RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13909
(328 letters)
>gnl|CDD|215525 PLN02972, PLN02972, Histidyl-tRNA synthetase.
Length = 763
Score = 226 bits (577), Expect = 4e-68
Identities = 103/222 (46%), Positives = 143/222 (64%), Gaps = 9/222 (4%)
Query: 109 LLDGLFESCGVPAKQFRTICSSVDKLDKWSWEDVRYEMTQEKGLSKIIADKIGIYVQQHG 168
LLDG+ E CGVP ++FRTICSS+DKLDK S+E V+ EM +EKGLS ADKIG +V++ G
Sbjct: 485 LLDGMLEICGVPPEKFRTICSSIDKLDKQSFEQVKKEMVEEKGLSNETADKIGNFVKERG 544
Query: 169 H-KELVEKFMQDDL-LKTSKSALVGLAAIKLLLSYCDIYELTDKVIFDLSLARGLDYYTG 226
EL+ K Q+ + S+ L ++++ + + K++FDLSLARGLDYYTG
Sbjct: 545 PPLELLSKLRQEGSEFLGNASSRAALDELEIMFKALEKSKAIGKIVFDLSLARGLDYYTG 604
Query: 227 IIYEAVLIGDRKKGESVGSVAGGGRYDKLVGMFDPRQRNVPCVGISIGVERIFSLIESKL 286
+IYEAV KG VGS+A GGRYD LVGMF +Q VP VG+S+G+ER+F+++E +
Sbjct: 605 VIYEAVF-----KGAQVGSIAAGGRYDNLVGMFSGKQ--VPAVGVSLGIERVFAIMEQQE 657
Query: 287 AAERTKLRTTEVQVYVASAQKNLLEERMRICSYLWKNGINAD 328
+ +R TE +V V+ + L + S LW GI A+
Sbjct: 658 EEKSQVIRPTETEVLVSIIGDDKLALAAELVSELWNAGIKAE 699
Score = 64.1 bits (156), Expect = 2e-11
Identities = 35/101 (34%), Positives = 53/101 (52%), Gaps = 9/101 (8%)
Query: 16 VIRKLKDLVPPNIEIMKKEMDKLKELKSKL-------CRTTNTTVEE--HDVEYDQVKLT 66
V++ +KD V + + L E ++L C ++ V++ VE ++V+
Sbjct: 267 VLQLIKDRVTNGGGVSSDSLQVLAEWATQLLLLFDPKCPGFDSLVDKVKEIVESNEVRRL 326
Query: 67 LKTPKGTRDYGPEPMVLRKNVLEQIISVFKRHGAQTIDTPV 107
K PKGTRD+ E M +R+ I SVFKRHGA +DTPV
Sbjct: 327 PKIPKGTRDFAKEQMAIREKAFSIITSVFKRHGATALDTPV 367
>gnl|CDD|223202 COG0124, HisS, Histidyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 140 bits (356), Expect = 2e-38
Identities = 62/220 (28%), Positives = 98/220 (44%), Gaps = 21/220 (9%)
Query: 109 LLDGLFESCGVPAKQFRTICSSVDKLDKWSWEDVRYEMTQEKGLSKIIADKIGIYVQQHG 168
+L+G E G+ ++ + +DKLDK ++ E ++ + + + +
Sbjct: 168 ILEGRLEYLGIDQRE--ALLRYLDKLDKIGKLELD-----EDSKRRLKTNPLRVLDSKKD 220
Query: 169 HKELVEKFMQDDLLKTSKSALVGLAAIKLLLSYCDIYELTDKVIFDLSLARGLDYYTGII 228
+ + K +LL L ++ LL+ D D SL RGLDYYTG +
Sbjct: 221 SDQELLKNA-PELLDYLDEE--SLEHLEELLALLDALG--ISYEIDPSLVRGLDYYTGTV 275
Query: 229 YEAVLIGDRKKGESVGSVAGGGRYDKLVGMFDPRQRNVPCVGISIGVERIFSLIESKLAA 288
+EAV G + GSV GGGRYD LV F + P VG +IGVER+ +E
Sbjct: 276 FEAVTDG----LGAQGSVCGGGRYDGLVEEF--GGKPTPAVGFAIGVERLILALE---EE 326
Query: 289 ERTKLRTTEVQVYVASAQKNLLEERMRICSYLWKNGINAD 328
+ T V VYV ++ E +++ L GI+ +
Sbjct: 327 GKEDPVETRVDVYVVPLGEDAEPEALKLAQKLRAAGISVE 366
Score = 51.8 bits (125), Expect = 2e-07
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 66 TLKTPKGTRDYGPEPMVLRKNVLEQIISVFKRHGAQTIDTPVCLLDGLFESCGVPAK 122
++ P+GTRD+ PE M LR+ + I VF+ +G I TP+ FE + A+
Sbjct: 3 KIQRPRGTRDFLPEDMALREYIESTIRKVFESYGFSEIRTPI------FEYTELFAR 53
>gnl|CDD|238396 cd00773, HisRS-like_core, Class II Histidinyl-tRNA synthetase
(HisRS)-like catalytic core domain. HisRS is a
homodimer. It is responsible for the attachment of
histidine to the 3' OH group of ribose of the
appropriate tRNA. This domain 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. 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. HisZ along with HisG catalyze
the first reaction in histidine biosynthesis. HisZ is
found only in a subset of bacteria and differs from
HisRS in lacking a C-terminal anti-codon binding domain.
Length = 261
Score = 116 bits (294), Expect = 7e-31
Identities = 42/93 (45%), Positives = 56/93 (60%), Gaps = 6/93 (6%)
Query: 191 GLAAIKLLLSYCDIYELTDKVIFDLSLARGLDYYTGIIYEAVLIGDRKKGESVGSVAGGG 250
LA ++ LL Y + + K DLSL RGLDYYTGI++EAV + GS+AGGG
Sbjct: 175 ALAHLEKLLDYLEALGVDIKYSIDLSLVRGLDYYTGIVFEAVA----DGLGAQGSIAGGG 230
Query: 251 RYDKLVGMFDPRQRNVPCVGISIGVERIFSLIE 283
RYD L+ F +VP VG +IG+ER+ +E
Sbjct: 231 RYDGLLEEF--GGEDVPAVGFAIGLERLLLALE 261
Score = 37.6 bits (88), Expect = 0.005
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 81 MVLRKNVLEQIISVFKRHGAQTIDTPV 107
LR+ + + + VF+R+G + IDTPV
Sbjct: 2 AALRRYIEDTLREVFERYGYEEIDTPV 28
>gnl|CDD|213530 TIGR00442, hisS, histidyl-tRNA synthetase. This model finds a
histidyl-tRNA synthetase in every completed genome.
