RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10034
(399 letters)
>gnl|CDD|215364 PLN02678, PLN02678, seryl-tRNA synthetase.
Length = 448
Score = 465 bits (1199), Expect = e-163
Identities = 208/468 (44%), Positives = 268/468 (57%), Gaps = 97/468 (20%)
Query: 3 LDLDLFRTEKGGDPEKVRKNQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLCSK 62
LD++LFR EKGGDPE +R++Q+ RF +VELVD+VI D +WRQ + + D+ K N +K
Sbjct: 2 LDINLFREEKGGDPELIRESQRRRFASVELVDEVIALDKEWRQRQFELDSLRKEFNKLNK 61
Query: 63 VIGEKMKAKEPVGD--------------------------SSTLP--GNHLHPSVPVSNN 94
+ + AKE + + L GN +H SVPVSN+
Sbjct: 62 EVAKLKIAKEDATELIAETKELKKEITEKEAEVQEAKAALDAKLKTIGNLVHDSVPVSND 121
Query: 95 EDENGIVRTKGDTEVRKK-YSHVDLITMIDGVDSEAGAIVAGGRGYFLKGPAVCLQVGLV 153
E N +VRT G+ K +HVDL+ ++ VD+E GA VAGGRGY+LKG V L L+
Sbjct: 122 EANNAVVRTWGEKRQEPKLKNHVDLVELLGIVDTERGADVAGGRGYYLKGAGVLLNQALI 181
Query: 154 QYALSKWIEKGYTPLYTPFFMRKEVMQEVAQLAQFDEELYKVIGKGEKVGDSAPEKDELD 213
+ L+ ++GYTPL TPFFMRK+VM + AQLAQFDEELYKV G+G D
Sbjct: 182 NFGLAFLRKRGYTPLQTPFFMRKDVMAKCAQLAQFDEELYKVTGEG-------------D 228
Query: 214 DKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQE-------------------- 253
DKYLIATSEQP+CA HR W+ LPIRY G STCFR+E
Sbjct: 229 DKYLIATSEQPLCAYHRGDWIDPKELPIRYAGYSTCFRKEAGSHGRDTLGIFRVHQFEKV 288
Query: 254 -------------------------DLTKS--IAYRVVNIVSGALNHAAAKKLDLEAWFP 286
D +S I Y+VV+IVSGALN AAAKK DLEAWFP
Sbjct: 289 EQFCITSPNGNESWEMHEEMLKNSEDFYQSLGIPYQVVSIVSGALNDAAAKKYDLEAWFP 348
Query: 287 GSGAFRELVSCSNCLDYQSRRLLVRYGQTKKMNEKIEFVHMLNATACATTRVICAILETH 346
S +RELVSCSNC DYQSRRL +RYGQ K + ++VH+LN+T AT R +C ILE +
Sbjct: 349 ASKTYRELVSCSNCTDYQSRRLEIRYGQKKSNEQTKQYVHLLNSTLTATERTLCCILENY 408
Query: 347 QTETGVRIPDCLRKFVPAVYVNEAGEIPFVKTAPIDEEETKKQKKQKE 394
QTE GVR+P+ L+ F+ + +PF K P + K +KK+K+
Sbjct: 409 QTEDGVRVPEVLQPFMGGIEF-----LPFKKKPP---AKGKGKKKKKK 448
>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 = 347 bits (892), Expect = e-119
Identities = 126/313 (40%), Positives = 168/313 (53%), Gaps = 65/313 (20%)
Query: 97 ENGIVRTKGDTEV--RKKYSHVDLITMIDGVDSEAGAIVAGGRGYFLKGPAVCLQVGLVQ 154
+N +R G+ V K HV+L +D +D E GA V+G R Y+LKG L+ L+
Sbjct: 1 DNVEIRRWGEPRVFDFKPKDHVELGEKLDILDFERGAKVSGSRFYYLKGDGALLERALIN 60
Query: 155 YALSKWIEKGYTPLYTPFFMRKEVMQEVAQLAQFDEELYKVIGKGEKVGDSAPEKDELDD 214
+AL ++G+TP+ PF +RKEVM+ QL +FDE+LYKV G +D
Sbjct: 61 FALDFLTKRGFTPVIPPFLVRKEVMEGTGQLPKFDEQLYKVEG---------------ED 105
Query: 215 KYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQE--------------------- 253
YLIAT+E P+ A+HRD L E LP++Y G S CFR+E
