RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8087
(658 letters)
>gnl|CDD|238399 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 = 361 bits (928), Expect = e-120
Identities = 118/277 (42%), Positives = 166/277 (59%), Gaps = 9/277 (3%)
Query: 169 NGIAKVTPPTLVQTQVEGGSTLFSLNFFGEPAYLTQSSQLYLETCLPALGDVYCIAQSYR 228
NG +V P + T EGG+ LF +++FG+PAYL QS QLY E + AL VY I +R
Sbjct: 41 NGFTEVHTPKITSTDTEGGAELFKVSYFGKPAYLAQSPQLYKEMLIAALERVYEIGPVFR 100
Query: 229 AENSRTRRHLAEYTHVEAECAFL-TFDDLLDKLEDLICDTVDRVMATHGD---LVRQMNP 284
AE S TRRHL+E+ +EAE AF+ +++++D +E+LI RV+ LV Q+N
Sbjct: 101 AEKSNTRRHLSEFWMLEAEMAFIEDYNEVMDLIEELIKYIFKRVLERCAKELELVNQLNR 160
Query: 285 NFEPPARPFLRMNYADAIEYLRKHEIRKPDNTEYEFGEDIPEMPERKMTDQI-NRPIMLC 343
P PF R+ Y +AIE LR+ E ++GED+ ER + + + P+ +
Sbjct: 161 ELLKPLEPFPRITYDEAIELLREKG----VEEEVKWGEDLSTEHERLLGEIVKGDPVFVT 216
Query: 344 RFPADIKSFYMSKCPENPALTESVDVLFPNVGEVIGGSMRIWDPEELLAGYKREGIDPAP 403
+P +IK FYM +NP ES D+L P VGE++GGS RI D +EL K G+DP
Sbjct: 217 DYPKEIKPFYMKPDDDNPETVESFDLLMPGVGEIVGGSQRIHDYDELEERIKEHGLDPES 276
Query: 404 YYWYTDQRKYGSTPHGGYGLGLERVLCWLLNQYHVRD 440
+ WY D RKYG PHGG+GLGLER++ WLL ++R+
Sbjct: 277 FEWYLDLRKYGMPPHGGFGLGLERLVMWLLGLDNIRE 313
Score = 44.9 bits (107), Expect = 9e-05
Identities = 14/44 (31%), Positives = 24/44 (54%)
Query: 613 PDVQLDNRHIMIRGENTSRVLLMRSVLLQALRAHFADRNYTEVN 656
+ LDNRH+ +R + +RS +L+A R + +TEV+
Sbjct: 4 LETLLDNRHLDLRTPKVQAIFRIRSEVLRAFREFLRENGFTEVH 47
>gnl|CDD|223096 COG0017, AsnS, Aspartyl/asparaginyl-tRNA synthetases [Translation,
ribosomal structure and biogenesis].
Length = 435
Score = 346 bits (891), Expect = e-113
Identities = 129/400 (32%), Positives = 198/400 (49%), Gaps = 55/400 (13%)
Query: 87 KGLMFVTLRDGSGFIQCVL--ADILCQTEHALLLSTESSVQFRGRIEKVPEENMKVQLIH 144
++F+ LRDGSGFIQ V+ + + A L+ ESSV G ++ P+ + +
Sbjct: 32 GKIIFLVLRDGSGFIQAVVPKNKVYEELFKAKKLTLESSVVVTGIVKASPKAPQGFE-LQ 90
Query: 145 PSSYAIVWLGDLKQGGYP----------------------PEVSLA-------------- 168
++ D YP P++
Sbjct: 91 VEKIEVLGEADPP---YPIDKKEHSELETLLDNRHLDLRTPKIQAVFKIRSSILRAIREF 147
Query: 169 ---NGIAKVTPPTLVQTQVEGGSTLFSLNFFGEPAYLTQSSQLYLETCLPALGDVYCIAQ 225
NG +V P + + EGG LF +++F + AYLTQS QLY E AL V+ I
Sbjct: 148 FYENGFTEVHTPIITASATEGGGELFKVDYFDKEAYLTQSPQLYKEALAAALERVFTIGP 207
Query: 226 SYRAENSRTRRHLAEYTHVEAECAFLTFDDLLDKLEDLICDTVDRVMATHGD---LVRQM 282
++RAE S TRRHL+E+ ++ E AF +D++D E+LI +V+ D + +
Sbjct: 208 TFRAEKSNTRRHLSEFWMLDPEMAFADLNDVMDLAEELIKYLFKKVLEECADELEFLGRD 267
Query: 283 NPNFE-PPARPFLRMNYADAIEYLRKHEIRKPDNTEYEFGEDIPEMPERKMTDQINRP-I 340
N + P + PF R+ Y +AIE L + K E+G+D+ ER + ++ +P +
Sbjct: 268 NSELKRPESAPFPRITYKEAIEILEEKGFEKV-----EWGDDLGTEHERYLGEEYFKPPV 322
Query: 341 MLCRFPADIKSFYMSKCPENPALTESVDVLFPNVGEVIGGSMRIWDPEELLAGYKREGID 400
+ +P +IK FYM P+NP S D+L P GE+IGGS R D + L+ K +G+D
Sbjct: 323 FVTNYPKEIKPFYMRPDPDNPGTVASFDLLAPGGGEIIGGSQREHDYDLLVERIKEKGLD 382
Query: 401 PAPYYWYTDQRKYGSTPHGGYGLGLERVLCWLLNQYHVRD 440
P Y WY D RKYG PH G+GLGLER++ ++L ++R+
Sbjct: 383 PESYEWYLDLRKYGMPPHAGFGLGLERLVMYILGLDNIRE 422
Score = 116 bits (293), Expect = 8e-28
Identities = 60/163 (36%), Positives = 88/163 (53%), Gaps = 16/163 (9%)
Query: 501 RIKIKDGEKYRD-KRVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVL--ADILCQTEHA 557
R IKD + + + VT+ GWVH R GK ++F+ LRDGSGFIQ V+ + + A
Sbjct: 4 RTYIKDIKPHVGGQEVTVRGWVHNKRDLGK-IIFLVLRDGSGFIQAVVPKNKVYEELFKA 62
Query: 558 LLLSTESSVQFRGRIEKVPEGKSAPGGHELKVDYWEVVGLAPAGGADAIL----NEEALP 613
L+ ESSV G ++ P+ AP G EL+V+ EV+G AD E +
Sbjct: 63 KKLTLESSVVVTGIVKASPK---APQGFELQVEKIEVLG-----EADPPYPIDKKEHSEL 114
Query: 614 DVQLDNRHIMIRGENTSRVLLMRSVLLQALRAHFADRNYTEVN 656
+ LDNRH+ +R V +RS +L+A+R F + +TEV+
Sbjct: 115 ETLLDNRHLDLRTPKIQAVFKIRSSILRAIREFFYENGFTEVH 157
>gnl|CDD|232982 TIGR00457, asnS, asparaginyl-tRNA synthetase. In a multiple
sequence alignment of representative asparaginyl-tRNA
synthetases (asnS), archaeal/eukaryotic type
aspartyl-tRNA synthetases (aspS_arch), and bacterial
type aspartyl-tRNA synthetases (aspS_bact), there is a
striking similarity between asnS and aspS_arch in gap
pattern and in sequence, and a striking divergence of
aspS_bact. Consequently, a separate model was built for
each of the three groups. This model, asnS, represents
asparaginyl-tRNA synthetases from the three domains of
life. Some species lack this enzyme and charge tRNA(asn)
by misacylation with Asp, followed by transamidation of
Asp to Asn [Protein synthesis, tRNA aminoacylation].