Apparent second copies from Bacillus subtilis,
Synechocystis sp., and Aquifex aeolicus are slightly
shorter, more closely related to each other than to
other hisS proteins, and actually serve as regulatory
subunits for an enzyme of histidine biosynthesis. They
were excluded from the seed alignment and score much
lower than do single copy histidyl-tRNA synthetases of
other genomes not included in the seed alignment. These
putative second copies of HisS score below the trusted
cutoff. The regulatory protein kinase GCN2 of
Saccharomyces cerevisiae (YDR283c), and related proteins
from other species designated eIF-2 alpha kinase, have a
domain closely related to histidyl-tRNA synthetase that
may serve to detect and respond to uncharged tRNA(his),
an indicator of amino acid starvation; these regulatory
proteins are not orthologous and so score below the
noise cutoff [Protein synthesis, tRNA aminoacylation].
Length = 397
Score = 109 bits (274), Expect = 6e-27
Identities = 40/119 (33%), Positives = 55/119 (46%), Gaps = 9/119 (7%)
Query: 210 KVIFDLSLARGLDYYTGIIYEAVLIGDRKKGESVGSVAGGGRYDKLVGMFDPRQRNVPCV 269
+ D SL RGLDYYTG ++E V + GS+ GGGRYD LV P V
Sbjct: 244 PYVIDPSLVRGLDYYTGTVFEFVT----DGLGAQGSICGGGRYDGLVEELG--GPPTPAV 297
Query: 270 GISIGVERIFSLIESKLAAERTKLRTTEVQVYVASAQKNLLEERMRICSYLWKNGINAD 328
G +IG+ER+ L+E + VYV + E +++ L K GI +
Sbjct: 298 GFAIGIERLLLLLEEL---GLLPPEESSPDVYVVPLGEEAELEALKLAQKLRKAGIRVE 353
Score = 50.2 bits (121), Expect = 7e-07
Identities = 26/90 (28%), Positives = 45/90 (50%), Gaps = 20/90 (22%)
Query: 68 KTPKGTRDYGPEPMVLRKNVLEQIISVFKRHGAQTIDTPVCLLDGLFESCGVPAKQF-RT 126
+ P+GTRD+ PE M+ + + E I VF+ +G + I TP+ FE + F R
Sbjct: 1 QAPRGTRDFLPEEMIKWQYIEETIREVFELYGFKEIRTPI------FEY----TELFARK 50
Query: 127 ICSSVDKLDK--WSWED-------VRYEMT 147
+ D ++K ++++D +R E T
Sbjct: 51 VGEETDIVEKEMYTFKDKGGRSLTLRPEGT 80
>gnl|CDD|234586 PRK00037, hisS, histidyl-tRNA synthetase; Reviewed.
Length = 412
Score = 104 bits (263), Expect = 2e-25
Identities = 45/144 (31%), Positives = 63/144 (43%), Gaps = 19/144 (13%)
Query: 185 SKSALVGLAAIKLLLSYCDIYELTDKVIFDLSLARGLDYYTGIIYEAVLIGDRKKGESVG 244
+ + +K LL I + D L RGLDYYTG ++E V + G
Sbjct: 225 DEESKEHFEELKELLDALGI-----PYVIDPRLVRGLDYYTGTVFEFVT----DDLGAQG 275
Query: 245 SVAGGGRYDKLVGMFDPRQRNVPCVGISIGVERIFSLIESKLAAERTKLRTTEVQVYVAS 304
+V GGGRYD LV F P VG +IGVER+ L+E +L V VYV
Sbjct: 276 TVCGGGRYDGLVEQF--GGPPTPAVGFAIGVERLLLLLE--------ELGEEPVDVYVVP 325
Query: 305 AQKNLLEERMRICSYLWKNGINAD 328
++ +++ L GI +
Sbjct: 326 LGEDAELAALKLAEKLRAAGIRVE 349
Score = 50.5 bits (122), Expect = 5e-07
Identities = 16/44 (36%), Positives = 25/44 (56%)
Query: 64 KLTLKTPKGTRDYGPEPMVLRKNVLEQIISVFKRHGAQTIDTPV 107
+ ++ P+GTRD PE + V + I VF+R+G I TP+
Sbjct: 1 MMKIQAPRGTRDILPEESAKWQYVEDTIREVFERYGFSEIRTPI 44
>gnl|CDD|237097 PRK12420, PRK12420, histidyl-tRNA synthetase; Provisional.
Length = 423
Score = 102 bits (257), Expect = 1e-24
Identities = 57/185 (30%), Positives = 92/185 (49%), Gaps = 13/185 (7%)
Query: 109 LLDGLFESCGVPAKQFRTICSSVDKLDKWSWEDVRYEMTQEKGLSKIIADKIGIYVQQHG 168
LL+G+ ++ G+P + + S+DK++K + VR ++ E+G+S+ +AD I V
Sbjct: 165 LLNGILQAIGIPTELTSDVILSLDKIEKIGIDGVRKDL-LERGISEEMADTICNTVLSCL 223
Query: 169 HKELVEKFMQDDLLKTSKSALV--GLAAIKLLLSYCDIYELTDKVIFDLSLARGLDYYTG 226
+ D + + LV G+ ++ L Y + + IF+ LARGL YTG
Sbjct: 224 QLSI------ADFKEAFNNPLVAEGVNELQQLQQYLIALGINENCIFNPFLARGLTMYTG 277
Query: 227 IIYEAVLIGDRKKGESVGSVAGGGRYDKLVGMFDPRQRNVPCVGISIGVERIFSLIESKL 286
+YE L K G S+ GGRYD ++G F N P VGIS G++ I++ + K
Sbjct: 278 TVYEIFL----KDGSITSSIGSGGRYDNIIGAFRGDDMNYPTVGISFGLDVIYTALSQKE 333
Query: 287 AAERT 291
T
Sbjct: 334 TISST 338
Score = 37.4 bits (87), Expect = 0.009
Identities = 16/44 (36%), Positives = 27/44 (61%)
Query: 64 KLTLKTPKGTRDYGPEPMVLRKNVLEQIISVFKRHGAQTIDTPV 107
+ ++ KGT+DY PE VLR + + VF+R+G + ++TP
Sbjct: 1 MMEMRNVKGTKDYLPEEQVLRNKIKRALEDVFERYGCKPLETPT 44
>gnl|CDD|178145 PLN02530, PLN02530, histidine-tRNA ligase.
