGFSA 330
Query: 141 YKKYDVEAWMPGRKHWGELSSCSDCTDYQARRLNIR---TEDGK--FAHTLNGTACAIPR 195
K YD+E W+P + + E+SSCS+CTD+QARR NIR DGK HTLNG+ A+ R
Sbjct: 331 AKTYDLEVWLPSQNTYREISSCSNCTDFQARRANIRYRDEGDGKPELVHTLNGSGLAVGR 390
Query: 196 LLMALVETHQNQDGTVNIPECLQPFMFNKRIIG 228
L+A++E +Q DG+V IPE L+P+M +I
Sbjct: 391 TLVAILENYQQADGSVTIPEVLRPYMGGLEVIP 423
>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 235 bits (603), Expect = 1e-75
Identities = 90/212 (42%), Positives = 131/212 (61%), Gaps = 10/212 (4%)
Query: 23 QIYHLEPNYYGNGWCLSGTAEMGIARYLMNQTLPESQLPKQIAAMSKCYRAEI-SVVADE 81
+Y +E L TAE+ + ++ L E LP + A S C+R+E S D
Sbjct: 219 DLYKVEDPDL----YLIPTAEVPLTNLHRDEILDEEDLPIKYTAYSPCFRSEAGSAGKDT 274
Query: 82 KGVYRVHCFTKIEMFGVTLPEDSEKQLEQFLQFEESLFGELGIHTRTLNMGANELGAQAY 141
+G+ RVH F K+E+ +T PE+SE++LE+ L E + EL + R +N+ +LG A
Sbjct: 275 RGLIRVHQFDKVELVVITKPEESEEELEEMLGNAEEVLQELELPYRVVNLCTGDLGFSAA 334
Query: 142 KKYDVEAWMPGRKHWGELSSCSDCTDYQARRLNIR---TEDGK--FAHTLNGTACAIPRL 196
KKYD+E W+PG+ + E+SSCS+CTD+QARRLNIR E+GK F HTLNG+ A+ R
Sbjct: 335 KKYDLEVWLPGQNKYREISSCSNCTDFQARRLNIRYRDKEEGKREFVHTLNGSGLAVGRT 394
Query: 197 LMALVETHQNQDGTVNIPECLQPFMFNKRIIG 228
L+A++E +Q +DG+V IPE L+P+M II
Sbjct: 395 LVAILENYQQEDGSVKIPEVLRPYMGGLEIIP 426
>gnl|CDD|232965 TIGR00414, serS, seryl-tRNA synthetase. This model represents the
seryl-tRNA synthetase found in most organisms. This
protein is a class II tRNA synthetase, and is recognized
by the pfam model tRNA-synt_2b. The seryl-tRNA
synthetases of two archaeal species, Methanococcus
jannaschii and Methanobacterium thermoautotrophicum,
differ considerably and are included in a different
model [Protein synthesis, tRNA aminoacylation].
Length = 418
Score = 228 bits (583), Expect = 6e-73
Identities = 87/207 (42%), Positives = 126/207 (60%), Gaps = 12/207 (5%)
Query: 22 SQIYHLEP-NYYGNGWCLSGTAEMGIARYLMNQTLPESQLPKQIAAMSKCYRAEI-SVVA 79
I+ LE + Y L TAE+ + N+ L E +LP + A S C+R+E S
Sbjct: 217 EDIFKLEDTDLY-----LIPTAEVPLTNLHRNEILEEEELPIKYTAHSPCFRSEAGSYGK 271
Query: 80 DEKGVYRVHCFTKIEMFGVTLPEDSEKQLEQFLQFEESLFGELGIHTRTLNMGANELGAQ 139
D KG+ RVH F K+E+ PE+S ++LE+ E + EL + R +N+ + +LG
Sbjct: 272 DTKGLIRVHQFNKVELVKFCKPEESAEELEEMTSDAEQILQELELPYRVVNLCSGDLGFS 331
Query: 140 AYKKYDVEAWMPGRKHWGELSSCSDCTDYQARRLNIR-----TEDGKFAHTLNGTACAIP 194
A KKYD+E WMPG+ + E+SSCS+CTD+QARRLNIR K+ HTLNGTA AI
Sbjct: 332 AAKKYDLEVWMPGQNTYREISSCSNCTDFQARRLNIRYKDKNKGKNKYVHTLNGTALAIG 391
Query: 195 RLLMALVETHQNQDGTVNIPECLQPFM 221
R ++A++E +Q +DG+V IPE L+ ++
Sbjct: 392 RTIVAILENYQTEDGSVEIPEVLRKYL 418
>gnl|CDD|177954 PLN02320, PLN02320, seryl-tRNA synthetase.