Sbjct: 106 LYLIATAEVPLAALHRDEILEEEELPLKYAGYSPCFRKEAGSAGRDTRGLFRVHQFEKVE 165
Query: 254 ----------------------DLTKS--IAYRVVNIVSGALNHAAAKKLDLEAWFPGSG 289
++ + + YRVVNI +G L AAAKK D+EAW PG G
Sbjct: 166 QFVFTKPEESWEELEELISNAEEILQELGLPYRVVNICTGDLGFAAAKKYDIEAWMPGQG 225
Query: 290 AFRELVSCSNCLDYQSRRLLVRYGQTKKMNEKIEFVHMLNATACATTRVICAILETHQTE 349
+RE+ SCSNC D+Q+RRL +RY K K ++VH LN TA AT R I AILE +QTE
Sbjct: 226 KYREISSCSNCTDFQARRLNIRYRDKKDG--KKQYVHTLNGTALATPRTIVAILENYQTE 283
Query: 350 TG-VRIPDCLRKF 361
G V IP+ LR +
Sbjct: 284 DGSVVIPEVLRPY 296
>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 305 bits (784), Expect = e-101
Identities = 142/440 (32%), Positives = 200/440 (45%), Gaps = 102/440 (23%)
Query: 3 LDLDLFRTEKGGDPEKVRKNQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLCSK 62
LDL L R +P+ VR+ K R + VDK++E D + R+ + + +N SK
Sbjct: 2 LDLKLIRE----NPDAVREKLKKRGGDALDVDKLLELDEERRKLLRELEELQAERNELSK 57
Query: 63 VIGEKMKAKEPVGDS------------------------------STLPGNHLHPSVPVS 92
IG +K E + T+P N H SVPV
Sbjct: 58 EIGRALKRGEDDAEELIAEVKELKEKLKELEAALDELEAELDTLLLTIP-NIPHESVPVG 116
Query: 93 NNEDENGIVRTKGDTEVR----KKYSHVDLITMIDGVDSEAGAIVAGGRGYFLKGPAVCL 148
+ED+N VR G+ V + HV+L + +D E A V+G R YF KG L
Sbjct: 117 KDEDDNVEVRRWGEPPVFVFDFEPKDHVELGEKLGLLDFERAAKVSGSRFYFYKGKGARL 176
Query: 149 QVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEVAQLAQFDEELYKVIGKGEKVGDSAPE 208
+ L+Q+ L + G+T + P+ + E M QL +F+E+LYKV
Sbjct: 177 ERALIQFMLDLHTKHGFTEVLPPYLVNLESMFGTGQLPKFEEDLYKV------------- 223
Query: 209 KDELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFR----------------- 251
E D YLI T+E P+ +HRD L E LPI+Y S CFR
Sbjct: 224 --EDPDLYLIPTAEVPLTNLHRDEILDEEDLPIKYTAYSPCFRSEAGSAGKDTRGLIRVH 281
Query: 252 --------------------------QEDLTKSIA--YRVVNIVSGALNHAAAKKLDLEA 283
E++ + + YRVVN+ +G L +AAKK DLE
Sbjct: 282 QFDKVELVVITKPEESEEELEEMLGNAEEVLQELELPYRVVNLCTGDLGFSAAKKYDLEV 341
Query: 284 WFPGSGAFRELVSCSNCLDYQSRRLLVRYGQTKKMNEKIEFVHMLNATACATTRVICAIL 343
W PG +RE+ SCSNC D+Q+RRL +RY ++ K EFVH LN + A R + AIL
Sbjct: 342 WLPGQNKYREISSCSNCTDFQARRLNIRYRDKEE--GKREFVHTLNGSGLAVGRTLVAIL 399
Query: 344 ETHQTETG-VRIPDCLRKFV 362
E +Q E G V+IP+ LR ++
Sbjct: 400 ENYQQEDGSVKIPEVLRPYM 419
>gnl|CDD|235461 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 298 bits (765), Expect = 5e-98
Identities = 134/440 (30%), Positives = 191/440 (43%), Gaps = 107/440 (24%)
Query: 3 LDLDLFRTEKGGDPEKVRKNQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLCSK 62
LD+ L R +PE V++ R VD+++E D + R+ + + + +N SK