Length = 487
Score = 85.6 bits (212), Expect = 1e-18
Identities = 70/248 (28%), Positives = 113/248 (45%), Gaps = 29/248 (11%)
Query: 88 LEQIISVFKRHGAQTIDTPV-----CLLDGLFESCGVPAKQFRTICSSVDKLDKWSWEDV 142
L I++ FKR G + D + +L + +S G+P + F +C VDKL+K E++
Sbjct: 207 LAAIVTFFKRVGITSSDVGIKVSSRKVLQAVLKSYGIPEESFAPVCVIVDKLEKLPREEI 266
Query: 143 RYEMTQEKGLSKIIADKIGIYVQQHGHKELVEKFMQDDLLKTSKSALVGLAAIKLLLSYC 202
E+ G+S+ + I + K L DDL + +A +K L S
Sbjct: 267 EKEL-DTLGVSEEAIEGI---LDVLSLKSL------DDLEALLGADSEAVADLKQLFSLA 316
Query: 203 DIYELTDKVIFDLSLARGLDYYTGIIYEAVLIGDRKKGESVGSVAGGGRYDKLVGMFDPR 262
+ Y D ++FD S+ RGL YYTGI++E DR + ++ GGGRYD+L+ F
Sbjct: 317 EAYGYQDWLVFDASVVRGLAYYTGIVFEGF---DRAG--KLRAICGGGRYDRLLSTFG-- 369
Query: 263 QRNVPCVGISIGVERIFSLIESKLAAERTKLR--TTEVQVYVASAQKNLLEERMRICSYL 320
+ P G G I L++ E+ L +V V + ++L + S L
Sbjct: 370 GEDTPACGFGFGDAVIVELLK-----EKGLLPELPHQVDDVVFALDEDLQGAAAGVASRL 424
Query: 321 WKNGINAD 328
+ G + D
Sbjct: 425 REKGRSVD 432
Score = 36.3 bits (84), Expect = 0.022
Identities = 18/53 (33%), Positives = 29/53 (54%)
Query: 62 QVKLTLKTPKGTRDYGPEPMVLRKNVLEQIISVFKRHGAQTIDTPVCLLDGLF 114
+ K+ + PKGTRD+ PE M LR + + V + G + +D PV + L+
Sbjct: 65 KPKIDVNPPKGTRDFPPEDMRLRNWLFDHFREVSRLFGFEEVDAPVLESEELY 117
>gnl|CDD|237043 PRK12292, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 391
Score = 78.8 bits (195), Expect = 2e-16
Identities = 47/192 (24%), Positives = 74/192 (38%), Gaps = 32/192 (16%)
Query: 109 LLDGLFESCGVPAKQFRTICSSVDKLDKWSWEDVRYEMTQEKGLSKIIADKIGIYVQQHG 168
L L E+ G+ + + ++ D V E LS+ + D +
Sbjct: 165 LFRALLEAAGLSEELEEVLRRALANKDY-----VALE-ELVLDLSEELRDAL-------- 210
Query: 169 HKELVEKFMQDDLLKTSKSALV---GLAAIKLLLSYCDIYE---LTDKVIFDLSLARGLD 222
L ++L+ ++ L A+ L + + E + DL L R LD
Sbjct: 211 -LALPRLRGGREVLEEARKLLPSLPIKRALDELEALAEALEKYGYGIPLSLDLGLLRHLD 269
Query: 223 YYTGIIYEAVLIGDRKKGESVG-SVAGGGRYDKLVGMFDPRQRNVPCVGISIGVERIFSL 281
YYTGI++E + VG +A GGRYD L+G F R P G S+ ++R+ L
Sbjct: 270 YYTGIVFEGY-------VDGVGNPIASGGRYDDLLGRFG---RARPATGFSLDLDRLLEL 319
Query: 282 IESKLAAERTKL 293
R L
Sbjct: 320 QLELPVEARKDL 331
Score = 37.9 bits (89), Expect = 0.006
Identities = 11/37 (29%), Positives = 21/37 (56%)
Query: 70 PKGTRDYGPEPMVLRKNVLEQIISVFKRHGAQTIDTP 106
P+G RD PE + + +++ +F+R G + + TP
Sbjct: 6 PEGIRDLLPEEARKIEEIRRRLLDLFRRWGYEEVITP 42
>gnl|CDD|232978 TIGR00443, hisZ_biosyn_reg, ATP phosphoribosyltransferase,
regulatory subunit. Apparant second copies of
histidyl-tRNA synthetase, found in Bacillus subtilis,
Synechocystis sp., Aquifex aeolicus, and others, are in
fact a regulatory subunit of ATP
phosphoribosyltransferase, and usually encoded by a gene
adjacent to that encoding the catalytic subunit [Amino
acid biosynthesis, Histidine family].
Length = 313
Score = 75.3 bits (186), Expect = 2e-15
Identities = 39/136 (28%), Positives = 67/136 (49%), Gaps = 13/136 (9%)
Query: 149 EKGLSKIIADKIGIYVQQHGHKELVEKFMQDDLLKTSKSALVGLAAIKLLLSYCDIYELT 208
E GLS + +++ + G E V + + L S++A L ++ +L + +
Sbjct: 190 ELGLSPEVRERLLALPRLRGDGEEVLEEARA--LAGSETAEAALDELEAVLELLEARGVE 247
Query: 209 DKVIFDLSLARGLDYYTGIIYEAVLIGDRKKGESVG-SVAGGGRYDKLVGMFDPRQRNVP 267
+ + DL L RG YYTG+I+E +G +AGGGRYD+L+G F R +P
Sbjct: 248 EYISLDLGLVRGYHYYTGLIFEGY-------APGLGAPLAGGGRYDELLGRF---GRPLP 297
Query: 268 CVGISIGVERIFSLIE 283
G ++ +ER+ +
Sbjct: 298 ATGFALNLERLLEALT 313
Score = 30.7 bits (70), Expect = 1.0
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 74 RDYGPEPMVLRKNVLEQIISVFKRHGAQTIDTPV 107
RD PE ++ + Q+ VF+ G Q I TP
Sbjct: 1 RDLLPEEAARKEEIERQLQDVFRSWGYQEIITPT 34
>gnl|CDD|222097 pfam13393, tRNA-synt_His, Histidyl-tRNA synthetase. This is a
family of class II aminoacyl-tRNA synthetase-like and
ATP phosphoribosyltransferase regulatory subunits.
Length = 308
Score = 75.3 bits (186), Expect = 2e-15
Identities = 41/170 (24%), Positives = 82/170 (48%), Gaps = 16/170 (9%)
Query: 109 LLDGLFESCGVPAKQFRTICSSVDKLDKWSWEDVRYEMTQEKGLSKIIADKIGIYVQQHG 168
++ L E+ G+ Q + ++ + D ++ E+ E GL +AD + + +G
Sbjct: 155 IVRALLEALGLSEAQEEALRDALQRKD---LPELE-ELLAELGLDPALADALLALPELYG 210
Query: 169 HKELVEKFMQDDLLKTSKSALVGLAAIKLLLSYCDIYELTDKVIFDLSLARGLDYYTGII 228
E++++ ++ LL S +A L ++ L + + ++ DL+ RG +YYTG++
Sbjct: 211 DPEVLDEALE--LLPGSPAAAA-LDELEALAALLEALGPGVRLTLDLAELRGYEYYTGLV 267
Query: 229 YEAVLIGDRKKGESVGSVAGGGRYDKLVGMFDPRQRNVPCVGISIGVERI 278
+ A G + ++A GGRYD L +F R P G S+ ++ +
Sbjct: 268 FAAYAPGAGQ------ALARGGRYDNLGEVFG---RARPATGFSLDLDAL 308
Score = 27.5 bits (62), Expect = 8.9
Identities = 7/35 (20%), Positives = 16/35 (45%)
Query: 72 GTRDYGPEPMVLRKNVLEQIISVFKRHGAQTIDTP 106
G RD P + + +++ +F+ G + + P
Sbjct: 1 GIRDLLPPEARRIEELRRRLLDLFRSWGYELVIPP 35
>gnl|CDD|183413 PRK12295, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 373
Score = 64.2 bits (157), Expect = 2e-11
Identities = 27/77 (35%), Positives = 41/77 (53%), Gaps = 6/77 (7%)
Query: 208 TDKVIFDLSLARGLDYYTGIIYEAVLIGDRKKGESVGSVAGGGRYDKLVGMFDPRQRNVP 267
+++ F S R LDYYTG ++E I G+ +AGGGRYD L+ +P
Sbjct: 303 LERLRFSASFGRPLDYYTGFVFE---IRAAGNGDPP--LAGGGRYDGLLTRLGAG-EPIP 356
Query: 268 CVGISIGVERIFSLIES 284
VG SI ++R+ +L +
Sbjct: 357 AVGFSIWLDRLAALGGA 373
>gnl|CDD|226228 COG3705, HisZ, ATP phosphoribosyltransferase involved in histidine
biosynthesis [Amino acid transport and metabolism].