Length = 502
Score = 222 bits (567), Expect = 1e-69
Identities = 102/222 (45%), Positives = 143/222 (64%), Gaps = 22/222 (9%)
Query: 18 KGERSQIYHLEPNYYGNGWCLSGTAEMGIARYLMNQTLPESQLPKQIAAMSKCYRAEISV 77
+G+ +Q+Y ++ G+ CL GTAE+ + M+ L ES LP + A S C+R E
Sbjct: 274 RGDNTQVYSID----GSDQCLIGTAEIPVGGIHMDSILLESALPLKYVAFSHCFRTEAGA 329
Query: 78 V-ADEKGVYRVHCFTKIEMFGVTLPEDSEKQLEQFLQFEESLFGELGIHTRTLNMGANEL 136
A +G+YRVH F+K+EMF + PE+SE E+ +Q EE LF LG+H +TL+M +L
Sbjct: 330 AGAATRGLYRVHQFSKVEMFVICRPEESESFHEELIQIEEDLFTSLGLHFKTLDMATADL 389
Query: 137 GAQAYKKYDVEAWMPGRKHWGELSSCSDCTDYQARRLNIR----------TEDGK----- 181
GA AY+K+D+EAWMPG +GE+SS S+CTDYQ+RRL IR + GK
Sbjct: 390 GAPAYRKFDIEAWMPGLGRYGEISSASNCTDYQSRRLGIRYRPSEPPQTNPKKGKGSLGP 449
Query: 182 --FAHTLNGTACAIPRLLMALVETHQNQDGTVNIPECLQPFM 221
F HTLN TACA+PR+++ L+E +Q +DG+V IPE L+PFM
Sbjct: 450 TKFVHTLNATACAVPRMIVCLLENYQQEDGSVVIPEPLRPFM 491
>gnl|CDD|215364 PLN02678, PLN02678, seryl-tRNA synthetase.
Length = 448
Score = 163 bits (415), Expect = 1e-47
Identities = 80/221 (36%), Positives = 113/221 (51%), Gaps = 14/221 (6%)
Query: 38 LSGTAEMGIARYLMNQTLPESQLPKQIAAMSKCYRAEI-SVVADEKGVYRVHCFTKIEMF 96
L T+E + Y + +LP + A S C+R E S D G++RVH F K+E F
Sbjct: 232 LIATSEQPLCAYHRGDWIDPKELPIRYAGYSTCFRKEAGSHGRDTLGIFRVHQFEKVEQF 291
Query: 97 GVTLPED--SEKQLEQFLQFEESLFGELGIHTRTLNMGANELGAQAYKKYDVEAWMPGRK 154
+T P S + E+ L+ E + LGI + +++ + L A KKYD+EAW P K
Sbjct: 292 CITSPNGNESWEMHEEMLKNSEDFYQSLGIPYQVVSIVSGALNDAAAKKYDLEAWFPASK 351
Query: 155 HWGELSSCSDCTDYQARRLNIR-------TEDGKFAHTLNGTACAIPRLLMALVETHQNQ 207
+ EL SCS+CTDYQ+RRL IR + ++ H LN T A R L ++E +Q +
Sbjct: 352 TYRELVSCSNCTDYQSRRLEIRYGQKKSNEQTKQYVHLLNSTLTATERTLCCILENYQTE 411
Query: 208 DGTVNIPECLQPFMFNKRIIGDTRGAPSLVKVKTGISKAKK 248
DG V +PE LQPFM + + P G K KK
Sbjct: 412 DG-VRVPEVLQPFMGGIEFLPFKKKPP---AKGKGKKKKKK 448
>gnl|CDD|216009 pfam00587, tRNA-synt_2b, tRNA synthetase class II core domain (G,
H, P, S and T). Other tRNA synthetase sub-families are
too dissimilar to be included. This domain is the core
catalytic domain of tRNA synthetases and includes
glycyl, histidyl, prolyl, seryl and threonyl tRNA
synthetases.
