RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780928|ref|YP_003065341.1| histidyl-tRNA synthetase
[Candidatus Liberibacter asiaticus str. psy62]
(496 letters)
>gnl|CDD|30473 COG0124, HisS, Histidyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 350 bits (900), Expect = 5e-97
Identities = 155/471 (32%), Positives = 241/471 (51%), Gaps = 47/471 (9%)
Query: 10 ELPRGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDE-DRPNK 68
+ PRG D +++ +R I +IR ++E+YGF I TP+ EY++ + +E D K
Sbjct: 5 QRPRGTRDFLPEDMALREYIESTIRKVFESYGFSEIRTPIFEYTELFARKSGEETDVVEK 64
Query: 69 GVFSLQDDDGQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQF 128
+++ +D G+ ++LR +LTAP+AR VAEN + P + Y GPVFR E+ GR+RQF
Sbjct: 65 EMYTFKDKGGRSLALRPELTAPVARAVAENKLDLPKPLKLYYFGPVFRYERPQKGRYRQF 124
Query: 129 IQCDVDNVGSSAETADAEMCMMMADTLEAVGIKRNDYHIGINNRKILDGILEKIGLHGDD 188
Q V+ +GS + ADAE+ + + LEA+GI + + IN+R IL+G LE +G
Sbjct: 125 YQFGVEVIGSDSPDADAEVIALAVEILEALGIG--GFTLEINSRGILEGRLEYLG----- 177
Query: 189 KLNERLIVLRAIDKLDKFGLQGVKLLLGEGRTDNSGDFTKGANLTSEQIDIMVSFLSIDL 248
+++R +LR +DKLDK KL L E L + + ++ S D
Sbjct: 178 -IDQREALLRYLDKLDKI----GKLELDEDSKR---------RLKTNPLRVLDSKKDSDQ 223
Query: 249 EKSMHELYELVKGTIAGEKGFNELVVISELVRKSGYNSNRIKISSTIVRGLEYYTGCVYE 308
E + EL+ E+ L + L+ G + +I ++VRGL+YYTG V+E
Sbjct: 224 E-LLKNAPELLDYL--DEESLEHLEELLALLDALGIS---YEIDPSLVRGLDYYTGTVFE 277
Query: 309 AILGFPVMNEKQKPVVFGSVGGGGRYDGLVSRFKGQNVPATGFSIGISRLIVALKSLESS 368
A+ GSV GGGRYDGLV F G+ PA GF+IG+ RLI+AL+
Sbjct: 278 AVT--------DGLGAQGSVCGGGRYDGLVEEFGGKPTPAVGFAIGVERLILALEEEGKE 329
Query: 369 TNNIKEMGPVLITTMDHDSDSLSKYQMYTQMLRTAGIRAEMFLGSSKNFGNQLKYADRRN 428
++ V + + D++ + Q LR AGI E+ S + Q KYAD+
Sbjct: 330 D-PVETRVDVYVVPLGEDAE--PEALKLAQKLRAAGISVEVDY-SGRKLKKQFKYADKLG 385
Query: 429 CPLAIIQGTGERSRGMLQIKDLAKGKELSREIKNNESWREARVAQITIPIS 479
A+I G E + G++ +KDLA G++ E + V ++ +
Sbjct: 386 ARFAVILGEDELANGVVTVKDLATGEQ-------EEVPLDELVEELKELLE 429
>gnl|CDD|37147 KOG1936, KOG1936, KOG1936, Histidyl-tRNA synthetase [Translation,
ribosomal structure and biogenesis].
Length = 518
Score = 233 bits (595), Expect = 9e-62
Identities = 143/473 (30%), Positives = 225/473 (47%), Gaps = 45/473 (9%)
Query: 2 GKKTKLRAELPRGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSL-GKFL 60
K K + P+G D +++ +R +I +I+ +++ +G + I+TP+ E + L GK+
Sbjct: 53 IFKKKFSLKTPKGTRDFSPEQMALREKIFSTIKEVFKRHGAETIDTPVFELKEILTGKYG 112
Query: 61 PDEDRPNKGVFSLQDDDGQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFR--NE 118
D +K ++ L+D G+ SLRYDLT P ARY+A N T + + Y I V+R
Sbjct: 113 ED----SKLIYDLKDQGGELCSLRYDLTVPFARYLAMNKITSI---KRYHIAKVYRRDQP 165
Query: 119 KHGPGRFRQFIQCDVDNVGSSAE-TADAEMCMMMADTLEAVGIKRNDYHIGINNRKILDG 177
GR+R+F QCD D G DAE ++ + L +GI DY I +N+RKILDG
Sbjct: 166 AMTRGRYREFYQCDFDIAGQFDPMIPDAECLKIVVEILSRLGIG--DYGIKVNHRKILDG 223
Query: 178 ILEKIGLHGDDKLNERLIVLRAIDKLDKFGLQGVKLLLGEGRTDNSGDFTKGANLTSEQI 237
+ G+ +DK + +IDKLDK + VK + F KG L+ E
Sbjct: 224 MFAVCGV-PEDKFRT---ICSSIDKLDKMPWEDVKKEMV---------FEKG--LSEEAA 268
Query: 238 DIMVSFLSIDLEKSMHELY---ELVKGTIAGEKGFNELVVISELVRKSGYNSNRIKISST 294
D + ++S+ + E + A ++ +L + E + G S RI +
Sbjct: 269 DRIGEYVSLKGLDELLEKLIADPKLSQNEAAKEALADLKQLFEYLEIFGI-SERISFDLS 327
Query: 295 IVRGLEYYTGCVYEAIL---------GFPVMNEKQKPVVFGSVGGGGRYDGLVSRF--KG 343
+ RGL+YYTG +YEA+L G +P GSV GGRYD LV F KG
Sbjct: 328 LARGLDYYTGVIYEAVLRGLRLICPAGRYDQAGSTEPGGVGSVAAGGRYDNLVGMFDKKG 387
Query: 344 QNVPATGFSIGISRLIVALKS-LESSTNNIKEMGPVLITTMDHDSDSLSKYQMYTQMLRT 402
VP G S+G+ R+ L+ + I+ + + L + L
Sbjct: 388 DKVPCVGQSVGVERIFSILEQRAATVATKIRTTE-TQVYVAAAGKNLLFERLKVVNALWD 446
Query: 403 AGIRAEMFLGSSKNFGNQLKYADRRNCPLAIIQGTGERSRGMLQIKDLAKGKE 455
AGI+AE ++ Q +YA+ PLA+I G E + G +++K++ +E
Sbjct: 447 AGIKAEYLYKANPKLLKQFQYAEEAGIPLAVILGEEELADGSVKVKNVGTREE 499
>gnl|CDD|73226 cd00773, HisRS-like_core, Class II Histidinyl-tRNA synthetase
(HisRS)-like catalytic core domain. HisRS is a
homodimer. It is responsible for the attachment of
histidine to the 3' OH group of ribose of the
appropriate tRNA. This domain is primarily responsible
for ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. Class II assignment is based upon
its structure and the presence of three characteristic
sequence motifs. This domain is also found at the
C-terminus of eukaryotic GCN2 protein kinase and at the
N-terminus of the ATP phosphoribosyltransferase
accessory subunit, HisZ. HisZ along with HisG catalyze
the first reaction in histidine biosynthesis. HisZ is
found only in a subset of bacteria and differs from
HisRS in lacking a C-terminal anti-codon binding
domain..
