RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11602
(1083 letters)
>gnl|CDD|215364 PLN02678, PLN02678, seryl-tRNA synthetase.
Length = 448
Score = 359 bits (922), Expect = e-113
Identities = 139/231 (60%), Positives = 167/231 (72%), Gaps = 17/231 (7%)
Query: 17 ELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQEVGSHGRDTRGIFRVHQF 76
E DDKYLIATSEQP+CA HR W+ LPIRY G STCFR+E GSHGRDT GIFRVHQF
Sbjct: 226 EGDDKYLIATSEQPLCAYHRGDWIDPKELPIRYAGYSTCFRKEAGSHGRDTLGIFRVHQF 285
Query: 77 EKVEQFVLTSPHDDESWKMLDEMIQNSEEFYADLGIAYRVVNIVSGALNHAAAKKLDLEA 136
EKVEQF +TSP+ +ESW+M +EM++NSE+FY LGI Y+VV+IVSGALN AAAKK DLEA
Sbjct: 286 EKVEQFCITSPNGNESWEMHEEMLKNSEDFYQSLGIPYQVVSIVSGALNDAAAKKYDLEA 345
Query: 137 WFPGSGAFRELVSCSNCLDYQSRRLLVRYGQTKQ----KIY-----ATACATTRVICAIL 187
WFP S +RELVSCSNC DYQSRRL +RYGQ K K Y +T AT R +C IL
Sbjct: 346 WFPASKTYRELVSCSNCTDYQSRRLEIRYGQKKSNEQTKQYVHLLNSTLTATERTLCCIL 405
Query: 188 ETHQTETGVRIPDCLRKFVPAVYLNEAGEIPFVKTAPIDEEETKKQKKQKE 238
E +QTE GVR+P+ L+ F+ + +PF K P + K +KK+K+
Sbjct: 406 ENYQTEDGVRVPEVLQPFMGGIEF-----LPFKKKPP---AKGKGKKKKKK 448
Score = 280 bits (718), Expect = 2e-84
Identities = 104/182 (57%), Positives = 133/182 (73%), Gaps = 8/182 (4%)
Query: 303 DTRGIFRVHQFEKVEQFVLTSPHDDESWKTLDEMIQNSEEFYADLGIAYRVVNIVSGALN 362
DT GIFRVHQFEKVEQF +TSP+ +ESW+ +EM++NSE+FY LGI Y+VV+IVSGALN
Sbjct: 275 DTLGIFRVHQFEKVEQFCITSPNGNESWEMHEEMLKNSEDFYQSLGIPYQVVSIVSGALN 334
Query: 363 HAAAKKLDLEAWFPGSGAFRELVSCSNCLAYQSRRLLVRYGQTKKMNEKIEFVHMLNATA 422
AAAKK DLEAWFP S +RELVSCSNC YQSRRL +RYGQ K + ++VH+LN+T
Sbjct: 335 DAAAKKYDLEAWFPASKTYRELVSCSNCTDYQSRRLEIRYGQKKSNEQTKQYVHLLNSTL 394
Query: 423 CATTRVICAILETHQTETGVRIPDCLRKFVPAVYVNEAGEIPFVKTAPIDEEETKKQKKQ 482
AT R +C ILE +QTE GVR+P+ L+ F+ + +PF K P + K +KK+
Sbjct: 395 TATERTLCCILENYQTEDGVRVPEVLQPFMGGIEF-----LPFKKKPP---AKGKGKKKK 446
Query: 483 KE 484
K+
Sbjct: 447 KK 448
Score = 82.8 bits (205), Expect = 2e-16
Identities = 30/43 (69%), Positives = 33/43 (76%)
Query: 533 ELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQE 575
E DDKYLIATSEQP+CA HR W+ LPIRY G STCFR+E
Sbjct: 226 EGDDKYLIATSEQPLCAYHRGDWIDPKELPIRYAGYSTCFRKE 268
>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 = 334 bits (859), Expect = e-106
Identities = 116/213 (54%), Positives = 144/213 (67%), Gaps = 15/213 (7%)
Query: 6 EKVGDSAPEKDEL-----DDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQEV 60
E G ++L +D YLIAT+E P+ A+HRD L E LP++Y G S CFR+E
Sbjct: 86 EGTGQLPKFDEQLYKVEGEDLYLIATAEVPLAALHRDEILEEEELPLKYAGYSPCFRKEA 145
Query: 61 GSHGRDTRGIFRVHQFEKVEQFVLTSPHDDESWKMLDEMIQNSEEFYADLGIAYRVVNIV 120
GS GRDTRG+FRVHQFEKVEQFV T P +ESW+ L+E+I N+EE +LG+ YRVVNI
Sbjct: 146 GSAGRDTRGLFRVHQFEKVEQFVFTKP--EESWEELEELISNAEEILQELGLPYRVVNIC 203
Query: 121 SGALNHAAAKKLDLEAWFPGSGAFRELVSCSNCLDYQSRRLLVRYGQTK--QKIY----- 173
+G L AAAKK D+EAW PG G +RE+ SCSNC D+Q+RRL +RY K +K Y
Sbjct: 204 TGDLGFAAAKKYDIEAWMPGQGKYREISSCSNCTDFQARRLNIRYRDKKDGKKQYVHTLN 263
Query: 174 ATACATTRVICAILETHQTETG-VRIPDCLRKF 205
TA AT R I AILE +QTE G V IP+ LR +
Sbjct: 264 GTALATPRTIVAILENYQTEDGSVVIPEVLRPY 296
Score = 263 bits (675), Expect = 3e-80
Identities = 88/150 (58%), Positives = 108/150 (72%), Gaps = 5/150 (3%)
Query: 303 DTRGIFRVHQFEKVEQFVLTSPHDDESWKTLDEMIQNSEEFYADLGIAYRVVNIVSGALN 362
DTRG+FRVHQFEKVEQFV T P +ESW+ L+E+I N+EE +LG+ YRVVNI +G L
Sbjct: 151 DTRGLFRVHQFEKVEQFVFTKP--EESWEELEELISNAEEILQELGLPYRVVNICTGDLG 208
Query: 363 HAAAKKLDLEAWFPGSGAFRELVSCSNCLAYQSRRLLVRYGQTKKMNEKIEFVHMLNATA 422
AAAKK D+EAW PG G +RE+ SCSNC +Q+RRL +RY K K ++VH LN TA
Sbjct: 209 FAAAKKYDIEAWMPGQGKYREISSCSNCTDFQARRLNIRYRDKKDG--KKQYVHTLNGTA 266
Query: 423 CATTRVICAILETHQTETG-VRIPDCLRKF 451
AT R I AILE +QTE G V IP+ LR +
Sbjct: 267 LATPRTIVAILENYQTEDGSVVIPEVLRPY 296
Score = 79.1 bits (196), Expect = 7e-16
Identities = 28/70 (40%), Positives = 40/70 (57%), Gaps = 8/70 (11%)
Query: 515 REVIGKGEKVGDSAPEKDEL-----DDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVS 569
+EV+ E G ++L +D YLIAT+E P+ A+HRD L E LP++Y G S
Sbjct: 82 KEVM---EGTGQLPKFDEQLYKVEGEDLYLIATAEVPLAALHRDEILEEEELPLKYAGYS 138
Query: 570 TCFRQECDAG 579
CFR+E +
Sbjct: 139 PCFRKEAGSA 148
>gnl|CDD|235461 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 269 bits (691), Expect = 1e-80
Identities = 88/199 (44%), Positives = 116/199 (58%), Gaps = 10/199 (5%)
Query: 15 KDELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQEVGSHGRDTRGIFRVH 74
K E DD YLI T+E P+ +HRD L E LP++Y S CFR E GS GRDTRG+ RVH
Sbjct: 219 KIEDDDLYLIPTAEVPLTNLHRDEILDEEELPLKYTAYSPCFRSEAGSAGRDTRGLIRVH 278
Query: 75 QFEKVEQFVLTSPHDDESWKMLDEMIQNSEEFYADLGIAYRVVNIVSGALNHAAAKKLDL 134
QF+KVE T P ++S+ L+E+ N+EE L + YRVV + +G L +AAK DL
Sbjct: 279 QFDKVELVKFTKP--EDSYAELEELTANAEEILQKLELPYRVVLLCTGDLGFSAAKTYDL 336
Query: 135 EAWFPGSGAFRELVSCSNCLDYQSRRLLVRY--GQTKQKIYA-----TACATTRVICAIL 187
E W P +RE+ SCSNC D+Q+RR +RY + + A R + AIL