Length = 171
Score = 110 bits (276), Expect = 6e-30
Identities = 41/131 (31%), Positives = 69/131 (52%), Gaps = 4/131 (3%)
Query: 23 QIYHLEPNYYGNGWCLSGTAEMGIARYLMNQTLPESQLPKQIAAMSKCYRAEISVVADEK 82
++Y + + G L TAE+GI R N+ L +LP ++ + C+R E +
Sbjct: 45 EMYKFK-DRGGEELYLRPTAEVGITRLFKNEILSYRELPLKLYQIGPCFRYEAR---PRR 100
Query: 83 GVYRVHCFTKIEMFGVTLPEDSEKQLEQFLQFEESLFGELGIHTRTLNMGANELGAQAYK 142
G+ RV FT+++ PE SE++LE+ L+ E + +LG+ R + +LG A K
Sbjct: 101 GLGRVREFTQVDAEIFGTPEQSEEELEELLKLAEEILQDLGLPYRVVLATTGDLGGSASK 160
Query: 143 KYDVEAWMPGR 153
+ D+EAW+P
Sbjct: 161 EGDLEAWLPAE 171
>gnl|CDD|238359 cd00670, Gly_His_Pro_Ser_Thr_tRS_core, Gly_His_Pro_Ser_Thr_tRNA
synthetase class II core domain. This domain is the core
catalytic domain of tRNA synthetases of the subgroup
containing glycyl, histidyl, prolyl, seryl and threonyl
tRNA synthetases. It is primarily responsible for
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. These enzymes belong to class II
aminoacyl-tRNA synthetases (aaRS) based upon their
structure and the presence of three characteristic
sequence motifs in the core domain. This domain is also
found at the C-terminus of eukaryotic GCN2 protein
kinase and at the N-terminus of the ATP
phosphoribosyltransferase accessory subunit, HisZ and
the accessory subunit of mitochondrial polymerase gamma
(Pol gamma b) . Most class II tRNA synthetases are
dimers, with this subgroup consisting of mostly
homodimers. These enzymes attach a specific amino acid
to the 3' OH group of ribose of the appropriate tRNA.