Length = 261
Score = 207 bits (529), Expect = 5e-54
Identities = 105/342 (30%), Positives = 166/342 (48%), Gaps = 81/342 (23%)
Query: 22 EIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWI 81
E +R I D++R ++E YG++ I+TP+ EY++ + DE K ++ +D G+ +
Sbjct: 1 EAALRRYIEDTLREVFERYGYEEIDTPVFEYTELFLRKSGDEVS--KEMYRFKDKGGRDL 58
Query: 82 SLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQFIQCDVDNVGSSAE 141
+LR DLTAP+AR VAEN ++ P + Y IGPVFR E+ GR+R+F Q V+ +GS +
Sbjct: 59 ALRPDLTAPVARAVAENLLSLPLPLKLYYIGPVFRYERPQKGRYREFYQVGVEIIGSDSP 118
Query: 142 TADAEMCMMMADTLEAVGIKRNDYHIGINNRKILDGILEKIGLHGDDKLNERLIVLRAID 201
ADAE+ + + LEA+ G+ + +I K+N R I
Sbjct: 119 LADAEVIALAVEILEAL---------GLKDFQI--------------KINHRGI------ 149
Query: 202 KLDKFGLQGVKLLLGEGRTDNSGDFTKGANLTSEQIDIMVSFLSIDLEKSMHELYELVKG 261
L G+ LL + E I+ ++ L + + +L + ++
Sbjct: 150 ------LDGIAGLLEDRE---------------EYIERLIDKLDKEALAHLEKLLDYLEA 188
Query: 262 TIAGEKGFNELVVISELVRKSGYNSNRIKISSTIVRGLEYYTGCVYEAILGFPVMNEKQK 321
K I ++VRGL+YYTG V+EA+
Sbjct: 189 LGVDIK---------------------YSIDLSLVRGLDYYTGIVFEAVA--------DG 219
Query: 322 PVVFGSVGGGGRYDGLVSRFKGQNVPATGFSIGISRLIVALK 363
GS+ GGGRYDGL+ F G++VPA GF+IG+ RL++AL+
Sbjct: 220 LGAQGSIAGGGRYDGLLEEFGGEDVPAVGFAIGLERLLLALE 261
>gnl|CDD|33500 COG3705, HisZ, ATP phosphoribosyltransferase involved in histidine
biosynthesis [Amino acid transport and metabolism].
Length = 390
Score = 135 bits (340), Expect = 3e-32
Identities = 97/366 (26%), Positives = 154/366 (42%), Gaps = 48/366 (13%)
Query: 7 LRAELPRGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRP 66
+ +LP G D E R + I D + ++ +G++ +ETP LE +D L ED
Sbjct: 1 MTWQLPEGIRDVLPLEARRKEEIRDQLLALFRAWGYERVETPTLEPADPLLD-GAGEDLR 59
Query: 67 NKGVFSLQDDDGQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFR 126
+ +F L+D+ G + LR D T P+AR A P R G VFR + GR
Sbjct: 60 RR-LFKLEDETGGRLGLRPDFTIPVARIHATLLAG--TPLRLSYAGKVFRAREGRHGRRA 116
Query: 127 QFIQCDVDNVGSSAETADAEMCMMMADTLEAVGIKRNDYHIGINNRKILDGILEKIGLHG 186
+F+Q ++ +G + ADAE+ + L+A+G+ D + + + I +L GL G
Sbjct: 117 EFLQAGIELLGDDSAAADAEVIALALAALKALGLA--DLKLELGHAGIFRALLAAAGLPG 174
Query: 187 DDKLNERLIVLRAIDKLDKFGLQGVKLLLGEGRTDNSGDFTKGANLTSEQIDIMVSFLSI 246
RL RA D GL+ A L+ E + L++
Sbjct: 175 G--WRARL--RRAFGDKDLLGLE---------------LLVLAAPLSPELRGRLSELLAL 215
Query: 247 -----DLEKSMHELYELVKGTIAGEKGFNELVVISELVRKSGYNSNRIKISSTIVRGLEY 301
LE L+ +A NE ++++ R+ I + +R +Y
Sbjct: 216 LGGREVLE----RARGLLDELMAQGIALNEGRALADIARRLIEK---IALDLGRLRHFDY 268
Query: 302 YTGCVYEAILGFPVMNEKQKPVVFGSVGGGGRYDGLVSRFKGQNVPATGFSIGISRLIVA 361
YTG V+ A + ++ GGRYDGL+ F G+ PATGF++ + L
Sbjct: 269 YTGLVFLAY----------ADGLGDALASGGRYDGLLGLF-GRAAPATGFALRLDALAQG 317
Query: 362 LKSLES 367
LE
Sbjct: 318 GLPLEE 323
>gnl|CDD|144252 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 = 170
Score = 98.1 bits (245), Expect = 5e-21
Identities = 45/168 (26%), Positives = 79/168 (47%), Gaps = 16/168 (9%)
Query: 25 IRNRILDSIRNIYENYGFDPIETPLLEYSDSL---GKFLPDEDRPNKGVFSLQDDDGQWI 81
+RN + + IR++++ YG+ ++TP+LE + G + D ++ +D G+ +
Sbjct: 1 LRNALENFIRDLFKRYGYQEVDTPILEPKELWEGSGHWDDYFDE----MYRFKDRGGEEL 56
Query: 82 SLRYDLTAPLARYVAENFDT-IVFPCRTYRIGPVFRNEK---HGPGRFRQFIQCDVDNVG 137
LR + R + P + Y+IGP FR E G GR R+F Q D + G
Sbjct: 57 YLRPTAEVGITRLFKNEILSYRDLPLKLYQIGPCFRYEARPRRGLGRVREFTQVDAEIFG 116
Query: 138 SS--AETADAEMCMMMADTLEAVGIKRNDYHIGINNRKILDGILEKIG 183
+ +E D E+ + + L+ +G+ Y + +N R L G K G
Sbjct: 117 TPEQSEEEDEELLKLAEEILQDLGL---PYRVVLNTRGDLGGYASKTG 161
>gnl|CDD|36253 KOG1035, KOG1035, KOG1035, eIF-2alpha kinase GCN2 [Translation,
ribosomal structure and biogenesis].