Length = 453
Score = 303 bits (777), Expect = 3e-96
Identities = 135/417 (32%), Positives = 195/417 (46%), Gaps = 71/417 (17%)
Query: 87 KGLMFVTLRDGS--GFIQCVLADILCQTEHALL--LSTESSVQFRGRIEKVPEENMKVQL 142
K ++F+ L DGS G IQ V+ LL L+T SSV G++ + P + V+L
Sbjct: 32 KKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTTGSSVSVTGKVVESPGKGQPVEL 91
Query: 143 IHPSSYAIVWLGDLKQGGYP-------------------------------PEVSLA--- 168
+V G+ + YP +S A
Sbjct: 92 -QVKKIEVV--GEAEPDDYPLQKKEHSLEFLRDIAHLRLRTNTLGAVMRVRNALSQAIHR 148
Query: 169 ----NGIAKVTPPTLVQTQVEGGSTLFSLN---------FFGEPAYLTQSSQLYLETCLP 215
NG V+PP L EG LF ++ FFG+ AYLT S QLYLET
Sbjct: 149 YFQENGFTWVSPPILTSNDCEGAGELFRVSTGNIDFSQDFFGKEAYLTVSGQLYLETYAL 208
Query: 216 ALGDVYCIAQSYRAENSRTRRHLAEYTHVEAECAFLTFDDLLDKLEDLICDTVDRVMATH 275
AL VY ++RAE S T RHL+E+ +E E AF +DLL E LI + V+
Sbjct: 209 ALSKVYTFGPTFRAEKSNTSRHLSEFWMIEPEMAFANLNDLLQLAETLIKYIIKAVLENC 268
Query: 276 GDLVRQMNPNFEPPARP---------FLRMNYADAIEYLRKHEIRKPDNTEYE--FGEDI 324
++ + NF+ F R+ Y DAIE L++ + N EYE +G+D+
Sbjct: 269 SQELKFLEKNFDKDLIKRLENIINNKFARITYTDAIEILKESD----KNFEYEDFWGDDL 324
Query: 325 PEMPERKMTDQI-NRPIMLCRFPADIKSFYMSKCPENPALTESVDVLFPNVGEVIGGSMR 383
ER + ++ P+ + +P DIK+FYM ++ ++D+L P +GE+IGGS R
Sbjct: 325 QTEHERFLAEEYFKPPVFVTNYPKDIKAFYMKLN-DDGKTVAAMDLLAPGIGEIIGGSER 383
Query: 384 IWDPEELLAGYKREGIDPAPYYWYTDQRKYGSTPHGGYGLGLERVLCWLLNQYHVRD 440
D ++L K G+D WY D RKYGS PH G+GLG ER+L ++ ++RD
Sbjct: 384 EDDLDKLENRMKEMGLDTDALNWYLDLRKYGSVPHSGFGLGFERLLAYITGLENIRD 440
Score = 89.7 bits (223), Expect = 5e-19
Identities = 48/164 (29%), Positives = 76/164 (46%), Gaps = 11/164 (6%)
Query: 499 AVRIK--IKDGEKYRDKRVTIFGWVHRLRRQGKGLMFVTLRDGS--GFIQCVLADILCQT 554
+ IK ++ K+ VT+ GWV +R K ++F+ L DGS G IQ V+
Sbjct: 1 SAAIKDLLQQVYKFVGDEVTVSGWVRT-KRSSKKIIFLELNDGSSLGPIQAVINGEDNPY 59
Query: 555 EHALL--LSTESSVQFRGRIEKVPEGKSAPGGHELKVDYWEVVGLAPAGGADAILNEEAL 612
LL L+T SSV G++ + P EL+V EVVG A + +E
Sbjct: 60 LFQLLKSLTTGSSVSVTGKVVESP---GKGQPVELQVKKIEVVGEAE-PDDYPLQKKEHS 115
Query: 613 PDVQLDNRHIMIRGENTSRVLLMRSVLLQALRAHFADRNYTEVN 656
+ D H+ +R V+ +R+ L QA+ +F + +T V+
Sbjct: 116 LEFLRDIAHLRLRTNTLGAVMRVRNALSQAIHRYFQENGFTWVS 159
>gnl|CDD|235176 PRK03932, asnC, asparaginyl-tRNA synthetase; Validated.