Length = 235
Score = 65.1 bits (159), Expect = 1e-12
Identities = 46/196 (23%), Positives = 73/196 (37%), Gaps = 16/196 (8%)
Query: 18 KGERSQIYHLEP---NYYGNGWCLSGTAEMGIARYLMNQTLPESQLPKQIAAMSKCYRAE 74
G R ++Y E L A I + + L LP ++ + C+R E
Sbjct: 42 DGYRKEMYTFEDKGRELRDTDLVLRPAACEPIYQIFSGEILSYRALPLRLDQIGPCFRHE 101
Query: 75 ISVVADEKGVYRVHCFTKIEMFGVTLPEDSEKQLEQFLQFEESLFGELGIHTRT------ 128
S +G+ RV F ++E PE++E++ ++L+ E + ELG+ R
Sbjct: 102 PS---GRRGLMRVREFRQVEYVVFGEPEEAEEERREWLELAEEIARELGLPVRVVVADDP 158
Query: 129 --LNMGANELGAQAYKKYDVEAWMPGRKHWGELSSCSDCTDYQARR--LNIRTEDGKFAH 184
G L A + E +P E + S I + G AH
Sbjct: 159 FFGRGGKRGLDAGRETVVEFELLLPLPGRAKETAVGSANVHLDHFGASFKIDEDGGGRAH 218
Query: 185 TLNGTACAIPRLLMAL 200
T G A RL++AL
Sbjct: 219 TGCGGAGGEERLVLAL 234
>gnl|CDD|238391 cd00768, class_II_aaRS-like_core, Class II tRNA amino-acyl
synthetase-like catalytic core domain. Class II amino
acyl-tRNA synthetases (aaRS) share a common fold and
generally attach an amino acid to the 3' OH of ribose of
the appropriate tRNA. PheRS is an exception in that it
attaches the amino acid at the 2'-OH group, like class I
aaRSs. These enzymes are usually homodimers. This domain
is primarily responsible for ATP-dependent formation of
the enzyme bound aminoacyl-adenylate. The substrate
specificity of this reaction is further determined by
additional domains. Intererestingly, this domain is also
found is asparagine synthase A (AsnA), in the accessory
subunit of mitochondrial polymerase gamma and in the
bacterial ATP phosphoribosyltransferase regulatory
subunit HisZ.
Length = 211
Score = 50.2 bits (120), Expect = 2e-07
Identities = 33/167 (19%), Positives = 58/167 (34%), Gaps = 16/167 (9%)
Query: 37 CLSGTAEMGIARYLMNQTLPESQLPKQIAAMSKCYRAEISVVADEKGVYRVHCFTKIEMF 96
L T E G+ R ++ +I +R E +G+ RV FT++E
Sbjct: 54 YLRPTLEPGLVRLFVSHIRKLPLRLAEIG---PAFRNEG----GRRGLRRVREFTQLEGE 106
Query: 97 GVTLPEDSEKQLEQFLQFEESLFGELGIH---TRTLNMGANELGAQAYKKYDVEAWMPGR 153
+ + E+ ++ E L LGI A +++E P
Sbjct: 107 VFGEDGEEASEFEELIELTEELLRALGIKLDIVFVEKTPGEFSPGGAGPGFEIEVDHPEG 166
Query: 154 KHWGELSSCSDCTDYQARRLNIRTED----GKFAHTLNGTACAIPRL 196
+ E+ S D QAR ++ D ++ T+ + RL
Sbjct: 167 RGL-EIGSGGYRQDEQARAADLYFLDEALEYRYPPTIGFGL-GLERL 211
>gnl|CDD|235240 PRK04173, PRK04173, glycyl-tRNA synthetase; Provisional.
Length = 456
Score = 35.1 bits (82), Expect = 0.028
Identities = 30/114 (26%), Positives = 53/114 (46%), Gaps = 8/114 (7%)
Query: 59 QLPKQIAAMSKCYRAEISVVADEKGVYRVHCFTKIEM-FGVTLPEDSEKQLEQFLQFEES 117
+LP IA + K +R EI+ ++R F ++E+ F V P + +++ ++
Sbjct: 184 KLPFGIAQIGKSFRNEIT---PRNFIFRTREFEQMELEFFVK-PGTDNEWFAYWIELRKN 239
Query: 118 LFGELGI---HTRTLNMGANELGAQAYKKYDVEAWMPGRKHWGELSSCSDCTDY 168
+LGI + R EL + +D+E P + WGEL ++ TDY
Sbjct: 240 WLLDLGIDPENLRFREHLPEELAHYSKATWDIEYKFPFGRFWGELEGIANRTDY 293
>gnl|CDD|223500 COG0423, GRS1, Glycyl-tRNA synthetase (class II) [Translation,
ribosomal structure and biogenesis].