Sbjct: 2 LDIKLIRE----NPEAVKEALAKRGF-PLDVDELLELDEERRELQTELEELQAERNALSK 56
Query: 63 VIGEKMKAKEPVGD-----------------------------SSTLPGNHLHPSVPVSN 93
IG+ + E +P N H SVPV
Sbjct: 57 EIGQAKRKGEDAEALIAEVKELKEEIKALEAELDELEAELEELLLRIP-NLPHDSVPVGK 115
Query: 94 NEDENGIVRTKG-----DTEVRKKYSHVDLITMIDGVDSEAGAIVAGGRGYFLKGPAVCL 148
+ED+N VR G D E + H +L + +D E A V+G R Y LKG L
Sbjct: 116 DEDDNVEVRRWGEPREFDFEPK---DHWELGEKLGILDFERAAKVSGSRFYVLKGDGARL 172
Query: 149 QVGLVQYALSKWI-EKGYTPLYTPFFMRKEVMQEVAQLAQFDEELYKVIGKGEKVGDSAP 207
+ L+Q+ L E GYT + P+ + +E M QL +F+E+LYK+
Sbjct: 173 ERALIQFMLDLHTEEHGYTEVIPPYLVNEESMYGTGQLPKFEEDLYKI------------ 220
Query: 208 EKDELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQE-------------- 253
E DD YLI T+E P+ +HRD L E LP++Y S CFR E
Sbjct: 221 ---EDDDLYLIPTAEVPLTNLHRDEILDEEELPLKYTAYSPCFRSEAGSAGRDTRGLIRV 277
Query: 254 ----------------------DLTKS---------IAYRVVNIVSGALNHAAAKKLDLE 282
+LT + + YRVV + +G L +AAK DLE
Sbjct: 278 HQFDKVELVKFTKPEDSYAELEELTANAEEILQKLELPYRVVLLCTGDLGFSAAKTYDLE 337
Query: 283 AWFPGSGAFRELVSCSNCLDYQSRRLLVRYGQTKKMNEKIEFVHMLNATACATTRVICAI 342
W P +RE+ SCSNC D+Q+RR +RY + + K E VH LN + A R + AI
Sbjct: 338 VWLPSQNTYREISSCSNCTDFQARRANIRY--RDEGDGKPELVHTLNGSGLAVGRTLVAI 395
Query: 343 LETHQTETG-VRIPDCLRKF 361
LE +Q G V IP+ LR +
Sbjct: 396 LENYQQADGSVTIPEVLRPY 415
>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 = 280 bits (717), Expect = 5e-91
Identities = 131/442 (29%), Positives = 196/442 (44%), Gaps = 109/442 (24%)
Query: 3 LDLDLFRTEKGGDPEKVRKNQKDRFKNVEL-VDKVIENDLKWRQFRHKADNFNKFKNLCS 61
LD L R +P+ V+++ K R +V++ ++K+I D + ++ + + +N S
Sbjct: 2 LDRKLLR----NNPDLVKESLKARGLSVDIDLEKLIALDDERKKLLSEIEELQAKRNELS 57
Query: 62 KVIGEKMKAKEPVGDS------------------------------STLPGNHLHPSVPV 91
K IG+ K+ + ++P N H SVPV
Sbjct: 58 KQIGKAKGQKKDKIEEIKKELKELKEELTELSAALKALEAELQDKLLSIP-NIPHESVPV 116
Query: 92 SNNEDEN------GIVRTKGDTEVRKKYSHVDLITMIDGVDSEAGAIVAGGRGYFLKGPA 145
+E++N G D + + H +L + G+D + V G R Y+LK
Sbjct: 117 GKDEEDNLEVKRWGTPPVF-DFKPK---PHWELGEKLGGLDFDRAVKVTGSRFYYLKNDG 172
Query: 146 VCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEVAQLAQFDEELYKVIGKGEKVGDS 205
L+ L+ + L + GY +Y P+ + +E + QL +F+E+++K+
Sbjct: 173 AKLERALINFMLDLLEKNGYQEIYPPYLVNEESLDGTGQLPKFEEDIFKLED-------- 224
Query: 206 APEKDELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQE-----DLTK--- 257
D YLI T+E P+ +HR+ L E LPI+Y S CFR E TK
Sbjct: 225 -------TDLYLIPTAEVPLTNLHRNEILEEEELPIKYTAHSPCFRSEAGSYGKDTKGLI 277
Query: 258 -------------------------------------SIAYRVVNIVSGALNHAAAKKLD 280
+ YRVVN+ SG L +AAKK D