Sbjct: 337 EVWLPSQNTYREISSCSNCTDFQARRANIRYRDEGDGKPELVHTLNGSGLAVGRTLVAIL 396
Query: 188 ETHQTETG-VRIPDCLRKF 205
E +Q G V IP+ LR +
Sbjct: 397 ENYQQADGSVTIPEVLRPY 415
Score = 214 bits (547), Expect = 7e-61
Identities = 66/150 (44%), Positives = 90/150 (60%), Gaps = 5/150 (3%)
Query: 303 DTRGIFRVHQFEKVEQFVLTSPHDDESWKTLDEMIQNSEEFYADLGIAYRVVNIVSGALN 362
DTRG+ RVHQF+KVE T P ++S+ L+E+ N+EE L + YRVV + +G L
Sbjct: 270 DTRGLIRVHQFDKVELVKFTKP--EDSYAELEELTANAEEILQKLELPYRVVLLCTGDLG 327
Query: 363 HAAAKKLDLEAWFPGSGAFRELVSCSNCLAYQSRRLLVRYGQTKKMNEKIEFVHMLNATA 422
+AAK DLE W P +RE+ SCSNC +Q+RR +RY + + K E VH LN +
Sbjct: 328 FSAAKTYDLEVWLPSQNTYREISSCSNCTDFQARRANIRY--RDEGDGKPELVHTLNGSG 385
Query: 423 CATTRVICAILETHQTETG-VRIPDCLRKF 451
A R + AILE +Q G V IP+ LR +
Sbjct: 386 LAVGRTLVAILENYQQADGSVTIPEVLRPY 415
Score = 64.7 bits (159), Expect = 1e-10
Identities = 25/49 (51%), Positives = 30/49 (61%), Gaps = 2/49 (4%)
Query: 531 KDELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQECDAG 579
K E DD YLI T+E P+ +HRD L E LP++Y S CFR E AG
Sbjct: 219 KIEDDDLYLIPTAEVPLTNLHRDEILDEEELPLKYTAYSPCFRSE--AG 265
>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 = 264 bits (677), Expect = 6e-79
Identities = 96/199 (48%), Positives = 124/199 (62%), Gaps = 10/199 (5%)
Query: 15 KDELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQEVGSHGRDTRGIFRVH 74
K E D YLI T+E P+ +HR+ L E LPI+Y S CFR E GS+G+DT+G+ RVH
Sbjct: 221 KLEDTDLYLIPTAEVPLTNLHRNEILEEEELPIKYTAHSPCFRSEAGSYGKDTKGLIRVH 280
Query: 75 QFEKVEQFVLTSPHDDESWKMLDEMIQNSEEFYADLGIAYRVVNIVSGALNHAAAKKLDL 134
QF KVE P +ES + L+EM ++E+ +L + YRVVN+ SG L +AAKK DL
Sbjct: 281 QFNKVELVKFCKP--EESAEELEEMTSDAEQILQELELPYRVVNLCSGDLGFSAAKKYDL 338
Query: 135 EAWFPGSGAFRELVSCSNCLDYQSRRLLVRYG--QTKQKIYA-----TACATTRVICAIL 187
E W PG +RE+ SCSNC D+Q+RRL +RY + Y TA A R I AIL
Sbjct: 339 EVWMPGQNTYREISSCSNCTDFQARRLNIRYKDKNKGKNKYVHTLNGTALAIGRTIVAIL 398
Query: 188 ETHQTETG-VRIPDCLRKF 205
E +QTE G V IP+ LRK+
Sbjct: 399 ENYQTEDGSVEIPEVLRKY 417
Score = 206 bits (526), Expect = 3e-58
Identities = 75/150 (50%), Positives = 97/150 (64%), Gaps = 5/150 (3%)
Query: 303 DTRGIFRVHQFEKVEQFVLTSPHDDESWKTLDEMIQNSEEFYADLGIAYRVVNIVSGALN 362
DT+G+ RVHQF KVE P +ES + L+EM ++E+ +L + YRVVN+ SG L
Sbjct: 272 DTKGLIRVHQFNKVELVKFCKP--EESAEELEEMTSDAEQILQELELPYRVVNLCSGDLG 329
Query: 363 HAAAKKLDLEAWFPGSGAFRELVSCSNCLAYQSRRLLVRYGQTKKMNEKIEFVHMLNATA 422
+AAKK DLE W PG +RE+ SCSNC +Q+RRL +RY K K ++VH LN TA
Sbjct: 330 FSAAKKYDLEVWMPGQNTYREISSCSNCTDFQARRLNIRYKDKNK--GKNKYVHTLNGTA 387
Query: 423 CATTRVICAILETHQTETG-VRIPDCLRKF 451
A R I AILE +QTE G V IP+ LRK+
Sbjct: 388 LAIGRTIVAILENYQTEDGSVEIPEVLRKY 417
Score = 63.5 bits (155), Expect = 3e-10
Identities = 22/45 (48%), Positives = 27/45 (60%)
Query: 531 KDELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQE 575
K E D YLI T+E P+ +HR+ L E LPI+Y S CFR E
Sbjct: 221 KLEDTDLYLIPTAEVPLTNLHRNEILEEEELPIKYTAHSPCFRSE 265
>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 262 bits (673), Expect = 3e-78
Identities = 94/198 (47%), Positives = 126/198 (63%), Gaps = 10/198 (5%)
Query: 17 ELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQEVGSHGRDTRGIFRVHQF 76
E D YLI T+E P+ +HRD L E LPI+Y S CFR E GS G+DTRG+ RVHQF
Sbjct: 224 EDPDLYLIPTAEVPLTNLHRDEILDEEDLPIKYTAYSPCFRSEAGSAGKDTRGLIRVHQF 283
Query: 77 EKVEQFVLTSPHDDESWKMLDEMIQNSEEFYADLGIAYRVVNIVSGALNHAAAKKLDLEA 136
+KVE V+T P +ES + L+EM+ N+EE +L + YRVVN+ +G L +AAKK DLE
Sbjct: 284 DKVELVVITKP--EESEEELEEMLGNAEEVLQELELPYRVVNLCTGDLGFSAAKKYDLEV 341
Query: 137 WFPGSGAFRELVSCSNCLDYQSRRLLVRYGQTKQK--IYATAC-----ATTRVICAILET 189
W PG +RE+ SCSNC D+Q+RRL +RY ++ + A R + AILE
Sbjct: 342 WLPGQNKYREISSCSNCTDFQARRLNIRYRDKEEGKREFVHTLNGSGLAVGRTLVAILEN 401
Query: 190 HQTETG-VRIPDCLRKFV 206
+Q E G V+IP+ LR ++
Sbjct: 402 YQQEDGSVKIPEVLRPYM 419
Score = 212 bits (542), Expect = 4e-60
Identities = 75/151 (49%), Positives = 102/151 (67%), Gaps = 5/151 (3%)
Query: 303 DTRGIFRVHQFEKVEQFVLTSPHDDESWKTLDEMIQNSEEFYADLGIAYRVVNIVSGALN 362
DTRG+ RVHQF+KVE V+T P +ES + L+EM+ N+EE +L + YRVVN+ +G L
Sbjct: 273 DTRGLIRVHQFDKVELVVITKP--EESEEELEEMLGNAEEVLQELELPYRVVNLCTGDLG 330
Query: 363 HAAAKKLDLEAWFPGSGAFRELVSCSNCLAYQSRRLLVRYGQTKKMNEKIEFVHMLNATA 422
+AAKK DLE W PG +RE+ SCSNC +Q+RRL +RY ++ K EFVH LN +
Sbjct: 331 FSAAKKYDLEVWLPGQNKYREISSCSNCTDFQARRLNIRYRDKEE--GKREFVHTLNGSG 388
Query: 423 CATTRVICAILETHQTETG-VRIPDCLRKFV 452
A R + AILE +Q E G V+IP+ LR ++
Sbjct: 389 LAVGRTLVAILENYQQEDGSVKIPEVLRPYM 419
Score = 59.1 bits (144), Expect = 7e-09
Identities = 24/47 (51%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 533 ELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQECDAG 579
E D YLI T+E P+ +HRD L E LPI+Y S CFR E AG
Sbjct: 224 EDPDLYLIPTAEVPLTNLHRDEILDEEDLPIKYTAYSPCFRSE--AG 268
>gnl|CDD|177954 PLN02320, PLN02320, seryl-tRNA synthetase.