Length = 558
Score = 32.3 bits (74), Expect = 0.24
Identities = 36/154 (23%), Positives = 51/154 (33%), Gaps = 43/154 (27%)
Query: 58 SQLPKQIAAMSKCYRAEISVVADEKGVYRVHCFTKIEMFGVTLPEDS------------- 104
++LP IA + K +R EIS G++R F + E+ PE+
Sbjct: 184 NKLPFGIAQIGKSFRNEIS---PRNGLFRTREFEQAEIEFFVDPEEKEHPKFNEVKDEKL 240
Query: 105 -----EKQLE------------------QFLQFEESLFGELGI---HTRTLNMGANELGA 138
E Q E F+ + +LGI R EL
Sbjct: 241 PLLPREAQEEGTEEEAVEEGIVENETLAYFIARTKFFLEDLGIDPEKLRFRQHLPEELAH 300
Query: 139 QAYKKYDVEAWMPGRKHWGELSSCSDCTDYQARR 172
+ +D E P W EL +D TDY R
Sbjct: 301 YSKDTWDAEYKFP-FGGWIELVGIADRTDYDLSR 333
>gnl|CDD|235929 PRK07080, PRK07080, hypothetical protein; Validated.
Length = 317
Score = 31.5 bits (72), Expect = 0.36
Identities = 14/34 (41%), Positives = 16/34 (47%), Gaps = 7/34 (20%)
Query: 174 NIRTEDGKFAHTLNGTAC---AIPRLLMALVETH 204
IRT DG AH T C + RL +AL H
Sbjct: 270 GIRTADGAVAH----TGCVGFGLERLALALFRHH 299
>gnl|CDD|239881 cd04434, LanC_like, LanC-like proteins. LanC is the cyclase enzyme
of the lanthionine synthetase. Lanthionine is a
lantibiotic, a unique class of peptide antibiotics. They
are ribosomally synthesized as a precursor peptide and
then post-translationally modified to contain thioether
cross-links called lanthionines (Lans) or
methyllanthionines (MeLans), in addition to
2,3-didehydroalanine (Dha) and (Z)-2,3-didehydrobutyrine
(Dhb). These unusual amino acids are introduced by the
dehydration of serine and threonine residues, followed
by thioether formation via addition of cysteine thiols,
catalysed by LanB and LanC or LanM. LanC, the cyclase
component, is a zinc metalloprotein, whose bound metal
has been proposed to activate the thiol substrate for
nucleophilic addition. A related domain is also present
in LanM and other pro- and eukaryotic proteins of
unknown function.
Length = 343
Score = 31.3 bits (71), Expect = 0.41
Identities = 10/66 (15%), Positives = 20/66 (30%), Gaps = 1/66 (1%)
Query: 6 CNALECNSKINSKGERSQIYHLEPNYYGNGWCLSGTAEMGIARYLMNQTLPESQLPKQIA 65
E + +S G N + WC G + +A L + L + + +
Sbjct: 187 LLKYERRLQDDSGGFWWPSRSNGGNRFLVAWC-HGAPGILLALLLAYKALGDDKYDEAAE 245
Query: 66 AMSKCY 71
+
Sbjct: 246 KALELA 251
>gnl|CDD|129509 TIGR00415, serS_MJ, seryl-tRNA synthetase, Methanococcus jannaschii
family. The seryl-tRNA synthetases from a few of the
Archaea, represented by this model, are very different
from the set of mutually more closely related seryl-tRNA
synthetases from Eubacteria, Eukaryotes, and other
Archaea. Although distantly homologous, the present set
differs enough not to be recognized by the pfam model
tRNA-synt_2b that recognizes the remainder of seryl-tRNA
synthetases among oither class II amino-acyl tRNA
synthetases [Protein synthesis, tRNA aminoacylation].
