RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 043456
(447 letters)
>gnl|CDD|215364 PLN02678, PLN02678, seryl-tRNA synthetase.
Length = 448
Score = 909 bits (2350), Expect = 0.0
Identities = 360/447 (80%), Positives = 405/447 (90%)
Query: 1 MLDINLFREEKGGIPEKIRESQRRRFASVDLVDEIISLDKKWRQLQFDVENYRKELNKIN 60
MLDINLFREEKGG PE IRESQRRRFASV+LVDE+I+LDK+WRQ QF++++ RKE NK+N
Sbjct: 1 MLDINLFREEKGGDPELIRESQRRRFASVELVDEVIALDKEWRQRQFELDSLRKEFNKLN 60
Query: 61 KQIAQLKLSGKDFSEMVTKTNEIKQQSADKEVEVREAWAAVKAKLEVVGNLVHDSVPVSN 120
K++A+LK++ +D +E++ +T E+K++ +KE EV+EA AA+ AKL+ +GNLVHDSVPVSN
Sbjct: 61 KEVAKLKIAKEDATELIAETKELKKEITEKEAEVQEAKAALDAKLKTIGNLVHDSVPVSN 120
Query: 121 DEANNAIVRTWGEKRTEPKLKNHVELVELLGIADLKKGADIAGGRGFYLKGDGVRLNQAL 180
DEANNA+VRTWGEKR EPKLKNHV+LVELLGI D ++GAD+AGGRG+YLKG GV LNQAL
Sbjct: 121 DEANNAVVRTWGEKRQEPKLKNHVDLVELLGIVDTERGADVAGGRGYYLKGAGVLLNQAL 180
Query: 181 INFGLDFLEKKSYTLLHTPFFMRKEVMAKCAQLAQFDEELYKVTGEGDDKYLIATAEQPL 240
INFGL FL K+ YT L TPFFMRK+VMAKCAQLAQFDEELYKVTGEGDDKYLIAT+EQPL
Sbjct: 181 INFGLAFLRKRGYTPLQTPFFMRKDVMAKCAQLAQFDEELYKVTGEGDDKYLIATSEQPL 240
Query: 241 CAYHIDDWIHPSELPIRYAGYSSCFRKEAGSHGRDTLGIFRVHQFEKVEQFCITSPNGND 300
CAYH DWI P ELPIRYAGYS+CFRKEAGSHGRDTLGIFRVHQFEKVEQFCITSPNGN+
Sbjct: 241 CAYHRGDWIDPKELPIRYAGYSTCFRKEAGSHGRDTLGIFRVHQFEKVEQFCITSPNGNE 300
Query: 301 SWDMHEEMIKNSEEFYQMLKIPYQVVAIVSGALNDAAAKKLDLEAWFPASQTYRELVSCS 360
SW+MHEEM+KNSE+FYQ L IPYQVV+IVSGALNDAAAKK DLEAWFPAS+TYRELVSCS
Sbjct: 301 SWEMHEEMLKNSEDFYQSLGIPYQVVSIVSGALNDAAAKKYDLEAWFPASKTYRELVSCS 360
Query: 361 NCTDYQSRRLEIRYGQKKSNEQTKQYVHLLNSTLTATERTICCILENYQKEDGVEVPEVL 420
NCTDYQSRRLEIRYGQKKSNEQTKQYVHLLNSTLTATERT+CCILENYQ EDGV VPEVL
Sbjct: 361 NCTDYQSRRLEIRYGQKKSNEQTKQYVHLLNSTLTATERTLCCILENYQTEDGVRVPEVL 420
Query: 421 QPFMGGKTFLPFKAKPAPEAKGKKSKA 447
QPFMGG FLPFK KP + KGKK K
Sbjct: 421 QPFMGGIEFLPFKKKPPAKGKGKKKKK 447
>gnl|CDD|235461 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 532 bits (1373), Expect = 0.0
Identities = 197/434 (45%), Positives = 272/434 (62%), Gaps = 14/434 (3%)
Query: 1 MLDINLFREEKGGIPEKIRESQRRRFASVDLVDEIISLDKKWRQLQFDVENYRKELNKIN 60
MLDI L RE PE ++E+ +R +D VDE++ LD++ R+LQ ++E + E N ++
Sbjct: 1 MLDIKLIREN----PEAVKEALAKRGFPLD-VDELLELDEERRELQTELEELQAERNALS 55
Query: 61 KQIAQLKLSGKDFSEMVTKTNEIKQQSADKEVEVREAWAAVKAKLEVVGNLVHDSVPVSN 120
K+I Q K G+D ++ + E+K++ E E+ E A ++ L + NL HDSVPV
Sbjct: 56 KEIGQAKRKGEDAEALIAEVKELKEEIKALEAELDELEAELEELLLRIPNLPHDSVPVGK 115
Query: 121 DEANNAIVRTWGEKRT-EPKLKNHVELVELLGIADLKKGADIAGGRGFYLKGDGVRLNQA 179
DE +N VR WGE R + + K+H EL E LGI D ++ A ++G R + LKGDG RL +A
Sbjct: 116 DEDDNVEVRRWGEPREFDFEPKDHWELGEKLGILDFERAAKVSGSRFYVLKGDGARLERA 175
Query: 180 LINFGLDFL-EKKSYTLLHTPFFMRKEVMAKCAQLAQFDEELYKVTGEGDDKYLIATAEQ 238
LI F LD E+ YT + P+ + +E M QL +F+E+LYK+ E DD YLI TAE
Sbjct: 176 LIQFMLDLHTEEHGYTEVIPPYLVNEESMYGTGQLPKFEEDLYKI--EDDDLYLIPTAEV 233
Query: 239 PLCAYHIDDWIHPSELPIRYAGYSSCFRKEAGSHGRDTLGIFRVHQFEKVEQFCITSPNG 298
PL H D+ + ELP++Y YS CFR EAGS GRDT G+ RVHQF+KVE T P
Sbjct: 234 PLTNLHRDEILDEEELPLKYTAYSPCFRSEAGSAGRDTRGLIRVHQFDKVELVKFTKP-- 291
Query: 299 NDSWDMHEEMIKNSEEFYQMLKIPYQVVAIVSGALNDAAAKKLDLEAWFPASQTYRELVS 358
DS+ EE+ N+EE Q L++PY+VV + +G L +AAK DLE W P+ TYRE+ S
Sbjct: 292 EDSYAELEELTANAEEILQKLELPYRVVLLCTGDLGFSAAKTYDLEVWLPSQNTYREISS 351
Query: 359 CSNCTDYQSRRLEIRYGQKKSNEQTKQYVHLLNSTLTATERTICCILENYQKEDG-VEVP 417
CSNCTD+Q+RR IRY + + + VH LN + A RT+ ILENYQ+ DG V +P
Sbjct: 352 CSNCTDFQARRANIRY--RDEGDGKPELVHTLNGSGLAVGRTLVAILENYQQADGSVTIP 409
Query: 418 EVLQPFMGGKTFLP 431
EVL+P+MGG +P
Sbjct: 410 EVLRPYMGGLEVIP 423
>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 = 510 bits (1316), Expect = 0.0
Identities = 179/303 (59%), Positives = 215/303 (70%), Gaps = 8/303 (2%)
Query: 124 NNAIVRTWGEKRTEP-KLKNHVELVELLGIADLKKGADIAGGRGFYLKGDGVRLNQALIN 182
+N +R WGE R K K+HVEL E L I D ++GA ++G R +YLKGDG L +ALIN
Sbjct: 1 DNVEIRRWGEPRVFDFKPKDHVELGEKLDILDFERGAKVSGSRFYYLKGDGALLERALIN 60
Query: 183 FGLDFLEKKSYTLLHTPFFMRKEVMAKCAQLAQFDEELYKVTGEGDDKYLIATAEQPLCA 242
F LDFL K+ +T + PF +RKEVM QL +FDE+LYKV EG+D YLIATAE PL A
Sbjct: 61 FALDFLTKRGFTPVIPPFLVRKEVMEGTGQLPKFDEQLYKV--EGEDLYLIATAEVPLAA 118