Length = 502
Score = 178 bits (454), Expect = 6e-48
Identities = 88/207 (42%), Positives = 124/207 (59%), Gaps = 22/207 (10%)
Query: 20 DKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQEVGSHGRDTRGIFRVHQFEKV 79
D+ LI T+E P+ +H DS L E++LP++Y+ S CFR E G+ G TRG++RVHQF KV
Sbjct: 287 DQCLIGTAEIPVGGIHMDSILLESALPLKYVAFSHCFRTEAGAAGAATRGLYRVHQFSKV 346
Query: 80 EQFVLTSPHDDESWKMLDEMIQNSEEFYADLGIAYRVVNIVSGALNHAAAKKLDLEAWFP 139
E FV+ P +ES +E+IQ E+ + LG+ ++ +++ + L A +K D+EAW P
Sbjct: 347 EMFVICRP--EESESFHEELIQIEEDLFTSLGLHFKTLDMATADLGAPAYRKFDIEAWMP 404
Query: 140 GSGAFRELVSCSNCLDYQSRRLLVRY-----------------GQTK--QKIYATACATT 180
G G + E+ S SNC DYQSRRL +RY G TK + ATACA
Sbjct: 405 GLGRYGEISSASNCTDYQSRRLGIRYRPSEPPQTNPKKGKGSLGPTKFVHTLNATACAVP 464
Query: 181 RVICAILETHQTETG-VRIPDCLRKFV 206
R+I +LE +Q E G V IP+ LR F+
Sbjct: 465 RMIVCLLENYQQEDGSVVIPEPLRPFM 491
Score = 142 bits (360), Expect = 1e-35
Identities = 70/160 (43%), Positives = 98/160 (61%), Gaps = 13/160 (8%)
Query: 304 TRGIFRVHQFEKVEQFVLTSPHDDESWKTLDEMIQNSEEFYADLGIAYRVVNIVSGALNH 363
TRG++RVHQF KVE FV+ P + ES+ +E+IQ E+ + LG+ ++ +++ + L
Sbjct: 334 TRGLYRVHQFSKVEMFVICRPEESESFH--EELIQIEEDLFTSLGLHFKTLDMATADLGA 391
Query: 364 AAAKKLDLEAWFPGSGAFRELVSCSNCLAYQSRRLLVRY-------GQTKKMNEKI---E 413
A +K D+EAW PG G + E+ S SNC YQSRRL +RY KK + +
Sbjct: 392 PAYRKFDIEAWMPGLGRYGEISSASNCTDYQSRRLGIRYRPSEPPQTNPKKGKGSLGPTK 451
Query: 414 FVHMLNATACATTRVICAILETHQTETG-VRIPDCLRKFV 452
FVH LNATACA R+I +LE +Q E G V IP+ LR F+
Sbjct: 452 FVHTLNATACAVPRMIVCLLENYQQEDGSVVIPEPLRPFM 491
Score = 49.2 bits (117), Expect = 1e-05
Identities = 20/43 (46%), Positives = 29/43 (67%)
Query: 536 DKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQECDA 578
D+ LI T+E P+ +H DS L E++LP++Y+ S CFR E A
Sbjct: 287 DQCLIGTAEIPVGGIHMDSILLESALPLKYVAFSHCFRTEAGA 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 = 123 bits (310), Expect = 3e-32
Identities = 42/127 (33%), Positives = 71/127 (55%), Gaps = 6/127 (4%)
Query: 14 EKDELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQEVGSHGRDTRGIFRV 73
+ ++ YL T+E I + ++ L LP++ + CFR E R RG+ RV
Sbjct: 50 KDRGGEELYLRPTAEVGITRLFKNEILSYRELPLKLYQIGPCFRYEA----RPRRGLGRV 105
Query: 74 HQFEKVEQFVLTSPHDDESWKMLDEMIQNSEEFYADLGIAYRVVNIVSGALNHAAAKKLD 133
+F +V+ + +P ++S + L+E+++ +EE DLG+ YRVV +G L +A+K+ D
Sbjct: 106 REFTQVDAEIFGTP--EQSEEELEELLKLAEEILQDLGLPYRVVLATTGDLGGSASKEGD 163
Query: 134 LEAWFPG 140
LEAW P
Sbjct: 164 LEAWLPA 170
Score = 84.2 bits (209), Expect = 1e-18
Identities = 29/75 (38%), Positives = 48/75 (64%), Gaps = 2/75 (2%)
Query: 303 DTRGIFRVHQFEKVEQFVLTSPHDDESWKTLDEMIQNSEEFYADLGIAYRVVNIVSGALN 362
RG+ RV +F +V+ + +P ++S + L+E+++ +EE DLG+ YRVV +G L
Sbjct: 98 PRRGLGRVREFTQVDAEIFGTP--EQSEEELEELLKLAEEILQDLGLPYRVVLATTGDLG 155
Query: 363 HAAAKKLDLEAWFPG 377
+A+K+ DLEAW P
Sbjct: 156 GSASKEGDLEAWLPA 170
Score = 47.2 bits (113), Expect = 7e-06
Identities = 12/46 (26%), Positives = 22/46 (47%)
Query: 530 EKDELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQE 575
+ ++ YL T+E I + ++ L LP++ + CFR E
Sbjct: 50 KDRGGEELYLRPTAEVGITRLFKNEILSYRELPLKLYQIGPCFRYE 95
>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 = 77.4 bits (191), Expect = 9e-16
Identities = 40/191 (20%), Positives = 70/191 (36%), Gaps = 19/191 (9%)
Query: 10 DSAPEKDELDDKYLIA-TSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQEVGSHGRDTR 68
++ D ++ + +PI + L +LP+R + CFR E R
Sbjct: 51 FEDKGRELRDTDLVLRPAACEPIYQIFSGEILSYRALPLRLDQIGPCFRHE----PSGRR 106
Query: 69 GIFRVHQFEKVEQFVLTSPHDDESWKMLDEMIQNSEEFYADLGIAYRVVNIVSGA----- 123
G+ RV +F +VE V P + E + E ++ +EE +LG+ RVV
Sbjct: 107 GLMRVREFRQVEYVVFGEPEEAEEER--REWLELAEEIARELGLPVRVVVADDPFFGRGG 164
Query: 124 ---LNHAAAKKLDLEAWFPGSGAFRELVSCSNCLDYQSRRLLVRYGQTKQKIYATAC--- 177
L+ ++ E P G +E S + + + T C
Sbjct: 165 KRGLDAGRETVVEFELLLPLPGRAKETAVGSANVHLDHFGASFKIDEDGGGRAHTGCGGA 224
Query: 178 -ATTRVICAIL 187
R++ A+L
Sbjct: 225 GGEERLVLALL 235
Score = 47.0 bits (112), Expect = 2e-05
Identities = 20/91 (21%), Positives = 32/91 (35%), Gaps = 17/91 (18%)
Query: 257 RDTRGIFRVHQFEKVEQFVLTSPHDDESWKMLDEMIQNSEEFYADLD------------- 303
RG+ RV +F +VE V P + E + E ++ +EE +L
Sbjct: 103 SGRRGLMRVREFRQVEYVVFGEPEEAEEER--REWLELAEEIARELGLPVRVVVADDPFF 160
Query: 304 --TRGIFRVHQFEKVEQFVLTSPHDDESWKT 332
E V +F L P + +T
Sbjct: 161 GRGGKRGLDAGRETVVEFELLLPLPGRAKET 191
>gnl|CDD|227470 COG5141, COG5141, PHD zinc finger-containing protein [General
function prediction only].
