RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 007710
(592 letters)
>gnl|CDD|215149 PLN02265, PLN02265, probable phenylalanyl-tRNA synthetase beta
chain.
Length = 597
Score = 1166 bits (3019), Expect = 0.0
Identities = 461/599 (76%), Positives = 523/599 (87%), Gaps = 9/599 (1%)
Query: 1 MPTVSVGRDRLFAALGKSYTKEEFEDLCFCFGIELDDVTTEKAIIRKEKHLDEEGDEN-- 58
MPTVSVGRDRLFAALG++YT+EEF++LCF FGIELDDVTTEKAIIRKEKHLDEE D
Sbjct: 1 MPTVSVGRDRLFAALGRTYTQEEFDELCFEFGIELDDVTTEKAIIRKEKHLDEEEDGGAD 60
Query: 59 -DEEVIYKIEVPANRYDLLCLEGIAQALRVFNKQQEIPKYTLSDVSKDSMLQMHVKPETS 117
DEEVIYKI+VPANRYDLLCLEG+A+ALRVF + IP Y L+++SK S+L+MHVKPETS
Sbjct: 61 DDEEVIYKIDVPANRYDLLCLEGLARALRVFLGTEPIPTYRLAEISKGSILKMHVKPETS 120
Query: 118 SIRPYVVCAVLRDISFDEASYNSFIDLQDKLHQNICRRRTLVAIGTHDLDTLQGPFTYEA 177
IRP+VVCAVLR ++FDEA YNSFIDLQDKLHQNICRRRTLVAIGTHDLDTLQGPFTYEA
Sbjct: 121 LIRPFVVCAVLRGVTFDEARYNSFIDLQDKLHQNICRRRTLVAIGTHDLDTLQGPFTYEA 180
Query: 178 LPPSHINFVPLKQTRDFTADELMEFYKSDLKLKKYLHIIENSPLYPVLYDQNRTVLSLPP 237
LPP INFVPLKQT+ F ADELMEFYKSD+KLKK+LHIIENSP++PV+YD NRTVLSLPP
Sbjct: 181 LPPEDINFVPLKQTKSFRADELMEFYKSDMKLKKFLHIIENSPVFPVIYDSNRTVLSLPP 240
Query: 238 IINGAHSAITLKTKNVFIECTATDLTKAKIVLNTMVTIFSEYCKRKYQVEPVEVVYADGR 297
IINGAHSAITL TKNVFIECTATDLTKAKIVLNTMVT+FSEYC RK++VEPVEVVY DG+
Sbjct: 241 IINGAHSAITLDTKNVFIECTATDLTKAKIVLNTMVTMFSEYCARKFEVEPVEVVYPDGK 300
Query: 298 SYVYPDLSAYNMEVSLSYINHTIGVSLEAEEVTSLLNRMQLHAERSASGNNQWNINVLVP 357
S VYPDLS MEV LSYIN +IGVSL+AEEV SLLN+MQL AE+ S ++ I V VP
Sbjct: 301 STVYPDLSVRTMEVDLSYINSSIGVSLDAEEVASLLNKMQLQAEQ--SSDDGCTIRVSVP 358
Query: 358 PTRSDVLHPCDVMEDVAIAYGYNNIPKRKPASV---KPLALNEFSDLMRLEIAMNGFTEV 414
PTRSD+LHPCDV EDVAIAYGYNNIPKRKP S+ K LN+FSDL+R E+AM GFTEV
Sbjct: 359 PTRSDILHPCDVAEDVAIAYGYNNIPKRKPKSMTVGKQQPLNQFSDLLRAEVAMAGFTEV 418
Query: 415 LTWILCSSKEISTMLNRQTDESTAV-VGNPRTSDFEVVRTTLMPGILKTIGHNKDHPKPI 473
LTWILCS KE MLNR+ D ++AV +GNPR++DFEVVRT+L+PG+LKT+GHNKD PKPI
Sbjct: 419 LTWILCSHKENFAMLNREDDGNSAVIIGNPRSADFEVVRTSLLPGLLKTLGHNKDAPKPI 478
Query: 474 KIYEVGDVVLLDEKKDVGASCRRRLAALYCGANSGFELIHCLVDRIMEVIGTPFVPVGDD 533
K++EV DVVLLDE KDVGA RRLAALYCG SGFE+IH LVDRIMEV+G PFV +GD+
Sbjct: 479 KLFEVSDVVLLDESKDVGARNSRRLAALYCGTTSGFEVIHGLVDRIMEVLGIPFVEIGDN 538
Query: 534 TGYYIQRSDEPEFLPGRQASITHKGKHVGTFGIVHPEVLNNFDISDPCSFMEIDIENFL 592
GYY++ S+EPE+ PGRQASI +KGKHVGTFGIVHPEVLNNFDI DPCSF+E+D+E L
Sbjct: 539 NGYYVEPSNEPEYFPGRQASIIYKGKHVGTFGIVHPEVLNNFDIPDPCSFLELDLEPLL 597
>gnl|CDD|236592 PRK09616, pheT, phenylalanyl-tRNA synthetase subunit beta;
Reviewed.