Query: 243 YHIDDWIHPSELPIRYAGYSSCFRKEAGSHGRDTLGIFRVHQFEKVEQFCITSPNGNDSW 302
H D+ + ELP++YAGYS CFRKEAGS GRDT G+FRVHQFEKVEQF T P +SW
Sbjct: 119 LHRDEILEEEELPLKYAGYSPCFRKEAGSAGRDTRGLFRVHQFEKVEQFVFTKPE--ESW 176
Query: 303 DMHEEMIKNSEEFYQMLKIPYQVVAIVSGALNDAAAKKLDLEAWFPASQTYRELVSCSNC 362
+ EE+I N+EE Q L +PY+VV I +G L AAAKK D+EAW P YRE+ SCSNC
Sbjct: 177 EELEELISNAEEILQELGLPYRVVNICTGDLGFAAAKKYDIEAWMPGQGKYREISSCSNC 236
Query: 363 TDYQSRRLEIRYGQKKSNEQTKQYVHLLNSTLTATERTICCILENYQKEDG-VEVPEVLQ 421
TD+Q+RRL IRY KK + KQYVH LN T AT RTI ILENYQ EDG V +PEVL+
Sbjct: 237 TDFQARRLNIRYRDKKDGK--KQYVHTLNGTALATPRTIVAILENYQTEDGSVVIPEVLR 294
Query: 422 PFM 424
P+M
Sbjct: 295 PYM 297
>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 511 bits (1319), Expect = 0.0
Identities = 188/439 (42%), Positives = 270/439 (61%), Gaps = 15/439 (3%)
Query: 1 MLDINLFREEKGGIPEKIRESQRRRFASVDLVDEIISLDKKWRQLQFDVENYRKELNKIN 60
MLD+ L RE P+ +RE ++R VD+++ LD++ R+L ++E + E N+++
Sbjct: 1 MLDLKLIREN----PDAVREKLKKRGGDALDVDKLLELDEERRKLLRELEELQAERNELS 56
Query: 61 KQIAQLKLSG-KDFSEMVTKTNEIKQQSADKEVEVREAWAAVKAKLEVVGNLVHDSVPVS 119
K+I + G D E++ + E+K++ + E + E A + L + N+ H+SVPV
Sbjct: 57 KEIGRALKRGEDDAEELIAEVKELKEKLKELEAALDELEAELDTLLLTIPNIPHESVPVG 116
Query: 120 NDEANNAIVRTWGEKRTEP---KLKNHVELVELLGIADLKKGADIAGGRGFYLKGDGVRL 176
DE +N VR WGE + K+HVEL E LG+ D ++ A ++G R ++ KG G RL
Sbjct: 117 KDEDDNVEVRRWGEPPVFVFDFEPKDHVELGEKLGLLDFERAAKVSGSRFYFYKGKGARL 176
Query: 177 NQALINFGLDFLEKKSYTLLHTPFFMRKEVMAKCAQLAQFDEELYKVTGEGDDKYLIATA 236
+ALI F LD K +T + P+ + E M QL +F+E+LYKV E D YLI TA
Sbjct: 177 ERALIQFMLDLHTKHGFTEVLPPYLVNLESMFGTGQLPKFEEDLYKV--EDPDLYLIPTA 234
Query: 237 EQPLCAYHIDDWIHPSELPIRYAGYSSCFRKEAGSHGRDTLGIFRVHQFEKVEQFCITSP 296
E PL H D+ + +LPI+Y YS CFR EAGS G+DT G+ RVHQF+KVE IT P
Sbjct: 235 EVPLTNLHRDEILDEEDLPIKYTAYSPCFRSEAGSAGKDTRGLIRVHQFDKVELVVITKP 294
Query: 297 NGNDSWDMHEEMIKNSEEFYQMLKIPYQVVAIVSGALNDAAAKKLDLEAWFPASQTYREL 356
+S + EEM+ N+EE Q L++PY+VV + +G L +AAKK DLE W P YRE+
Sbjct: 295 E--ESEEELEEMLGNAEEVLQELELPYRVVNLCTGDLGFSAAKKYDLEVWLPGQNKYREI 352
Query: 357 VSCSNCTDYQSRRLEIRYGQKKSNEQTKQYVHLLNSTLTATERTICCILENYQKEDG-VE 415
SCSNCTD+Q+RRL IRY K+ + +++VH LN + A RT+ ILENYQ+EDG V+
Sbjct: 353 SSCSNCTDFQARRLNIRYRDKEEGK--REFVHTLNGSGLAVGRTLVAILENYQQEDGSVK 410
Query: 416 VPEVLQPFMGGKTFLPFKA 434
+PEVL+P+MGG +P
Sbjct: 411 IPEVLRPYMGGLEIIPKPK 429
>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 = 472 bits (1216), Expect = e-165
Identities = 183/428 (42%), Positives = 258/428 (60%), Gaps = 14/428 (3%)
Query: 1 MLDINLFREEKGGIPEKIRESQRRRFASVDLVDEIIS-LDKKWRQLQFDVENYRKELNKI 59
MLD L R P+ ++ES + R SVD+ E + LD + ++L ++E + + N++
Sbjct: 1 MLDRKLLRNN----PDLVKESLKARGLSVDIDLEKLIALDDERKKLLSEIEELQAKRNEL 56
Query: 60 NKQIAQLKLSGKDFSEMVTK-TNEIKQQSADKEVEVREAWAAVKAKLEVVGNLVHDSVPV 118
+KQI + K KD E + K E+K++ + ++ A ++ KL + N+ H+SVPV
Sbjct: 57 SKQIGKAKGQKKDKIEEIKKELKELKEELTELSAALKALEAELQDKLLSIPNIPHESVPV 116
Query: 119 SNDEANNAIVRTWGEKRTEP-KLKNHVELVELLGIADLKKGADIAGGRGFYLKGDGVRLN 177
DE +N V+ WG K K H EL E LG D + + G R +YLK DG +L
Sbjct: 117 GKDEEDNLEVKRWGTPPVFDFKPKPHWELGEKLGGLDFDRAVKVTGSRFYYLKNDGAKLE 176
Query: 178 QALINFGLDFLEKKSYTLLHTPFFMRKEVMAKCAQLAQFDEELYKVTGEGDDKYLIATAE 237
+ALINF LD LEK Y ++ P+ + +E + QL +F+E+++K+ E D YLI TAE
Sbjct: 177 RALINFMLDLLEKNGYQEIYPPYLVNEESLDGTGQLPKFEEDIFKL--EDTDLYLIPTAE 234
Query: 238 QPLCAYHIDDWIHPSELPIRYAGYSSCFRKEAGSHGRDTLGIFRVHQFEKVEQFCITSPN 297
PL H ++ + ELPI+Y +S CFR EAGS+G+DT G+ RVHQF KVE P
Sbjct: 235 VPLTNLHRNEILEEEELPIKYTAHSPCFRSEAGSYGKDTKGLIRVHQFNKVELVKFCKPE 294
Query: 298 GNDSWDMHEEMIKNSEEFYQMLKIPYQVVAIVSGALNDAAAKKLDLEAWFPASQTYRELV 357
+S + EEM ++E+ Q L++PY+VV + SG L +AAKK DLE W P TYRE+
Sbjct: 295 --ESAEELEEMTSDAEQILQELELPYRVVNLCSGDLGFSAAKKYDLEVWMPGQNTYREIS 352
Query: 358 SCSNCTDYQSRRLEIRYGQKKSNEQTKQYVHLLNSTLTATERTICCILENYQKEDG-VEV 416
SCSNCTD+Q+RRL IRY K N+ +YVH LN T A RTI ILENYQ EDG VE+
Sbjct: 353 SCSNCTDFQARRLNIRYKDK--NKGKNKYVHTLNGTALAIGRTIVAILENYQTEDGSVEI 410
Query: 417 PEVLQPFM 424
PEVL+ ++
Sbjct: 411 PEVLRKYL 418
>gnl|CDD|177954 PLN02320, PLN02320, seryl-tRNA synthetase.