Length = 520
Score = 31.5 bits (71), Expect = 0.44
Identities = 21/85 (24%), Positives = 39/85 (45%), Gaps = 13/85 (15%)
Query: 82 KGVYRVHCFTKIEMFGVTLPEDSEKQLEQFLQFEESLFGELGIHTRTLNMGANELGAQAY 141
KG+ RVH F ++E + PE++E+ ++ L+ E EL + T +G + +
Sbjct: 354 KGLDRVHEFLRVECVWIAEPEETEEIRDKTLELAEDAADELDLEWWT-EVGDDPFYLEGR 412
Query: 142 K------------KYDVEAWMPGRK 154
K KY++ +PG +
Sbjct: 413 KKEDRGIEFPDVPKYEMRLSLPGIE 437
>gnl|CDD|216278 pfam01066, CDP-OH_P_transf, CDP-alcohol phosphatidyltransferase.
All of these members have the ability to catalyze the
displacement of CMP from a CDP-alcohol by a second
alcohol with formation of a phosphodiester bond and
concomitant breaking of a phosphoride anhydride bond.
Length = 97
Score = 29.1 bits (66), Expect = 0.76
Identities = 7/25 (28%), Positives = 9/25 (36%), Gaps = 1/25 (4%)
Query: 159 LSSCSDCTD-YQARRLNIRTEDGKF 182
L+ D D ARR + G
Sbjct: 38 LAVLLDGLDGKLARRTGQSSPLGAL 62
>gnl|CDD|232951 TIGR00389, glyS_dimeric, glycyl-tRNA synthetase, dimeric type.
This model describes a glycyl-tRNA synthetase distinct
from the two alpha and two beta chains of the tetrameric
E. coli glycyl-tRNA synthetase. This enzyme is a
homodimeric class II tRNA synthetase and is recognized
by pfam model tRNA-synt_2b, which recognizes His, Ser,
Pro, and this set of glycyl-tRNA synthetases [Protein
synthesis, tRNA aminoacylation].
Length = 551
Score = 29.0 bits (65), Expect = 2.4
Identities = 37/154 (24%), Positives = 52/154 (33%), Gaps = 45/154 (29%)
Query: 58 SQLPKQIAAMSKCYRAEISVVADEKGVYRVHCFTKIEMFGVTLPEDSE-------KQLEQ 110
+LP +A + K +R EIS G++RV F + E+ P D KQ
Sbjct: 180 RKLPFGVAQIGKSFRNEIS---PRNGLFRVREFEQAEIEFFVHPLDKSHPKFEEVKQDIL 236
Query: 111 FL---QFEESLFGELG----------------IHTRTLNMG------------ANELGAQ 139
L Q +ES GE + L +G NE+
Sbjct: 237 PLLPRQMQESGIGEAVESGMIENETLGYFIARVKQFLLEIGINPDKLRFRQHDKNEMAHY 296
Query: 140 AYKKYDVEAWMP-GRKHWGELSSCSDCTDYQARR 172
A +D E P G W E +D DY +
Sbjct: 297 AKDCWDFEFLTPYG---WIECVGIADRGDYDLTQ 327
>gnl|CDD|215450 PLN02837, PLN02837, threonine-tRNA ligase.
Length = 614
Score = 29.1 bits (65), Expect = 3.0
Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 2/73 (2%)
Query: 59 QLPKQIAAMSKCYRAEISVVADEKGVYRVHCFTKIEMFGVTLPEDSEKQLEQFLQFEESL 118
LP ++A + YR E+S G++RV FT+ + L + + ++ L E +
Sbjct: 327 DLPIRVAELGTVYRYELS--GSLHGLFRVRGFTQDDAHIFCLEDQIKDEIRGVLDLTEEI 384
Query: 119 FGELGIHTRTLNM 131
+ G +N+
Sbjct: 385 LKQFGFSKYEINL 397
>gnl|CDD|225394 COG2838, Icd, Monomeric isocitrate dehydrogenase [Energy production
and conversion].