Length = 450
Score = 270 bits (692), Expect = 1e-83
Identities = 134/420 (31%), Positives = 198/420 (47%), Gaps = 80/420 (19%)
Query: 87 KGLMFVTLRDGSGF--IQCVLADILCQTEHALLLSTESSVQFRGRIEKVPEENM------ 138
+ F+ LRDGS F +Q V + E L+T SSV G + + P
Sbjct: 32 GKIAFLQLRDGSCFKQLQVVKDNGEEYFEEIKKLTTGSSVIVTGTVVESPRAGQGYELQA 91
Query: 139 -KVQLIH--PSSYAI---------------VWLGDLKQG-------GYPPEVSLA----- 168
K+++I P Y I + K G ++ A
Sbjct: 92 TKIEVIGEDPEDYPIQKKRHSIEFLREIAHLRPRTNKFGAVMRIRN----TLAQAIHEFF 147
Query: 169 --NGIAKVTPPTLVQTQVEGGSTLF---------SLNFFGEPAYLTQSSQLYLETCLPAL 217
NG V P + + EG LF S +FFG+ AYLT S QLY E AL
Sbjct: 148 NENGFVWVDTPIITASDCEGAGELFRVTTLDLDFSKDFFGKEAYLTVSGQLYAEAYAMAL 207
Query: 218 GDVYCIAQSYRAENSRTRRHLAEYTHVEAECAFLTFDDLLDKLEDLICDTVDRVMATHGD 277
G VY ++RAENS TRRHLAE+ +E E AF +D +D E+++ V V+ D
Sbjct: 208 GKVYTFGPTFRAENSNTRRHLAEFWMIEPEMAFADLEDNMDLAEEMLKYVVKYVLENCPD 267
Query: 278 ----LVRQMNP-------NFEPPARPFLRMNYADAIEYLRKHEIRKPDNTEYEFGEDI-- 324
L R+++ NF PF R+ Y +AIE L+K +K + E+G+D+
Sbjct: 268 DLEFLNRRVDKGDIERLENFIES--PFPRITYTEAIEILQKSG-KKFEFPV-EWGDDLGS 323
Query: 325 PEMPERKMTDQI-NRPIMLCRFPADIKSFYMSKCPENPALTESV---DVLFPNVGEVIGG 380
ER + ++ +P+ + +P DIK+FYM P+ ++V D+L P +GE+IGG
Sbjct: 324 EH--ERYLAEEHFKKPVFVTNYPKDIKAFYMRLNPDG----KTVAAMDLLAPGIGEIIGG 377
Query: 381 SMRIWDPEELLAGYKREGIDPAPYYWYTDQRKYGSTPHGGYGLGLERVLCWLLNQYHVRD 440
S R + L A K G++ Y+WY D R+YGS PH G+GLG ER++ ++ ++RD
Sbjct: 378 SQREERLDVLEARIKELGLNKEDYWWYLDLRRYGSVPHSGFGLGFERLVAYITGLDNIRD 437
Score = 89.4 bits (223), Expect = 8e-19
Identities = 49/164 (29%), Positives = 76/164 (46%), Gaps = 18/164 (10%)
Query: 501 RIKIKD--GEKYRDKRVTIFGWVHRLRRQGKGLMFVTLRDGSGF--IQCVLADILCQTEH 556
R+ IKD KY + VT+ GWV +R + F+ LRDGS F +Q V + E
Sbjct: 3 RVSIKDILKGKYVGQEVTVRGWVRT-KRDSGKIAFLQLRDGSCFKQLQVVKDNGEEYFEE 61
Query: 557 ALLLSTESSVQFRGRIEKVPEGKSAPGGHELKVDYWEVVGLAPAGGAD-AILNEEALPDV 615
L+T SSV G + + P A G+EL+ EV+G P D I + +
Sbjct: 62 IKKLTTGSSVIVTGTVVESPR---AGQGYELQATKIEVIGEDP---EDYPIQKKRHSIEF 115
Query: 616 QLDNRHIMIRGENTSR---VLLMRSVLLQALRAHFADRNYTEVN 656
+ H+ R T++ V+ +R+ L QA+ F + + V+
Sbjct: 116 LREIAHLRPR---TNKFGAVMRIRNTLAQAIHEFFNENGFVWVD 156
>gnl|CDD|215753 pfam00152, tRNA-synt_2, tRNA synthetases class II (D, K and N).
Length = 345
Score = 240 bits (614), Expect = 1e-73
Identities = 94/304 (30%), Positives = 142/304 (46%), Gaps = 38/304 (12%)
Query: 169 NGIAKVTPPTLVQTQVEGGSTLFS--LNFFGEPAYLTQSSQLYLETCLPA-LGDVYCIAQ 225
G +V P L ++ EGG+ F F+ + AYL QS QLY + + A V+ IA
Sbjct: 39 RGFLEVETPILTKSTPEGGARDFLVPSKFYAKEAYLPQSPQLYKQLLMVAGFDRVFQIAP 98
Query: 226 SYRAENSRTRRHLAEYTHVEAECAFLTFDDLLDKLEDLICDTVDRVMATHGDLVRQMNPN 285
+R E+ RT RH E+T ++ E +F+ ++D++D EDLI +V+ +L
Sbjct: 99 CFRDEDLRTDRHPPEFTQLDLEMSFVDYEDVMDLTEDLIKYVFKKVLGKREELE---LLG 155
Query: 286 FEPPARPFLRMNYADAIE--------------------YLRKHEIRKPDNTEY----EFG 321
E P F R+ YA+AIE + E + G
Sbjct: 156 IELP--EFPRITYAEAIERYGSDKPDLRFGLELKDVTEIFKGSEFKVFAEAGDVVDKALG 213
Query: 322 EDIPEMPERKMTDQ-INRPIMLCRFPADIKSFYMSKCPENPALTESVDVLFPNVGEVIGG 380
E+ E + D+ + P+ + FP FYM K + P L E D++ GE+ GG
Sbjct: 214 ALRSELGEENLGDKDKDNPVFVTDFPLFEHPFYMPKDEDPPGLAERFDLVLNG-GEIGGG 272
Query: 381 SMRIWDPEELLAGYKREGIDP----APYYWYTDQRKYGSTPHGGYGLGLERVLCWLLNQY 436
S+RI DPEE ++ G+DP + +Y D KYG PHGG GLGL+R++ L
Sbjct: 273 SIRIHDPEEQRKRFEELGLDPEEAEEKFGFYLDALKYGMPPHGGIGLGLDRLVMLLTGLE 332
Query: 437 HVRD 440
+R+
Sbjct: 333 SIRE 336
Score = 44.1 bits (105), Expect = 1e-04
Identities = 11/44 (25%), Positives = 23/44 (52%)
Query: 613 PDVQLDNRHIMIRGENTSRVLLMRSVLLQALRAHFADRNYTEVN 656
+ +L R++ +R L +RS +++A+R +R + EV
Sbjct: 2 EETRLKYRYLDLRRPKMQANLKLRSKIIKAIREFLDERGFLEVE 45
>gnl|CDD|235354 PRK05159, aspC, aspartyl-tRNA synthetase; Provisional.