Length = 552
Score = 472 bits (1218), Expect = e-161
Identities = 219/597 (36%), Positives = 322/597 (53%), Gaps = 53/597 (8%)
Query: 1 MPTVSVGRDRLFAALGKSYTKEEFEDLCFCFGIELDDVTTEKAIIRKEKHLDEEGDENDE 60
MP + V +D L +G +E EDL E+++ D+
Sbjct: 1 MPVIRVNKDDLERLIGIDLEDDELEDLLPMLKCEVEE-------------------IEDD 41
Query: 61 EVIYKIEVPANRYDLLCLEGIAQALR-VFNKQQEIPKYTLSDVSKDSMLQMHVKPETSSI 119
E+ KIE +R DLL +EG+A+ALR + +PKY + KDS +++ V E I
Sbjct: 42 EI--KIEFNPDRPDLLSVEGLARALRGFLGIETGLPKYEV----KDSDVKVEVDEEVPEI 95
Query: 120 RPYVVCAVLRDISFDEASYNSFIDLQDKLHQNICRRRTLVAIGTHDLDTLQGPFTYEALP 179
RPY+ AV+R + D+ + S I LQ+KLH I R+R VAIG HDLD ++ P Y+A+
Sbjct: 96 RPYIAGAVVRGVKLDDEALKSLIQLQEKLHWTIGRKRKKVAIGIHDLDKIKPPIYYKAVD 155
Query: 180 PSHINFVPLKQTRDFTADELMEFYKSDLKLKKYLHIIENSPLYPVLYDQNRTVLSLPPII 239
P FVPL + T E++E + K K+Y H++++ YP++ D VLS PPII
Sbjct: 156 PDEK-FVPLGFDEEMTLREILEKHP---KGKEYGHLLKDFDRYPLIVDSEGNVLSFPPII 211
Query: 240 NGAHSAITLKTKNVFIECTATDLTKAKIVLNTMVTIFSEYCKRKYQVEPVEVVYADGRSY 299
N + +T T+N+FI+ T TDL + LN + T +E R +E V+V+Y DG
Sbjct: 212 NSELTRVTEGTRNLFIDVTGTDLEAVLLALNIIATALAE---RGGTIESVKVIYPDG-EL 267
Query: 300 VYPDLSAYNMEVSLSYINHTIGVSLEAEEVTSLLNRMQLHAERSASGNNQWNINVLVPPT 359
PDL+ EVS+ YIN +G+ L AEE+ LL RM+ AE G++ + V VPP
Sbjct: 268 TTPDLTPRTREVSVEYINKLLGIDLSAEEIIELLERMRYDAE---IGDD--KVKVTVPPY 322
Query: 360 RSDVLHPCDVMEDVAIAYGYNNIPKRKPASV---KPLALNEFSDLMR-LEIAMNGFTEVL 415
R D+LH DV+EDVAIAYGYNN+ P + + + +R L + + GF EV+
Sbjct: 323 RVDILHEVDVIEDVAIAYGYNNLEPELPKVFTIGRLHPIEKLERAIRDLMVGL-GFQEVM 381
Query: 416 TWILCSSKEISTMLNRQTDESTAVVGNPRTSDFEVVRTTLMPGILKTIGHNKDHPKPIKI 475
+ L S + + +N + +E V NP + D+ VVRT+L+P +L+ + +NK P KI
Sbjct: 382 NFTLTSEEVLFEKMNLEPEEDYVEVLNPISEDYTVVRTSLLPSLLEFLSNNKHREYPQKI 441
Query: 476 YEVGDVVLLDEKKDVGASCRRRLAALYCGANSGFELIHCLVDRIMEVIGTPFVPVGDDTG 535
+E+GDVVL+DE + G R+LAA + + F I +V ++ +G
Sbjct: 442 FEIGDVVLIDESTETGTRTERKLAAAIAHSEASFTEIKSVVQALLRELGIE--------- 492
Query: 536 YYIQRSDEPEFLPGRQASITHKGKHVGTFGIVHPEVLNNFDISDPCSFMEIDIENFL 592
Y ++ S+ P F+PGR A I GK +G G +HPEVL NF I P EID+E L
Sbjct: 493 YEVEESEHPSFIPGRCADILVNGKKIGVIGEIHPEVLENFGIEVPVVAFEIDLEALL 549
>gnl|CDD|232989 TIGR00471, pheT_arch, phenylalanyl-tRNA synthetase, beta subunit.
Every known example of the phenylalanyl-tRNA synthetase,
except the monomeric form of mitochondrial, is an alpha
2 beta 2 heterotetramer. The beta subunits break into
two subfamilies that are considerably different in
sequence, length, and pattern of gaps. This model
represents the subfamily that includes the beta subunit
from eukaryotic cytosol, the Archaea, and spirochetes
[Protein synthesis, tRNA aminoacylation].
Length = 551
Score = 458 bits (1181), Expect = e-156
Identities = 213/597 (35%), Positives = 326/597 (54%), Gaps = 51/597 (8%)
Query: 1 MPTVSVGRDRLFAALGKSYTKEEFEDLCFCFGIELDDVTTEKAIIRKEKHLDEEGDENDE 60
MPTV+V +D L L + +++ + D++ E DE
Sbjct: 1 MPTVTVYKDDLEDLL----IGTDRDEILEELPMMGDEI--------------EGFDEESP 42
Query: 61 EVIYKIEVPANRYDLLCLEGIAQALRVFNKQQEIPKYTLSDVSKDSMLQMHVKPETSSIR 120
E+ K+E NR DLL +EG+A++LR + ++ K S K +++ V IR
Sbjct: 43 EI--KVEFNPNRPDLLSVEGLARSLRGYLGIEKGLKSYDS---KKGDVKLTVDESVLQIR 97
Query: 121 PYVVCAVLRDISFDEASYNSFIDLQDKLHQNICRRRTLVAIGTHDLDTLQGPFTYEALPP 180
P++ AV++ I ++ S I+LQ+KLH NI R R VAIG HDLD ++ PF Y+A+ P
Sbjct: 98 PFITGAVVKGIILNDKVLESLIELQEKLHWNIGRNRRKVAIGIHDLDKVEFPFHYKAVSP 157
Query: 181 SHINFVPLKQTRDFTADELMEFYKSDLKLKKYLHIIENSPLYPVLYDQNRTVLSLPPIIN 240
+ I FVPL ++ T DE++E + K +Y HIIE+S +P++ D VLS+PPIIN
Sbjct: 158 NGIKFVPLNSDQEMTPDEILEEHP---KGIRYAHIIEDSDKFPLILDSKDDVLSMPPIIN 214