Length = 1351
Score = 81.2 bits (200), Expect = 6e-16
Identities = 78/409 (19%), Positives = 148/409 (36%), Gaps = 41/409 (10%)
Query: 25 IRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWISLR 84
+R +++ + I+ +G +ETP L ++ L D G + L
Sbjct: 934 LREYVVEEVVKIFRKHGAIELETPPL-------SLRNACAYFSRKAVELLDHSGDVVELP 986
Query: 85 YDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQFIQCDVDNVGSSAETAD 144
YDL P ARYV+ N + Y I V+R H ++ ++CD D +G + +
Sbjct: 987 YDLRLPFARYVSRNSVLSF---KRYCISRVYRPAIHNHP--KECLECDFDIIGPTTSLTE 1041
Query: 145 AEMCMMMADTLEAVGIKRNDYHIGINNRKILDGILEKIGLHGDDKLNERLIVLRAIDKLD 204
AE+ + + + + + I +N+ +L+ IL G+ D+ + +L +
Sbjct: 1042 AEL-LKVIVEITTEILHEGNCDIHLNHADLLEAILSHCGIP-KDQRRKVAELLSDMGSSR 1099
Query: 205 KFGLQGVKLLLGEGRTDNSGDFTKGANLTSEQIDIMVSFLSIDLEKSMHELYELVKGTIA 264
+ + R+ + A L + L + +L++G +
Sbjct: 1100 PQRSEKELKWVFIRRSSL-----QLAKL------PEFVLNRLFLVAGRFQALKLIRGKLR 1148
Query: 265 GE---KGFNELVVISELVRKSGYNSNRIKISSTIVRGLEYYTGCVYEAILGFPVMNEKQK 321
+ + EL + L+R G + + I G ++ +
Sbjct: 1149 ADSLVRALKELENVVGLLRSLGIEEH-VHIYVGPTESRHRNGGIQFQ----ITAEIKSNT 1203
Query: 322 PVVFGSVGGGGRYDGLVSRFKGQ---NVP-ATGFSIGISRLIVALKSLESSTNNIKEMGP 377
+ GGRYD L+ + + N+P A G S + A K LE
Sbjct: 1204 SGDPVLLAAGGRYDSLLQEVRDEQKMNLPGAIGVSALSTIRQHAPKDLEPIKTPSS--CD 1261
Query: 378 VLITTMDHDSDSLSKYQMYTQMLRTAGIRAEMFLGSSKNFGNQLKYADR 426
VLI + + + L + GI+AE+ S + +YA+
Sbjct: 1262 VLICSRGSGLLTQRMELV--AKLWSKGIKAEIVPDPSPSLEELTEYANE 1308
>gnl|CDD|29799 cd00859, HisRS_anticodon, HisRS Histidyl-anticodon binding domain.
HisRS belongs to class II aminoacyl-tRNA synthetases
(aaRS). This alignment contains the anticodon binding
domain, which is responsible for specificity in
tRNA-binding, so that the activated amino acid is
transferred to a ribose 3' OH group of the appropriate
tRNA only..
Length = 91
Score = 72.1 bits (177), Expect = 3e-13
Identities = 33/110 (30%), Positives = 49/110 (44%), Gaps = 21/110 (19%)
Query: 377 PVLITTMDHDSDSLSKYQMYTQMLRTAGIRAEMFLGSSKNFGNQLKYADRRNCPLAIIQG 436
V + + +LS+ + LR AGI+AE+ G K Q KYADR A+I G
Sbjct: 3 DVYVVPLG--EGALSEALELAEQLRDAGIKAEIDYGGRK-LKKQFKYADRSGARFAVILG 59
Query: 437 TGERSRGMLQIKDLAKGKELSREIKNNESWREARVAQITIPISELVSTVK 486
E + G++ +KDL G+ Q T+ + ELV +K
Sbjct: 60 EDELAAGVVTVKDLETGE------------------QETVALDELVEELK 91
>gnl|CDD|164576 CHL00201, syh, histidine-tRNA synthetase; Provisional.