Length = 437
Score = 200 bits (512), Expect = 1e-57
Identities = 108/406 (26%), Positives = 186/406 (45%), Gaps = 65/406 (16%)
Query: 87 KGLMFVTLRDGSGFIQCVL-ADILCQT-EHALLLSTESSVQFRGRIEKVPEENMKVQLIH 144
G+ F+ LRD SG IQ V+ + + E L ES V G ++ P+ V++I
Sbjct: 32 GGIAFLILRDRSGIIQVVVKKKVDEELFETIKKLKRESVVSVTGTVKANPKAPGGVEVI- 90
Query: 145 PSSYAIV--------------------------WLGDLKQGGYPPEVS----LANGIAK- 173
P ++ +L DL++ P V + + + +
Sbjct: 91 PEEIEVLNKAEEPLPLDISGKVLAELDTRLDNRFL-DLRR----PRVRAIFKIRSEVLRA 145
Query: 174 ------------VTPPTLVQTQVEGGSTLFSLNFFGEPAYLTQSSQLYLETCLPALGD-V 220
+ P +V + EGG+ LF +++F + AYL QS QLY + + A + V
Sbjct: 146 FREFLYENGFTEIFTPKIVASGTEGGAELFPIDYFEKEAYLAQSPQLYKQMMVGAGFERV 205
Query: 221 YCIAQSYRAENSRTRRHLAEYTHVEAECAFLT-FDDLLDKLEDLICDTVDRVMATHGDLV 279
+ I +RAE T RHL EYT ++ E F+ +D++D LE+L+ + V +
Sbjct: 206 FEIGPVFRAEEHNTSRHLNEYTSIDVEMGFIDDHEDVMDLLENLLRYMYEDVAENCEKEL 265
Query: 280 RQMNPNFEPPARPFLRMNYADAIEYLRKHEIRKPDNTEYEFGEDIPEMPERKMTDQINR- 338
+ P P R+ Y +AIE L+ E +G+D+ ER + + +
Sbjct: 266 ELLGIELPVPETPIPRITYDEAIEILKSKGN------EISWGDDLDTEGERLLGEYVKEE 319
Query: 339 ----PIMLCRFPADIKSFYMSKCPENPALTESVDVLFPNVGEVIGGSMRIWDPEELLAGY 394
+ +P++ + FY ++P +++S D+LF + E+ G RI + L+
Sbjct: 320 YGSDFYFITDYPSEKRPFYTMPDEDDPEISKSFDLLFRGL-EITSGGQRIHRYDMLVESI 378
Query: 395 KREGIDPAPYYWYTDQRKYGSTPHGGYGLGLERVLCWLLNQYHVRD 440
K +G++P + +Y + KYG PHGG+GLGLER+ LL ++R+
Sbjct: 379 KEKGLNPESFEFYLEAFKYGMPPHGGFGLGLERLTMKLLGLENIRE 424
Score = 92.9 bits (232), Expect = 4e-20
Identities = 49/153 (32%), Positives = 71/153 (46%), Gaps = 19/153 (12%)
Query: 513 KRVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVL-ADILCQT-EHALLLSTESSVQFRG 570
+ VT+ GWVH +R G G+ F+ LRD SG IQ V+ + + E L ES V G
Sbjct: 17 EEVTLAGWVHEIRDLG-GIAFLILRDRSGIIQVVVKKKVDEELFETIKKLKRESVVSVTG 75
Query: 571 RIEKVPEGKSAPGGHELKVDYWEVVGLA-------PAGGADAILNEEALPDVQLDNRHIM 623
V APGG E+ + EV+ A +G A L D +LDNR +
Sbjct: 76 ---TVKANPKAPGGVEVIPEEIEVLNKAEEPLPLDISGKVLAEL------DTRLDNRFLD 126
Query: 624 IRGENTSRVLLMRSVLLQALRAHFADRNYTEVN 656
+R + +RS +L+A R + +TE+
Sbjct: 127 LRRPRVRAIFKIRSEVLRAFREFLYENGFTEIF 159
>gnl|CDD|129550 TIGR00458, aspS_nondisc, nondiscriminating aspartyl-tRNA
synthetase. In a multiple sequence alignment of
representative asparaginyl-tRNA synthetases (asnS),
archaeal/eukaryotic type aspartyl-tRNA synthetases
(aspS_arch), and bacterial type aspartyl-tRNA
synthetases (aspS_bact), there is a striking similarity
between asnS and aspS_arch in gap pattern and in
sequence, and a striking divergence of aspS_bact.
Consequently, a separate model was built for each of the
three groups. This model, aspS_arch, represents
aspartyl-tRNA synthetases from the eukaryotic cytosol
and from the Archaea. In some species, this enzyme
aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn)
is subsequently transamidated to Asn-tRNA(asn) [Protein
synthesis, tRNA aminoacylation].
Length = 428
Score = 154 bits (391), Expect = 5e-41
Identities = 82/272 (30%), Positives = 139/272 (51%), Gaps = 8/272 (2%)
Query: 170 GIAKVTPPTLVQTQVEGGSTLFSLNFFGEPAYLTQSSQLYLETCLPA-LGDVYCIAQSYR 228
G +V P LV + EGG+ LF + +F A+L QS QLY + + A VY I +R
Sbjct: 151 GFIEVHTPKLVASATEGGTELFPITYFEREAFLGQSPQLYKQQLMAAGFERVYEIGPIFR 210
Query: 229 AENSRTRRHLAEYTHVEAECAFLTFDDLLDKLEDLICDTVDRVMATHGDLVRQMNPNFEP 288
AE T RHL E T ++ E AF D++D LE+L+ + V + + E
Sbjct: 211 AEEHNTHRHLNEATSIDIEMAFEDHHDVMDILEELVVRVFEDVPERCAHQLETLEFKLEK 270
Query: 289 PARPFLRMNYADAIEYLRKHEIRKPDNTEYEFGEDIPEMPERKMTDQINRPIMLCRFPAD 348
P F+R+ Y +AIE + GED+ E+ + ++++ + +P +
Sbjct: 271 PEGKFVRLTYDEAIEMANAKGVEIGW------GEDLSTEAEKALGEEMDGLYFITDWPTE 324
Query: 349 IKSFYMSKCPENPALTESVDVLFPNVGEVIGGSMRIWDPEELLAGYKREGIDPAPYYWYT 408
I+ FY +NP +++S D+++ ++ E+ G+ RI + L+ K +G++P + Y
Sbjct: 325 IRPFYTMPDEDNPEISKSFDLMYRDL-EISSGAQRIHLHDLLVERIKAKGLNPEGFKDYL 383
Query: 409 DQRKYGSTPHGGYGLGLERVLCWLLNQYHVRD 440
+ YG PH G+GLG ER + +LL ++R+
Sbjct: 384 EAFSYGMPPHAGWGLGAERFVMFLLGLKNIRE 415
Score = 71.4 bits (175), Expect = 4e-13
Identities = 48/150 (32%), Positives = 69/150 (46%), Gaps = 12/150 (8%)
Query: 513 KRVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVLADILCQTE---HALLLSTESSVQFR 569
+ VT GWVH +R G GL+FV LRD G IQ A L+ ES V R
Sbjct: 13 QEVTFMGWVHEIRDLG-GLIFVLLRDREGLIQITAPAKKVSKNLFKWAKKLNLESVVAVR 71
Query: 570 GRIEKVPEGKSAPGGHELKVDYWEVVGLAPAGGADAILNEEALP---DVQLDNRHIMIRG 626
G V + APGG E+ EV+ A + E +P D +LD R + +R
Sbjct: 72 G---IVKIKEKAPGGFEIIPTKIEVINEAKE--PLPLDPTEKVPAELDTRLDYRFLDLRR 126
Query: 627 ENTSRVLLMRSVLLQALRAHFADRNYTEVN 656
+ +RS +L+++R A+ + EV+
Sbjct: 127 PTVQAIFRIRSGVLESVREFLAEEGFIEVH 156
>gnl|CDD|178213 PLN02603, PLN02603, asparaginyl-tRNA synthetase.