Query: 241 GAHSAITLKTKNVFIECTATDLTKAKIVLNTMVTIFSEYCKRKYQVEPVEVVYADGRSYV 300
+ +T+ T+N+ I+ T TD T +I LN T+F++ + V VE
Sbjct: 215 SELTKLTVNTRNLLIDVTGTDKTAVEITLNIACTMFADRGDGRITVVEVER---PDEHLG 271
Query: 301 YPDLSAYNMEVSLSYINHTIGVSLEAEEVTSLLNRMQLHAERSASGNNQWNINVLVPPTR 360
P+L+ MEVS+ YIN +G++L A+E+ L +M+L A +S + V++P R
Sbjct: 272 QPNLAPRFMEVSVEYINSLLGLNLSADEIAHSLKKMRLDAVQSDE-----KLKVVIPAYR 326
Query: 361 SDVLHPCDVMEDVAIAYGYNNIPKRKPAS-----VKPLALNEFSDLMRLEIAMNGFTEVL 415
D+LH D++EDVAI YGYNN P P +KP LN+ SD++R + GF EV+
Sbjct: 327 VDILHEVDIIEDVAIGYGYNNFPPELPLINTIGRLKP--LNKVSDIIREIMVGLGFQEVI 384
Query: 416 TWILCSSKEISTMLNRQTDESTAVVGNPRTSDFEVVRTTLMPGILKTIGHNKDHPKPIKI 475
L S + + R D + V NP+T ++ +VRT+L+PG+L+T+ NK H P KI
Sbjct: 385 PLTLTSEEVNFKRM-RIEDNNDVKVANPKTLEYTIVRTSLLPGLLETLSENKHHELPQKI 443
Query: 476 YEVGDVVLLDEKKDVGASCRRRLAALYCGANSGFELIHCLVDRIMEVIGTPFVPVGDDTG 535
+E+GDVV+ D+K + + +LA + + F I +V + +G
Sbjct: 444 FEIGDVVVKDDKSETRSRVVTKLAVGITHSEANFNEIKSIVAALARELG---------IE 494
Query: 536 YYIQRSDEPEFLPGRQASITHKGKHVGTFGIVHPEVLNNFDISDPCSFMEIDIENFL 592
Y I+ S+ P F+PGR A I +GK +G FG +HPEVL NF++ P S E++IE FL
Sbjct: 495 YEIEESEHPSFIPGRGAKIVFEGKAIGHFGEIHPEVLTNFELEFPVSAFEVNIEVFL 551
>gnl|CDD|223150 COG0072, PheT, Phenylalanyl-tRNA synthetase beta subunit
[Translation, ribosomal structure and biogenesis].
Length = 650
Score = 321 bits (825), Expect = e-101
Identities = 155/607 (25%), Positives = 249/607 (41%), Gaps = 77/607 (12%)
Query: 1 MPTVSVGRDRLFAALGKSYTKEEFEDLCFCFGIELDDVTTEKAIIRKEKHLDEEGDENDE 60
MPT+ L + + D GI +
Sbjct: 1 MPTIVREYLDLDDLIIEISITPNRADCLSMLGIARELAAEYDL----------------- 43
Query: 61 EVIYKIEVPANRYDLLCLEGIAQALRVF--NKQQEIPKYTLSDVSKDSMLQMHVKPETSS 118
K+E P R DL EG+A+ + + + P+Y V K VK
Sbjct: 44 ----KLEFPKIR-DLESAEGLARKIFLEIEAGKYACPRYAGR-VIKG------VKVNA-- 89
Query: 119 IRPYVVCAVLRDISFDEASYNSFIDLQDKLHQNICRRRTLVAIGTHDLDTLQGPFTYEAL 178
P + A LR + N+ +D+ + +H + + R IG D + P Y
Sbjct: 90 PSPLWLQARLRGVGIR--PINNLVDITNYVHLELGQPRHAFDIGKIDG---KIPVRYAKE 144
Query: 179 PPSHINFVPLKQTRDFTADELMEFYKSDLKLKKYLHIIENSPLYPVLYDQNRTVLSLPPI 238
+ + F+ K+ T D ++ ++ L L + +S + P D V S PPI
Sbjct: 145 GET-LVFLDGKERELLTGDLVIADHEKGLALA-GVMGGADSEVDPNTTDVLLEVASFPPI 202
Query: 239 INGAHS-AITLKTKNVFIECTATDLTKAKIVLNTMVTIFSEYCKRKYQVEPVEVVYADGR 297
I S + L T+ F D + LN T+ +E C +V V +V D +
Sbjct: 203 IISKTSRRLGLDTEASFRFERGVDPELVEKALNRATTLLAEICG--GEVSSVVIVGGDEK 260
Query: 298 SYVYPDLSAYNMEVSLSYINHTIGVSLEAEEVTSLLNRMQLHAERSASGNNQWNINVLVP 357
+E+ L IN +G+ L AEE+ +L R+ E G + V VP
Sbjct: 261 LTPPR-----KIELRLERINRLLGLELSAEEIEKILKRLGFKVEVKGDG-----LTVTVP 310
Query: 358 PTRSDVLHPCDVMEDVAIAYGYNNIPKRKP-----ASVKPLALNEFSDLMRLEIAMNGFT 412
R D+L D++E+VA YGYNNIP P L +F +R + GF
Sbjct: 311 SYRVDILIEADLIEEVARIYGYNNIPPELPSAFTIGRGGLTPLQKFRRKVRRALVGLGFQ 370
Query: 413 EVLTWILCSSKEISTMLNRQTDESTAVVGNPRTSDFEVVRTTLMPGILKTIGHNKDHPKP 472
EV+T+ L S E + + + DE + NP + ++ V+RT+L+PG+L+ + +NK+ P
Sbjct: 371 EVITYSLTS-PEEAKLFGLENDE-ALELANPISEEYSVLRTSLLPGLLEALSYNKNRKNP 428
Query: 473 -IKIYEVGDVVLLDEKKDVGASCRRRLAALYCG-------ANSGFELIHCLVDRIMEVIG 524
++I+E+GDV + DE+ + LAA G F ++ ++E +G
Sbjct: 429 DVRIFEIGDVFVKDEEAERETRHLAGLAAGLAGEESWQGKRPVDFYDAKGDLEALLEALG 488
Query: 525 TPFVPVGDDTGYYIQRSDEPEFLPGRQASITHKGKHVGTFGIVHPEVLNNFDISDPCSFM 584
Y + ++ P F PGR A+I + +G G +HPEVL FD+ P
Sbjct: 489 V---------EYEFEPAEHPAFHPGRSAAIYLNKEVIGFIGELHPEVLKEFDLPGPVYVF 539
Query: 585 EIDIENF 591
EID++
Sbjct: 540 EIDLDAL 546
>gnl|CDD|234804 PRK00629, pheT, phenylalanyl-tRNA synthetase subunit beta;
Reviewed.