Length = 502
Score = 265 bits (679), Expect = 9e-84
Identities = 156/448 (34%), Positives = 248/448 (55%), Gaps = 26/448 (5%)
Query: 2 LDINLFREEKGGIPEKIRESQRRRFASVDLVDEIISLDKKWRQLQFDVENYRKELNKI-N 60
+D R+ K + IR R A+++LV + L + LQ +VE R E N + N
Sbjct: 67 IDFKWIRDNKEAVAINIRN--RNSNANLELV---LELYENMLALQKEVERLRAERNAVAN 121
Query: 61 KQIAQLKLSGKDFSEMVTKTNEIKQQSADKEVEVREAWAAVKAKLEVVGNLVHDSVPVSN 120
K +L+ S + +V + +K+ E ++ + ++ + + + N+ H VPV
Sbjct: 122 KMKGKLEPSER--QALVEEGKNLKEGLVTLEEDLVKLTDELQLEAQSIPNMTHPDVPVGG 179
Query: 121 DEANNAIVRTWGEKRT-EPKLKNHVELVELLGIADLKKGADIAGGRGFYLKGDGVRLNQA 179
++++ A+ + G R +K+H++L + L + D A+++G + +YLK + V L A
Sbjct: 180 EDSS-AVRKEVGSPREFSFPIKDHLQLGKELDLFDFDAAAEVSGSKFYYLKNEAVLLEMA 238
Query: 180 LINFGLDFLEKKSYTLLHTPFFMRKEVMAKCA-QLAQFDEELYKVTGEGDDKYLIATAEQ 238
L+N+ L + KK +T L TP +R V+ KC Q + ++Y + +G D+ LI TAE
Sbjct: 239 LVNWTLSEVMKKGFTPLTTPEIVRSSVVEKCGFQPRGDNTQVYSI--DGSDQCLIGTAEI 296
Query: 239 PLCAYHIDDWIHPSELPIRYAGYSSCFRKEAGSHGRDTLGIFRVHQFEKVEQFCITSPNG 298
P+ H+D + S LP++Y +S CFR EAG+ G T G++RVHQF KVE F I P
Sbjct: 297 PVGGIHMDSILLESALPLKYVAFSHCFRTEAGAAGAATRGLYRVHQFSKVEMFVICRPEE 356
Query: 299 NDSWDMHEEMIKNSEEFYQMLKIPYQVVAIVSGALNDAAAKKLDLEAWFPASQTYRELVS 358
++S+ HEE+I+ E+ + L + ++ + + + L A +K D+EAW P Y E+ S
Sbjct: 357 SESF--HEELIQIEEDLFTSLGLHFKTLDMATADLGAPAYRKFDIEAWMPGLGRYGEISS 414
Query: 359 CSNCTDYQSRRLEIRY----------GQKKSNEQTKQYVHLLNSTLTATERTICCILENY 408
SNCTDYQSRRL IRY + K + ++VH LN+T A R I C+LENY
Sbjct: 415 ASNCTDYQSRRLGIRYRPSEPPQTNPKKGKGSLGPTKFVHTLNATACAVPRMIVCLLENY 474
Query: 409 QKEDG-VEVPEVLQPFMGGKTFLPFKAK 435
Q+EDG V +PE L+PFMGG + K+K
Sbjct: 475 QQEDGSVVIPEPLRPFMGGLELIKPKSK 502
>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 = 163 bits (416), Expect = 8e-49
Identities = 60/176 (34%), Positives = 90/176 (51%), Gaps = 8/176 (4%)
Query: 176 LNQALINFGLDFLEKKSYTLLHTPFFMRKEVMAKC-AQLAQFDEELYKVTG-EGDDKYLI 233
L AL NF + L++ Y + TP KE+ F+EE+YK G++ YL
Sbjct: 1 LRNALENFIRELLKRYGYQEVDTPILEPKELWEGSGHWDDYFEEEMYKFKDRGGEELYLR 60
Query: 234 ATAEQPLCAYHIDDWIHPSELPIRYAGYSSCFRKEAGSHGRDTLGIFRVHQFEKVEQFCI 293
TAE + ++ + ELP++ CFR EA R G+ RV +F +V+
Sbjct: 61 PTAEVGITRLFKNEILSYRELPLKLYQIGPCFRYEA----RPRRGLGRVREFTQVDAEIF 116
Query: 294 TSPNGNDSWDMHEEMIKNSEEFYQMLKIPYQVVAIVSGALNDAAAKKLDLEAWFPA 349
+P S + EE++K +EE Q L +PY+VV +G L +A+K+ DLEAW PA
Sbjct: 117 GTP--EQSEEELEELLKLAEEILQDLGLPYRVVLATTGDLGGSASKEGDLEAWLPA 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 = 105 bits (264), Expect = 2e-27
Identities = 37/112 (33%), Positives = 63/112 (56%), Gaps = 4/112 (3%)
Query: 1 MLDINLFREEKGGIPEKIRESQRRRFASVDLVDEIISLDKKWRQLQFDVENYRKELNKIN 60
MLDI L RE PE ++E R+R V VDE++ LD++ R+LQ ++E + E N+++
Sbjct: 1 MLDIKLIREN----PEAVKEKLRKRGVDVLDVDELLELDEERRELQVELEELQAERNELS 56
Query: 61 KQIAQLKLSGKDFSEMVTKTNEIKQQSADKEVEVREAWAAVKAKLEVVGNLV 112
K+I + K +D ++ + E+K + E E+RE A + L + N+
Sbjct: 57 KEIGKAKKKKEDAEALIAEVKELKDELKALEAELRELEAELDKLLLSIPNIP 108
>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 = 86.3 bits (214), Expect = 2e-19
Identities = 44/210 (20%), Positives = 70/210 (33%), Gaps = 19/210 (9%)
Query: 173 GVRLNQALINFGLDFLEKKSYTLLHTPFFMRKEVMAKCAQLAQFDEELYKVT-----GEG 227
G L +AL F D + + Y + PF + K L + +E+Y
Sbjct: 1 GTALWRALERFLDDRMAEYGYQEILFPFLAPTVLFFKGGHLDGYRKEMYTFEDKGRELRD 60
Query: 228 DDKYLIATAEQPLCAYHIDDWIHPSELPIRYAGYSSCFRKEAGSHGRDTLGIFRVHQFEK 287
D L A +P+ + + LP+R CFR E G+ RV +F +
Sbjct: 61 TDLVLRPAACEPIYQIFSGEILSYRALPLRLDQIGPCFRHEP----SGRRGLMRVREFRQ 116
Query: 288 VEQFCITSPNGNDSWDMHEEMIKNSEEFYQMLKIPYQVV-----AIVSGALNDAAA---K 339
VE P + E ++ +EE + L +P +VV G A
Sbjct: 117 VEYVVFGEPEEAEEE--RREWLELAEEIARELGLPVRVVVADDPFFGRGGKRGLDAGRET 174
Query: 340 KLDLEAWFPASQTYRELVSCSNCTDYQSRR 369
++ E P +E S
Sbjct: 175 VVEFELLLPLPGRAKETAVGSANVHLDHFG 204
>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 = 57.1 bits (138), Expect = 2e-09
Identities = 41/203 (20%), Positives = 74/203 (36%), Gaps = 16/203 (7%)
Query: 178 QALINFGLDFLEKKSYTLLHTPFFMRKEVMAKCAQLAQFDEELYKVTGEGDDKYLIATAE 237
+ F+ + + + TP R+ ++ K + +L V E ++ +
Sbjct: 3 SKIEQKLRRFMAELGFQEVETPIVEREPLLEKAGHEPK---DLLPVGAENEEDLYLRPTL 59
Query: 238 QPLCAYHIDDWIHPSELPIRYAGYSSCFRKEAGSHGRDTLGIFRVHQFEKVEQFCITSPN 297
+P I LP+R A FR E G G+ RV +F ++E
Sbjct: 60 EPGLVRLFVSHIRK--LPLRLAEIGPAFRNEGGR-----RGLRRVREFTQLEGEVFGEDG 112