Length = 565
Score = 153 bits (387), Expect = 1e-39
Identities = 95/297 (31%), Positives = 149/297 (50%), Gaps = 34/297 (11%)
Query: 162 PPEVSLANGIAKVTPPTLVQTQVEGGSTLFSLNFFGEPAYLTQSSQLYLETCLPALGDVY 221
P + P T + G +S +FFG+PA+LT S QL ET AL DVY
Sbjct: 272 PNSAENGGSLVDDIPKT------KDGLIDWSQDFFGKPAFLTVSGQLNGETYATALSDVY 325
Query: 222 CIAQSYRAENSRTRRHLAEYTHVEAECAFLTFDDLLDKLEDLICDTVDRVMAT------- 274
++RAENS T RHLAE+ +E E AF +D + + V ++
Sbjct: 326 TFGPTFRAENSNTSRHLAEFWMIEPELAFADLNDDMACATAYLQYVVKYILENCKEDMEF 385
Query: 275 -----HGDLVRQMNPNFEPPARPFLRMNYADAIEYLRKHEIRKPDNTEYEF----GEDIP 325
++ +++ E + F++++Y DAIE L K ++EF G D+
Sbjct: 386 FNTWIEKGIIDRLSDVVE---KNFVQLSYTDAIELLLK------AKKKFEFPVKWGLDLQ 436
Query: 326 EMPERKMTDQI--NRPIMLCRFPADIKSFYMSKCPENPALTESVDVLFPNVGEVIGGSMR 383
ER +T++ RP+++ +P +IK+FYM + + + ++D+L P VGE+IGGS R
Sbjct: 437 SEHERYITEEAFGGRPVIIRDYPKEIKAFYMRENDDGKTVA-AMDMLVPRVGELIGGSQR 495
Query: 384 IWDPEELLAGYKREGIDPAPYYWYTDQRKYGSTPHGGYGLGLERVLCWLLNQYHVRD 440
E L A ++ Y+WY D R+YGS PH G+GLG ER++ + ++RD
Sbjct: 496 EERLEYLEARLDELKLNKESYWWYLDLRRYGSVPHAGFGLGFERLVQFATGIDNIRD 552
Score = 38.4 bits (89), Expect = 0.013
Identities = 43/145 (29%), Positives = 62/145 (42%), Gaps = 17/145 (11%)
Query: 457 AARDNAKSESKAKKEEEDAEKREKNLEEAKKIVLKEDPSLPPAVRIKIKDGEKYRDKRVT 516
AA + +S AK E E E KK+ + + V+ +G K +
Sbjct: 59 AASASLQSPESAKVEAAKGAFGEAVGEFRKKLRIAD-------VKGGEDEGLARVGKTLN 111
Query: 517 IFGWVHRLRRQGKGLMFVTLRDGSGF--IQCVL---ADILCQTEHALLLSTESSVQFRGR 571
+ GWV LR Q + F+ + DGS +QCV+ A+ Q E L+ T +SV +G
Sbjct: 112 VMGWVRTLRAQ-SSVTFIEVNDGSCLSNMQCVMTPDAEGYDQVESGLIT-TGASVLVQGT 169
Query: 572 IEKVPEGKSAPGGHELKVDYWEVVG 596
+ GK ELKV VVG
Sbjct: 170 VVSSQGGKQKV---ELKVSKIVVVG 191
>gnl|CDD|240414 PTZ00425, PTZ00425, asparagine-tRNA ligase; Provisional.
Length = 586
Score = 152 bits (384), Expect = 5e-39
Identities = 88/256 (34%), Positives = 139/256 (54%), Gaps = 11/256 (4%)
Query: 194 NFFGEPAYLTQSSQLYLETCLPALGDVYCIAQSYRAENSRTRRHLAEYTHVEAECAFLTF 253
+FF + A+LT S QL LE ++GDVY ++RAENS T RHLAE+ +E E AF
Sbjct: 320 DFFSKQAFLTVSGQLSLENLCSSMGDVYTFGPTFRAENSHTSRHLAEFWMIEPEIAFADL 379
Query: 254 DDLLDKLEDLICDTVDRVMATHGDLVRQMNPNFE----PPARPFLRMNYADAIEYLRKHE 309
D ++ E I + V+ + D + N E + L ++A I Y +
Sbjct: 380 YDNMELAESYIKYCIGYVLNNNFDDIYYFEENVETGLISRLKNILDEDFAK-ITYTNVID 438
Query: 310 IRKPDNTEYE----FGEDIPEMPERKMTDQI-NRPIMLCRFPADIKSFYMSKCPENPALT 364
+ +P + +E +G D+ ER + +QI +P+++ +P D+K+FYM K E+
Sbjct: 439 LLQPYSDSFEVPVKWGMDLQSEHERFVAEQIFKKPVIVYNYPKDLKAFYM-KLNEDQKTV 497
Query: 365 ESVDVLFPNVGEVIGGSMRIWDPEELLAGYKREGIDPAPYYWYTDQRKYGSTPHGGYGLG 424
++DVL P +GEVIGGS R + E L K + ++ Y+WY RK+GS PH G+GLG
Sbjct: 498 AAMDVLVPKIGEVIGGSQREDNLERLDKMIKEKKLNMESYWWYRQLRKFGSHPHAGFGLG 557
Query: 425 LERVLCWLLNQYHVRD 440
ER++ + +++D
Sbjct: 558 FERLIMLVTGVDNIKD 573
Score = 35.0 bits (80), Expect = 0.14
Identities = 16/33 (48%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 509 KYRDKRVTIFGWVHRLRRQGKG-LMFVTLRDGS 540
KY D+ +T+ GW +R+QG G FV L DGS
Sbjct: 78 KYIDQIITVCGWSKAVRKQGGGRFCFVNLNDGS 110
>gnl|CDD|235808 PRK06462, PRK06462, asparagine synthetase A; Reviewed.