Length = 744
Score = 28.6 bits (64), Expect = 4.5
Identities = 11/38 (28%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 53 QTLPESQLPKQIAAMSKCY--RAEISVVADEKGVYRVH 88
++LP SQ + A + Y R ++++V +KG+ +H
Sbjct: 307 ESLPASQRAEIEADIHAVYAHRPDLAMVDSDKGITNLH 344
>gnl|CDD|143558 cd07449, CRD_FZ3, Cysteine-rich Wnt-binding domain (CRD) of the
frizzled 3 (Fz3) receptor. The cysteine-rich domain
(CRD) is an essential extracellular portion of the
frizzled 3 (Fz3) receptor, and is required for binding
Wnt proteins, which play fundamental roles in many
aspects of early development, such as cell and tissue
polarity, neural synapse formation, and the regulation
of proliferation. Fz proteins serve as Wnt receptors for
multiple signal transduction pathways, including both
beta-catenin dependent and -independent cellular
signaling, as well as the planar cell polarity pathway
and Ca(2+) modulating signaling pathway. CRD containing
Fzs have been found in diverse species from amoebas to
mammals. 10 different frizzled proteins are found in
vertebrata. Fz3 plays a vital role in the
anterior-posterior guidance of commissural axons.
Knockout mice without Fz3 show defects in fiber tracts
in the rostral CNS.
Length = 127
Score = 26.9 bits (59), Expect = 5.8
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 89 CFTKIEMFGVTLPEDSE 105
C +EMFGV PED E
Sbjct: 87 CSKLMEMFGVPWPEDME 103
>gnl|CDD|235860 PRK06778, PRK06778, hypothetical protein; Validated.
Length = 289
Score = 27.6 bits (61), Expect = 6.3
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 9/48 (18%)
Query: 21 RSQIYHLEPNYYGNGWCLSGTAEMGIARYLMNQTLPESQLPKQIAAMS 68
++ IY N W LSG + R L +PE ++ Q++AM+
Sbjct: 197 KNNIY--------NNWNLSGDRALSARRVLEEAGMPEDKV-MQVSAMA 235
>gnl|CDD|233540 TIGR01709, typeII_sec_gspL, type II secretion system protein L.
This model represents GspL, protein L of the main
terminal branch of the general secretion pathway, also
called type II secretion. It transports folded proteins
across the bacterial outer membrane and is widely
distributed in Gram-negative pathogens [Protein fate,
Protein and peptide secretion and trafficking].
Length = 384
Score = 27.8 bits (62), Expect = 6.4
Identities = 15/54 (27%), Positives = 19/54 (35%), Gaps = 5/54 (9%)
Query: 70 CYRAEISVVADEKGVYRVHCF---TKIEMFGVTLPEDSEKQLEQFLQF--EESL 118
RA + +A V + + V LP QL Q L F EE L
Sbjct: 26 TGRAALQALAPPDPAAAVVLLVPAEDVLLRSVPLPPGKAAQLRQALPFLLEEEL 79
>gnl|CDD|129583 TIGR00492, alr, alanine racemase. This enzyme interconverts
L-alanine and D-alanine. Its primary function is to
generate D-alanine for cell wall formation. With
D-alanine-D-alanine ligase, it makes up the D-alanine
branch of the peptidoglycan biosynthetic route. It is a
monomer with one pyridoxal phosphate per subunit. In E.
coli, the ortholog is duplicated so that a second
isozyme, DadX, is present. DadX, a paralog of the
biosynthetic Alr, is induced by D- or L-alanine and is
involved in catabolism [Cell envelope, Biosynthesis and
degradation of murein sacculus and peptidoglycan].