Query: 298 GNDSWDMHEEMIKNSEEFYQML--KIPYQVVAIVSGALNDAAAK-KLDLEAWFPASQTYR 354
S EE+I+ +EE + L K+ V G + A ++E P
Sbjct: 113 EEASE--FEELIELTEELLRALGIKLDIVFVEKTPGEFSPGGAGPGFEIEVDHP-EGRGL 169
Query: 355 ELVSCSNCTDYQSRRLEIRYGQK 377
E+ S D Q+R ++ + +
Sbjct: 170 EIGSGGYRQDEQARAADLYFLDE 192
>gnl|CDD|223518 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 589
Score = 48.0 bits (115), Expect = 7e-06
Identities = 33/172 (19%), Positives = 58/172 (33%), Gaps = 24/172 (13%)
Query: 133 EKRTEPKLKNHVELVELLGIADLKKGADIAGGRGFYLKGDGVRLNQALINFGLDFLEKKS 192
++ E K ++H +L + L + G F+ G + L ++ L
Sbjct: 182 KRLEEAKKRDHRKLGKELDLFSFSPE--EGPGLPFWHP-KGATIRNLLEDYVRTKLRSYG 238
Query: 193 YTLLHTPFFMRKEVMAKCAQLAQFDEELYKVTGEGDDKYLIATAEQPLCAYHI----DDW 248
Y + TP E+ + E+++ + + L C HI
Sbjct: 239 YQEVKTPVLADLELWELSGHWDNYKEDMFLTESDDREYALKPMN----CPGHILIFKSGL 294
Query: 249 IHPSELPIRYAGYSSCFRKEA-GSHGRDTLGIFRV--------HQFEKVEQF 291
ELP+R A + +R E G+ G+ RV H F +Q
Sbjct: 295 RSYRELPLRLAEFGYVYRYEKSGA----LHGLMRVRGFTQDDAHIFCTPDQI 342
>gnl|CDD|238394 cd00771, ThrRS_core, Threonyl-tRNA synthetase (ThrRS) class II core
catalytic domain. ThrRS is a homodimer. It is
responsible for the attachment of threonine to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. Class II assignment is
based upon its structure and the presence of three
characteristic sequence motifs in the core domain.
Length = 298
Score = 39.5 bits (93), Expect = 0.002
Identities = 23/108 (21%), Positives = 41/108 (37%), Gaps = 12/108 (11%)
Query: 167 FYLKGDGVRLNQALINFGLDFLEKKSYTLLHTPFFMRKEVMAKCAQLAQFDEELYKVTGE 226
+ KG +R L +F + K+ Y + TP KE+ + E ++ E
Sbjct: 25 WLPKGAIIR--NELEDFLRELQRKRGYQEVETPIIYNKELWETSGHWDHYRENMFPFEEE 82
Query: 227 GDDKYLIATAEQPL-CAYHI----DDWIHPSELPIRYAGYSSCFRKEA 269
++ L +P+ C H +LP+R A + + R E
Sbjct: 83 DEEYGL-----KPMNCPGHCLIFKSKPRSYRDLPLRLAEFGTVHRYEQ 125
>gnl|CDD|232967 TIGR00418, thrS, threonyl-tRNA synthetase. This model represents
the threonyl-tRNA synthetase found in most organisms.
This protein is a class II tRNA synthetase, and is
recognized by the pfam model tRNA-synt_2b. Note that B.
subtilis has closely related isozymes thrS and thrZ. The
N-terminal regions are quite dissimilar between archaeal
and eubacterial forms, while some eukaryotic forms are
missing sequence there altogether. [Protein synthesis,
tRNA aminoacylation].
Length = 563
Score = 38.8 bits (91), Expect = 0.004
Identities = 28/142 (19%), Positives = 48/142 (33%), Gaps = 11/142 (7%)
Query: 133 EKRTEPKLKN-HVELVELLGIADLKKGADIAGGRGFYLKGDGVRLNQALINFGLDFLEKK 191
R E K H +L + L + + +I G F+L G + L +F K
Sbjct: 161 LLRLEEAKKRDHRKLGKELELFSFEP--EIGPGLPFWLP-KGATIRNLLEDFVRQKQIKY 217
Query: 192 SYTLLHTPFFMRKEVMAKCAQLAQFDEELYKVTGEGDDKYLIATAEQPLCAYHI----DD 247
Y + TP E+ + E ++ T + ++++ C H
Sbjct: 218 GYMEVETPIMYDLELWEISGHWDNYKERMFPFTELDNREFMLKPMN---CPGHFLIFKSS 274
Query: 248 WIHPSELPIRYAGYSSCFRKEA 269
+LP+R A R E
Sbjct: 275 LRSYRDLPLRIAELGYSHRYEQ 296
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 35.8 bits (83), Expect = 0.054
Identities = 15/91 (16%), Positives = 40/91 (43%)
Query: 16 EKIRESQRRRFASVDLVDEIISLDKKWRQLQFDVENYRKELNKINKQIAQLKLSGKDFSE 75
K ++ +L + +L ++ +L+ ++ R EL ++ ++I L+ + SE
Sbjct: 359 AKEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSE 418
Query: 76 MVTKTNEIKQQSADKEVEVREAWAAVKAKLE 106
+ E ++ + E++ + +LE
Sbjct: 419 RLEDLKEELKELEAELEELQTELEELNEELE 449
Score = 30.5 bits (69), Expect = 2.3
Identities = 16/94 (17%), Positives = 41/94 (43%), Gaps = 8/94 (8%)
Query: 21 SQRRRFASVDL-VDEIISLDKKWRQLQFDVENYRKE-------LNKINKQIAQLKLSGKD 72
R + L + ++ L K+ +L+ ++ +E L + K+I +LK ++
Sbjct: 219 KAELRELELALLLAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEE 278
Query: 73 FSEMVTKTNEIKQQSADKEVEVREAWAAVKAKLE 106
E + + E + ++ E+ + ++ +LE
Sbjct: 279 LREELEELQEELLELKEEIEELEGEISLLRERLE 312
Score = 29.3 bits (66), Expect = 5.5
Identities = 13/83 (15%), Positives = 39/83 (46%), Gaps = 5/83 (6%)
Query: 34 EIISLDKKWRQLQF-----DVENYRKELNKINKQIAQLKLSGKDFSEMVTKTNEIKQQSA 88
L + R+L+ ++ RKEL ++ +++++L+ ++ E + + + ++
Sbjct: 214 RYQELKAELRELELALLLAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELK 273
Query: 89 DKEVEVREAWAAVKAKLEVVGNL 111
+ E+RE ++ +L +
Sbjct: 274 SELEELREELEELQEELLELKEE 296
>gnl|CDD|183530 PRK12444, PRK12444, threonyl-tRNA synthetase; Reviewed.