Sbjct: 278 RVHQFNKVELVKFCKPEESAEELEEMTSDAEQILQELELPYRVVNLCSGDLGFSAAKKYD 337
Query: 281 LEAWFPGSGAFRELVSCSNCLDYQSRRLLVRYGQTKKMNEKIEFVHMLNATACATTRVIC 340
LE W PG +RE+ SCSNC D+Q+RRL +RY K K ++VH LN TA A R I
Sbjct: 338 LEVWMPGQNTYREISSCSNCTDFQARRLNIRYKDKNK--GKNKYVHTLNGTALAIGRTIV 395
Query: 341 AILETHQTETG-VRIPDCLRKF 361
AILE +QTE G V IP+ LRK+
Sbjct: 396 AILENYQTEDGSVEIPEVLRKY 417
>gnl|CDD|177954 PLN02320, PLN02320, seryl-tRNA synthetase.
Length = 502
Score = 165 bits (420), Expect = 2e-46
Identities = 109/340 (32%), Positives = 165/340 (48%), Gaps = 77/340 (22%)
Query: 83 NHLHPSVPVSNNEDENGIVRTKGDTEVRKKYS---HVDLITMIDGVDSEAGAIVAGGRGY 139
N HP VPV +++ VR + + + H+ L +D D +A A V+G + Y
Sbjct: 169 NMTHPDVPVGG--EDSSAVRKEVGSPREFSFPIKDHLQLGKELDLFDFDAAAEVSGSKFY 226
Query: 140 FLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEVA-QLAQFDEELYKVIGK 198
+LK AV L++ LV + LS+ ++KG+TPL TP +R V+++ Q + ++Y + G
Sbjct: 227 YLKNEAVLLEMALVNWTLSEVMKKGFTPLTTPEIVRSSVVEKCGFQPRGDNTQVYSIDGS 286
Query: 199 GEKVGDSAPEKDELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFR------- 251
D+ LI T+E P+ +H DS L E++LP++Y+ S CFR
Sbjct: 287 ---------------DQCLIGTAEIPVGGIHMDSILLESALPLKYVAFSHCFRTEAGAAG 331
Query: 252 ------------------------------------QEDLTKSIA--YRVVNIVSGALNH 273
+EDL S+ ++ +++ + L
Sbjct: 332 AATRGLYRVHQFSKVEMFVICRPEESESFHEELIQIEEDLFTSLGLHFKTLDMATADLGA 391
Query: 274 AAAKKLDLEAWFPGSGAFRELVSCSNCLDYQSRRLLVRY-------GQTKKMNEKI---E 323
A +K D+EAW PG G + E+ S SNC DYQSRRL +RY KK + +
Sbjct: 392 PAYRKFDIEAWMPGLGRYGEISSASNCTDYQSRRLGIRYRPSEPPQTNPKKGKGSLGPTK 451
Query: 324 FVHMLNATACATTRVICAILETHQTETG-VRIPDCLRKFV 362
FVH LNATACA R+I +LE +Q E G V IP+ LR F+
Sbjct: 452 FVHTLNATACAVPRMIVCLLENYQQEDGSVVIPEPLRPFM 491
>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 = 88.8 bits (221), Expect = 6e-21
Identities = 41/178 (23%), Positives = 62/178 (34%), Gaps = 54/178 (30%)
Query: 152 LVQYALSKWIEKGYTPLYTPFFMRKEVMQEV-AQLAQFDEELYKVIGKGEKVGDSAPEKD 210
L + GY + TP KE+ + F+EE+YK +G +
Sbjct: 5 LENFIRELLKRYGYQEVDTPILEPKELWEGSGHWDDYFEEEMYKFKDRGGE--------- 55
Query: 211 ELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQE----------------- 253
+ YL T+E I + ++ L LP++ + CFR E
Sbjct: 56 ---ELYLRPTAEVGITRLFKNEILSYRELPLKLYQIGPCFRYEARPRRGLGRVREFTQVD 112
Query: 254 ------------------DLTKSI------AYRVVNIVSGALNHAAAKKLDLEAWFPG 287
L + I YRVV +G L +A+K+ DLEAW P
Sbjct: 113 AEIFGTPEQSEEELEELLKLAEEILQDLGLPYRVVLATTGDLGGSASKEGDLEAWLPA 170
>gnl|CDD|217020 pfam02403, Seryl_tRNA_N, Seryl-tRNA synthetase N-terminal domain.