Length = 367
Score = 27.7 bits (62), Expect = 6.7
Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 105 EKQLEQFLQFEESLFGELGIHTRTLNMGANELGAQAYKKYDVEAWMPG 152
+KQ+E+F F E L + I ++ AN + + + PG
Sbjct: 175 QKQIERFNSFLEGLKQQ-NIEPPFRHI-ANSAAILNWPESHFDMVRPG 220
>gnl|CDD|197282 cd09186, PLDc_FAM83F_N, N-terminal phospholipase D-like domain of
the uncharacterized protein, Family with sequence
similarity 83F. N-terminal phospholipase D (PLD)-like
domain of the uncharacterized protein, Family with
sequence similarity 83F (FAM83F). Since the N-terminal
PLD-like domain of FAM83 proteins shows only trace
similarity to the PLD catalytic domain and lacks the
functionally important histidine residue, FAM83 proteins
may share a similar three-dimensional fold with PLD
enzymes, but are most unlikely to carry PLD activity.
The N-terminus of FAM83F shows high homology to other
FAM83 family members, indicating that FAM83F might have
arisen early in vertebrate evolution by duplication of a
gene in the FAM83 family.
Length = 268
Score = 27.6 bits (61), Expect = 7.4
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 152 GRKHWGELSSCSDCTDYQARRLNIRTEDG 180
G KH+ E+ S +D+ R + +R+ G
Sbjct: 173 GVKHFLEMCSRLQLSDFHIRNIRVRSVTG 201
>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 = 27.2 bits (61), Expect = 7.8
Identities = 18/73 (24%), Positives = 30/73 (41%), Gaps = 3/73 (4%)
Query: 59 QLPKQIAAMSKCYRAEISVVADEKGVYRVHCFTKIEMFGVTLPEDSEKQLEQFLQFEESL 118
+LP +A + K +R EIS G++RV FT+ E+ PE S + +
Sbjct: 105 KLPFGVAQIGKSFRNEIS---PRNGLFRVREFTQAEIEFFVDPEKSHPWFDYWADQRLKW 161
Query: 119 FGELGIHTRTLNM 131
+ L +
Sbjct: 162 LPKFAQSPENLRL 174
>gnl|CDD|129282 TIGR00178, monomer_idh, isocitrate dehydrogenase, NADP-dependent,
monomeric type. The monomeric type of isocitrate
dehydrogenase has been found so far in a small number of
species, including Azotobacter vinelandii,
Corynebacterium glutamicum, Rhodomicrobium vannielii,
and Neisseria meningitidis. It is NADP-specific [Energy
metabolism, TCA cycle].
Length = 741
Score = 27.5 bits (61), Expect = 8.1
Identities = 11/38 (28%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 53 QTLPESQLPKQIAAMSKCY--RAEISVVADEKGVYRVH 88
++LP +Q + A + Y R E+++V +KG+ +H
Sbjct: 305 ESLPAAQQEEIEADLQAVYAQRPELAMVNSDKGITNLH 342
>gnl|CDD|219722 pfam08124, Lyase_8_N, Polysaccharide lyase family 8, N terminal
alpha-helical domain. This family consists of a group
of secreted bacterial lyase enzymes EC:4.2.2.1 capable
of acting on hyaluronan and chondroitin in the
extracellular matrix of host tissues, contributing to
the invasive capacity of the pathogen.
Length = 319
Score = 27.2 bits (61), Expect = 9.9
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 10/54 (18%)
Query: 22 SQIYHLEPNYYGNGWCLSGTAEMGIAR------YLMNQTLPESQLPKQIAAMSK 69
+Y+ + YGN W E+G R LM L E ++ K AA+
Sbjct: 98 DNVYNSNKSEYGNWW----DWEIGTPRALNDTLVLMYDDLSEEEITKYTAAIDH 147
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
0.318 0.133 0.399
Gapped
Lambda K H
0.267 0.0744 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,046,868
Number of extensions: 1201850
Number of successful extensions: 905
Number of sequences better than 10.0: 1
Number of HSP's gapped: 885
Number of HSP's successfully gapped: 30
Length of query: 264
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 169
Effective length of database: 6,723,972
Effective search space: 1136351268
Effective search space used: 1136351268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.1 bits)