Length = 430
Score = 62.6 bits (152), Expect = 2e-10
Identities = 51/164 (31%), Positives = 72/164 (43%), Gaps = 20/164 (12%)
Query: 290 KISSTIVRGLEYYTGCVYEAILGFPVMNEKQKPVVFGSVGGGGRYDGLVSRFKGQNVPAT 349
KI+ +VRGL+YY +E ++ GGGRYD L+ + G PA
Sbjct: 251 KINYKLVRGLDYYNDTAFEI-----KTLSSNGQ---DTICGGGRYDSLIHQLGGPKTPAV 302
Query: 350 GFSIGISRLIVALKSLESSTNNI---KEMGPVLITTMDHDSDSLSKYQMYTQMLRTAGIR 406
G +IG+ RL++ K +NI K+ V I T + K Q L I+
Sbjct: 303 GCAIGLERLLLIAK------DNIILPKQSIDVYIAT--QGLKAQKKGWEIIQFLEKQNIK 354
Query: 407 AEMFLGSSKNFGNQLKYADRRNCPLAIIQGTGERSRGMLQIKDL 450
E+ L SS NF Q+K A ++ II G E + IK L
Sbjct: 355 FELDL-SSSNFHKQIKQAGKKRAKACIILGDNEIMDNCITIKWL 397
Score = 60.3 bits (146), Expect = 1e-09
Identities = 45/164 (27%), Positives = 69/164 (42%), Gaps = 10/164 (6%)
Query: 13 RGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLLEYSD----SLGKFLPDEDRPNK 68
RG D EI I D + + I TP+ E S +G+ D NK
Sbjct: 8 RGTKDILPDEINYWQFIHDKALTLLSLANYSEIRTPIFENSSLYDRGIGE---TTDIVNK 64
Query: 69 GVFSLQDDDGQWISLRYDLTAPLARYVAEN-FDTIVFPCRTYRIGPVFRNEKHGPGRFRQ 127
++ D + I+LR + TA + R EN D R + GP+FR E+ GR RQ
Sbjct: 65 EMYRFTDRSNRDITLRPEGTAGIVRAFIENKMDYHSNLQRLWYSGPMFRYERPQSGRQRQ 124
Query: 128 FIQCDVDNVGSSAETADAEMCMMMADTLEAVGIKRNDYHIGINN 171
F Q ++ +GS AD E+ + + + + + IN+
Sbjct: 125 FHQLGIEFIGSIDARADTEVIHLAMQIFNELQV--KNLILDINS 166
>gnl|CDD|29813 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 = 50.1 bits (119), Expect = 1e-06
Identities = 41/141 (29%), Positives = 59/141 (41%), Gaps = 10/141 (7%)
Query: 25 IRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWISLR 84
IR++I +R GF +ETP++E L K + ++D LR
Sbjct: 1 IRSKIEQKLRRFMAELGFQEVETPIVEREPLLEKAGHEPKDLLPVGAENEEDL----YLR 56
Query: 85 YDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKH--GPGRFRQFIQCDVDNVGSSAET 142
L L R + + P R IGP FRNE G R R+F Q + + G E
Sbjct: 57 PTLEPGLVRLFVSHIRKL--PLRLAEIGPAFRNEGGRRGLRRVREFTQLEGEVFGEDGEE 114
Query: 143 AD--AEMCMMMADTLEAVGIK 161
A E+ + + L A+GIK
Sbjct: 115 ASEFEELIELTEELLRALGIK 135
>gnl|CDD|145985 pfam03129, HGTP_anticodon, Anticodon binding domain. This domain
is found in histidyl, glycyl, threonyl and prolyl tRNA
synthetases it is probably the anticodon binding domain.
Length = 93
Score = 47.6 bits (114), Expect = 7e-06
Identities = 23/111 (20%), Positives = 46/111 (41%), Gaps = 19/111 (17%)
Query: 378 VLITTMDHDSDSLSKYQMYTQMLRTAGIRAEMFLGSSKNFGNQLKYADRRNCPLAIIQGT 437
V++ + + Q + LR AGIR E+ +++ G + + AD P ++ G
Sbjct: 2 VVVIPLGEKDELEDYAQKLAEELREAGIRVELDD-RNESLGKKFRDADLIGIPFRLVVGE 60
Query: 438 GERSRGMLQIKDLAKGKELSREIKNNESWREARVAQITIPISELVSTVKKI 488
E G + ++D G+ + T+ + ELV +K++
Sbjct: 61 KELENGTVTVRDRDTGE------------------KETVSLEELVEKLKEL 93
>gnl|CDD|143920 pfam00152, tRNA-synt_2, tRNA synthetases class II (D, K and N).
Length = 341
Score = 42.6 bits (101), Expect = 2e-04
Identities = 31/136 (22%), Positives = 52/136 (38%), Gaps = 29/136 (21%)
Query: 23 IRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWIS 82
+++R++I+ +IR + GF +ETP+L S G R F + +
Sbjct: 22 LKLRSKIIRAIREFLDERGFLEVETPILTKSTPEGGA-----RD----FLVPKFYAKEAY 72
Query: 83 LRYDLTAP---LARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGR-FRQFIQCDVDNVGS 138
L +P + FD R ++I P FR+E R +F Q D
Sbjct: 73 LP---QSPQLYKQLLMVAGFD------RVFQIAPCFRDEDLRTDRHPPEFTQLD------ 117
Query: 139 SAETADAEMCMMMADT 154
E + + +M T
Sbjct: 118 -LEMSFVDYEDVMDLT 132
>gnl|CDD|30790 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 589
Score = 41.8 bits (98), Expect = 4e-04
Identities = 38/165 (23%), Positives = 67/165 (40%), Gaps = 13/165 (7%)
Query: 21 KEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQW 80
K IRN + D +R +YG+ ++TP+L L + D + +F + DD +
Sbjct: 218 KGATIRNLLEDYVRTKLRSYGYQEVKTPVL-ADLELWELSGHWDNYKEDMFLTESDD-RE 275
Query: 81 ISLRYDLTAPLARYVAENFDTIV--FPCRTYRIGPVFRNEK----HGPGRFRQFIQCDVD 134
+L+ + P + ++ P R G V+R EK HG R R F Q D
Sbjct: 276 YALKP-MNCPGHILIFKSGLRSYRELPLRLAEFGYVYRYEKSGALHGLMRVRGFTQDDAH 334
Query: 135 NVGSSAETAD--AEMCMMMADTLEAVGIKRNDYHIGINNRKILDG 177
+ + D + ++ + + G DY + ++ R G
Sbjct: 335 IFCTPDQIKDEFKGILELILEVYKDFGF--TDYEVKLSTRPKFIG 377
>gnl|CDD|29810 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 = 41.8 bits (98), Expect = 4e-04
Identities = 29/159 (18%), Positives = 57/159 (35%), Gaps = 14/159 (8%)
Query: 25 IRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQW---- 80
+ + + + YG+ I P L + K + K +++ +D +
Sbjct: 4 LWRALERFLDDRMAEYGYQEILFPFLAPTVLFFKGGHLDGYR-KEMYTFEDKGRELRDTD 62
Query: 81 ISLRYDLTAPLARYVAENFD-TIVFPCRTYRIGPVFRNE---KHGPGRFRQFIQCDVDNV 136
+ LR P+ + + P R +IGP FR+E + G R R+F Q +
Sbjct: 63 LVLRPAACEPIYQIFSGEILSYRALPLRLDQIGPCFRHEPSGRRGLMRVREFRQVEYVVF 122
Query: 137 G--SSAETADAEMCMMMADTLEAVGIKRNDYHIGINNRK 173
G AE E + + +G+ + + +
Sbjct: 123 GEPEEAEEERREWLELAEEIARELGL---PVRVVVADDP 158
>gnl|CDD|37535 KOG2324, KOG2324, KOG2324, Prolyl-tRNA synthetase [Translation,
ribosomal structure and biogenesis].