Length = 669
Score = 80.4 bits (198), Expect = 2e-15
Identities = 38/166 (22%), Positives = 59/166 (35%), Gaps = 53/166 (31%)
Query: 693 VCCVCLGERSDDVNEIVECDSCGVTVHEGCYGVQDTASISSTVSSCSTEPWFCESCRAGI 752
+C C +++ N IV CD C + VH+ CYG+Q W C C G
Sbjct: 195 ICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPEGF----------WLCRKCIYGE 244
Query: 753 AE-PTCELCPNFGENHLRGLFENIKNGHAQRDRMRYHACHLRDSRDSSDGDRGGIFKETD 811
+ C CP G FK+T
Sbjct: 245 YQIRCCSFCP----------------------------------------SSDGAFKQTS 264
Query: 812 VGKWVHLVCALYIPGVAFGEVDRLSNV-TLFEMPYSRWGAKSCALC 856
G+W H++CA++ P ++FG + + + + SRW C +C
Sbjct: 265 DGRWGHVICAMFNPELSFGHLLSKDPIDNIASVSSSRWKL-GCLIC 309
Score = 35.7 bits (82), Expect = 0.16
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 632 VCCVCLGERSDDVNEIVECDSCGVTVHE 659
+C C +++ N IV CD C + VH+
Sbjct: 195 ICTKCTSTHNENSNAIVFCDGCEICVHQ 222
Score = 30.3 bits (68), Expect = 6.7
Identities = 24/100 (24%), Positives = 33/100 (33%), Gaps = 36/100 (36%)
Query: 547 ICAVHRDSWLPEASL-------PIRYLGVSTCFRQE---------------CDAGMCRTY 584
ICA+ + PE S PI + + R + C C
Sbjct: 272 ICAM----FNPELSFGHLLSKDPIDNIASVSSSRWKLGCLICKEFGGTCIQCSYFNCTRA 327
Query: 585 FHVTCAQREGLL------SEATSEEVDQADPFYAHCRLHA 618
+HVTCA+R G S +D +P CR H
Sbjct: 328 YHVTCARRAGYFDLNIYSHNGISYCIDH-EPL---CRKHY 363
>gnl|CDD|206003 pfam13832, zf-HC5HC2H_2, PHD-zinc-finger like domain.
Length = 109
Score = 57.0 bits (138), Expect = 8e-10
Identities = 20/54 (37%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 803 RGGIFKETDVGKWVHLVCALYIPGVAFGEVDRLSNVTLFEMPYSRWGAKSCALC 856
RGG K+T G+WVH++CA+++P V FG + + + +P RW C C
Sbjct: 9 RGGALKKTTDGRWVHVLCAIFVPEVRFGNGATMEPIDVSRIPKERW-KLKCCFC 61
Score = 41.6 bits (98), Expect = 2e-04
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 575 ECDAGMCRTYFHVTCAQREGLLSEATSEEVDQADPFYAHCRLH 617
+C G C+T FHVTCA+ G+ E Q A+C+ H
Sbjct: 70 QCSYGRCQTSFHVTCARAAGVYMEIEDWPNLQ---VIAYCQKH 109
>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 = 54.0 bits (130), Expect = 6e-08
Identities = 34/149 (22%), Positives = 56/149 (37%), Gaps = 13/149 (8%)
Query: 15 KDELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQEVGSHGRDTRGIFRVH 74
E ++ + + +P S + LP+R + FR E RG+ RV
Sbjct: 46 GAENEEDLYLRPTLEPGLVRLFVSHI--RKLPLRLAEIGPAFRNE-----GGRRGLRRVR 98
Query: 75 QFEKVEQFVLTSPHDDESWKMLDEMIQNSEEFYADLGI---AYRVVNIVSGALNHAAAKK 131
+F ++E V ++ S +E+I+ +EE LGI V A
Sbjct: 99 EFTQLEGEVFGEDGEEASEF--EELIELTEELLRALGIKLDIVFVEKTPGEFSPGGAGPG 156
Query: 132 LDLEAWFPGSGAFRELVSCSNCLDYQSRR 160
++E P G E+ S D Q+R
Sbjct: 157 FEIEVDHP-EGRGLEIGSGGYRQDEQARA 184
Score = 41.7 bits (98), Expect = 0.001
Identities = 25/125 (20%), Positives = 45/125 (36%), Gaps = 9/125 (7%)
Query: 298 FYADLDTRGIFRVHQFEKVEQFVLTSPHDDESWKTLDEMIQNSEEFYADLGI---AYRVV 354
F + RG+ RV +F ++E V ++ S +E+I+ +EE LGI V
Sbjct: 85 FRNEGGRRGLRRVREFTQLEGEVFGEDGEEASEF--EELIELTEELLRALGIKLDIVFVE 142
Query: 355 NIVSGALNHAAAKKLDLEAWFPGSGAFRELVSCSNCLAYQSRRLLVRYGQTKKMNEKIEF 414
A ++E P G E+ S Q+R + + + +
Sbjct: 143 KTPGEFSPGGAGPGFEIEVDHP-EGRGLEIGSGGYRQDEQARAADLYFLDE---ALEYRY 198
Query: 415 VHMLN 419
+
Sbjct: 199 PPTIG 203
Score = 30.5 bits (69), Expect = 3.2
Identities = 23/124 (18%), Positives = 45/124 (36%), Gaps = 21/124 (16%)
Query: 255 HGRDTRGIFRVHQFEKVEQFVLTSPHDDESWKMLDEMIQNSEEFYADL----------DT 304
+ RG+ RV +F ++E V ++ S +E+I+ +EE L T
Sbjct: 87 NEGGRRGLRRVREFTQLEGEVFGEDGEEASEF--EELIELTEELLRALGIKLDIVFVEKT 144
Query: 305 RGIFRVHQFEKVEQFVLTSPHDDESWKTL-------DEMIQNSEEFYADLGIAYRVVNIV 357
G F + + P + + DE + ++ ++ D + YR +
Sbjct: 145 PGEFSPGGAGPGFEIEVDHP--EGRGLEIGSGGYRQDEQARAADLYFLDEALEYRYPPTI 202
Query: 358 SGAL 361
L
Sbjct: 203 GFGL 206
>gnl|CDD|214584 smart00249, PHD, PHD zinc finger. The plant homeodomain (PHD) finger
is a C4HC3 zinc-finger-like motif found in nuclear
proteins thought to be involved in epigenetics and
chromatin-mediated transcriptional regulation. The PHD
finger binds two zinc ions using the so-called
'cross-brace' motif and is thus structurally related to
the RING finger and the FYVE finger. It is not yet known
if PHD fingers have a common molecular function. Several
reports suggest that it can function as a protein-protein
interacton domain and it was recently demonstrated that
the PHD finger of p300 can cooperate with the adjacent
BROMO domain in nucleosome binding in vitro. Other
reports suggesting that the PHD finger is a ubiquitin
ligase have been refuted as these domains were RING
fingers misidentified as PHD fingers.