Length = 390
Score = 53.5 bits (129), Expect = 4e-08
Identities = 29/102 (28%), Positives = 47/102 (46%), Gaps = 16/102 (15%)
Query: 178 QDDLLKTSKSALVGLAAIKLLLSYCDIYELTDKVIFDLSLARGLDYYTGIIYEAVLIGDR 237
D L AL A+ + L +K+ DL R DYYTG+++ A
Sbjct: 228 LLDELMAQGIALNEGRALADIARR-----LIEKIALDLGRLRHFDYYTGLVFLAY----- 277
Query: 238 KKGESVG-SVAGGGRYDKLVGMFDPRQRNVPCVGISIGVERI 278
+ +G ++A GGRYD L+G+F R P G ++ ++ +
Sbjct: 278 --ADGLGDALASGGRYDGLLGLF---GRAAPATGFALRLDAL 314
Score = 35.4 bits (82), Expect = 0.033
Identities = 10/38 (26%), Positives = 23/38 (60%)
Query: 70 PKGTRDYGPEPMVLRKNVLEQIISVFKRHGAQTIDTPV 107
P+G RD P ++ + +Q++++F+ G + ++TP
Sbjct: 6 PEGIRDVLPLEARRKEEIRDQLLALFRAWGYERVETPT 43
Score = 29.7 bits (67), Expect = 2.4
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 10/79 (12%)
Query: 209 DKVIFDLSLARGLDYYTGIIYEAVLIGDRKKGESVGSVAGGGRYDKLVGMFDPRQRNVPC 268
++ + R LDYYTG +EA +AGGGRYD+L+ +P
Sbjct: 322 EERRYAALFGRELDYYTGAAFEAA---------QALRLAGGGRYDRLLTGL-GASEEIPG 371
Query: 269 VGISIGVERIFSLIESKLA 287
VG S+ ++R +++ A
Sbjct: 372 VGFSLWLDRGVAVVGEGKA 390
>gnl|CDD|164576 CHL00201, syh, histidine-tRNA synthetase; Provisional.
Length = 430
Score = 47.2 bits (112), Expect = 6e-06
Identities = 31/109 (28%), Positives = 50/109 (45%), Gaps = 11/109 (10%)
Query: 217 LARGLDYYTGIIYEAVLIGDRKKGESVGSVAGGGRYDKLVGMFDPRQRNVPCVGISIGVE 276
L RGLDYY +E + G+ ++ GGGRYD L+ + P VG +IG+E
Sbjct: 256 LVRGLDYYNDTAFEIKTL--SSNGQD--TICGGGRYDSLIHQLGGPK--TPAVGCAIGLE 309
Query: 277 RIFSLIESKLAAERTKLRTTEVQVYVASAQKNLLEERMRICSYLWKNGI 325
R+ + + + L + VY+A+ ++ I +L K I
Sbjct: 310 RLLLIAKDNII-----LPKQSIDVYIATQGLKAQKKGWEIIQFLEKQNI 353
>gnl|CDD|238436 cd00859, HisRS_anticodon, HisRS Histidyl-anticodon binding domain.
HisRS belongs to class II aminoacyl-tRNA synthetases
(aaRS). This alignment contains the anticodon binding
domain, which is responsible for specificity in
tRNA-binding, so that the activated amino acid is
transferred to a ribose 3' OH group of the appropriate
tRNA only.
Length = 91
Score = 38.3 bits (90), Expect = 5e-04
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 297 EVQVYVASAQKNLLEERMRICSYLWKNGINAD 328
EV VYV + L E + + L GI A+
Sbjct: 1 EVDVYVVPLGEGALSEALELAEQLRDAGIKAE 32
>gnl|CDD|215929 pfam00458, WHEP-TRS, WHEP-TRS domain.
Length = 56
Score = 32.7 bits (75), Expect = 0.025
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 8 NEIKEQRDVIRKLKDLVPPNIEIMKKEMDKLKELKSKLCRTTNT 51
+I Q D++RKLK P ++ + KL LK + T
Sbjct: 3 EKIAAQGDLVRKLKAKKAPKEDV-DAAVKKLLALKKQYKEKTGK 45
>gnl|CDD|238605 cd01200, WHEPGMRS_RNA, EPRS-like_RNA binding domain. This short
RNA-binding domain is found in several higher eukaryote
aminoacyl-tRNA synthetases (aaRSs). It is found in
three copies in the mammalian bifunctional EPRS in a
region that separates the N-terminal GluRS from the
C-terminal ProRS. In the Drosophila EPRS, this domain
is repeated six times. It is found at the N-terminus of
TrpRS, HisRS and GlyR and at the C-terminus of MetRS.
This domain consists of a helix- turn- helix structure,
which is similar to other RNA-binding proteins. It is
involved in both protein-RNA interactions by binding
tRNA and protein-protein interactions, which are
important for the formation of aaRSs into multienzyme
complexes.
Length = 42
Score = 31.7 bits (73), Expect = 0.029
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 8 NEIKEQRDVIRKLKDLVPPNIEIMKKEMDKLKELKSKLCRTT 49
+I EQ D++RKLK P EI + KL LK++ T
Sbjct: 2 EKIAEQGDLVRKLKAEKAPKEEI-DAAVKKLLALKAQYKEAT 42
>gnl|CDD|237098 PRK12421, PRK12421, ATP phosphoribosyltransferase regulatory
subunit; Provisional.
Length = 392
Score = 34.9 bits (81), Expect = 0.049
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 9/74 (12%)
Query: 211 VIFDLSLARGLDYYTGIIYEAVLIGDRKKGESVGSVAGGGRYDKLVGMFDPRQRNVPCVG 270
V DL+ RG Y+TG+++ A I R + ++A GGRYD +G R R P G
Sbjct: 265 VSIDLAELRGYHYHTGLVF-AAYIPGRGQ-----ALARGGRYDG-IGEAFGRAR--PATG 315
Query: 271 ISIGVERIFSLIES 284
S+ ++ + +L
Sbjct: 316 FSMDLKELLALQFL 329
>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 = 33.3 bits (77), Expect = 0.078
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 83 LRKNVLEQIISVFKRHGAQTIDTPVCLLDGLFESCG 118
LR + I + KR+G Q +DTP+ L+E G
Sbjct: 1 LRNALENFIRELLKRYGYQEVDTPILEPKELWEGSG 36
>gnl|CDD|214960 smart00991, WHEP-TRS, A conserved domain of 46 amino acids,
called WHEP-TRS has been shown.to exist in a number of
higher eukaryote aminoacyl-transfer RNA synthetases.