Length = 335
Score = 145 bits (369), Expect = 8e-39
Identities = 73/260 (28%), Positives = 128/260 (49%), Gaps = 10/260 (3%)
Query: 191 FSLNFFGEPAYLTQSSQLYLETCLPALGDVYCIAQSYRAEN--SRTRRHLAEYTHVEAEC 248
S++F+G YL S L+ + L LG ++ ++ ++R E T RHL E+T ++ E
Sbjct: 76 ISIDFYGVEYYLADSMILHKQLALRMLGKIFYLSPNFRLEPVDKDTGRHLYEFTQLDIEI 135
Query: 249 AFLTFDDLLDKLEDLICDTVDRVMATHGDLVRQMNPNFEPPARPFLRMNYADAIEYLRKH 308
D+++D +EDLI V ++ H D + + RPF R+ + +A+E L +
Sbjct: 136 EGADLDEVMDLIEDLIKYLVKELLEEHEDELEFFGRDLPHLKRPFKRITHKEAVEILNEE 195
Query: 309 EIRKPDNTEYEFGEDIPEMPERKMTDQINRPIMLCRFPADIKSFYMSKCPENPALTESVD 368
R D E G + E+ +++ P + P + FY + PE P + + D
Sbjct: 196 GCRGID--LEELGSEG----EKSLSEHFEEPFWIIDIPKGSREFYDREDPERPGVLRNYD 249
Query: 369 VLFPN-VGEVIGGSMRIWDPEELLAGYKREGIDPAPYYWYTDQRKYGSTPHGGYGLGLER 427
+L P GE + G R ++ EE++ + G+DP Y WY + K G P G+G+G+ER
Sbjct: 250 LLLPEGYGEAVSGGEREYEYEEIVERIREHGVDPEKYKWYLEMAKEGPLPSAGFGIGVER 309
Query: 428 VLCWLLNQYHVRDKYQLIAK 447
+ ++ H+R+ Q +
Sbjct: 310 LTRYICGLRHIRE-VQPFPR 328
>gnl|CDD|177867 PLN02221, PLN02221, asparaginyl-tRNA synthetase.
Length = 572
Score = 148 bits (375), Expect = 6e-38
Identities = 91/265 (34%), Positives = 141/265 (53%), Gaps = 12/265 (4%)
Query: 187 GSTLFSLNFFGEPAYLTQSSQLYLETCLPALGDVYCIAQSYRAENSRTRRHLAEYTHVEA 246
G +S +FFG A+LT S QL +ET AL VY ++RAENS T RHLAE+ VE
Sbjct: 296 GKIDYSKDFFGRQAFLTVSGQLQVETYACALSSVYTFGPTFRAENSHTSRHLAEFWMVEP 355
Query: 247 ECAFLTFDDLLDKLEDLICDTVDRVMATHGDLVRQMNPNFEP---------PARPFLRMN 297
E AF +D ++ E + ++ D + M NF+ + PF R+
Sbjct: 356 EIAFADLEDDMNCAEAYVKYMCKWLLDKCFDDMELMAKNFDSGCIDRLRMVASTPFGRIT 415
Query: 298 YADAIEYLRKHEIR-KPDNTEYEFGEDIPEMPERKMTDQI-NRPIMLCRFPADIKSFYMS 355
Y +AIE L + + K + E+G D+ ER +T+ + +P+++ +P IK+FYM
Sbjct: 416 YTEAIELLEEAVAKGKEFDNNVEWGIDLASEHERYLTEVLFQKPLIVYNYPKGIKAFYM- 474
Query: 356 KCPENPALTESVDVLFPNVGEVIGGSMRIWDPEELLAGYKREGIDPAPYYWYTDQRKYGS 415
+ ++ ++DVL P VGE+IGGS R + + + G+ PY WY D R+YG+
Sbjct: 475 RLNDDEKTVAAMDVLVPKVGELIGGSQREERYDVIKQRIEEMGLPIEPYEWYLDLRRYGT 534
Query: 416 TPHGGYGLGLERVLCWLLNQYHVRD 440
H G+GLG ER++ + ++RD
Sbjct: 535 VKHCGFGLGFERMILFATGIDNIRD 559
Score = 38.4 bits (89), Expect = 0.012
Identities = 40/150 (26%), Positives = 68/150 (45%), Gaps = 8/150 (5%)
Query: 507 GEKYRDKRVTIFGWVHRLRRQGKG-LMFVTLRDGS--GFIQCVLADILCQTEHALLLSTE 563
G ++V I GWV R QGKG F+ + DGS +Q ++ L + + L++T
Sbjct: 45 GAGLAGQKVRIGGWVKTGREQGKGTFAFLEVNDGSCPANLQVMVDSSL--YDLSTLVATG 102
Query: 564 SSVQFRGRIEKVPEGKSAPGGHELKVDYWEVVGLAPAGGADAILNEEAL-PDVQLDNRHI 622
+ V G ++ PEGK EL V+ +V+ + L + L + D H+
Sbjct: 103 TCVTVDGVLKVPPEGKGTKQKIELSVE--KVIDVGTVDPTKYPLPKTKLTLEFLRDVLHL 160
Query: 623 MIRGENTSRVLLMRSVLLQALRAHFADRNY 652
R + S V +R+ L A + F + ++
Sbjct: 161 RSRTNSISAVARIRNALAFATHSFFQEHSF 190
>gnl|CDD|239818 cd04323, AsnRS_cyto_like_N, AsnRS_cyto_like_N: N-terminal,
anticodon recognition domain of the type found in human
and Saccharomyces cerevisiae cytoplasmic
asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai
AsnRs and, in various putative bacterial AsnRSs. This
domain is a beta-barrel domain (OB fold) involved in
binding the tRNA anticodon stem-loop. The enzymes in
this group are homodimeric class2b aminoacyl-tRNA
synthetases (aaRSs). aaRSs catalyze the specific
attachment of amino acids (AAs) to their cognate tRNAs
during protein biosynthesis. This 2-step reaction
involves i) the activation of the AA by ATP in the
presence of magnesium ions, followed by ii) the transfer
of the activated AA to the terminal ribose of tRNA. In
the case of the class2b aaRSs, the activated AA is
attached to the 3'OH of the terminal ribose. Eukaryotes
contain 2 sets of aaRSs, both of which are encoded by
the nuclear genome. One set concerns with cytoplasmic
synthesis, whereas the other exclusively with
mitochondrial protein synthesis. AsnRS is
immunodominant antigen of the filarial nematode B.