Length = 47
Score = 42.2 bits (99), Expect = 2e-05
Identities = 15/40 (37%), Positives = 19/40 (47%)
Query: 1040 CGLCHLSHDPHTMAKCDTCHLYYHLACLDPPLLRMPKKTK 1079
C +C D + +CD C +YH CL PPLL K
Sbjct: 2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGK 41
Score = 40.7 bits (95), Expect = 1e-04
Identities = 15/56 (26%), Positives = 21/56 (37%), Gaps = 9/56 (16%)
Query: 693 VCCVCLGERSDDVNEIVECDSCGVTVHEGCYGVQDTASISSTVSSCSTEPWFCESC 748
C VC + DD E+++CD C H+ C G W+C C
Sbjct: 1 YCSVC--GKPDDGGELLQCDGCDRWYHQTCLGPPLLEEE-------PDGKWYCPKC 47
Score = 28.7 bits (64), Expect = 1.5
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 632 VCCVCLGERSDDVNEIVECDSCGVTVH 658
C VC + DD E+++CD C H
Sbjct: 1 YCSVC--GKPDDGGELLQCDGCDRWYH 25
>gnl|CDD|222368 pfam13771, zf-HC5HC2H, PHD-like zinc-binding domain. The members
of this family are annotated as containing PHD domain,
but the zinc-binding region here is not typical of PHD
domains. The conformation here is a well-conserved
cysteine-histidine rich region spanning 90 residues,
where the Cys and His are arranged as
HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.
Length = 89
Score = 42.7 bits (101), Expect = 4e-05
Identities = 14/43 (32%), Positives = 18/43 (41%), Gaps = 4/43 (9%)
Query: 576 CDAGMCRTYFHVTCAQREGLLSEATSEEVDQADPFYAHCRLHA 618
C CR FHVTCA+ G L + F ++C H
Sbjct: 51 CCVKNCRRAFHVTCAREAGCL----FQFDGDNGKFKSYCPKHR 89
Score = 36.2 bits (84), Expect = 0.008
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 4/43 (9%)
Query: 817 HLVCALYIPGVAFGEVDRLSNVTLFEM---PYSRWGAKSCALC 856
H+ CAL+ P V D + L ++ R K C+LC
Sbjct: 1 HVNCALWSPEVVQRGDDDMEGFPLEDVDKAVKRRRKLK-CSLC 42
>gnl|CDD|201356 pfam00628, PHD, PHD-finger. PHD folds into an interleaved type of
Zn-finger chelating 2 Zn ions in a similar manner to that
of the RING and FYVE domains. Several PHD fingers have
been identified as binding modules of methylated histone
H3.
Length = 51
Score = 41.3 bits (97), Expect = 5e-05
Identities = 14/38 (36%), Positives = 18/38 (47%)
Query: 1040 CGLCHLSHDPHTMAKCDTCHLYYHLACLDPPLLRMPKK 1077
C +C D + CD C ++HLACL PPL
Sbjct: 2 CAVCGKVDDDGELLLCDGCDRWFHLACLGPPLEPEEIP 39
Score = 40.9 bits (96), Expect = 7e-05
Identities = 14/59 (23%), Positives = 18/59 (30%), Gaps = 8/59 (13%)
Query: 693 VCCVCLGERSDDVNEIVECDSCGVTVHEGCYGVQDTASISSTVSSCSTEPWFCESCRAG 751
C VC D E++ CD C H C G W+C C+
Sbjct: 1 YCAVCGKVDDD--GELLLCDGCDRWFHLACLG------PPLEPEEIPEGEWYCPECKPK 51
Score = 30.9 bits (70), Expect = 0.25
Identities = 9/27 (33%), Positives = 11/27 (40%), Gaps = 2/27 (7%)
Query: 632 VCCVCLGERSDDVNEIVECDSCGVTVH 658
C VC D E++ CD C H
Sbjct: 1 YCAVCGKVDDD--GELLLCDGCDRWFH 25
>gnl|CDD|222406 pfam13831, PHD_2, PHD-finger. PHD folds into an interleaved type
of Zn-finger chelating 2 Zn ions in a similar manner to
that of the RING and FYVE domains. Several PHD fingers
have been identified as binding modules of methylated
histone H3.
Length = 33
Score = 40.3 bits (95), Expect = 9e-05
Identities = 15/43 (34%), Positives = 18/43 (41%), Gaps = 10/43 (23%)
Query: 706 NEIVECDSCGVTVHEGCYGVQDTASISSTVSSCSTEPWFCESC 748
N ++ C C V VH CYGV + S PW C C
Sbjct: 1 NPLLVCSKCSVAVHASCYGVPEL----------SDGPWLCRRC 33
>gnl|CDD|222901 PHA02597, 30.2, hypothetical protein; Provisional.
Length = 197
Score = 37.4 bits (87), Expect = 0.022
Identities = 29/117 (24%), Positives = 44/117 (37%), Gaps = 37/117 (31%)
Query: 89 DDESWKMLDEMIQNSEEF-----YADLGIAYRVVNIVSGALNHAAAKKL----------- 132
D E K L E NS+ Y D A V+N + + A L
Sbjct: 53 DQELAKKLIEKYNNSDFIRYLSAYDD---ALDVINKLKEDYDFVAVTALGDSIDALLNRQ 109
Query: 133 -DLEAWFPGSGAFRELVSCSNCLDYQSRRLLVRYGQTKQKIYATACAT--TRVICAI 186
+L A FPG AF E++ C + ++K+K++ A RV+C +
Sbjct: 110 FNLNALFPG--AFSEVLMC-------------GHDESKEKLFIKAKEKYGDRVVCFV 151
>gnl|CDD|197519 smart00109, C1, Protein kinase C conserved region 1 (C1) domains
(Cysteine-rich domains). Some bind phorbol esters and
diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Length = 50
Score = 32.1 bits (73), Expect = 0.093
Identities = 12/38 (31%), Positives = 16/38 (42%)
Query: 685 FSKFSKILVCCVCLGERSDDVNEIVECDSCGVTVHEGC 722
F F+K CCVC + + C C V H+ C
Sbjct: 5 FRTFTKPTFCCVCRKSIWGSFKQGLRCSECKVKCHKKC 42
Score = 28.2 bits (63), Expect = 2.3
Identities = 11/36 (30%), Positives = 15/36 (41%)
Query: 624 FSKFSKILVCCVCLGERSDDVNEIVECDSCGVTVHE 659
F F+K CCVC + + C C V H+
Sbjct: 5 FRTFTKPTFCCVCRKSIWGSFKQGLRCSECKVKCHK 40
>gnl|CDD|235240 PRK04173, PRK04173, glycyl-tRNA synthetase; Provisional.
Length = 456
Score = 35.5 bits (83), Expect = 0.18
Identities = 25/85 (29%), Positives = 35/85 (41%), Gaps = 9/85 (10%)
Query: 69 GIFRVHQFEK--VEQFVLTSPHDDESWKMLDEMIQNSEEFYADLGIA---YRVVNIVSGA 123
IFR +FE+ +E FV P D W I+ + + DLGI R +
Sbjct: 205 FIFRTREFEQMELEFFVK--PGTDNEW--FAYWIELRKNWLLDLGIDPENLRFREHLPEE 260
Query: 124 LNHAAAKKLDLEAWFPGSGAFRELV 148
L H + D+E FP + EL
Sbjct: 261 LAHYSKATWDIEYKFPFGRFWGELE 285
Score = 35.5 bits (83), Expect = 0.18
Identities = 25/85 (29%), Positives = 35/85 (41%), Gaps = 9/85 (10%)
Query: 306 GIFRVHQFEK--VEQFVLTSPHDDESWKTLDEMIQNSEEFYADLGIA---YRVVNIVSGA 360
IFR +FE+ +E FV P D W I+ + + DLGI R +
Sbjct: 205 FIFRTREFEQMELEFFVK--PGTDNEW--FAYWIELRKNWLLDLGIDPENLRFREHLPEE 260
Query: 361 LNHAAAKKLDLEAWFPGSGAFRELV 385
L H + D+E FP + EL
Sbjct: 261 LAHYSKATWDIEYKFPFGRFWGELE 285
>gnl|CDD|222105 pfam13402, M60-like, Peptidase M60-like family. Members of this
family are related to the Enhancin peptidase family.