This domain is present one to six times in the several
enzymes. There are three copies in mammalian
multifunctional aminoacyl-tRNA synthetase in a region
that separates the N-terminal glutamyl-tRNA synthetase
domain from the C-terminal prolyl-tRNA synthetase
domain, and six copies in the intercatalytic region of
the Drosophila enzyme. The domain is found at the
N-terminal extremity of the mammalian tryptophanyl-
tRNA synthetase and histidyl-tRNA synthetase, and the
mammalian, insect, nematode and plant glycyl- tRNA
synthetases. This domain could contain a central
alpha-helical region and may play a role in the
association of tRNA-synthetases into multienzyme
complexes.
Length = 56
Score = 28.8 bits (65), Expect = 0.50
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 8 NEIKEQRDVIRKLKDLVPPNIEIMKKEMDKLKELKSKLCRTT 49
+ Q +++RKLK EI + KL LK++L T
Sbjct: 2 EAVAAQGELVRKLKAEKASKDEI-DAAVAKLLALKAQLKEAT 42
>gnl|CDD|223446 COG0369, CysJ, Sulfite reductase, alpha subunit (flavoprotein)
[Inorganic ion transport and metabolism].
Length = 587
Score = 31.6 bits (72), Expect = 0.52
Identities = 33/151 (21%), Positives = 57/151 (37%), Gaps = 15/151 (9%)
Query: 74 RDYGPEPMVLRKNVLEQIISVFKRHGAQTIDTPVCLLDGLFESCGVPAKQFRTICSSVDK 133
+D+ R +VLE + S F Q ES I K
Sbjct: 175 QDFEAAAAPWRDDVLELLKSKFPG---QEAAPAQVATSPQSESPYSKPAPSVAILLENRK 231
Query: 134 LD-KWSWEDVR-YEMTQ-EKGLSKIIADKIGIYVQQHGHKELVEKFMQDDLLKTSKSALV 190
L + S +DVR E+ + GL D +G++ + ELV++F++ LL V
Sbjct: 232 LTGRDSDKDVRHIELDLPDSGLRYEPGDALGVWPEND--PELVDEFLE--LLGLDPEEPV 287
Query: 191 G-----LAAIKLLLSYCDIYELTDKVIFDLS 216
L ++ L S+ + ++ +L+
Sbjct: 288 TVDGETLPLVEALKSHFEFTSAPKSLLENLA 318
>gnl|CDD|176562 cd08625, PI-PLCc_beta3, Catalytic domain of metazoan
phosphoinositide-specific phospholipase C-beta3. This
subfamily corresponds to the catalytic domain present in
metazoan phosphoinositide-specific phospholipase C
(PI-PLC, EC 3.1.4.11)-beta isozyme 3. PI-PLC is a
signaling enzyme that hydrolyzes the membrane
phospholipids phosphatidylinositol-4,5-bisphosphate
(PIP2) to generate two important second messengers in
eukaryotic signal transduction cascades, Inositol
1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG).
InsP3 triggers inflow of calcium from intracellular
stores, while DAG, together with calcium, activates
protein kinase C, which goes on to phosphorylate other
molecules, leading to altered cellular activity. Calcium
is required for the catalysis. PLC-beta represents a
class of mammalian PI-PLC that has an N-terminal
pleckstrin homology (PH) domain, an array of EF hands, a
PLC catalytic core domain, a C2 domain, and a unique
C-terminal coiled-coil (CT) domain necessary for
homodimerization. The PLC catalytic core domain is a TIM
barrel with two highly conserved regions (X and Y) split
by a highly degenerate linker sequence. PI-PLC-beta3 is
widely expressed at highest levels in brain, liver, and
parotid gland. It is activated by the heterotrimeric G
protein alpha q subunits through their C2 domain and
long C-terminal extension. It is also activated by the
beta-gamma subunits of heterotrimeric G proteins.
Length = 258
Score = 30.4 bits (68), Expect = 1.2
Identities = 28/86 (32%), Positives = 46/86 (53%), Gaps = 14/86 (16%)
Query: 34 EMDKLKELKSKLCRTTNTTVEEHDVEYDQVKLTLKTPKGTR----DYGPEPMVLRKNVLE 89
EM E K+ + + T + +E VEY++ +L+ PKGTR +Y P+ L NV
Sbjct: 181 EMSSFVETKA-MEQLTKSPMEF--VEYNKKQLSRIYPKGTRVDSSNYMPQ---LFWNVGC 234
Query: 90 QIISVFKRHGAQTIDTPVCLLDGLFE 115
Q++++ QT+D + L G+FE
Sbjct: 235 QMVAL----NFQTLDLAMQLNMGVFE 256
>gnl|CDD|188996 cd06457, M3A_MIP, Peptidase M3 mitochondrial intermediate peptidase
(MIP). Peptidase M3 mitochondrial intermediate
peptidase (MIP; EC 3.4.24.59) belongs to the widespread
subfamily M3A, that show similarity to the Thimet
oligopeptidase (TOP). It is one of three peptidases
responsible for the proteolytic processing of both,
nuclear and mitochondrial encoded precursor polypeptides
targeted to the various subcompartments of the
mitochondria. It cleaves intermediate-size proteins
initially processed by mitochondrial processing
peptidase (MPP) to yield a processing intermediate with
a typical N-terminal octapeptide that is sequentially
cleaved by MIP to mature-size protein. MIP cleaves
precursor proteins of respiratory components, including
subunits of the electron transport chain and
tri-carboxylic acid cycle enzymes, and components of the
mitochondrial genetic machinery, including ribosomal
proteins, translation factors, and proteins required for
mitochondrial DNA metabolism. It has been suggested that
the human MIP (HMIP polypeptide; gene symbol MIPEP) may
be one of the loci predicted to influence the clinical
manifestations of Friedreich's ataxia (FRDA), an
autosomal recessive neurodegenerative disease caused by
lack of human frataxin. These proteins are enriched in
cysteine residues, two of which are highly conserved,
suggesting their importance to stability as well as in
formation of metal binding sites, thus playing a role in
MIP activity.