Length = 791
Score = 169 bits (432), Expect = 7e-45
Identities = 98/400 (24%), Positives = 168/400 (42%), Gaps = 59/400 (14%)
Query: 230 RTVLSLPPIINGAHSAITLKTKNVFIEC---TATDLTKAKIVLNTMVTIFSEYCKRKYQ- 285
+ L+L ++ G S +T T NV +E + K L + ++ R ++
Sbjct: 307 KKPLALAGVMGGEDSEVTENTTNVLLESAYFDPVSIRKTARRLG----LRTDASYR-FER 361
Query: 286 -VEPVEVVYA-----------------DGRSYVYPDLSAYNMEVSLSYINHTIGVSLEAE 327
V+P + A +G VYP + + L IN +G + E
Sbjct: 362 GVDPALTLLALERATALILELGGGEVVEGVVDVYPLPKEPTITLRLERINRLLGTEISDE 421
Query: 328 EVTSLLNRMQLHAERSASGNNQWNINVLVPPTRSDVLHPCDVMEDVAIAYGYNNIPKRKP 387
E+ +L R L E + + V VP R D+ D++E+VA YGY+NIP P
Sbjct: 422 EIVDILKR--LGFEVTEVDGDGLT--VTVPSWRFDIEIEEDLVEEVARIYGYDNIPSTPP 477
Query: 388 -ASVKPLALNE---FSDLMRLEIAMNGFTEVLTWILCSSKEISTMLNRQTDESTAVVGNP 443
A++ L E +R +A G+ EV+T+ S E + + + ++ NP
Sbjct: 478 VAALTMGGLTEAQRLLRRLRRALAALGYQEVITYSFVS-PEDAKLFG--LNPEPLLLLNP 534
Query: 444 RTSDFEVVRTTLMPGILKTIGHNKDH-PKPIKIYEVGDVVLLDEKKDVGASCRRRLAALY 502
+ + V+RT+L+PG+L+ + +N + K + ++E+G V L D LA +
Sbjct: 535 ISEELSVMRTSLLPGLLEAVAYNLNRGNKDVALFEIGRVFLPDGDLPRE---PEHLAGVL 591
Query: 503 CGANS----------GFELIHCLVDRIMEVIGTPFVPVGDDTGYYIQRSDEPEFLPGRQA 552
G F + V+ ++E +G P V ++ + PGR A
Sbjct: 592 TGNRVEESWGGKRPVDFFDLKGDVEALLEALGLPEV-------EFVAEFEAAALHPGRSA 644
Query: 553 SITHKGKHVGTFGIVHPEVLNNFDISDPCSFMEIDIENFL 592
I GK +G G +HP+VL D+ E+D++ L
Sbjct: 645 EIYLDGKVIGFIGELHPKVLKKLDLPGRTYVFELDLDALL 684
>gnl|CDD|238392 cd00769, PheRS_beta_core, Phenylalanyl-tRNA synthetase (PheRS) beta
chain core domain. PheRS belongs to class II
aminoacyl-tRNA synthetases (aaRS) based upon its
structure. While class II aaRSs generally aminoacylate
the 3'-OH 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. PheRS is an alpha-2/
beta-2 tetramer. While the alpha chain contains a
catalytic core domain, the beta chain has a
non-catalytic core domain.
Length = 198
Score = 153 bits (390), Expect = 2e-43
Identities = 57/209 (27%), Positives = 96/209 (45%), Gaps = 24/209 (11%)
Query: 395 LNEFSDLMRLEIAMNGFTEVLTWILCSSKEISTMLNRQTDESTAVVGNPRTSDFEVVRTT 454
L + +R +A GF EV+T+ L S +E + + NP + ++ V+RT+
Sbjct: 2 LQKLERKLRRLLAGLGFQEVITYSLTSPEEAELFDG--GLDEAVELSNPLSEEYSVLRTS 59
Query: 455 LMPGILKTIGHNKDHP-KPIKIYEVGDVVLLDEKKDVGASCRRRLAALYCGA-------- 505
L+PG+L + N + KP++++E+G V L DE G LAAL G
Sbjct: 60 LLPGLLDALARNLNRKNKPLRLFEIGRVFLKDED---GPEEEEHLAALLSGNREPESWQG 116
Query: 506 ---NSGFELIHCLVDRIMEVIGTPFVPVGDDTGYYIQRSDEPEFLPGRQASITHKGKHVG 562
F +++ ++ +G + ++ D F PGR A I G+ +G
Sbjct: 117 KGRPVDFYDAKGILEALLRALGIIV-------EFELEELDADLFHPGRSAKIYVNGEVIG 169
Query: 563 TFGIVHPEVLNNFDISDPCSFMEIDIENF 591
G +HPEVL FD+ +P E+D++
Sbjct: 170 FIGELHPEVLKEFDLKEPVYAFELDLDAL 198
>gnl|CDD|232990 TIGR00472, pheT_bact, phenylalanyl-tRNA synthetase, beta subunit,
non-spirochete bacterial. Every known example of the
phenylalanyl-tRNA synthetase, except the monomeric form
of mitochondrial, is an alpha 2 beta 2 heterotetramer.