Therefore these proteins may act as peptidases.
Length = 303
Score = 34.9 bits (81), Expect = 0.20
Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 8/73 (10%)
Query: 274 FVLTSPHDDESWKMLDEMIQNSEEFYADLDT-RGIFRVHQFEKVEQFVLTSPHDDESWKT 332
F+L DE WK M++N +A+L R I V E + + P +E K
Sbjct: 97 FILGK-TTDEDWK---NMLRNYPAPWAELVGGRVILTVPS-ENLRKLTRNDP--EELLKL 149
Query: 333 LDEMIQNSEEFYA 345
D +I++ E
Sbjct: 150 WDRIIRSQNELAG 162
>gnl|CDD|237996 cd00029, C1, Protein kinase C conserved region 1 (C1) .
Cysteine-rich zinc binding domain. Some members of this
domain family bind phorbol esters and diacylglycerol,
some are reported to bind RasGTP. May occur in tandem
arrangement. Diacylglycerol (DAG) is a second messenger,
released by activation of Phospholipase D. Phorbol
Esters (PE) can act as analogues of DAG and mimic its
downstream effects in, for example, tumor promotion.
Protein Kinases C are activated by DAG/PE, this
activation is mediated by their N-terminal conserved
region (C1). DAG/PE binding may be phospholipid
dependent. C1 domains may also mediate DAG/PE signals in
chimaerins (a family of Rac GTPase activating proteins),
RasGRPs (exchange factors for Ras/Rap1), and Munc13
isoforms (scaffolding proteins involved in exocytosis).
Length = 50
Score = 30.5 bits (69), Expect = 0.34
Identities = 10/35 (28%), Positives = 13/35 (37%)
Query: 688 FSKILVCCVCLGERSDDVNEIVECDSCGVTVHEGC 722
F K C VC + + C C V H+ C
Sbjct: 8 FFKPTFCDVCRKSIWGLFKQGLRCSWCKVKCHKKC 42
Score = 26.7 bits (59), Expect = 8.0
Identities = 9/33 (27%), Positives = 12/33 (36%)
Query: 627 FSKILVCCVCLGERSDDVNEIVECDSCGVTVHE 659
F K C VC + + C C V H+
Sbjct: 8 FFKPTFCDVCRKSIWGLFKQGLRCSWCKVKCHK 40
>gnl|CDD|232962 TIGR00409, proS_fam_II, prolyl-tRNA synthetase, family II.
Prolyl-tRNA synthetase is a class II tRNA synthetase and
is recognized by pfam model tRNA-synt_2b, which
recognizes tRNA synthetases for Gly, His, Ser, and Pro.
The prolyl-tRNA synthetases are divided into two widely
divergent groups. This group includes enzymes from
Escherichia coli, Bacillus subtilis, Aquifex aeolicus,
the spirochete Treponema pallidum, Synechocystis
PCC6803, and one of the two prolyL-tRNA synthetases of
Saccharomyces cerevisiae. The other group includes the
Pro-specific domain of a human multifunctional tRNA
ligase and the prolyl-tRNA synthetases from the Archaea,
the Mycoplasmas, and the spirochete Borrelia burgdorferi
[Protein synthesis, tRNA aminoacylation].
Length = 568
Score = 34.4 bits (79), Expect = 0.41
Identities = 44/186 (23%), Positives = 67/186 (36%), Gaps = 30/186 (16%)
Query: 15 KDELDDKY-LIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQEVGSHGRDTRGIFRV 73
KD ++ L T E+ I + R+ LP+ + T FR E+ R G+ R
Sbjct: 97 KDRKGREFVLGPTHEEVITDLARNEIKSYKQLPLNLYQIQTKFRDEI----RPRFGLMRG 152
Query: 74 HQFEKVEQFVLTSPHDDESWKMLDEMIQNSEEFY----ADLGIAYRVVNIVSGALNHAAA 129
+F + + S H DE + LD Q + Y + LG+ +R V SGA+ +A+
Sbjct: 153 REFIMKDAY---SFHSDE--ESLDATYQKMYQAYSNIFSRLGLDFRPVQADSGAIGGSAS 207
Query: 130 KKLDLEAWFPGSGAFRELVSCSNCLDY-----------QSRRLLVRYGQTKQKIYATACA 178
+ + A SG +V DY R K T
Sbjct: 208 HEFMVLA---ESGE-DTIVYSDES-DYAANIELAEALAPGERNAPTAELDKVDTPNTKTI 262
Query: 179 TTRVIC 184
V C
Sbjct: 263 AELVEC 268
>gnl|CDD|185429 PTZ00074, PTZ00074, 60S ribosomal protein L34; Provisional.
Length = 135
Score = 31.6 bits (72), Expect = 0.86
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 195 GVRIPDCLRKFVPAVYLNEAGEIPFVKTAPIDEEETKKQKKQKEGMKKK 243
GV C+R + +L E E VK ++ + KKQKK+K+ KKK
Sbjct: 78 GVLCHKCVRDRIVRAFLVE--EQKIVKQVLKEKAKQKKQKKKKKKKKKK 124
Score = 29.7 bits (67), Expect = 3.6
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 441 GVRIPDCLRKFVPAVYVNEAGEIPFVKTAPIDEEETKKQKKQKEGMKKKVLIDEA 495
GV C+R + ++ E E VK ++ + KKQKK+K+ KKK +A
Sbjct: 78 GVLCHKCVRDRIVRAFLVE--EQKIVKQVLKEKAKQKKQKKKKKKKKKKKTSKKA 130
>gnl|CDD|237851 PRK14894, PRK14894, glycyl-tRNA synthetase; Provisional.
Length = 539
Score = 33.1 bits (75), Expect = 0.93
Identities = 28/115 (24%), Positives = 47/115 (40%), Gaps = 10/115 (8%)
Query: 45 LPIRYLGVSTCFRQEVGSHGRDTRGIFRVHQFEKVEQFVLTSPHDDESWKMLDEMIQNSE 104
LP V FR E+ +FRV +FE++E P DE W ++
Sbjct: 164 LPFGIAQVGKAFRNEINPRNF----LFRVREFEQMEIEYFVMPGTDEEWH--QRWLEARL 217
Query: 105 EFYADLGIA---YRVVNIVSGALNHAAAKKLDLEAWFPGSGAFRELVSCSNCLDY 156
++ +GI + ++ L H + + DL +P G +E+ +N DY
Sbjct: 218 AWWEQIGIPRSRITIYDVPPDELAHYSKRTFDLMYDYPNIG-VQEIEGIANRTDY 271
>gnl|CDD|215738 pfam00130, C1_1, Phorbol esters/diacylglycerol binding domain (C1
domain). This domain is also known as the Protein kinase
C conserved region 1 (C1) domain.
Length = 53
Score = 29.0 bits (65), Expect = 1.5
Identities = 9/33 (27%), Positives = 9/33 (27%), Gaps = 2/33 (6%)
Query: 1037 SHKCGLC--HLSHDPHTMAKCDTCHLYYHLACL 1067
C C L KC C L H C
Sbjct: 11 PTFCDHCGEFLWGLGKQGLKCSWCGLNVHKRCH 43
>gnl|CDD|172788 PRK14300, PRK14300, chaperone protein DnaJ; Provisional.