Length = 606
Score = 30.6 bits (70), Expect = 1.3
Identities = 11/41 (26%), Positives = 18/41 (43%)
Query: 20 LKDLVPPNIEIMKKEMDKLKELKSKLCRTTNTTVEEHDVEY 60
L+ L +KE+ L LK K + T++ D +Y
Sbjct: 227 LEALSKKLRPKAEKELSVLARLKRKHSGKSLPTLQPWDRDY 267
>gnl|CDD|188994 cd06455, M3A_TOP, Peptidase M3 Thimet oligopeptidase (TOP) also
includes neurolysin. Peptidase M3 Thimet oligopeptidase
(TOP; PZ-peptidase; endo-oligopeptidase A; endopeptidase
24.15; soluble metallo-endopeptidase; EC 3.4.24.15)
family also includes neurolysin (endopeptidase 24.16,
microsomal endopeptidase, mitochondrial oligopeptidase
M, neurotensin endopeptidase, soluble angiotensin
II-binding protein, thimet oligopeptidase II) which
hydrolyzes oligopeptides such as neurotensin, bradykinin
and dynorphin A. TOP and neurolysin are neuropeptidases
expressed abundantly in the testis, but also found in
the liver, lung and kidney. They are involved in the
metabolism of neuropeptides under 20 amino acid residues
long and cleave most bioactive peptides at the same
sites, but recognize different positions on some
naturally occurring and synthetic peptides; they cleave
at distinct sites on the 13-residue bioactive peptide
neurotensin, which modulates central dopaminergic and
cholinergic circuits. TOP has been shown to degrade
peptides released by the proteasome, limiting the extent
of antigen presentation by major histocompatibility
complex class I molecules, and has been associated with
amyloid protein precursor processing.
Length = 637
Score = 30.2 bits (69), Expect = 1.9
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 20 LKDLVPPNIEIMKKEMDKLKELKSKLCRTTNTTVEEHDVEY--DQVK 64
L DL + +KE+ +L LK K C + D+ Y ++VK
Sbjct: 260 LDDLAEKLKPLAEKELAELLALKKKECPEAGDRIYAWDLRYYMNRVK 306
>gnl|CDD|237254 PRK12899, secA, preprotein translocase subunit SecA; Reviewed.
Length = 970
Score = 29.4 bits (66), Expect = 2.9
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 16 VIRKLKDLVPPNIEIMKKEM-DKLKELKSKLCRTTNTTVEEHDVEYDQV 63
+IR + PP E M M ++L E K N T+ +H +EYD V
Sbjct: 696 LIRHFR---PPEGEAMSDPMFNRLIETAQKRVEGRNYTIRKHTLEYDDV 741
>gnl|CDD|189012 cd09605, M3A, Peptidase M3A family includes Thimet oligopeptidase,
dipeptidyl carboxypeptidase and mitochondrial
intermediate peptidase. The peptidase M3-like family,
also called neurolysin-like family, is part of the
"zincins" metallopeptidases, and includes M3, M2 and M32
families of metallopeptidases. The M3 family is
subdivided into two subfamilies: the widespread M3A,
which comprises a number of high-molecular mass endo-
and exopeptidases from bacteria, archaea, protozoa,
fungi, plants and animals, and the small M3B, whose
members are enzymes primarily from bacteria. Well-known
mammalian/eukaryotic M3A endopeptidases are the thimet
oligopeptidase (TOP; endopeptidase 3.4.24.15),
neurolysin (alias endopeptidase 3.4.24.16), and the
mitochondrial intermediate peptidase. The first two are
intracellular oligopeptidases, which act only on
relatively short substrates of less than 20 amino acid
residues, while the latter cleaves N-terminal
octapeptides from proteins during their import into the
mitochondria. The M3A subfamily also contains several
bacterial endopeptidases, collectively called
oligopeptidases A, as well as a large number of
bacterial carboxypeptidases, called dipeptidyl
peptidases (Dcp; Dcp II; peptidyl dipeptidase; EC
3.4.15.5). The peptidases in the M3 family contain the
HEXXH motif that forms the active site in conjunction
with a C-terminally-located Glutamic acid (Glu) residue.
A single zinc ion is ligated by the side-chains of the
two Histidine (His) residues, and the more C-terminal
Glu. Most of the peptidases are synthesized without
signal peptides or propeptides, and function
intracellularly. The structure of neurolysin shows
similarities to those of angiotensin-converting enzyme
(ACE; peptidyl-dipeptidase A) peptidase unit 2 belonging
to peptidase family M2. ACE is an enzyme responsible for
cleavage of dipeptides from the C-termini of proteins,
notably converting angiotensin I to angiotensin II in
mammals. There are similarities to the thermostable
carboxypeptidases from Pyrococcus furiosus
carboxypeptidase (PfuCP), and Thermus aquaticus (TaqCP),
belonging to peptidase family M32. Little is known about
function of this family, including carboxypeptidases Taq
and Pfu.
Length = 590
Score = 29.4 bits (67), Expect = 3.4
Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 2/45 (4%)
Query: 16 VIRKLKDLVPPNIEIMKKEMDKLKELKSKLCRTTNTTVEEHDVEY 60
V+ L+DL +KE+ +L+ K K + ++ D Y
Sbjct: 209 VLDFLEDLAEKAKPRAEKELAELQAFKKKEG--GDDELQPWDWAY 251
>gnl|CDD|233335 TIGR01271, CFTR_protein, cystic fibrosis transmembrane conductor
regulator (CFTR). The model describes the cystis
fibrosis transmembrane conductor regulator (CFTR) in
eukaryotes. The principal role of this protein is
chloride ion conductance. The protein is predicted to
consist of 12 transmembrane domains. Mutations or lesions
in the genetic loci have been linked to the aetiology of
asthma, bronchiectasis, chronic obstructive pulmonary
disease etc. Disease-causing mutations have been studied
by 36Cl efflux assays in vitro cell cultures and
electrophysiology, all of which point to the impairment
of chloride channel stability and not the biosynthetic
processing per se [Transport and binding proteins,
Anions].
Length = 1490
Score = 29.1 bits (65), Expect = 3.6
Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 13/67 (19%)
Query: 119 VPAKQF---RTICSSVDKLDKWSWEDVRYEMTQEKGLSKII---ADKI------GIYVQQ 166
+P K F T ++D ++WS E++ +++ +E GL +I DK+ G YV
Sbjct: 1297 IPQKVFIFSGTFRKNLDPYEQWSDEEI-WKVAEEVGLKSVIEQFPDKLDFVLVDGGYVLS 1355
Query: 167 HGHKELV 173
+GHK+L+
Sbjct: 1356 NGHKQLM 1362
>gnl|CDD|205451 pfam13271, DUF4062, Domain of unknown function (DUF4062). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria, archaea and
eukaryotes, and is approximately 80 amino acids in
length. There is a conserved SST sequence motif.
Length = 83
Score = 27.2 bits (61), Expect = 3.8
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 299 QVYVASAQKNLLEERMRICSYLWKNG 324
Q++++S +L EER + L + G
Sbjct: 1 QIFISSTYTDLKEEREAVIEALLELG 26
>gnl|CDD|176561 cd08624, PI-PLCc_beta2, Catalytic domain of metazoan
phosphoinositide-specific phospholipase C-beta2. This
subfamily corresponds to the catalytic domain present in
metazoan phosphoinositide-specific phospholipase C
(PI-PLC, EC 3.1.4.11)-beta isozyme 2. PI-PLC is a
signaling enzyme that hydrolyzes the membrane
phospholipids phosphatidylinositol-4,5-bisphosphate
(PIP2) to generate two important second messengers in
eukaryotic signal transduction cascades, Inositol
1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG).