Length = 639
Score = 34.7 bits (80), Expect = 0.090
Identities = 43/156 (27%), Positives = 70/156 (44%), Gaps = 21/156 (13%)
Query: 137 EPKLKNHVELVELLGIADLKKGADIAGGRGFYL-KGDGVRLNQALINFGLDFLEKKSYTL 195
E +NH +L + L L ++ A G FYL KG +R L F + ++ +Y
Sbjct: 241 EAAKRNHRKLGKELE---LFMFSEEAPGMPFYLPKGQIIR--NELEAFLREIQKEYNYQE 295
Query: 196 LHTPFFMRKEVMAKCAQLAQFDEELYKVTGEGDDKYLIATAEQPL-CAYHI---DDWIHP 251
+ TPF M +E+ + + + +Y E D+K A +P+ C H+ + +H
Sbjct: 296 VRTPFMMNQELWERSGHWDHYKDNMY--FSEVDNKSF---ALKPMNCPGHMLMFKNKLHS 350
Query: 252 -SELPIRYAGYSSCFRKE-AGSHGRDTLGIFRVHQF 285
ELPIR + R E +G+ G+ RV F
Sbjct: 351 YRELPIRMCEFGQVHRHEFSGALN----GLLRVRTF 382
>gnl|CDD|217817 pfam03961, DUF342, Protein of unknown function (DUF342). This
family of bacterial proteins has no known function. The
proteins are in the region of 500-600 amino acid
residues in length.
Length = 450
Score = 34.5 bits (80), Expect = 0.092
Identities = 21/107 (19%), Positives = 45/107 (42%), Gaps = 13/107 (12%)
Query: 37 SLDKKWRQLQFDVENYRKELNKINKQIAQLKLS-----GKDFSEMVTKTNEIKQQSADKE 91
L ++ ++L+ +++ +EL KI K + +L + E + K E K++ +++
Sbjct: 331 ELKEELKELEEELKELEEELEKIKKLLKKLPKKARGQLPPEKREQLEKLLETKEKLSEEL 390
Query: 92 VEVREAWAAVKAKLE--------VVGNLVHDSVPVSNDEANNAIVRT 130
E+ E +K +LE V ++ V + I R
Sbjct: 391 EELEEELKELKEELESLYSEGKISVNKTIYPGVKIHIGNKVLRIKRE 437
>gnl|CDD|237851 PRK14894, PRK14894, glycyl-tRNA synthetase; Provisional.
Length = 539
Score = 34.6 bits (79), Expect = 0.094
Identities = 40/183 (21%), Positives = 72/183 (39%), Gaps = 24/183 (13%)
Query: 253 ELPIRYAGYSSCFRKEAGSHGRDTLGIFRVHQFEKVEQFCITSPNGNDSWDMHEEMIKNS 312
+LP A FR E +FRV +FE++E P ++ W H+ ++
Sbjct: 163 KLPFGIAQVGKAFRNEINPRNF----LFRVREFEQMEIEYFVMPGTDEEW--HQRWLEAR 216
Query: 313 EEFYQMLKIPYQVVAIV---SGALNDAAAKKLDLEAWFPASQTYRELVSCSNCTDYQSRR 369
+++ + IP + I L + + DL +P + +E+ +N TDY
Sbjct: 217 LAWWEQIGIPRSRITIYDVPPDELAHYSKRTFDLMYDYP-NIGVQEIEGIANRTDYD--- 272
Query: 370 LEIRYGQKKSNEQTKQYVHLLNSTLTATERTICCILENYQKEDGVE-VPEVLQPFMG-GK 427
G +++ +N +T R L + + G VP V++P G G+
Sbjct: 273 ----LGSHSKDQEQLNLTARVNPNEDSTAR-----LTYFDQASGRHVVPYVIEPSAGVGR 323
Query: 428 TFL 430
L
Sbjct: 324 CML 326
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 34.6 bits (80), Expect = 0.11
Identities = 12/90 (13%), Positives = 40/90 (44%), Gaps = 4/90 (4%)
Query: 16 EKIRESQRRRFASVDLVDEIISLDKKWRQLQFDVENYRKELNKINKQIAQLKLSGKDFSE 75
+K +R L ++ L+ + +L+ ++ +EL ++ +++ +LK +
Sbjct: 303 QKQILRERLAN----LERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEA 358
Query: 76 MVTKTNEIKQQSADKEVEVREAWAAVKAKL 105
+ + ++ + E+ E +++K+
Sbjct: 359 ELEELEAELEELESRLEELEEQLETLRSKV 388
Score = 33.9 bits (78), Expect = 0.19
Identities = 23/137 (16%), Positives = 57/137 (41%), Gaps = 12/137 (8%)
Query: 2 LDINLFREEKGGIPEKIRESQRRRFAS-----------VDLVDEIISLDKKWRQLQFDVE 50
L + REE + E+++E++ +L E+ L+++ +LQ ++
Sbjct: 232 LRLEELREELEELQEELKEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELY 291
Query: 51 NYRKELNKINKQIAQLKLSGKDFSEMVTKTNEIKQQSADKEVEVREAWAAVKAKLEVVGN 110
E++++ +Q L+ + + + ++ K E+ E A ++ KLE +
Sbjct: 292 ALANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKE 351
Query: 111 LVHDSVPVSNDEANNAI 127
+S+ +E +
Sbjct: 352 -ELESLEAELEELEAEL 367
>gnl|CDD|163645 cd07402, MPP_GpdQ, Enterobacter aerogenes GpdQ and related
proteins, metallophosphatase domain. GpdQ
(glycerophosphodiesterase Q, also known as Rv0805 in
Mycobacterium tuberculosis) is a binuclear
metallophosphoesterase from Enterobacter aerogenes that
catalyzes the hydrolysis of mono-, di-, and triester
substrates, including some organophosphate pesticides
and products of the degradation of nerve agents. The
GpdQ homolog, Rv0805, has 2',3'-cyclic nucleotide
phosphodiesterase activity. GpdQ and Rv0805 belong to
the metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 240
Score = 32.2 bits (74), Expect = 0.45
Identities = 8/32 (25%), Positives = 13/32 (40%)
Query: 300 DSWDMHEEMIKNSEEFYQMLKIPYQVVAIVSG 331
M ++N+E +L V AI+ G
Sbjct: 158 GIAWMDAIGLRNAEALAAVLARHPNVRAILCG 189
>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 = 31.2 bits (71), Expect = 0.52
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 50 ENYRKELNKINKQIAQLKLSGKDFSEMVTKTNEIKQQSADKEVE 93
++ +K+L +KQI LK KD E+ K ++KQQ+ + E
Sbjct: 30 DSLKKQLKNRDKQIEDLKKKVKDNEELQKKIEKLKQQNKTAKEE 73
>gnl|CDD|237050 PRK12305, thrS, threonyl-tRNA synthetase; Reviewed.