Length = 372
Score = 32.3 bits (73), Expect = 1.6
Identities = 28/125 (22%), Positives = 44/125 (35%), Gaps = 30/125 (24%)
Query: 688 FSKILVCCVCLGERSDDVNEIVECDSCG----VTVHEGCYGVQDTASISSTVSSCSTEPW 743
FS + C C G S+ + CD+C + +G + ++
Sbjct: 142 FSSEVKCDTCHGSGSEKGETVTTCDACSGVGATRMQQGFFTIEQA--------------- 186
Query: 744 FCESCRAG--IAEPTCELCPNFGENH-LRGLFENIKNGHAQRDRMRYHACHLRDSRDSSD 800
C C+ I + C+ C G H R L NI G R+R+ + +
Sbjct: 187 -CHKCQGNGQIIKNPCKKCHGMGRYHKQRNLSVNIPAGVENGTRIRH-------TGEGEA 238
Query: 801 GDRGG 805
G RGG
Sbjct: 239 GIRGG 243
Score = 30.8 bits (69), Expect = 4.0
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 627 FSKILVCCVCLGERSDDVNEIVECDSCGVTVHEVKIQQEFLAIK 670
FS + C C G S+ + CD+C V ++QQ F I+
Sbjct: 142 FSSEVKCDTCHGSGSEKGETVTTCDACS-GVGATRMQQGFFTIE 184
>gnl|CDD|187828 cd09697, Cas8a1_I-A, CRISPR/Cas system-associated protein Cas8a1.
CRISPR (Clustered Regularly Interspaced Short Palindromic
Repeats) and associated Cas proteins comprise a system
for heritable host defense by prokaryotic cells against
phage and other foreign DNA; Large proteins, some contain
Zn-finger domain; signature gene for I-A subtype; also
known as Csx8 family.
Length = 441
Score = 32.2 bits (73), Expect = 1.7
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 12/70 (17%)
Query: 966 IPLAFNVEFVAYFLNRNGRLGKLTREQRALA-VENDSLQSEQSR----------LQKTYD 1014
IP AF F A+F+N N + L + +A+ +N+ + E + LQ+ D
Sbjct: 194 IPFAFTGSFEAFFINDNLDIEILKKSNKAIKEKKNEETEGENNSVPLRKTLFNILQEKVD 253
Query: 1015 ELVY-MEVVF 1023
+ Y +EV+
Sbjct: 254 YIKYDVEVIL 263
>gnl|CDD|233970 TIGR02670, cas_csx8, CRISPR-associated protein Cas8a1/Csx8, subtype
I. In three genomes so far, a member of this protein
appears in the midst of a CRISPR-associated (cas) gene
operon, immediately upstream of a member of family
TIGR01875 (CRISPR-associated autoregulator, DevR family).
The genomes so far are Nocardia farcinica IFM10152,
Clostridium perfringens SM101, and Clostridium tetani E88
[Mobile and extrachromosomal element functions, Other].
Length = 441
Score = 32.2 bits (73), Expect = 1.7
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 12/70 (17%)
Query: 966 IPLAFNVEFVAYFLNRNGRLGKLTREQRALA-VENDSLQSEQSR----------LQKTYD 1014
IP AF F A+F+N N + L + +A+ +N+ + E + LQ+ D
Sbjct: 194 IPFAFTGSFEAFFINDNLDIEILKKSNKAIKEKKNEETEGENNSVPLRKTLFNILQEKVD 253
Query: 1015 ELVY-MEVVF 1023
+ Y +EV+
Sbjct: 254 YIKYDVEVIL 263
>gnl|CDD|219273 pfam07028, DUF1319, Protein of unknown function (DUF1319). This
family contains a number of viral proteins of unknown
function approximately 200 residues long. Family members
seem to be restricted to badnaviruses.
Length = 119
Score = 30.0 bits (68), Expect = 2.5
Identities = 27/88 (30%), Positives = 37/88 (42%), Gaps = 21/88 (23%)
Query: 953 DLATLADMNKKWHIPLAFNVEFVAYFLNRNGR-----LGKLTREQRA----LAVENDSLQ 1003
DLAT K + LA N+ A L+ R L K+ QRA L E +L+
Sbjct: 10 DLATEE---KVSNSDLAHNLHVTADRLSLGSRVEIKNLLKIQESQRADLKELKDELRTLK 66
Query: 1004 SEQSRLQKTYDELVYMEVVFPQPPLSKQ 1031
E + L+K Y + PLSK+
Sbjct: 67 RELTALRKEY---------LERRPLSKE 85
>gnl|CDD|222758 pfam14446, Prok-RING_1, Prokaryotic RING finger family 1. RING
finger family found sporadically in bacteria and
archaea, and associated in gene neighborhoods with other
components of the ubiquitin-based signaling and
degradation system, including ubiquitin, the E1 and E2
proteins and the JAB-like metallopeptidase. The
bacterial versions contain transmembrane helices.
Length = 55
Score = 28.2 bits (63), Expect = 2.9
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 695 CVCLGERSDDVNEIVECDSCGVTVHEGCYG 724
C G++ ++IV C CG H C+
Sbjct: 8 CPVCGKKFKPGDDIVVCPECGAPYHRECWE 37
>gnl|CDD|164584 MTH00008, COX2, cytochrome c oxidase subunit II; Validated.
Length = 228
Score = 30.6 bits (69), Expect = 3.3
Identities = 20/50 (40%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 938 RLMEVDTGAVAQAQSD---LATLADMNKKWHIP-LAFNVEFVAYFLNRNG 983
RL+EVD AV Q++ L T AD+ W +P L V+ V LN+ G
Sbjct: 134 RLLEVDNRAVLPMQTEIRVLVTAADVIHSWTVPSLGVKVDAVPGRLNQIG 183
>gnl|CDD|219186 pfam06810, Phage_GP20, Phage minor structural protein GP20. This
family consists of several phage minor structural
protein GP20 sequences of around 180 residues in length.
The function of this family is unknown.
Length = 156
Score = 30.0 bits (68), Expect = 3.4
Identities = 11/62 (17%), Positives = 26/62 (41%), Gaps = 8/62 (12%)
Query: 483 KEGMKKKVLIDEAMIQNEKDLIATEKERNNALREVIGK--------GEKVGDSAPEKDEL 534
+E + K + IQN K + E ++L++ + +KV D+ + ++
Sbjct: 1 EEQIDKIMAEYGKDIQNPKSKLDKANEERDSLKKQLKNRDKQIEDLKKKVKDNEELQKKI 60
Query: 535 DD 536
+
Sbjct: 61 EK 62
>gnl|CDD|234029 TIGR02830, spore_III_AG, stage III sporulation protein AG. CC A
comparative genome analysis of all sequenced genomes of
shows a number of proteins conserved strictly among the
endospore-forming subset of the Firmicutes. This
protein, a member of this panel, is found in a spore
formation operon and is designated stage III sporulation
protein AG [Cellular processes, Sporulation and
germination].
Length = 186
Score = 30.4 bits (69), Expect = 3.7
Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 7/54 (12%)
Query: 473 EEETKKQKKQKEGMKKKVLIDEAMIQNEKDLIATEKERNNALREVIGKGEKVGD 526
+ +K + E ++ +V Q E ++ EK+ N L+E++ K E VGD
Sbjct: 32 SDTPNNEKTEPEFVQGEV-------QKEDEISDYEKQYENELKEILEKIEGVGD 78
>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 = 31.1 bits (70), Expect = 3.8
Identities = 29/121 (23%), Positives = 48/121 (39%), Gaps = 30/121 (24%)
Query: 19 DDKYLIATSE-QPICAVHRDSWLPEASLPIRYLGVST-CFRQEVGSHGRDTRGIFRVHQF 76
D Y+IA ++ +P + PI++ S +R E G +G+ RVH+F
Sbjct: 307 DPGYVIAPAQCEPFYQFFEGEVIDAEDKPIKFFDRSGWTYRWEAGG----AKGLDRVHEF 362
Query: 77 EKVEQFVLTSPHDDESWKMLDEMIQNSEEFYADLGIAYRVVNIVSGALNHAAAKKLDLEA 136
+VE + P + E + D+ ++ L AA +LDLE
Sbjct: 363 LRVECVWIAEPEETEEIR--DKTLE----------------------LAEDAADELDLEW 398
Query: 137 W 137
W
Sbjct: 399 W 399
>gnl|CDD|220329 pfam09657, Cas_Csx8, CRISPR-associated protein Csx8 (Cas_Csx8).