Length = 457
Score = 40.3 bits (94), Expect = 0.001
Identities = 37/128 (28%), Positives = 61/128 (47%), Gaps = 10/128 (7%)
Query: 23 IRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWIS 82
+R+ N++ + N ++ G I P+L S L + D +F L D G+ +
Sbjct: 52 LRVLNKLCRLLDNEMQSGGAQKISLPILS-SKELWEKTGRWDAMGSELFRLHDRKGKQMC 110
Query: 83 L----RYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNE---KHGPGRFRQFIQCDVDN 135
L D+TA +A Y+ ++ P R Y+IG FR+E + G R R+F+ D+ +
Sbjct: 111 LTPTHEEDITALMATYIPLSYKQ--LPIRVYQIGRKFRDELRPRFGLLRGREFLMKDMYS 168
Query: 136 VGSSAETA 143
S ETA
Sbjct: 169 FDSDEETA 176
Score = 34.2 bits (78), Expect = 0.086
Identities = 32/177 (18%), Positives = 65/177 (36%), Gaps = 31/177 (17%)
Query: 270 NELVVISELVRKSGYNSNRIKISSTIVRGLEYYTGCVYEAILGFPVMNEKQKPVVFGSVG 329
+E + +S++ N R+ + +I G + G Y L +N + KP
Sbjct: 239 SEDLDLSKIASCPKCNEGRLTKTKSIEVGHTFLLGTKYSKPLNAKFVNVEGKP------- 291
Query: 330 GGGRYDGLVSRFKGQNVPATGFSIGISRLIVALKSLESSTNNI---KEMGP--VLITTMD 384
+ + + IG++RL+ A + S + + P V +
Sbjct: 292 --------------EFLHMGCYGIGVTRLLAAAAEVLSDDKGLRWPSLIAPYKVCLIGPK 337
Query: 385 HDSDSLSKYQMYTQMLRTAGIRA---EMFLGSSKN--FGNQLKYADRRNCPLAIIQG 436
S S ++ +++L + E+ L + G ++K A+R P I+ G
Sbjct: 338 KGSKSQRAQEVISELLNDEAVGNLHGEILLDDREELTIGKRIKDANRLGIPFVIVVG 394
>gnl|CDD|29816 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 = 38.6 bits (90), Expect = 0.004
Identities = 29/130 (22%), Positives = 45/130 (34%), Gaps = 39/130 (30%)
Query: 24 RIRNRILDSIRNIYENYGFDPIETPLL-------------EYSDSLGKFLPDED----RP 66
IRN + D +R + G+ +ETP++ Y +++ F +++ +P
Sbjct: 31 IIRNELEDFLRELQRKRGYQEVETPIIYNKELWETSGHWDHYRENMFPFEEEDEEYGLKP 90
Query: 67 NKGVFSLQDDDGQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEK----HGP 122
+ S R DL P R G V R E+ HG
Sbjct: 91 MNCPGHCLIFKSKPRSYR-DL-----------------PLRLAEFGTVHRYEQSGALHGL 132
Query: 123 GRFRQFIQCD 132
R R F Q D
Sbjct: 133 TRVRGFTQDD 142
>gnl|CDD|31383 COG1190, LysU, Lysyl-tRNA synthetase (class II) [Translation,
ribosomal structure and biogenesis].
Length = 502
Score = 37.9 bits (88), Expect = 0.006
Identities = 27/96 (28%), Positives = 40/96 (41%), Gaps = 14/96 (14%)
Query: 23 IRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWIS 82
R++I+ +IR ++ GF +ETP+L G RP + D D +
Sbjct: 180 FIKRSKIIRAIREFLDDRGFLEVETPML--QPIPGG---AAARPFITHHNALDMD---LY 231
Query: 83 LRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNE 118
LR L R + F+ R + IG FRNE
Sbjct: 232 LRIAPELYLKRLIVGGFE------RVFEIGRNFRNE 261
>gnl|CDD|30366 COG0016, PheS, Phenylalanyl-tRNA synthetase alpha subunit
[Translation, ribosomal structure and biogenesis].
Length = 335
Score = 37.9 bits (88), Expect = 0.006
Identities = 30/113 (26%), Positives = 52/113 (46%), Gaps = 14/113 (12%)
Query: 27 NRILDSIRNIYENYGFDPIETPLLEYS----DSLGKFLPDEDRPNK---GVFSLQDDDGQ 79
+ ++ I +I+ GF +E P +E D+L +P +D P + F L+DD +
Sbjct: 114 TQTIEEIEDIFLGMGFTEVEGPEIETDFYNFDAL--NIP-QDHPARDMQDTFYLKDDREK 170
Query: 80 WISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQFIQCD 132
+ LR + AR +AEN P + + G V+RN+ +F Q +
Sbjct: 171 LL-LRTHTSPVQARTLAENAKI---PIKIFSPGRVYRNDTVDATHSPEFHQIE 219
>gnl|CDD|29820 cd00775, LysRS_core, Lys_tRNA synthetase (LysRS) class II core
domain. Class II LysRS is a dimer which attaches a
lysine to the 3' OH group of ribose of the appropriate
tRNA. Its assignment to class II aaRS is based upon its
structure and the presence of three characteristic
sequence motifs in the core domain. It is found in
eukaryotes as well as some prokaryotes and archaea.
However, LysRS belongs to class I aaRS's in some
prokaryotes and archaea. The catalytic core domain is
primarily responsible for the ATP-dependent formation of
the enzyme bound aminoacyl-adenylate..