Length = 575
Score = 32.4 bits (75), Expect = 0.57
Identities = 26/123 (21%), Positives = 54/123 (43%), Gaps = 20/123 (16%)
Query: 172 DGVRLNQALINFGLDFLEKKSYTLLHTPFFMRKEVMAKCAQLAQFDEELYKVTGEGDDKY 231
G + + + ++ K+ Y ++TP + ++ L + E ++ +++Y
Sbjct: 204 KGAIIRREIEDYLRKEHLKRGYEFVYTPHIGKSDLWKTSGHLDNYKENMFPPMEIDEEEY 263
Query: 232 LIATAEQPL-CAYHIDDWIHPS------ELPIRYAGYSSCFRKE-AGS-HGRDTLGIFRV 282
+ +P+ C HI I+ S +LP+R A + + +R E +G H G+ RV
Sbjct: 264 YL----KPMNCPGHIL--IYKSRLRSYRDLPLRLAEFGTVYRYEKSGVLH-----GLTRV 312
Query: 283 HQF 285
F
Sbjct: 313 RGF 315
>gnl|CDD|133408 cd04781, HTH_MerR-like_sg6, Helix-Turn-Helix DNA binding domain
of putative transcription regulators from the MerR
superfamily. Putative helix-turn-helix (HTH) MerR-like
transcription regulators (subgroup 6) with at least two
conserved cysteines present in the C-terminal portion
of the protein. Based on sequence similarity, these
proteins are predicted to function as transcription
regulators that mediate responses to stress in
eubacteria. They belong to the MerR superfamily of
transcription regulators that promote transcription of
various stress regulons by reconfiguring the operator
sequence located between the -35 and -10 promoter
elements. A typical MerR regulator is comprised of two
distinct domains that harbor the regulatory
(effector-binding) site and the active (DNA-binding)
site. Their N-terminal domains are homologous and
contain a DNA-binding winged HTH motif, while the
C-terminal domains are often dissimilar and bind
specific coactivator molecules such as metal ions,
drugs, and organic substrates.
Length = 120
Score = 29.6 bits (67), Expect = 1.4
Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 15/74 (20%)
Query: 9 EEKGGIPEKIRESQRRRFAS-----VDLV----------DEIISLDKKWRQLQFDVENYR 53
EEKG I R RR++ + L+ DEI ++ + D + +
Sbjct: 21 EEKGLIASIGRRGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDGKPPIDRQLLK 80
Query: 54 KELNKINKQIAQLK 67
+ ++++QI +L+
Sbjct: 81 AKAAELDQQIQRLQ 94
>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 = 1.5
Identities = 25/100 (25%), Positives = 48/100 (48%), Gaps = 8/100 (8%)
Query: 228 DDKYLIATAE-QPLCAYHIDDWIHPSELPIRYAGYSS-CFRKEAGSHGRDTLGIFRVHQF 285
D Y+IA A+ +P + + I + PI++ S +R EAG G+ RVH+F
Sbjct: 307 DPGYVIAPAQCEPFYQFFEGEVIDAEDKPIKFFDRSGWTYRWEAGG----AKGLDRVHEF 362
Query: 286 EKVEQFCITSPNGNDSWDMHEEMIKNSEEFYQMLKIPYQV 325
+VE I P + ++ ++ ++ +E+ L + +
Sbjct: 363 LRVECVWIAEPEETE--EIRDKTLELAEDAADELDLEWWT 400
>gnl|CDD|226396 COG3879, COG3879, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 247
Score = 30.4 bits (69), Expect = 1.6
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 24 RRFASVDLVDEIISLDKKWRQLQFDVENYRKELNK 58
RR +DLV E+ SL KK L +VE+ +L+
Sbjct: 48 RRARDLDLVKELRSLQKKVNTLAAEVEDLENKLDS 82
>gnl|CDD|234876 PRK00960, PRK00960, seryl-tRNA synthetase; Provisional.
Length = 517
Score = 30.4 bits (69), Expect = 2.1
Identities = 32/147 (21%), Positives = 59/147 (40%), Gaps = 46/147 (31%)
Query: 221 YKVTGE----------GDDKYLIATAE-QPLCAYHIDDWIHPSELPIRY---AGYSSCFR 266
V E D Y++A A+ +P + + + ELPI++ +G++ +R
Sbjct: 290 MMVKKEVPIEKLKEKLRDPGYVLAPAQCEPFYQFFQGETVDVDELPIKFFDRSGWT--YR 347
Query: 267 KEAG-SHGRDTLGIFRVHQFEKVEQFCITSPNGNDSWDMHEEMIKNSEEFYQMLKIPYQV 325
E G +HG + RV++F ++E + +P E++ + +E + I
Sbjct: 348 WEGGGAHGLE-----RVNEFHRIEIVWLGTP---------EQVEEIRDELLKYAHI---- 389
Query: 326 VAIVSGALNDAAAKKLDLEAWFPASQT 352
A+KLDLE W
Sbjct: 390 -----------LAEKLDLEYWREVGDD 405
>gnl|CDD|234752 PRK00413, thrS, threonyl-tRNA synthetase; Reviewed.
Length = 638
Score = 30.4 bits (70), Expect = 2.2
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 7/35 (20%)
Query: 253 ELPIRYAGYSSCFRKEA-GS-HGRDTLGIFRVHQF 285
+LP+R A + + R E G+ H G+ RV F
Sbjct: 350 DLPLRLAEFGTVHRYEPSGALH-----GLMRVRGF 379
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 30.3 bits (69), Expect = 2.2
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 16/81 (19%)
Query: 29 VDLVDEIISLDKKWRQLQFDVENYRKELNKINKQIAQLKLSGKDFSEMVTKTN-EIKQQS 87
+DL E+ L+K+ +L+ KE+++I K KLS + F V K E+ ++
Sbjct: 810 IDLAAELARLEKELEKLE-------KEIDRIEK-----KLSNEGF---VAKAPEEVVEKE 854
Query: 88 ADKEVEVREAWAAVKAKLEVV 108
+K E + A ++ +L V+
Sbjct: 855 KEKLAEYQVKLAKLEERLAVL 875
>gnl|CDD|226044 COG3513, COG3513, Predicted CRISPR-associated nuclease, contains
McrA/HNH-nuclease and RuvC-like nuclease domain [Defense
mechanisms].
Length = 1088
Score = 30.6 bits (69), Expect = 2.3
Identities = 18/79 (22%), Positives = 31/79 (39%), Gaps = 2/79 (2%)
Query: 2 LDINLFREEKGGIPEKIRESQRRRFASVDLVDEIISLDKKWRQLQFD-VENYRKELNKIN 60
L + +E I + ES F+ DL E+ + +K R+ + +EL I
Sbjct: 183 LSAKMIEKEDTHI-RNLPESYEEIFSQSDLYKELKLIFEKQREFGNPHFSKHLEELVAIL 241
Query: 61 KQIAQLKLSGKDFSEMVTK 79
+ KD S+ + K
Sbjct: 242 LMQQRPYPFLKDNSKKIGK 260
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 30.2 bits (69), Expect = 2.4
Identities = 11/39 (28%), Positives = 23/39 (58%)
Query: 29 VDLVDEIISLDKKWRQLQFDVENYRKELNKINKQIAQLK 67
+L ++I L+ K R L+ + E +EL ++ ++ +LK
Sbjct: 11 SELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLK 49
>gnl|CDD|224176 COG1256, FlgK, Flagellar hook-associated protein [Cell motility and
secretion].
Length = 552
Score = 30.1 bits (68), Expect = 2.7
Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 11/57 (19%)
Query: 27 ASVDLVDEIISLDKKWRQLQFD-----------VENYRKELNKINKQIAQLKLSGKD 72
+ LV++I + ++ L+ D V + K++ +NKQI ++K +G D
Sbjct: 139 KAQTLVNQINNTYEQLTDLRKDINAEIAATVDEVNSLLKQIADLNKQIRKVKAAGND 195
>gnl|CDD|225101 COG2190, NagE, Phosphotransferase system IIA components
[Carbohydrate transport and metabolism].
Length = 156
Score = 29.1 bits (66), Expect = 3.0
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 164 GRGFYLK---GDGVRLNQALINFGLDFLEKKSYTLLHTPF 200
G GF GD V+ L+ F LD ++ K Y+ + TP
Sbjct: 86 GEGFESLVKEGDKVKAGDPLLEFDLDLIKAKGYSTI-TPV 124
>gnl|CDD|151031 pfam10458, Val_tRNA-synt_C, Valyl tRNA synthetase tRNA binding arm.