malayai and of interest as a target for anti-parasitic
drug design. Human AsnRS has been shown to be a
pro-inflammatory chemokine which interacts with CCR3
chemokine receptors on T cells, immature dendritic cells
and macrophages.
Length = 84
Score = 133 bits (337), Expect = 2e-37
Identities = 46/84 (54%), Positives = 60/84 (71%), Gaps = 2/84 (2%)
Query: 514 RVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVLADILCQ-TEHALLLSTESSVQFRGRI 572
RV +FGWVHRLR Q K LMF+ LRDG+GF+QCVL+ L A L+ ESSV+ G +
Sbjct: 1 RVKVFGWVHRLRSQKK-LMFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGEV 59
Query: 573 EKVPEGKSAPGGHELKVDYWEVVG 596
++ P K APGG+EL+VDY E++G
Sbjct: 60 KEDPRAKQAPGGYELQVDYLEIIG 83
Score = 69.2 bits (170), Expect = 1e-14
Identities = 23/50 (46%), Positives = 32/50 (64%), Gaps = 1/50 (2%)
Query: 87 KGLMFVTLRDGSGFIQCVLADILCQ-TEHALLLSTESSVQFRGRIEKVPE 135
K LMF+ LRDG+GF+QCVL+ L A L+ ESSV+ G +++ P
Sbjct: 15 KKLMFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGEVKEDPR 64
>gnl|CDD|215456 PLN02850, PLN02850, aspartate-tRNA ligase.
Length = 530
Score = 140 bits (355), Expect = 2e-35
Identities = 92/286 (32%), Positives = 146/286 (51%), Gaps = 22/286 (7%)
Query: 167 LANGIAKVTPPTLVQTQVEGGSTLFSLNFFGEPAYLTQSSQLYLETCLPA-LGDVYCIAQ 225
L+ G ++ P L+ EGGS +F L++ G+PA L QS QL+ + + V+ I
Sbjct: 240 LSKGFVEIHTPKLIAGASEGGSAVFRLDYKGQPACLAQSPQLHKQMAICGDFRRVFEIGP 299
Query: 226 SYRAENSRTRRHLAEYTHVEAECA----FLTFDDLLDKLEDLICDTVDRVMATHGDLVRQ 281
+RAE+S T RHL E+T ++ E + D++D+L I D ++ + +R+
Sbjct: 300 VFRAEDSFTHRHLCEFTGLDLEMEIKEHYSEVLDVVDELFVAIFDGLNERCKKELEAIRE 359
Query: 282 MNPNFEPPA--RPFLRMNYADAIEYLRKHEIRKPD----NTEYE--FGEDIPEMPERKMT 333
P FEP LR+ +A+ I+ L++ + NTE E G+ + E + T
Sbjct: 360 QYP-FEPLKYLPKTLRLTFAEGIQMLKEAGVEVDPLGDLNTESERKLGQLVKE---KYGT 415
Query: 334 DQINRPIMLCRFPADIKSFYMSKCPENPALTESVDVLFPNVGEVIGGSMRIWDPEELLAG 393
D +L R+P ++ FY CP++P + S DV F E+I G+ R+ DPE L
Sbjct: 416 DFY----ILHRYPLAVRPFYTMPCPDDPKYSNSFDV-FIRGEEIISGAQRVHDPELLEKR 470
Query: 394 YKREGIDPAPYYWYTDQRKYGSTPHGGYGLGLERVLCWLLNQYHVR 439
+ GID Y D +YG+ PHGG+G+GLERV+ ++R
Sbjct: 471 AEECGIDVKTISTYIDSFRYGAPPHGGFGVGLERVVMLFCGLNNIR 516
Score = 42.0 bits (99), Expect = 0.001
Identities = 36/137 (26%), Positives = 57/137 (41%), Gaps = 10/137 (7%)
Query: 446 AKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKIVLKEDPSLPPAVRIKIK 505
AK K KL AK+ + + ++E+D N + L+ + +
Sbjct: 18 AKKAAAKAEKLRREATAKAAAASLEDEDDPLA--SNYGDVPLEELQSKVTGREWTDVS-D 74
Query: 506 DGEKYRDKRVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVL-ADILCQTEH----ALLL 560
GE+ V I G VH +R +GK F+ LR +QCV+ + ++ A L
Sbjct: 75 LGEELAGSEVLIRGRVHTIRGKGKSA-FLVLRQSGFTVQCVVFVSEVTVSKGMVKYAKQL 133
Query: 561 STESSVQFRGRIEKVPE 577
S ES V G + VP+
Sbjct: 134 SRESVVDVEG-VVSVPK 149
>gnl|CDD|238358 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 = 117 bits (295), Expect = 2e-29
Identities = 69/280 (24%), Positives = 120/280 (42%), Gaps = 43/280 (15%)
Query: 168 ANGIAKVTPPTLVQTQVEGGSTLFSLNFF--GEPAYLTQSSQLYLETCLPA-LGDVYCIA 224
G +V P L + G+ F + + G YL S QL+ + + L V+ I
Sbjct: 17 DRGFLEVETPMLQKITGGAGARPFLVKYNALGLDYYLRISPQLFKKRLMVGGLDRVFEIN 76
Query: 225 QSYRAENSRTRRHLAEYTHVEAECAFLTFDDLLDKLEDLICDTVDRVMATHGDLVRQMNP 284
+++R E+ R R H E+T ++ E AF ++D+++ E L+ V+
Sbjct: 77 RNFRNEDLRAR-HQPEFTMMDLEMAFADYEDVIELTERLVRHLAREVLGVTA---VTYGF 132
Query: 285 NFEPPARPFLRMNYADAIEYLRKHEIRKPDNTEYEFGEDIPEMPERKMTDQINRPIMLCR 344
E PF R+ Y +A+E +P+ L
Sbjct: 133 ELEDFGLPFPRLTYREALERYG-------------------------------QPLFLTD 161
Query: 345 FPADIKSFYMSKCPENPALTESVDVLFPNVGEVIGGSMRIWDPEELLAGYKREGIDPAP- 403
+PA++ S S NP + ++ D LF N EV GS R+ DP+ ++ +GI+
Sbjct: 162 YPAEMHSPLASPHDVNPEIADAFD-LFINGVEVGNGSSRLHDPDIQAEVFQEQGINKEAG 220
Query: 404 ---YYWYTDQRKYGSTPHGGYGLGLERVLCWLLNQYHVRD 440
+ +Y +YG PHGG G+G++R++ + N +R+
Sbjct: 221 MEYFEFYLKALEYGLPPHGGLGIGIDRLIMLMTNSPTIRE 260
>gnl|CDD|173592 PTZ00401, PTZ00401, aspartyl-tRNA synthetase; Provisional.