The beta subunits break into two subfamilies that are
considerably different in sequence, length, and pattern
of gaps. This model represents the subfamily that
includes the beta subunit from Bacteria other than
spirochetes, as well as a chloroplast-encoded form from
Porphyra purpurea. The chloroplast-derived sequence is
considerably shorter at the amino end, however, so This
model was built in fragment mode [Protein synthesis,
tRNA aminoacylation].
Length = 797
Score = 149 bits (379), Expect = 5e-38
Identities = 133/612 (21%), Positives = 242/612 (39%), Gaps = 108/612 (17%)
Query: 33 IELDDVTTEKAIIRKEKHLDEEGDENDEEVIYKIEVPANRYDLLCLEGIAQAL-RVFNKQ 91
I LD+ I + LD++ I ++ + NR D L + GIA+ L +F+
Sbjct: 136 IVLDEDAPLGTDIAEYLGLDDD--------IIEVSITPNRGDCLSILGIARELAALFDLN 187
Query: 92 QEIPKYTLSDVSKDSMLQMHVKPETSSIRPYVVCAVLRDISFDEASYNSFIDLQDKLHQ- 150
E P + ++ ++ E + P+ + V++ + S + L+++L +
Sbjct: 188 LETPVPFEPETTETIDEGFKIEIEDPEVCPFYLGRVIKGVKVKP----SPLWLKERLRRS 243
Query: 151 ------NICRRRTLVAIGT------HDLDTLQGPFTYEALPPSHINFVPLKQTRDFTADE 198
NI V + D D ++G +A E
Sbjct: 244 GIRPINNIVDITNYVMLELGQPLHAFDADKIEGNIVVR------------------SAKE 285
Query: 199 LMEFYKSDLKLKKYLHIIENSPLYPVLYDQNRTVLSLPPIINGAHSAITLKTKNVFIEC- 257
F + L K+ ++ L V+ D + L++ ++ G S +T T N+F+E
Sbjct: 286 GESF--TTLDGKER--ELKKGDL--VIADDKKP-LAIAGVMGGKESGVTDTTTNIFLESA 338
Query: 258 --TATDLTKAKIVLNTMVTIFSEYCKRKYQ-VEPVEVVYA----------------DGRS 298
+ K L I ++ R + V+P A
Sbjct: 339 YFNPESIRKTARRLG----ISTDSSYRFERGVDPELTELALDRALNLILEIFGGEVISVV 394
Query: 299 YVYPDLSAYNMEVSLSY--INHTIGVSLEAEEVTSLLNRMQLHAERSASGNNQWNINVLV 356
A ++SL +N +G+ L EEV +L R L + + V V
Sbjct: 395 SDNYKEKAKEKKISLRIKKLNKILGIELSDEEVRDILKR--LGFKVEKQKDG---WEVTV 449
Query: 357 PPTRSDVLHPCDVMEDVAIAYGYNNIPKRKPASVKPLALN--EFSDLMRLEIAMN--GFT 412
P R D+ D++E++A YGY+NIP + L N + L +L + G
Sbjct: 450 PSYRHDIEIEEDLIEEIARIYGYDNIPAEPLSVSSKLNKNNENYLLLRKLRTLLVGLGLN 509
Query: 413 EVLTWILCSSKEISTMLNRQTDESTAVVGNPRTSDFEVVRTTLMPGILKTIGHNKDHPKP 472
EV+T+ ++ N E+ + NP +++ V+RT+L+P +L+ + +N++
Sbjct: 510 EVITYSFVDPEKAEK-FNFPKLENLVEIKNPLSNERSVLRTSLLPSLLEVLAYNQNRKNK 568
Query: 473 -IKIYEVGDVVLLDEKKDVGASCRRRLAALYCG-----------ANSGFELIHCLVDRIM 520
+KI+E+G V K + RLA L G F + V+ ++
Sbjct: 569 DVKIFEIGKVF---AKDGEAVKEQLRLAILISGEKNPSSWNHKEEKVDFYDLKGDVESLL 625
Query: 521 EVIGTPFVPVGDDTGYYIQRSDEPEFLPGRQASITHKGKHVGTFGIVHPEVLNNFDISDP 580
E++G D Y+ ++ E PG+ A+I KGK +G G +HPE+ +D+ +P
Sbjct: 626 ELLGL------SDDVYFKNTAENEELHPGQSATIYLKGKKIGFIGELHPEIAKKYDLKEP 679
Query: 581 CSFMEIDIENFL 592
E+D++ L
Sbjct: 680 TFVFELDLDRLL 691
>gnl|CDD|214876 smart00873, B3_4, B3/4 domain. This domain is found in tRNA
synthetase beta subunits as well as in some non tRNA
synthetase proteins.
Length = 174
Score = 107 bits (270), Expect = 4e-27
Identities = 32/179 (17%), Positives = 65/179 (36%), Gaps = 24/179 (13%)
Query: 120 RPYVVCAVLRDISFDEASYNSFIDLQDKLHQNICRRRTLVAIGTHDLDTLQGPFTYEALP 179
P + V+R + S LQ++LH+ R + + +L+ A
Sbjct: 1 CPRYLGRVIRGVKNT---RPSPEWLQERLHRAGIRP-INNVVDITNYVSLETGQPLHAFD 56
Query: 180 PSHI--NFVPLKQTRDFTADELMEFYKSDLKLKKYLHIIENSPLYPVLYD---------- 227
I +PL++ ++ ++ + +L + +I + L
Sbjct: 57 LDKIKGKDIPLRRAKE--GEKFETLDGKEYELDEGDLVIADDEGPLALAGVMGGEESEVT 114
Query: 228 QNRTVLSLPPIINGAHS-AITLKTKNVFIECTA-----TDLTKAKIVLNTMVTIFSEYC 280
+N TV+ L P I + IT +T N+F + + D ++ L+ + E C
Sbjct: 115 ENTTVIFLEPAIFSPRTIRITARTLNLFTDASGRFERGVDPELVELALDRAAALLLEIC 173
>gnl|CDD|197942 smart00874, B5, tRNA synthetase B5 domain. This domain is found in
phenylalanine-tRNA synthetase beta subunits.