This domain is found at the C-terminus of Valyl tRNA
synthetases.
Length = 66
Score = 27.2 bits (61), Expect = 3.0
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 54 KELNKINKQIAQL--KLSGKDFSEMVTKTNEIKQQSADKEVEVREAWAAVKAKLEVVG 109
KEL K+ K+I +L KLS F E+ ++ K E E +K +L +G
Sbjct: 11 KELAKLQKEIERLQKKLSNPGFVAKAPA--EVVEEEKAKLAEYEEQLEKLKERLSQLG 66
>gnl|CDD|218124 pfam04518, Effector_1, Effector from type III secretion system.
This is a family of effector proteins which are secreted
by the type III secretion system. The precise function
of this family is unknown.
Length = 380
Score = 29.6 bits (67), Expect = 3.8
Identities = 9/40 (22%), Positives = 20/40 (50%)
Query: 54 KELNKINKQIAQLKLSGKDFSEMVTKTNEIKQQSADKEVE 93
+E+ K+ ++IAQL+L + + + + + D V
Sbjct: 82 REIRKLQQKIAQLELKSAELNPQKASLDPGMKPAKDSFVN 121
>gnl|CDD|204784 pfam11932, DUF3450, Protein of unknown function (DUF3450). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are about 260 amino acids in
length.
Length = 250
Score = 29.1 bits (66), Expect = 4.2
Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 16 EKIRESQRRRFASV----DLVDEIISLDKKWRQLQFDVENYRKELNKINKQIAQLK 67
+KI + + + L+ EI +L QLQ V N ++E+ + +QI Q++
Sbjct: 43 KKIDKWADQTQELLAEIRQLLKEIENLRVYNDQLQRLVANQQQEIASLQQQIEQIE 98
>gnl|CDD|223519 COG0442, ProS, Prolyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 500
Score = 29.5 bits (67), Expect = 4.4
Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 9/74 (12%)
Query: 215 QFDEELYKVTGEGDDKYLIA-TAEQPLCAYHIDDWIHPS--ELPIRYAGYSSCFRKEAGS 271
F EL++V GD + T+E+ + WI S +LP++ S FR E
Sbjct: 88 GFGPELFRVKDRGDRPLALRPTSEEVITDM-FRKWIR-SYKDLPLKLYQIQSKFRDEK-- 143
Query: 272 HGRDTLGIFRVHQF 285
R G+ R +F
Sbjct: 144 --RPRFGLLRGREF 155
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 29.7 bits (67), Expect = 4.6
Identities = 17/109 (15%), Positives = 45/109 (41%), Gaps = 7/109 (6%)
Query: 2 LDINLFREEKGGIPEKIRESQRRRFASVDLVDEII----SLDKKWRQLQFDVENYRKELN 57
L+ +E + E+ + + + + ++ + L+++ +L+ + + L
Sbjct: 826 LEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEAALRDLESRLG 885
Query: 58 KINKQIAQLKLSGKDFSEMVTKTNEIKQQSADKEVEVREAWAAVKAKLE 106
+ K+ +L+ E+ K E++ Q K + E A ++A E
Sbjct: 886 DLKKERDELE---AQLRELERKIEELEAQIEKKRKRLSELKAKLEALEE 931
>gnl|CDD|185467 PTZ00131, PTZ00131, glycophorin-binding protein; Provisional.
Length = 413
Score = 29.4 bits (65), Expect = 4.6
Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 12/81 (14%)
Query: 73 FSEMVTKTNEIKQQSADKEVEVREAWAA---VKAKLEVVGNLVHDSVPVSNDEAN----N 125
F +++T T+ SAD E ++ +AWAA + LEV ++ + P NDE +
Sbjct: 185 FYKILTHTDPNDDTSADPEGQIMKAWAADPEYRKHLEVFHKILTHTDP--NDETSADPEG 242
Query: 126 AIVRTWGEKRTEPKLKNHVEL 146
I++ W +P+ H+E+
Sbjct: 243 QIMKAWA---ADPEYLKHLEI 260
Score = 28.6 bits (63), Expect = 7.1
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 12/81 (14%)
Query: 73 FSEMVTKTNEIKQQSADKEVEVREAWAA---VKAKLEVVGNLVHDSVPVSNDEAN----N 125
F +++T T+ + SAD E ++ +AWAA LE+ ++ + P NDE +
Sbjct: 223 FHKILTHTDPNDETSADPEGQIMKAWAADPEYLKHLEIFYKILTHTDP--NDETSADPEG 280
Query: 126 AIVRTWGEKRTEPKLKNHVEL 146
I++ W +P+ H+E+
Sbjct: 281 QIMKAWA---ADPEYLKHLEI 298
>gnl|CDD|223726 COG0653, SecA, Preprotein translocase subunit SecA (ATPase, RNA
helicase) [Intracellular trafficking and secretion].
Length = 822
Score = 29.5 bits (67), Expect = 4.8
Identities = 19/58 (32%), Positives = 34/58 (58%), Gaps = 6/58 (10%)
Query: 48 DVENYRKELNKINKQIAQLK-LSGKDFSEMVTKTNEIKQQSADKEVE--VREAWAAVK 102
++ RK + +IN A+++ LS E+ KTNE K++ A E++ + EA+A V+
Sbjct: 16 ILKRLRKIVMQINALEAEMESLS---DEELKAKTNEFKERLASGELDDLLPEAFAVVR 70
>gnl|CDD|109652 pfam00604, Flu_PB2, Influenza RNA-dependent RNA polymerase subunit
PB2. PB2 can bind 5' end cap structure of RNA.
Length = 759
Score = 29.5 bits (66), Expect = 4.8
Identities = 14/45 (31%), Positives = 17/45 (37%)
Query: 252 SELPIRYAGYSSCFRKEAGSHGRDTLGIFRVHQFEKVEQFCITSP 296
S +P G S F + RD LG F Q K+ F P
Sbjct: 582 SLIPKAARGQYSGFARTLFQQMRDVLGTFDTVQIIKLLPFAAAPP 626
>gnl|CDD|215969 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 427
Score = 29.0 bits (66), Expect = 5.3
Identities = 18/59 (30%), Positives = 34/59 (57%), Gaps = 7/59 (11%)
Query: 16 EKIRESQRRRFASVDLVDEIIS------LDKKWRQL-QFDVENYRKELNKINKQIAQLK 67
E IR S + A +L++E+ LD + R+L + ++E KE+ ++ K+IA+L+
Sbjct: 354 EVIRGSIDLKKAKKELIEELSEIQADYLLDMRLRRLTKEEIEKLEKEIEELEKEIAELE 412
>gnl|CDD|179877 PRK04778, PRK04778, septation ring formation regulator EzrA;
Provisional.
Length = 569
Score = 29.0 bits (66), Expect = 5.7
Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 4/89 (4%)
Query: 29 VDLVDEIISLDKKWRQLQFDVENYRKELNKINKQIAQLKLSG--KDFSEMVTKT-NEIKQ 85
L + + L K + + +E YR +L++I + + + L G +D+ EM + +EI+
Sbjct: 400 EKLSEMLQGLRKDELEAREKLERYRNKLHEIKRYLEKSNLPGLPEDYLEMFFEVSDEIEA 459
Query: 86 QSADKEVEVREAWAAVKAKLEVVGNLVHD 114
+ + E E AV LE V
Sbjct: 460 LAEELE-EKPINMEAVNRLLEEATEDVET 487
>gnl|CDD|236408 PRK09200, PRK09200, preprotein translocase subunit SecA;
Reviewed.