Length = 329
Score = 35.9 bits (83), Expect = 0.023
Identities = 29/103 (28%), Positives = 42/103 (40%), Gaps = 18/103 (17%)
Query: 24 RIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWISL 83
+R++I+ IR ++ GF +ETP+L+ RP + D D + L
Sbjct: 9 IVRSKIISYIRKFLDDRGFLEVETPMLQPIAGGA-----AARPFITHHNALDMD---LYL 60
Query: 84 RYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNE----KHGP 122
R L R + F+ R Y IG FRNE H P
Sbjct: 61 RIAPELYLKRLIVGGFE------RVYEIGRNFRNEGIDLTHNP 97
>gnl|CDD|58337 cd00669, Asp_Lys_Asn_RS_core, Asp_Lys_Asn_tRNA synthetase class II
core domain. This domain is the core catalytic domain of
class II aminoacyl-tRNA synthetases of the subgroup
containing aspartyl, lysyl, and asparaginyl tRNA
synthetases. 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. Nearly all class II tRNA synthetases
are dimers and enzymes in this subgroup are homodimers.
These enzymes attach a specific amino acid to the 3' OH
group of ribose of the appropriate tRNA..
Length = 269
Score = 35.3 bits (81), Expect = 0.041
Identities = 24/111 (21%), Positives = 41/111 (36%), Gaps = 14/111 (12%)
Query: 23 IRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWIS 82
++R++I+ +IR+ ++ GF +ETP+L+ K + G
Sbjct: 1 FKVRSKIIKAIRDFMDDRGFLEVETPMLQKITGGAG---ARPFLVK-----YNALGLDYY 52
Query: 83 LRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQFIQCDV 133
LR R + D R + I FRNE +F D+
Sbjct: 53 LRISPQLFKKRLMVGGLD------RVFEINRNFRNEDLRARHQPEFTMMDL 97
>gnl|CDD|73228 cd00777, AspRS_core, Asp tRNA synthetase (aspRS) class II core
domain. Class II assignment is based upon its structure
and the presence of three characteristic sequence
motifs. AspRS is a homodimer, which attaches a specific
amino acid to the 3' OH group of ribose of the
appropriate tRNA. The catalytic core domain is primarily
responsible for the ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. AspRS in this family
differ from those found in the AsxRS family by a GAD
insert in the core domain..
Length = 280
Score = 34.4 bits (79), Expect = 0.078
Identities = 33/115 (28%), Positives = 51/115 (44%), Gaps = 20/115 (17%)
Query: 23 IRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLG--KFL-PDEDRPNKGVFSLQDDDGQ 79
+R+R+R++ +IRN + GF IETP+L S G FL P P K ++L
Sbjct: 1 LRLRSRVIKAIRNFLDEQGFVEIETPILTKSTPEGARDFLVPSRLHPGK-FYALPQSPQL 59
Query: 80 WISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQFIQCDVD 134
+ L + FD R ++I FR+E R +F Q D++
Sbjct: 60 FKQL----------LMVSGFD------RYFQIARCFRDEDLRADRQPEFTQIDIE 98
>gnl|CDD|37096 KOG1885, KOG1885, KOG1885, Lysyl-tRNA synthetase (class II)
[Translation, ribosomal structure and biogenesis].
Length = 560
Score = 34.1 bits (78), Expect = 0.082
Identities = 37/150 (24%), Positives = 54/150 (36%), Gaps = 41/150 (27%)
Query: 24 RIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWISL 83
RIR +I+ IR ++ GF +ETP++ +P F +D L
Sbjct: 226 RIRAKIISYIRKFLDSRGFLEVETPMMN-----MIAGGATAKP----FITHHND-----L 271
Query: 84 RYDLT---AP---LARYVAENFDTIVFPCRTYRIGPVFRNE----KHGPGRFRQFIQC-- 131
DL AP L V D R Y IG FRNE H P +F C
Sbjct: 272 DMDLYLRIAPELYLKMLVVGGLD------RVYEIGRQFRNEGIDLTHNP----EFTTCEF 321
Query: 132 -----DVDNVGSSAETADAEMCMMMADTLE 156
D +++ E + M + + +
Sbjct: 322 YMAYADYEDLMDMTEELLSGMVKNITGSYK 351
>gnl|CDD|37622 KOG2411, KOG2411, KOG2411, Aspartyl-tRNA synthetase, mitochondrial
[Translation, ribosomal structure and biogenesis].
Length = 628
Score = 33.5 bits (76), Expect = 0.14
Identities = 28/117 (23%), Positives = 45/117 (38%), Gaps = 19/117 (16%)
Query: 21 KEIRIRNRILDSIRNIYENY-GFDPIETPLLEYSDSLG--KFLPDEDRPNKGVFSLQDDD 77
+R+R+ ++ IR N GF +ETP L G +F+ P ++L
Sbjct: 176 NNLRLRSNVVKKIRRYLNNRHGFVEVETPTLFKRTPGGAREFVVPTRTPRGKFYALPQSP 235
Query: 78 GQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQFIQCDVD 134
Q+ L + D R Y+I FR+E R +F Q D++
Sbjct: 236 QQFKQL----------LMVSGID------RYYQIARCFRDEDLRADRQPEFTQVDME 276
>gnl|CDD|30522 COG0173, AspS, Aspartyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 585
Score = 32.1 bits (73), Expect = 0.40
Identities = 12/30 (40%), Positives = 22/30 (73%)
Query: 21 KEIRIRNRILDSIRNIYENYGFDPIETPLL 50
K +++R+++ +IRN ++ GF IETP+L
Sbjct: 139 KNLKLRSKVTKAIRNFLDDQGFLEIETPIL 168
>gnl|CDD|31968 COG1782, COG1782, Predicted metal-dependent RNase, consists of a
metallo-beta-lactamase domain and an RNA-binding KH
domain [General function prediction only].
Length = 637
Score = 30.6 bits (69), Expect = 0.95
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 450 LAKGKELSREIKNNESWREARVAQITIPISELVSTVKKILQENKEE 495
+ KG REI W V I S + ++++IL+ ++E
Sbjct: 114 IGKGGSTLREITAETGWAPKIVRTPPIQ-SRTIKSIREILRSERKE 158
>gnl|CDD|30367 COG0017, AsnS, Aspartyl/asparaginyl-tRNA synthetases [Translation,
ribosomal structure and biogenesis].