Length = 68
Score = 78.3 bits (194), Expect = 4e-18
Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 309 MEVSLSYINHTIGVSLEAEEVTSLLNRMQLHAERSASGNNQWNINVLVPPTRSDVLHPCD 368
+ + L IN +G+ + AEE+ +L R+ E S + V VP R D+L D
Sbjct: 3 ITLRLERINRLLGLEILAEEIEEILKRLGFEVEVSGDT-----LEVTVPSYRFDILIEAD 57
Query: 369 VMEDVAIAYGY 379
++E+VA YGY
Sbjct: 58 LIEEVARIYGY 68
>gnl|CDD|202662 pfam03483, B3_4, B3/4 domain. This domain is found in tRNA
synthetase beta subunits as well as in some non tRNA
synthetase proteins.
Length = 159
Score = 76.8 bits (190), Expect = 1e-16
Identities = 24/170 (14%), Positives = 49/170 (28%), Gaps = 56/170 (32%)
Query: 137 SYNSFIDLQDKLHQNICRRRTLVAIGTHDLDTLQGPFTYEALPPSHINFVPLKQTRDFTA 196
N+ +D+ + + + + + DLD + G V
Sbjct: 19 PINNVVDITNYVMLELGQ-----PLHAFDLDKIAGDIV-----------VR----LAKGG 58
Query: 197 DELMEFYKSDLKLKKYLHIIENSPLYPVLYDQNRTVLSLPPIINGAHSAITLKTKNVFIE 256
++ + +L P V+ D + ++L I+ G S +T T N+F+E
Sbjct: 59 EKFTTLDGKERELD---------PGDLVIADDDG-PVALAGIMGGEESEVTEDTTNIFLE 108
Query: 257 CTA--------------------------TDLTKAKIVLNTMVTIFSEYC 280
D ++ L+ + E C
Sbjct: 109 SAYFDPVAIRKTSRKLGLRTDASYRFERGVDPELVELALDRATALILELC 158
>gnl|CDD|202663 pfam03484, B5, tRNA synthetase B5 domain. This domain is found in
phenylalanine-tRNA synthetase beta subunits.
Length = 70
Score = 72.2 bits (178), Expect = 6e-16
Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 309 MEVSLSYINHTIGVSLEAEEVTSLLNRMQLHAERSASGNNQWNINVLVPPTRSDVLHPCD 368
+ + L IN +G+ L EE+ +L R+ E S + V VP R D+LH D
Sbjct: 4 ITLDLEKINRLLGIELSPEEIKKILKRLGFKVEVSDEDT----LKVTVPSYRPDILHEVD 59
Query: 369 VMEDVAIAYGY 379
++E++A YGY
Sbjct: 60 LIEEIARLYGY 70
>gnl|CDD|214391 CHL00192, syfB, phenylalanyl-tRNA synthetase beta chain;
Provisional.
Length = 704
Score = 60.5 bits (147), Expect = 2e-09
Identities = 116/594 (19%), Positives = 214/594 (36%), Gaps = 102/594 (17%)
Query: 57 ENDEEVIYKIEVP--ANRYDLLCLEGIAQALR-VFNKQQEIPKYTLSDVSKDSMLQMHVK 113
+ E +++ ANR D+L ++G+++ + +FN KY +S +K
Sbjct: 40 KIGGESDIILDISSTANRSDVLSIQGLSREISALFNSDPIKLKYYNPSIS----WFDKLK 95
Query: 114 PETSSIRPYVVCAVLRDISFDEASYNSFID-LQDKLHQNICRRRTLVAIGTHDLDTLQGP 172
S+ + C++ + + LQ++L + G L+ L
Sbjct: 96 NLISNDSSKLNCSMFIAVIIENIEIKDSPKWLQNRL----------SSSGFKSLNNLTDI 145
Query: 173 FTYEALPPSH-INFVPLKQTRDFTADELMEFYKSDLKLKKYLHIIENSPLY----PVLYD 227
Y L I L + + S L+K I NS +L
Sbjct: 146 QNYIMLETGQPIEIYDLDKIYSKNTTSSLAL-SSKFALQKSSFIASNSKNIELENNILVV 204
Query: 228 Q-NRTVLSLPPIINGAHSAITLKTKNVFIE---CTATDLTKAKIVLNTMVTIFSEYCKRK 283
Q N ++S+ II+ TK++ IE A + K+ L Y K
Sbjct: 205 QANNVIISIAGIISNEEIICDKNTKSILIEASIFDAAVIRKSSRKLGLRTDRSIRYEKSL 264
Query: 284 YQVEPVEVVY-------------ADGRSYVYPDLSAYNMEVSLSY-----------INHT 319
+E Y ++Y + + + LSY IN
Sbjct: 265 KNDNLLEAYYRLVSLLRILNPKLKCKFHFIYKKIKNSSRRIKLSYKKIKDILGPIKINTN 324
Query: 320 IGVSLEAEEVTSLLNRMQLHAERSASGNNQWNINVLVPPTRS-DVLHPCDVMEDVAIAYG 378
L +E+T+ L R+ + + N VL+P R D++ DV+E++A YG
Sbjct: 325 T-RYLSPKEITNALKRLNFKITYD---SLKLNWEVLIPSYRKDDIVREIDVIEEIARIYG 380
Query: 379 YNNIPKRKPASVKPLALNEFSDLMR---LEIAMN-GFTEVLTWILCSSK-----EISTML 429
+NN + P ++K + + R N G TE++ + L + EI
Sbjct: 381 FNNFLSKLP-NIKFIGRLDIDYNTRDKIRSYLRNLGLTELIHYSLVKQESFSKNEIK--- 436
Query: 430 NRQTDESTAVVGNPRTSDFEVVRTTLMPGILKTIGHN-KDHPKPIKIYEVGDVVLLDEKK 488
+ NP D+ +R++L+PG+++ + N K ++ +E+G V LD
Sbjct: 437 ----------LKNPLIKDYSTLRSSLLPGLIEAVQENLKQGNSTLEGFEIGHVFNLDSSS 486
Query: 489 DVGASCRRRLAALYCGA----NSGFELIHCL--------VDRIMEVIGTPFVPVGDDTGY 536
+ + LA G +S E L ++ + + P
Sbjct: 487 IIEET---ELAGGIFGGIDIRSSWSEKAQSLNWFEAKGIIENFFQKLNLPIYWKKYSDLD 543
Query: 537 YIQRSDEPEFLPGRQASI-THKGKHVGTFGIVHPEVLNNFDISDPCSFMEIDIE 589
++ F P + I G+ +G FG +HP + N +++ EI+++
Sbjct: 544 -----EKINFHPYCTSEIFLSNGQKIGIFGQLHPLLANKLNLNTEIYLFEINLD 592
>gnl|CDD|163697 cd08066, MPN_AMSH_like, Mov34/MPN/PAD-1 family. AMSH (associated
molecule with the Src homology 3 domain (SH3) of STAM
(signal-transducing adapter molecule, also known as
STAMBP)) and AMSH-like proteins (AMSH-LP) are members of
JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent
ubiquitin isopeptidase activity. AMSH specifically
cleaves Lys 63 and not Lys48-linked polyubiquitin
(poly-Ub) chains, thus facilitating the recycling and
subsequent trafficking of receptors to the cell surface.