Length = 790
Score = 29.1 bits (66), Expect = 5.9
Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 20/66 (30%)
Query: 46 QFDVENYRKELNKINKQIAQLKLSGK--DFS--EMVTKTNEIKQQSADKE------VE-- 93
+ ++ YRK + +IN KL GK S E+ KT E K++ A + E
Sbjct: 11 KRRLKKYRKIVKQIN------KLEGKMSSLSDEELRQKTIEFKERLASGKTLDDILPEAF 64
Query: 94 --VREA 97
VREA
Sbjct: 65 AVVREA 70
>gnl|CDD|223266 COG0188, GyrA, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), A subunit [DNA replication,
recombination, and repair].
Length = 804
Score = 29.2 bits (66), Expect = 6.1
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 11/60 (18%)
Query: 18 IRESQRRRFASVDLVD---------EIISLDKKWRQL-QFDVENYRKELNKINKQIAQLK 67
IRES+ + A +L+ E I LD + R+L + E KEL ++ K+IA L+
Sbjct: 396 IRESKDKPEAKEELMARFGLSEKQAEAI-LDLRLRRLTGLEEEKIEKELKELEKEIADLE 454
>gnl|CDD|219294 pfam07095, IgaA, Intracellular growth attenuator protein IgaA.
This family consists of several bacterial intracellular
growth attenuator (IgaA) proteins. IgaA is involved in
negative control of bacterial proliferation within
fibroblasts. IgaA is homologous to the E. coli YrfF and
P. mirabilis UmoB proteins. Whereas the biological
function of YrfF is currently unknown, UmoB has been
shown elsewhere to act as a positive regulator of FlhDC,
the master regulator of flagella and swarming. FlhDC has
been shown to repress cell division during P. mirabilis
swarming, suggesting that UmoB could repress cell
division via FlhDC. This biological function, if
maintained in S. enterica, could sustain a putative
negative control of cell division and growth exerted by
IgaA in intracellular bacteria.
Length = 705
Score = 28.9 bits (65), Expect = 6.2
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 10/52 (19%)
Query: 43 RQLQFDVENYRKELNKINKQIAQ-LKLSG----KDFSEMVTKTNEIKQQSAD 89
RQL + N++N +A ++ SG DFS++V KT ++ D
Sbjct: 456 RQLHPQDSD-----NRVNPSLASAIQKSGMILLDDFSDIVLKTQDLCSAEND 502
>gnl|CDD|233894 TIGR02492, flgK_ends, flagellar hook-associated protein FlgK. The
flagellar hook-associated protein FlgK of bacterial
flagella has conserved N- and C-terminal domains. The
central region is highly variable in length and
sequence, and often contains substantial runs of
low-complexity sequence. This model is built from an
alignment of FlgK sequences with the central region
excised. Note that several other proteins of the
flagellar apparatus also are homologous in the N- and
C-terminal regions to FlgK, but are excluded from this
model [Cellular processes, Chemotaxis and motility].
Length = 324
Score = 28.5 bits (64), Expect = 7.3
Identities = 8/48 (16%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 48 DVENYRKELNKINKQIAQLKLSGKDFSEMVTKTNEIKQQSADKEVEVR 95
++ + K++ +NK+I Q++ SG+D ++++ + + + ++ + + + +
Sbjct: 167 EINSLLKQIASLNKEIKQVEASGQDANDLLDQRDLLLKELS-QLIGIS 213
>gnl|CDD|221480 pfam12238, MSA-2c, Merozoite surface antigen 2c. This family of
proteins is found in eukaryotes. Proteins in this family
are typically between 263 and 318 amino acids in length.
There is a conserved SFT sequence motif. MSA-2 is a
plasma membrane glycoprotein which can be found in
Babesia bovis species.
Length = 201
Score = 28.2 bits (63), Expect = 7.3
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 7/36 (19%)
Query: 168 YLKGDGVRLNQALINFGLDFLEKKSYTLLHTPFFMR 203
Y K + V+ L+ F DFL+ +S FMR
Sbjct: 95 YDKDNVVKDYTFLVKFCNDFLDSES-------PFMR 123
>gnl|CDD|197544 smart00150, SPEC, Spectrin repeats.
Length = 101
Score = 26.9 bits (60), Expect = 7.7
Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 10/75 (13%)
Query: 32 VDEIISLDKKWRQLQFDVENYRKELNKINKQIAQLKLSGKDFSEMVTKTNEIKQQSADKE 91
++ + +L KK + ++E + + + +N+ QL G +E + + E
Sbjct: 30 LESVEALLKKHEAFEAELEAHEERVEALNELGEQLIEEGHPDAEEIEERLE--------- 80
Query: 92 VEVREAWAAVKAKLE 106
E+ E W +K E
Sbjct: 81 -ELNERWEELKELAE 94
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 28.7 bits (64), Expect = 7.7
Identities = 25/105 (23%), Positives = 43/105 (40%), Gaps = 21/105 (20%)
Query: 4 INLFREEKGGIPEKIRESQRRRFASVDLVDEIISLDKKWRQLQF--------DVENYRKE 55
IN + E+K + EKIRE + E+ +D+K L+ ++ E
Sbjct: 471 INHYNEKKSRLEEKIREIEI----------EVKDIDEKIVDLKKRKEYLESEEINKSINE 520
Query: 56 LNKINKQIAQLKLSGKDFSEMV---TKTNEIKQQSADKEVEVREA 97
NKI A L+ +E+ K EIK + ++E ++
Sbjct: 521 YNKIESARADLEDIKIKINELKDKHDKYEEIKNRYKSLKLEDLDS 565
>gnl|CDD|183581 PRK12542, PRK12542, RNA polymerase sigma factor; Provisional.
Length = 185
Score = 27.7 bits (61), Expect = 8.7
Identities = 22/88 (25%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 28 SVDLVDEIISLDKKWRQLQFDVENYRKELNKINKQIAQLKLSGKDFSEMVTKTNEIKQQS 87
S++ VDE I +K + + ++ KELN+ N+Q+ + K+ F + + EI
Sbjct: 95 SIEAVDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKV----FYNLTYQ--EISSVM 148
Query: 88 ADKEVEVREAWAAVKAKLE-VVGNLVHD 114
E VR+ + + +++ ++G + HD
Sbjct: 149 GITEANVRKQFERARKRVQNMIGGIQHD 176
>gnl|CDD|219818 pfam08393, DHC_N2, Dynein heavy chain, N-terminal region 2.
Dyneins are described as motor proteins of eukaryotic
cells, as they can convert energy derived from the
hydrolysis of ATP to force and movement along
cytoskeletal polymers, such as microtubules. This
region is found C-terminal to the dynein heavy chain
N-terminal region 1 (pfam08385) in many members of this
family. No functions seem to have been attributed
specifically to this region.
Length = 408
Score = 28.3 bits (64), Expect = 9.0
Identities = 11/48 (22%), Positives = 21/48 (43%), Gaps = 3/48 (6%)
Query: 30 DLVDEIISLDKKWRQLQF---DVENYRKELNKINKQIAQLKLSGKDFS 74
DL E ++W+ + D E E+ K KQ+ +L + + +
Sbjct: 18 DLYSEWSESIEEWKNTPWSTIDPEELESEIEKFLKQLRKLPKNLRQYE 65
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 0.134 0.390
Gapped
Lambda K H
0.267 0.0798 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,995,336
Number of extensions: 2249091
Number of successful extensions: 2475
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2398
Number of HSP's successfully gapped: 124
Length of query: 447
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 347
Effective length of database: 6,502,202
Effective search space: 2256264094
Effective search space used: 2256264094
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: 61 (27.1 bits)