Length = 435
Score = 29.8 bits (67), Expect = 1.6
Identities = 28/119 (23%), Positives = 43/119 (36%), Gaps = 32/119 (26%)
Query: 23 IRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWIS 82
+IR+ IL +IR + GF + TP++ S + G +F +
Sbjct: 134 FKIRSSILRAIREFFYENGFTEVHTPIITASATEG---------GGELFKVDY------- 177
Query: 83 LRYDLTAPLA-------RYVAENFDTIVFPCRTYRIGPVFRNEKHGPGR-FRQFIQCDV 133
+D A L +A + R + IGP FR EK R +F D
Sbjct: 178 --FDKEAYLTQSPQLYKEALAAALE------RVFTIGPTFRAEKSNTRRHLSEFWMLDP 228
>gnl|CDD|29821 cd00776, AsxRS_core, Asx tRNA synthetase (AspRS/AsnRS) class II
core domain. Assignment to class II aminoacyl-tRNA
synthetases (aaRS) based upon its structure and the
presence of three characteristic sequence motifs in the
core domain. This family includes AsnRS as well as a
subgroup of AspRS. AsnRS and AspRS are homodimers,
which attach either asparagine or aspartate to the 3'OH
group of ribose of the appropriate tRNA. While archaea
lack asnRS, they possess a non-discriminating aspRS,
which can mischarge Asp-tRNA with Asn. Subsequently, a
tRNA-dependent aspartate amidotransferase converts the
bound aspartate to asparagine. The catalytic core domain
is primarily responsible for the ATP-dependent formation
of the enzyme bound aminoacyl-adenylate..
Length = 322
Score = 29.7 bits (67), Expect = 1.7
Identities = 24/98 (24%), Positives = 37/98 (37%), Gaps = 19/98 (19%)
Query: 24 RIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQ-WIS 82
RIR+ +L + R GF + TP + +D+ G +F + +++
Sbjct: 25 RIRSEVLRAFREFLRENGFTEVHTPKITSTDTEG---------GAELFKVSYFGKPAYLA 75
Query: 83 LRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKH 120
L + E R Y IGPVFR EK
Sbjct: 76 QSPQLYKEMLIAALE---------RVYEIGPVFRAEKS 104
>gnl|CDD|36850 KOG1637, KOG1637, KOG1637, Threonyl-tRNA synthetase [Translation,
ribosomal structure and biogenesis].
Length = 560
Score = 28.8 bits (64), Expect = 3.5
Identities = 29/126 (23%), Positives = 47/126 (37%), Gaps = 14/126 (11%)
Query: 11 LPRGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGV 70
LP G RI N ++D IR Y GF + TP + Y+ L + ++ +
Sbjct: 188 LPHG--------TRIYNTLVDFIRAEYRKRGFTEVITPNI-YNKKLWETSGHWQNYSENM 238
Query: 71 FSLQDDDGQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGP----GRFR 126
F + + ++ + + + P R G + RNE G R R
Sbjct: 239 FKFEVEKEEFALKPMNCPGHCLMFAHRDRSYRELPLRFADFGVLHRNEASGALSGLTRVR 298
Query: 127 QFIQCD 132
+F Q D
Sbjct: 299 RF-QQD 303
>gnl|CDD|48070 cd01966, Nitrogenase_NifN_1, Nitrogenase_nifN1: A subgroup of the
NifN subunit of the NifEN complex: NifN forms an
alpha2beta2 tetramer with NifE. NifN and nifE are
structurally homologous to nitrogenase MoFe protein beta
and alpha subunits respectively. NifEN participates in
the synthesis of the iron-molybdenum cofactor (FeMoco)
of the MoFe protein. NifB-co (an iron and sulfur
containing precursor of the FeMoco) from NifB is
transferred to the NifEN complex where it is further
processed to FeMoco. The nifEN bound precursor of FeMoco
has been identified as a molybdenum-free, iron- and
sulfur- containing analog of FeMoco. It has been
suggested that this nifEN bound precursor also acts as a
cofactor precursor in nitrogenase systems which require
a cofactor other than FeMoco: i.e. iron-vanadium
cofactor (FeVco) or iron only cofactor (FeFeco)..
Length = 417
Score = 28.6 bits (64), Expect = 4.0
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 30 LDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRP 66
++ +++I E +G +PI P L S SL L D+ P
Sbjct: 173 VEELKDIIEAFGLEPIILPDL--SGSLDGHLADDWSP 207
>gnl|CDD|30791 COG0442, ProS, Prolyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 500
Score = 28.3 bits (63), Expect = 4.8
Identities = 32/150 (21%), Positives = 57/150 (38%), Gaps = 31/150 (20%)
Query: 11 LPRGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLL------EYSDSLGKFLPDED 64
LP G R+ +I + IR + G + P L + S F P+
Sbjct: 43 LPLGL--------RVLEKIENIIREEMDKIGAQEVLFPTLIPAELWKESGRWEGFGPE-- 92
Query: 65 RPNKGVFSLQDDDGQWISLR----YDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKH 120
+F ++D + ++LR +T +++ D P + Y+I FR+EK
Sbjct: 93 -----LFRVKDRGDRPLALRPTSEEVITDMFRKWIRSYKD---LPLKLYQIQSKFRDEKR 144
Query: 121 GPG---RFRQFIQCDVDNVGSSAETADAEM 147
R R+F+ D + + E A+
Sbjct: 145 PRFGLLRGREFLMKDAYSFHADEEDAEETY 174
>gnl|CDD|38484 KOG3274, KOG3274, KOG3274, Uncharacterized conserved protein,
AMMECR1 [Function unknown].
Length = 210
Score = 28.4 bits (63), Expect = 4.8
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 7/51 (13%)
Query: 263 IAGEKGFNELVVISELVRKSGYNSN-----RIKISSTIVRGLEYYTGCVYE 308
+A E+G++++ I L+RK+GY R I T R + YE
Sbjct: 147 VAAEQGWDQIETIDSLIRKAGYKGPITEELRKSIKLTRYRSEKI--SITYE 195
>gnl|CDD|48408 cd02410, archeal_CPSF_KH, The archaeal cleavage and polyadenylation
specificity factor (CPSF) contains an N-terminal K
homology RNA-binding domain (KH). The archeal CPSFs are
predicted to be metal-dependent RNases belonging to the
beta-CASP family, a subgroup enzymes within the
metallo-beta-lactamase fold. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices. In general, KH
domains are known to bind single-stranded RNA or DNA and
are found in a wide variety of proteins including
ribosomal proteins, transcription factors and
post-transcriptional modifiers of mRNA..