AMSH and AMSH-LP are anchored on the early endosomal
membrane via interaction with the clathrin coat. AMSH
shares a common SH3-binding site with another endosomal
DUB, UBPY (ubiquitin-specific protease Y; also known as
USP8), the latter being a cysteine protease that does
not discriminate between Lys48 and Lys63-linked
ubiquitin. AMSH is involved in the degradation of EGF
receptor (EGFR) and possibly other ubiquitinated
endocytosed proteins. AMSH also interacts with CHMP1,
CHMP2, and CHMP3 proteins, all of which are components
of ESCRT-III, suggested to be required for EGFR
down-regulation. The function of AMSH-LP has not been
elucidated; however, it exhibits two fundamentally
distinct features from AMSH: first, there is a
substitution in the critical amino acid residue in the
SH3-binding motif (SBM) in the human AMSH-LP, but not in
its mouse ortholog, and lacks STAM-binding ability;
second, AMSH-LP lacks the ability to interact with CHMP
proteins. It is therefore likely that AMSH and AMSH-LP
play different roles on early endosomes.
Length = 173
Score = 32.6 bits (75), Expect = 0.31
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 435 ESTAVVGNPRTSDFEVVRTTLMPGILKTIGHNKD-----HPKPIKIYEVGDVVLLDEKKD 489
E+ A+V P+ ++F + R T PG L I + K HPK +YE V+ ++
Sbjct: 108 EAIAIVCAPKYNEFGIFRLTDPPG-LDEILNCKKTGFHPHPKDPPLYEDCGHVIWKDQLK 166
Query: 490 V 490
V
Sbjct: 167 V 167
>gnl|CDD|216483 pfam01409, tRNA-synt_2d, tRNA synthetases class II core domain (F).
Other tRNA synthetase sub-families are too dissimilar
to be included. This family includes only
phenylalanyl-tRNA synthetases. This is the core
catalytic domain.
Length = 245
Score = 31.4 bits (72), Expect = 0.95
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 561 VGTFGIVHPEVLNNFDISD 579
+G G+VHP VL I +
Sbjct: 189 IGGAGMVHPNVLEAVGIDE 207
>gnl|CDD|200600 cd10978, CE4_Sll1306_like, Putative catalytic domain of
Synechocystis sp. Sll1306 protein and other bacterial
homologs. The family contains Synechocystis sp. Sll1306
protein and uncharacterized bacterial polysaccharide
deacetylases. Although their biological function remains
unknown, they show very high sequence homology to the
catalytic domain of bacterial PuuE (purine utilization
E) allantoinases. PuuE allantoinase specifically
catalyzes the hydrolysis of (S)-allantoin into allantoic
acid. It functions as a homotetramer. Its monomer is
composed of a 7-stranded barrel with detectable sequence
similarity to the 6-stranded barrel NodB homology domain
of polysaccharide deacetylase-like proteins in the CE4
superfamily, which removes N-linked or O-linked acetyl
groups from cell wall polysaccharides. PuuE allantoinase
appears to be metal-independent and acts on a small
substrate molecule, which is distinct from the common
feature of polysaccharide deacetylases that are normally
metal ion dependent and recognize multimeric substrates.
Length = 271
Score = 31.3 bits (71), Expect = 1.3
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 9/76 (11%)
Query: 97 YTLSDVSKDSMLQMHVKPETSSIRPYVVCAVLRDI-SFDEASYNSFIDLQ------DKLH 149
Y + DVS+D + V + + PY + DI F+ +Y+S LQ D+L+
Sbjct: 157 YHIDDVSRDEPFIIPVNGKDFVVVPYTL--RNNDIVRFEGRAYSSDAYLQELKDEFDQLY 214
Query: 150 QNICRRRTLVAIGTHD 165
+ RR +++I HD
Sbjct: 215 EEAAHRRRMMSISLHD 230
>gnl|CDD|234924 PRK01229, PRK01229, N-glycosylase/DNA lyase; Provisional.