Clusters of short DNA repeats with nonhomologous spacers,
which are found at regular intervals in the genomes of
phylogenetically distinct prokaryotic species, comprise a
family with recognisable features. This family is known
as CRISPR (short for Clustered, Regularly Interspaced
Short Palindromic Repeats). A number of protein families
appear only in association with these repeats and are
designated Cas (CRISPR-Associated) proteins. This entry
describes proteins of unknown function which are encoded
in the midst of a cas gene operon.
Length = 441
Score = 31.0 bits (70), Expect = 4.1
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 12/70 (17%)
Query: 966 IPLAFNVEFVAYFLNRNGRLGKLTREQRALAVE-NDSLQSEQSR----------LQKTYD 1014
IP AF F A+F+N N + L + +A+ + N+ + Q+ LQ+ D
Sbjct: 194 IPFAFTGSFEAFFINDNLDIEILKKSNKAIKEKKNEETEGNQNSVPLRKTLFNILQEKVD 253
Query: 1015 ELVY-MEVVF 1023
+ Y +EV+
Sbjct: 254 YIKYDVEVIL 263
>gnl|CDD|187875 cd09744, Cas8a1_I-A, CRISPR/Cas system-associated protein Cas8a1.
CRISPR (Clustered Regularly Interspaced Short Palindromic
Repeats) and associated Cas proteins comprise a system
for heritable host defense by prokaryotic cells against
phage and other foreign DNA; Large proteins, some contain
Zn-finger domain; signature gene for I-A subtype; also
known as Csx8 family.
Length = 441
Score = 31.0 bits (70), Expect = 4.1
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 12/70 (17%)
Query: 966 IPLAFNVEFVAYFLNRNGRLGKLTREQRALAVE-NDSLQSEQSR----------LQKTYD 1014
IP AF F A+F+N N + L + +A+ + N+ + Q+ LQ+ D
Sbjct: 194 IPFAFTGSFEAFFINDNLDIEILKKSNKAIKEKKNEETEGNQNSVPLRKTLFNILQEKVD 253
Query: 1015 ELVY-MEVVF 1023
+ Y +EV+
Sbjct: 254 YIKYDVEVIL 263
>gnl|CDD|173839 cd01150, AXO, Peroxisomal acyl-CoA oxidase. Peroxisomal acyl-CoA
oxidases (AXO) catalyze the first set in the peroxisomal
fatty acid beta-oxidation, the alpha,beta
dehydrogenation of the corresponding trans-enoyl-CoA by
FAD, which becomes reduced. In a second oxidative
half-reaction, the reduced FAD is reoxidized by
molecular oxygen. AXO is generally a homodimer, but it
has been reported to form a different type of oligomer
in yeast. There are several subtypes of AXO's, based on
substrate specificity. Palmitoyl-CoA oxidase acts on
straight-chain fatty acids and prostanoids; whereas, the
closely related Trihydroxycoprostanoly-CoA oxidase has
the greatest activity for 2-methyl branched side chains
of bile precursors. Pristanoyl-CoA oxidase, acts on
2-methyl branched fatty acids. AXO has an additional
domain, C-terminal to the region with similarity to
acyl-CoA dehydrogenases, which is included in this
alignment.
Length = 610
Score = 31.1 bits (71), Expect = 4.2
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 35 HRDSWLPEASLPIRYLGVSTCFRQEVGSHGRDTRGIFRVHQFEKVEQ-FVLTSPHDDESW 93
H+D WL A L + CF Q HG + +G+ ++ + Q FV+ +P D +
Sbjct: 121 HQDYWLQGA----NNLEIIGCFAQTELGHGSNLQGLETTATYDPLTQEFVINTP-DFTAT 175
Query: 94 K 94
K
Sbjct: 176 K 176
>gnl|CDD|234876 PRK00960, PRK00960, seryl-tRNA synthetase; Provisional.
Length = 517
Score = 30.4 bits (69), Expect = 5.6
Identities = 24/99 (24%), Positives = 41/99 (41%), Gaps = 29/99 (29%)
Query: 40 LPEASLPIRYLGVS-TCFRQEVGSHGRDTRGIFRVHQFEKVEQFVLTSPHDDESWKMLDE 98
+ LPI++ S +R E G G+ RV++F ++E L +P E ++ DE
Sbjct: 329 VDVDELPIKFFDRSGWTYRWEGGG----AHGLERVNEFHRIEIVWLGTPEQVE--EIRDE 382
Query: 99 MIQNSEEFYADLGIAYRVVNIVSGALNHAAAKKLDLEAW 137
+++ + A+KLDLE W
Sbjct: 383 LLKYAHIL----------------------AEKLDLEYW 399
>gnl|CDD|129694 TIGR00606, rad50, rad50. All proteins in this family for which
functions are known are involvedin recombination,
recombinational repair, and/or non-homologous end
joining.They are components of an exonuclease complex
with MRE11 homologs. This family is distantly related to
the SbcC family of bacterial proteins.This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University).
Length = 1311
Score = 30.4 bits (68), Expect = 6.5
Identities = 28/114 (24%), Positives = 43/114 (37%), Gaps = 3/114 (2%)
Query: 407 KMNEKIEFVHMLNATACATTRVICAILETHQTETGVRIPDCLRKFVPAVYVNEAGEIPFV 466
++ E+IE A T V + E P C R F + E
Sbjct: 643 RLKEEIEKSSKQRAMLAGATAVYSQFITQLTDENQSCCPVCQRVFQTEAELQEFISDLQS 702
Query: 467 KT--APIDEEETKKQKKQKEGMKKKVLIDEAMIQNEKDLIATE-KERNNALREV 517
K AP + T+ + K+KE + ++L Q+ DL E E N L++V
Sbjct: 703 KLRLAPDKLKSTESELKKKEKRRDEMLGLAPGRQSIIDLKEKEIPELRNKLQKV 756
>gnl|CDD|216941 pfam02233, PNTB, NAD(P) transhydrogenase beta subunit. This family
corresponds to the beta subunit of NADP transhydrogenase
in prokaryotes, and either the protein N- or C terminal
in eukaryotes. The domain is often found in conjunction
with pfam01262. Pyridine nucleotide transhydrogenase
catalyzes the reduction of NAD+ to NADPH. A complete
loss of activity occurs upon mutation of Gly314 in E.
coli.
Length = 464
Score = 30.4 bits (69), Expect = 6.5
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 6/40 (15%)
Query: 946 AVAQAQSDLATLADMNKKWHIPLAFNVEFVAYFLNRNGRL 985
AVAQAQ +A LA + ++ + + F + VA GR+
Sbjct: 320 AVAQAQHPVADLAKLLEERGVNVRFAIHPVA------GRM 353
>gnl|CDD|222665 pfam14303, NAM-associated, No apical meristem-associated C-terminal
domain. This domain is found in a number of different
types of plant proteins including NAM-like proteins.
Length = 147
Score = 28.9 bits (65), Expect = 7.6
Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 473 EEETKKQKKQKEGMKKKVLIDEAMIQNEK-----DLIATEKE 509
EE K+++K++ MK ++ + EK L+ EK+
Sbjct: 82 EEAEKEKEKEERFMKALAEAEKERAELEKKKAEAKLMKEEKK 123
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
0.320 0.135 0.415
Gapped
Lambda K H
0.267 0.0799 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 54,483,864
Number of extensions: 5331670
Number of successful extensions: 5053
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4991
Number of HSP's successfully gapped: 94
Length of query: 1083
Length of database: 10,937,602
Length adjustment: 107
Effective length of query: 976
Effective length of database: 6,191,724
Effective search space: 6043122624
Effective search space used: 6043122624
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: 64 (28.3 bits)