InsP3 triggers inflow of calcium from intracellular
stores, while DAG, together with calcium, activates
protein kinase C, which goes on to phosphorylate other
molecules, leading to altered cellular activity. Calcium
is required for the catalysis. PLC-beta represents a
class of mammalian PI-PLC that has an N-terminal
pleckstrin homology (PH) domain, an array of EF hands, a
PLC catalytic core domain, a C2 domain, and a unique
C-terminal coiled-coil (CT) domain necessary for
homodimerization. The PLC catalytic core domain is a TIM
barrel with two highly conserved regions (X and Y) split
by a highly degenerate linker sequence. PI-PLC-beta2 is
expressed at highest levels in cells of hematopoietic
origin. It is activated by the heterotrimeric G protein
alpha q subunits through their C2 domain and long
C-terminal extension. It is also activated by the
beta-gamma subunits of heterotrimeric G proteins.
Length = 261
Score = 28.9 bits (64), Expect = 3.9
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 11/62 (17%)
Query: 58 VEYDQVKLTLKTPKGTR----DYGPEPMVLRKNVLEQIISVFKRHGAQTIDTPVCLLDGL 113
VEY++ +++ PKGTR +Y P+ NV Q++++ QT+D P+ L
Sbjct: 205 VEYNKRQMSRIYPKGTRMDSSNYMPQMFW---NVGCQMVAL----NFQTMDLPMQQNMAL 257
Query: 114 FE 115
FE
Sbjct: 258 FE 259
>gnl|CDD|109527 pfam00474, SSF, Sodium:solute symporter family. Membership of this
family is supported by a significant blast score.
Length = 406
Score = 28.8 bits (65), Expect = 4.0
Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 5/54 (9%)
Query: 185 SKSALVGLAAIKLLLSYCDIYELTDKV---IFDLSLARGLDYYTGIIYEAVLIG 235
K LV L+A+ LLL Y Y V + LA GL+YYT ++ L
Sbjct: 81 GKRILVYLSALSLLL-YFFTYMSVQIVGGARL-IELALGLNYYTAVLLLGALTA 132
>gnl|CDD|128454 smart00149, PLCYc, Phospholipase C, catalytic domain (part); domain
Y. Phosphoinositide-specific phospholipases C. These
enzymes contain 2 regions (X and Y) which together form
a TIM barrel-like structure containing the active site
residues. Phospholipase C enzymes (PI-PLC) act as signal
transducers that generate two second messengers,
inositol-1,4,5-trisphosphate and diacylglycerol. The
bacterial enzyme appears to be a homologue of the
mammalian PLCs.
Length = 115
Score = 27.6 bits (62), Expect = 4.6
Identities = 24/73 (32%), Positives = 30/73 (41%), Gaps = 24/73 (32%)
Query: 58 VEYDQVKLTLKTPKGTR-DYGP-EPMVLRKNVLEQIISVFKRHGAQ-------TIDTPVC 108
V Y+Q +L+ PKGTR D P V F HG Q T D P+
Sbjct: 47 VRYNQRQLSRVYPKGTRVDSSNYNPQV------------FWNHGCQMVALNFQTPDKPMQ 94
Query: 109 LLDGLFES---CG 118
L G+F + CG
Sbjct: 95 LNQGMFRANGGCG 107
>gnl|CDD|213256 cd03289, ABCC_CFTR2, ATP-binding cassette domain 2 of
CFTR,subfamily C. The cystic fibrosis transmembrane
regulator (CFTR), the product of the gene mutated in
patients with cystic fibrosis, has adapted the ABC
transporter structural motif to form a tightly regulated
anion channel at the apical surface of many epithelia.
Use of the term assembly of a functional ion channel
implies the coming together of subunits or at least
smaller not-yet functional components of the active
whole. In fact, on the basis of current knowledge only
the CFTR polypeptide itself is required to form an ATP-
and protein kinase A-dependent low-conductance chloride
channel of the type present in the apical membrane of
many epithelial cells. CFTR displays the typical
organization (IM-ABC)2 and carries a characteristic
hydrophilic R-domain that separates IM1-ABC1 from
IM2-ABC2.
Length = 275
Score = 28.3 bits (63), Expect = 5.1
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 13/67 (19%)
Query: 119 VPAKQF---RTICSSVDKLDKWSWEDVRYEMTQEKGLSKII---ADKI------GIYVQQ 166
+P K F T ++D KWS E++ +++ +E GL +I ++ G V
Sbjct: 82 IPQKVFIFSGTFRKNLDPYGKWSDEEI-WKVAEEVGLKSVIEQFPGQLDFVLVDGGCVLS 140
Query: 167 HGHKELV 173
HGHK+L+
Sbjct: 141 HGHKQLM 147
>gnl|CDD|164492 CHL00086, apcA, allophycocyanin alpha subunit.
Length = 161
Score = 27.6 bits (61), Expect = 5.8
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 9/71 (12%)
Query: 219 RGLDYYTGIIYEAVLIGDRKKGESVGSVAGGGRYDKLVGMFDPRQRNVPCVGISIGVERI 278
R LDYY ++ ++ GD E +G V Y+ L P G++ GV +
Sbjct: 83 RDLDYYLRLVTYGIVAGDVTPIEEIGLVGVKEMYNSL---------GTPISGVAEGVRSM 133
Query: 279 FSLIESKLAAE 289
S+ S LA E
Sbjct: 134 KSVACSLLAGE 144
>gnl|CDD|238474 cd00938, HisRS_RNA, HisRS_RNA binding domain. This short
RNA-binding domain is found at the N-terminus of HisRS
in several higher eukaryote aminoacyl-tRNA synthetases
(aaRSs). This domain consists of a helix- turn- helix
structure, which is similar to other RNA-binding
proteins. It is involved in both protein-RNA
interactions by binding tRNA and protein-protein
interactions, which are important for the formation of
aaRSs into multienzyme complexes.
Length = 45
Score = 25.5 bits (56), Expect = 6.2
Identities = 14/36 (38%), Positives = 24/36 (66%), Gaps = 1/36 (2%)
Query: 10 IKEQRDVIRKLKDLVPPNIEIMKKEMDKLKELKSKL 45
+K Q +++RKLK + E + +E+ KL ELK++L
Sbjct: 7 VKLQGELVRKLKA-EKASKEQIAEEVAKLLELKAQL 41
>gnl|CDD|176560 cd08623, PI-PLCc_beta1, Catalytic domain of metazoan
phosphoinositide-specific phospholipase C-beta1. This
subfamily corresponds to the catalytic domain present in
metazoan phosphoinositide-specific phospholipase C
(PI-PLC, EC 3.1.4.11)-beta isozyme 1. PI-PLC is a
signaling enzyme that hydrolyzes the membrane
phospholipids phosphatidylinositol-4,5-bisphosphate
(PIP2) to generate two important second messengers in
eukaryotic signal transduction cascades, Inositol
1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG).