Length = 208
Score = 29.9 bits (68), Expect = 3.3
Identities = 26/109 (23%), Positives = 46/109 (42%), Gaps = 15/109 (13%)
Query: 12 FAALGKSYTKEE-FEDLCFCFGIELDDVTTE--KAI--IRKEKHLDEEGDENDEEVIYKI 66
F LG+ +E+ F +L FC + T A I+ +K + + EE + +
Sbjct: 25 FKLLGEKGDEEDLFSELSFC-------ILTANSSAEGGIKAQKEIGDGFLYLSEEELEEK 77
Query: 67 --EVPANRYDLLCLEGIAQALRVFNKQQEIPKYTLSDVSKDSMLQMHVK 113
EV +R+ E I +A +++ K +EI K L ++K
Sbjct: 78 LKEV-GHRFYNKRAEYIVEARKLYGKLKEIIKADKDQFEAREFLVKNIK 125
>gnl|CDD|233874 TIGR02456, treS_nterm, trehalose synthase. Trehalose synthase
interconverts maltose and alpha, alpha-trehalose by
transglucosylation. This is one of at least three
mechanisms for biosynthesis of trehalose, an important
and widespread compatible solute. However, it is not
driven by phosphate activation of sugars and its
physiological role may tend toward trehalose
degradation. This view is accentuated by numerous
examples of fusion to a probable maltokinase domain. The
sequence region described by this model is found both as
the whole of a trehalose synthase and as the N-terminal
region of a larger fusion protein that includes
trehalose synthase activity. Several of these fused
trehalose synthases have a domain homologous to proteins
with maltokinase activity from Actinoplanes
missouriensis and Streptomyces coelicolor
(PMID:15378530) [Energy metabolism, Biosynthesis and
degradation of polysaccharides].
Length = 539
Score = 30.1 bits (68), Expect = 3.4
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 8/61 (13%)
Query: 495 RRRLAALYCGANSGFELIHCLVDRIMEVIGTPFVPVGDDTGYYIQRSDEPEFLPGRQASI 554
RRRLA L EL+ L ++ + G+P + GD+ G D +L R
Sbjct: 339 RRRLAPLLDNDRRRIELLTAL---LLSLPGSPILYYGDEIGM----GDNI-WLGDRNGVR 390
Query: 555 T 555
T
Sbjct: 391 T 391
>gnl|CDD|218563 pfam05343, Peptidase_M42, M42 glutamyl aminopeptidase. These
peptidases are found in Archaea and Bacteria. The
example in Lactococcus lactis, PepA, aids growth on
milk. Pyrococcus horikoshii contain a thermostable
de-blocking aminopeptidase member of this family used
commercially for N-terminal protein sequencing.
Length = 292
Score = 29.8 bits (68), Expect = 3.5
Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 12/65 (18%)
Query: 527 FVPVGDDTGYYIQRSDEPEFLPGRQASI-THKGKHVGTFGIVHPEVLNNFDISDPCSFME 585
F P+G G+ P+ L G++ +I T KGK G G P +L + + P E
Sbjct: 40 FTPIG---GWD------PQVLEGQRVTIYTDKGKIPGVIGSKPPHLLKDAERKKPIDIDE 90
Query: 586 --IDI 588
IDI
Sbjct: 91 LFIDI 95
>gnl|CDD|188126 TIGR01283, nifE, nitrogenase molybdenum-iron cofactor biosynthesis
protein NifE. This protein is part of the NifEN complex
involved in biosynthesis of the molybdenum-iron cofactor
used by the homologous NifDK complex of nitrogenase. In
a few species, the protein is found as a NifEN fusion
protein [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other, Central intermediary metabolism,
Nitrogen fixation].
Length = 453
Score = 30.0 bits (68), Expect = 4.3
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 495 RRRL----AALYCGANSGFELIHCLVDRIMEVIGT 525
R RL AA+Y G + ++ L D MEV+ T
Sbjct: 318 RERLKGKKAAIYTGGVKSWSVVSALQDLGMEVVAT 352
>gnl|CDD|241092 cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 in UHM domain of
poly(U)-binding-splicing factor PUF60 and similar
proteins. This subgroup corresponds to the RRM3 of
PUF60, also termed FUSE-binding protein-interacting
repressor (FBP-interacting repressor or FIR), or
Ro-binding protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1), an essential splicing factor that functions
as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors another RRM and binds to tryptophan-containing
linear peptide motifs (UHM ligand motifs, ULMs) in
several nuclear proteins. The research indicates that
PUF60 binds FUSE as a dimer, and only the first two RRM
domains participate in the single-stranded DNA
recognition. .
Length = 98
Score = 27.8 bits (62), Expect = 4.7
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 10/47 (21%)
Query: 22 EEFEDLCFCFGIELDDVTTEKAIIRKEKHLDEEGDENDEEVIYKIEV 68
E + C FG + II +EK +G+E D E+I KI V
Sbjct: 21 GEVTEECGKFG------AVNRVIIYQEK----QGEEEDAEIIVKIFV 57
>gnl|CDD|240277 PTZ00118, PTZ00118, 40S ribosomal protein S4; Provisional.
Length = 262
Score = 28.7 bits (64), Expect = 7.2
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 549 GRQASITHKGKHVGTFGIVH 568
GR +I K KH G+F ++H
Sbjct: 190 GRVGTIVSKEKHPGSFDLIH 209
>gnl|CDD|217039 pfam02446, Glyco_hydro_77, 4-alpha-glucanotransferase. These
enzymes EC:2.4.1.25 transfer a segment of a
(1,4)-alpha-D-glucan to a new 4-position in an acceptor,
which may be glucose or (1,4)-alpha-D-glucan.
Length = 493
Score = 28.8 bits (65), Expect = 8.0
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 154 RRRTLVAIGTHDLDTLQG 171
++V GTHD DTL+G
Sbjct: 374 PENSVVYTGTHDNDTLRG 391
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 0.400
Gapped
Lambda K H
0.267 0.0838 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 30,488,407
Number of extensions: 3016696
Number of successful extensions: 2704
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2643
Number of HSP's successfully gapped: 37
Length of query: 592
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 490
Effective length of database: 6,413,494
Effective search space: 3142612060
Effective search space used: 3142612060
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 62 (27.5 bits)