This domain is found associated with the Pfam tRNA
synthetase class II domain (pfam00587) and represents
the N-terminal domain of seryl-tRNA synthetase.
Length = 108
Score = 73.4 bits (181), Expect = 4e-16
Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 2 VLDLDLFRTEKGGDPEKVRKNQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLCS 61
+LD+ L R +PE V++ + R +V VD+++E D + R+ + + + +N S
Sbjct: 1 MLDIKLIRE----NPEAVKEKLRKRGVDVLDVDELLELDEERRELQVELEELQAERNELS 56
Query: 62 KVIGEKMKAKE 72
K IG+ K KE
Sbjct: 57 KEIGKAKKKKE 67
>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 = 38.9 bits (91), Expect = 0.002
Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 8/92 (8%)
Query: 162 EKGYTPLYTPFFMRKEVMQEVAQLAQFDEELYKVIGKGEKVGDSAPEKDELDDKYLIATS 221
E GY + PF + + L + +E+Y KG ++ D D L +
Sbjct: 18 EYGYQEILFPFLAPTVLFFKGGHLDGYRKEMYTFEDKGRELRD--------TDLVLRPAA 69
Query: 222 EQPICAVHRDSWLPEASLPIRYLGVSTCFRQE 253
+PI + L +LP+R + CFR E
Sbjct: 70 CEPIYQIFSGEILSYRALPLRLDQIGPCFRHE 101
>gnl|CDD|180320 PRK05948, PRK05948, precorrin-2 methyltransferase; Provisional.
Length = 238
Score = 32.7 bits (75), Expect = 0.28
Identities = 14/56 (25%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 149 QVGLVQYALSKWI--EKGYTPLYTPFFMRKEVMQEVAQLAQFDEELYKVIGKGEKV 202
Q GL + ++ W+ ++ PLY P+ +E +++ Q A ++++ + +GE V
Sbjct: 42 QPGLAEQIIAPWLSPQQIKLPLYFPYVQDEEQLEQAWQAAA--DQVWHYLEQGEDV 95
>gnl|CDD|183145 PRK11462, PRK11462, putative transporter; Provisional.
Length = 460
Score = 33.0 bits (75), Expect = 0.28
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 9/54 (16%)
Query: 138 GYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEVAQLAQFDEE 191
F PA+C Y LS I K Y L T K VM+++AQ + ++
Sbjct: 407 ALFTIVPAIC-------YLLSAIIAKRYYSLTTHNL--KTVMEQLAQGKRRCQQ 451
>gnl|CDD|214462 MTH00217, ND4, NADH dehydrogenase subunit 4; Provisional.
Length = 482
Score = 32.3 bits (74), Expect = 0.39
Identities = 21/49 (42%), Positives = 24/49 (48%), Gaps = 15/49 (30%)
Query: 230 RDSW--LPEAS------------LPIRYLGVSTCFRQEDLTKSIAYRVV 264
R SW LPEAS L I Y ++TC RQ DL + IAY V
Sbjct: 258 RFSWPLLPEASEYFSPLIQTLSLLAIIYGSLTTC-RQVDLKRIIAYSSV 305
>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 = 30.5 bits (69), Expect = 1.0
Identities = 17/102 (16%), Positives = 33/102 (32%), Gaps = 18/102 (17%)
Query: 158 SKWIEKGYTPLYTPFFMRKEVMQEVAQLAQFDEELYKVIGKGEKVGDSAPEKDELDDKYL 217
E G+ + TP R+ + L + E K + E ++
Sbjct: 11 RFMAELGFQEVETPIVEREPL------LEKAGHE-PKDLLPV---------GAENEEDLY 54
Query: 218 IATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQEDLTKSI 259
+ + +P S + LP+R + FR E + +
Sbjct: 55 LRPTLEPGLVRLFVSHI--RKLPLRLAEIGPAFRNEGGRRGL 94
>gnl|CDD|184228 PRK13671, PRK13671, hypothetical protein; Provisional.