Length = 145
Score = 28.3 bits (63), Expect = 5.6
Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 1/46 (2%)
Query: 450 LAKGKELSREIKNNESWREARVAQITIPISELVSTVKKILQENKEE 495
+ KG REI W V I S V ++++ L+ +EE
Sbjct: 91 IGKGGSTLREITRETGWAPKVVRTPPIQ-SRTVKSIRRFLRREREE 135
>gnl|CDD|73229 cd00779, ProRS_core_prok, Prolyl-tRNA synthetase (ProRS) class II
core catalytic domain. ProRS is a homodimer. It is
responsible for the attachment of proline 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. This
subfamily contains the core domain of ProRS from
prokaryotes and from the mitochondria of eukaryotes..
Length = 255
Score = 28.2 bits (63), Expect = 5.8
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 104 FPCRTYRIGPVFRNE---KHGPGRFRQFIQCDVDNVGSSAETADAE 146
P Y+I FR+E + G R R+F+ D + E+ +
Sbjct: 112 LPLNLYQIQTKFRDEIRPRFGLMRGREFLMKDAYSFDIDEESLEET 157
>gnl|CDD|39385 KOG4183, KOG4183, KOG4183, RNA polymerase I 49 kDa subunit
[Transcription].
Length = 413
Score = 28.1 bits (62), Expect = 6.1
Identities = 22/74 (29%), Positives = 30/74 (40%), Gaps = 6/74 (8%)
Query: 48 PLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWISLRYDLTAPLAR--YVAENFDTIVFP 105
PL+ +SD G F E+ ++ +D + L R YV NF T
Sbjct: 24 PLVAFSDPNGGFRSPEN-TRFTLYKKKDSSKPRN--QRVLAGETERLEYVGNNFSTGALK 80
Query: 106 CRTYRIGPVFRNEK 119
C TY +G VF E
Sbjct: 81 CNTYCVG-VFNKES 93
>gnl|CDD|34415 COG4806, RhaA, L-rhamnose isomerase [Carbohydrate transport and
metabolism].
Length = 419
Score = 28.1 bits (62), Expect = 6.1
Identities = 10/45 (22%), Positives = 20/45 (44%), Gaps = 5/45 (11%)
Query: 11 LPRGFADCPTKEIRIRNRILDSIRNIY-----ENYGFDPIETPLL 50
+P G D P + R R+L+++ + + D +E+ L
Sbjct: 186 IPDGMKDIPVDRLAPRQRLLEALDEVISEKLDPAHHIDAVESKLF 230
>gnl|CDD|146135 pfam03343, SART-1, SART-1 family. SART-1 is a protein involved in
cell cycle arrest and pre-mRNA splicing. It has been
shown to be a component of U4/U6 x U5 tri-snRNP complex
in human, Schizosaccharomyces pombe and Saccharomyces
cerevisiae. SART-1 is a known tumour antigen in a range
of cancers recognized by T cells.
Length = 577
Score = 27.8 bits (62), Expect = 7.1
Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 9/66 (13%)
Query: 439 ERSRGMLQIKDLAKGKE-LSREIKNNESWREARVAQ-------ITI-PISELVSTVKKIL 489
+ R + Q K E ++R+I +S E A+ I I SE V +++K
Sbjct: 321 AKQRRLKQKKRKKLRPEDIARQIAEEKSEDEEEAAEAENNDNGIVIDETSEFVRSLQKEP 380
Query: 490 QENKEE 495
E + E
Sbjct: 381 LEEEPE 386
>gnl|CDD|33846 COG4089, COG4089, Predicted membrane protein [Function unknown].
Length = 235
Score = 27.6 bits (61), Expect = 7.3
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 7/41 (17%)
Query: 302 YTGCVYEAILGFPVMNEKQ-----KPVVFGSVGGGGRYDGL 337
Y V ++G ++N K+ PVV S+GG G +DG+
Sbjct: 186 YITGVLGTLIGADLLNLKKIINEGPPVV--SIGGAGTFDGI 224
>gnl|CDD|176105 cd08413, PBP2_CysB_like, The C-terminal substrate domain of
LysR-type transcriptional regulators CysB-like contains
type 2 periplasmic binding fold. CysB is a
transcriptional activator of genes involved in sulfate
and thiosulfate transport, sulfate reduction, and
cysteine synthesis. In Escherichia coli, the regulation
of transcription in response to sulfur source is
attributed to two transcriptional regulators, CysB and
Cbl. CysB, in association with Cbl, downregulates the
expression of ssuEADCB operon which is required for the
utilization of sulfur from aliphatic sulfonates, in the
presence of cysteine. Also, Cbl and CysB together
directly function as transcriptional activators of
tauABCD genes, which are required for utilization of
taurine as sulfur source for growth. Like many other
members of the LTTR family, CysB is composed of two
functional domains joined by a linker helix involved in
oligomerization: an N-terminal HTH (helix-turn-helix)
domain, which is responsible for the DNA-binding
specificity, and a C-terminal substrate-binding domain,
which is structurally homologous to the type 2
periplasmic binding proteins. As also observed in the
periplasmic binding proteins, the C-terminal domain of
the bacterial transcriptional repressor undergoes a
conformational change upon substrate binding which in
turn changes the DNA binding affinity of the repressor.
The structural topology of this substrate-binding domain
is most similar to that of the type 2 periplasmic
binding proteins (PBP2), which are responsible for the
uptake of a variety of substrates such as phosphate,
sulfate, polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis. Besides transport proteins, the PBP2
superfamily includes the substrate-binding domains from
ionotropic glutamate receptors, LysR-like
transcriptional regulators, and unorthodox sensor
proteins involved in signal transduction.
Length = 198
Score = 27.6 bits (62), Expect = 8.9
Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 7/37 (18%)
Query: 165 YHIGINNRKILDGILEKIGLHGDDKLNERLIVLRAID 201
Y G R +D + GL + IVL A+D
Sbjct: 104 YDFGFTGRSSIDRAFARAGLEPN-------IVLTALD 133
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.318 0.138 0.393
Gapped
Lambda K H
0.267 0.0670 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,835,000
Number of extensions: 318339
Number of successful extensions: 829
Number of sequences better than 10.0: 1
Number of HSP's gapped: 791
Number of HSP's successfully gapped: 49
Length of query: 496
Length of database: 6,263,737
Length adjustment: 98
Effective length of query: 398
Effective length of database: 4,146,055
Effective search space: 1650129890
Effective search space used: 1650129890
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 (21.7 bits)
S2: 59 (26.6 bits)