InsP3 triggers inflow of calcium from intracellular
stores, while DAG, together with calcium, activates
protein kinase C, which goes on to phosphorylate other
molecules, leading to altered cellular activity. Calcium
is required for the catalysis. PLC-beta represents a
class of mammalian PI-PLC that has an N-terminal
pleckstrin homology (PH) domain, an array of EF hands, a
PLC catalytic core domain, a C2 domain, and a unique
C-terminal coiled-coil (CT) domain necessary for
homodimerization. The PLC catalytic core domain is a TIM
barrel with two highly conserved regions (X and Y) split
by a highly degenerate linker sequence. PI-PLC-beta1 is
expressed at highest levels in specific regions of the
brain. It is activated by the heterotrimeric G protein
alpha q subunits through their C2 domain and long
C-terminal extension.
Length = 258
Score = 28.1 bits (62), Expect = 6.7
Identities = 30/98 (30%), Positives = 49/98 (50%), Gaps = 19/98 (19%)
Query: 27 NIEIMKK-----EMDKLKELKSKLCRTTNTTVEEHDVEYDQVKLTLKTPKGTR----DYG 77
+ E KK EM E K L + T + VE VEY++++L+ PKGTR +Y
Sbjct: 169 SFEASKKRNKSFEMSSFVETKG-LEQLTKSPVEF--VEYNKMQLSRIYPKGTRVDSSNYM 225
Query: 78 PEPMVLRKNVLEQIISVFKRHGAQTIDTPVCLLDGLFE 115
P+ L N Q++++ QT+D + + G++E
Sbjct: 226 PQ---LFWNAGCQMVAL----NFQTVDLSMQINMGMYE 256
>gnl|CDD|234215 TIGR03453, partition_RepA, plasmid partitioning protein RepA.
Members of this family are the RepA (or ParA) protein
involved in replicon partitioning. All known examples
occur in bacterial species with two or more replicons,
on a plasmid or the smaller chromosome. Note that an
apparent exception may be seen as a pseudomolecule from
assembly of an incompletely sequenced genome. Members of
this family belong to a larger family that also includes
the enzyme cobyrinic acid a,c-diamide synthase, but
assignment of that name to members of this family would
be in error [Mobile and extrachromosomal element
functions, Plasmid functions].
Length = 387
Score = 28.0 bits (63), Expect = 7.0
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 14 RDVIRKLK----DLVPPNIEIMKKEMDKLKELKSK 44
++IRK DLVP N+E+M+ E + + L
Sbjct: 179 SEIIRKTYFPGLDLVPGNLELMEFEHETPRALSRG 213
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 27.9 bits (63), Expect = 8.4
Identities = 17/59 (28%), Positives = 27/59 (45%)
Query: 3 RLRIINEIKEQRDVIRKLKDLVPPNIEIMKKEMDKLKELKSKLCRTTNTTVEEHDVEYD 61
RL I+ + E RK P IE +K + DK++++ +T EE V+ D
Sbjct: 528 RLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKID 586
>gnl|CDD|240521 cd13394, Syo1_like, Fungal symportin 1 (syo1) and similar proteins.
This family of eukaryotic proteins includes
Saccharomyces cerevisiae Ydl063c and Chaetomium
thermophilum Syo1, which mediate the co-import of two
ribosomal proteins, Rpl5 and Rpl11 (which both interact
with 5S rRNA) into the nucleus. Import precedes their
association with rRNA and subsequent ribosome assembly
in the nucleolus. The primary structure of syo1 is a
mixture of Armadillo- (ARM, N-terminal part of syo1) and
HEAT-repeats (C-terminal part of syo1).
Length = 597
Score = 28.0 bits (63), Expect = 8.4
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 296 TEVQVYVASAQKNL-LEERMRICSYLWKNGI 325
TEV V A +NL +EE +C +LW+ I
Sbjct: 93 TEVVVEAFGALRNLAIEEGYDVCVHLWRKDI 123
>gnl|CDD|239845 cd04380, RhoGAP_OCRL1, RhoGAP_OCRL1: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain present
in OCRL1-like proteins. OCRL1 (oculocerebrorenal
syndrome of Lowe 1)-like proteins contain two conserved
domains: a central inositol polyphosphate 5-phosphatase
domain and a C-terminal Rho GAP domain, this GAP domain
lacks the catalytic residue and therefore maybe
inactive. OCRL-like proteins are type II inositol
polyphosphate 5-phosphatases that can hydrolyze lipid
PI(4,5)P2 and PI(3,4,5)P3 and soluble Ins(1,4,5)P3 and
Ins(1,3,4,5)P4, but their individual specificities vary.
The functionality of the RhoGAP domain is still unclear.
Small GTPases cluster into distinct families, and all
act as molecular switches, active in their GTP-bound
form but inactive when GDP-bound. The Rho family of
GTPases activates effectors involved in a wide variety
of developmental processes, including regulation of
cytoskeleton formation, cell proliferation and the JNK
signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 220
Score = 27.3 bits (61), Expect = 9.4
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 111 DGLFESCGVPAKQFRTICSSVDKLDKWS 138
+GLFE G+P++ + D LD S
Sbjct: 69 EGLFEEPGLPSEPGELLAEIRDALDTGS 96
>gnl|CDD|241454 cd13300, PH1_TECPR1, Tectonin beta-propeller repeat-containing
protein 1 Pleckstrin homology (PH) domain, repeat 1.
TECPR1 is a tethering factor involved in autophagy. It
promotes the autophagosome fusion with lysosomes by
associating with both the ATG5-ATG12 conjugate and
phosphatidylinositol-3-phosphate (PtdIns3P) present at
the surface of autophagosomes. TECPR1 is also involved
in selective autophagy against bacterial pathogens, by
being required for phagophore/preautophagosomal
structure biogenesis and maturation. It contains 2 DysFN
(Dysferlin domains of unknown function, N-terminal), 2
Hyd_WA domains that is a probably beta-propeller, a
PH-like domain, a TECPR domain, and a DysFC
(C-terminal). The PH domain mediates the binding to
phosphatidylinositol-3-phosphate (PtdIns3P). Binding to
the ATG5-ATG12 conjugate exposes the PH domain, allowing
the association with PtdIns3P. 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 = 121
Score = 26.6 bits (59), Expect = 10.0
Identities = 10/39 (25%), Positives = 17/39 (43%)
Query: 139 WEDVRYEMTQEKGLSKIIADKIGIYVQQHGHKELVEKFM 177
W DVR + Q G+ + IY + K+ + F+
Sbjct: 23 WVDVRVALEQGVGVDGRQDSILFIYYTHYDEKKYIHAFL 61
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 0.137 0.394
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,872,364
Number of extensions: 1656434
Number of successful extensions: 1840
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1807
Number of HSP's successfully gapped: 82
Length of query: 328
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 231
Effective length of database: 6,635,264
Effective search space: 1532745984
Effective search space used: 1532745984
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 (21.7 bits)
S2: 59 (26.5 bits)