Length = 298
Score = 30.0 bits (68), Expect = 2.0
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 17 EKVRKNQKDRFKNVELVDKVIENDLKWRQFRH-KADNFNKFKNLC 60
+ VR K++ + LV + IEN K ++ A N++ F N C
Sbjct: 235 KIVRNTSKEKLAKIWLVSEGIENLFK----KNINAPNYDSFVNKC 275
>gnl|CDD|219131 pfam06676, DUF1178, Protein of unknown function (DUF1178). This
family consists of several hypothetical bacterial
proteins of around 150 residues in length. The function
of this family is unknown.
Length = 145
Score = 28.7 bits (65), Expect = 3.0
Identities = 12/33 (36%), Positives = 14/33 (42%), Gaps = 5/33 (15%)
Query: 282 EAWFPGSGAF-----RELVSCSNCLDYQSRRLL 309
E WF S F R LVSC C + + L
Sbjct: 15 EGWFASSADFDKQQARGLVSCPVCGSTEVEKAL 47
>gnl|CDD|214427 MTH00124, ND4, NADH dehydrogenase subunit 4; Provisional.
Length = 457
Score = 29.4 bits (67), Expect = 3.9
Identities = 10/16 (62%), Positives = 10/16 (62%), Gaps = 2/16 (12%)
Query: 247 STCFRQEDLTKS-IAY 261
C RQ DL KS IAY
Sbjct: 274 LICLRQTDL-KSLIAY 288
>gnl|CDD|233729 TIGR02103, pullul_strch, alpha-1,6-glucosidases, pullulanase-type.
Members of this protein family include secreted (or
membrane-anchored) pullulanases of Gram-negative
bacteria and pullulanase-type starch debranching enzymes
of plants. Both enzymes hydrolyze alpha-1,6 glycosidic
linkages. Pullulan is an unusual, industrially important
polysaccharide in which short alpha-1,4 chains
(maltotriose) are connected in alpha-1,6 linkages.
Enzymes that cleave alpha-1,6 linkages in pullulan and
release maltotriose are called pullulanases although
pullulan itself may not be the natural substrate. This
family is closely homologous to, but architecturally
different from, the Gram-positive pullulanases of
Gram-positive bacteria (TIGR02102) [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 898
Score = 29.4 bits (66), Expect = 4.7
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 322 IEFVHMLNATACATTRVICAILETHQTETGVRIPDCLRKFVPAVY--VNEAGEI 373
EF M+ A V+ ++ H +G L K VP Y +NE G +
Sbjct: 404 KEFREMVQALNKTGLNVVMDVVYNHTNASGPNDRSVLDKIVPGYYHRLNEDGGV 457
>gnl|CDD|215474 PLN02877, PLN02877, alpha-amylase/limit dextrinase.
Length = 970
Score = 29.0 bits (65), Expect = 6.1
Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 1/46 (2%)
Query: 322 IEFVHMLNATACATTRVICAILETHQTETG-VRIPDCLRKFVPAVY 366
IEF M+ A RV+ ++ H +G L K VP Y
Sbjct: 466 IEFRKMVQALNRIGLRVVLDVVYNHLHSSGPFDENSVLDKIVPGYY 511
>gnl|CDD|185429 PTZ00074, PTZ00074, 60S ribosomal protein L34; Provisional.
Length = 135
Score = 27.3 bits (61), Expect = 7.5
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 351 GVRIPDCLRKFVPAVYVNEAGEIPFVKTAPIDEEETKKQKKQKEGMKKK 399
GV C+R + ++ E E VK ++ + KKQKK+K+ KKK
Sbjct: 78 GVLCHKCVRDRIVRAFLVE--EQKIVKQVLKEKAKQKKQKKKKKKKKKK 124
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
0.317 0.135 0.395
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,429,053
Number of extensions: 1976415
Number of successful extensions: 1778
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1746
Number of HSP's successfully gapped: 35
Length of query: 399
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 300
Effective length of database: 6,546,556
Effective search space: 1963966800
Effective search space used: 1963966800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 60 (26.8 bits)