Length = 550
Score = 120 bits (302), Expect = 1e-28
Identities = 98/338 (28%), Positives = 148/338 (43%), Gaps = 51/338 (15%)
Query: 145 PSSYAIVWLGDLKQGGYPPEVSLANGIAKVTPPTLVQTQVEGGSTLFSLNFFGEPAYLTQ 204
P+S AI L + Y + + + ++ P ++ EGG+ +F L +F AYL Q
Sbjct: 207 PASGAIFRLQS-RVCQYFRQFLIDSDFCEIHSPKIINAPSEGGANVFKLEYFNRFAYLAQ 265
Query: 205 SSQLYLETCLPA-LGDVYCIAQSYRAENSRTRRHLAEYTHVEAECAFLT-FDDLLDKLED 262
S QLY + L + V+ + +R+ENS T RHL E+ ++ E + ++LD E
Sbjct: 266 SPQLYKQMVLQGDVPRVFEVGPVFRSENSNTHRHLTEFVGLDVEMRINEHYYEVLDLAES 325
Query: 263 LICDTVDRVMATHGD-------------LVRQMNP-------------NFEPP----AR- 291
L +R +ATH LV ++ P EP AR
Sbjct: 326 LFNYIFER-LATHTKELKAVCQQYPFEPLVWKLTPERMKELGVGVISEGVEPTDKYQARV 384
Query: 292 -----PFLRMNYADAIEYLRKHEIRKPDNTEYEFGEDIPEMPERKMTDQINRP-----IM 341
LR+NY IE L K T+ DI E+ + + +
Sbjct: 385 HNMDSRMLRINYMHCIELLNTVLEEKMAPTD-----DINTTNEKLLGKLVKERYGTDFFI 439
Query: 342 LCRFPADIKSFYMSKCPENPALTESVDVLFPNVGEVIGGSMRIWDPEELLAGYKREGIDP 401
RFP+ + FY +C ++ T S D +F E+ G+ RI DP+ LLA K +D
Sbjct: 440 SDRFPSSARPFYTMECKDDERFTNSYD-MFIRGEEISSGAQRIHDPDLLLARAKMLNVDL 498
Query: 402 APYYWYTDQRKYGSTPHGGYGLGLERVLCWLLNQYHVR 439
P Y D + G+ PHGG+G+GLERV+ L +VR
Sbjct: 499 TPIKEYVDSFRLGAWPHGGFGVGLERVVMLYLGLSNVR 536
Score = 39.6 bits (92), Expect = 0.005
Identities = 58/234 (24%), Positives = 94/234 (40%), Gaps = 30/234 (12%)
Query: 446 AKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREK--NLEEAKKIVLKEDPSLPPAVRIK 503
A A KK S AR A+ + + E A EK ++ A +V + +
Sbjct: 10 APAVEKKQSDKEARKAARLAEEKARAAEKAALVEKYKDVFGAAPMVQSTTYKSRTFIPVA 69
Query: 504 IKDGEKYRDKRVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVLA----------DILCQ 553
+ + DK V I V R++GK + F+ LRDGS +Q + A D + Q
Sbjct: 70 VLSKPELVDKTVLIRARVSTTRKKGK-MAFMVLRDGSDSVQAMAAVEGDVPKEMIDFIGQ 128
Query: 554 TEHALLLSTESSVQFRGRIEKV--PEGKSAPGGHELKVDYWEVVGLA----PAGGADAIL 607
+ TES V + KV P ++ ELKV V + P DA
Sbjct: 129 ------IPTESIVDVEATVCKVEQPITSTSHSDIELKVKKIHTVTESLRTLPFTLEDASR 182
Query: 608 NE--EALP---DVQLDNRHIMIRGENTSRVLLMRSVLLQALRAHFADRNYTEVN 656
E E D +L++R + +R + + ++S + Q R D ++ E++
Sbjct: 183 KESDEGAKVNFDTRLNSRWMDLRTPASGAIFRLQSRVCQYFRQFLIDSDFCEIH 236
>gnl|CDD|215291 PLN02532, PLN02532, asparagine-tRNA synthetase.
Length = 633
Score = 109 bits (273), Expect = 9e-25
Identities = 76/266 (28%), Positives = 130/266 (48%), Gaps = 24/266 (9%)
Query: 191 FSLNFFGEPAYLTQSSQLYLETCLPALGDVYCIAQSYRAENSRTRRHLAEYTHVEAECAF 250
FS +FF P YLT S +L+LE+ ALG+VY +RA+ + RHLAE VE E AF
Sbjct: 363 FSKDFFSRPTYLTVSGRLHLESYACALGNVYTFGPRFRADRIDSARHLAEMWMVEVEMAF 422
Query: 251 LTFDDLLDKLED---LICDTV------------DRVMATHGDLVRQMNPNFEPPARPFLR 295
+D ++ ED +C V R+ T + + + R
Sbjct: 423 SELEDAMNCAEDYFKFLCKWVLENCSEDMKFVSKRIDKTISTRLEAI------ISSSLQR 476
Query: 296 MNYADAIEYLRKHEIRKPDNTEYEFGEDIPEMPERKMTDQI-NRPIMLCRFPADIKSFYM 354
++Y +A++ L++ +K + T+ E+G + + D+I +P+++ +P ++K FY+
Sbjct: 477 ISYTEAVDLLKQATDKKFE-TKPEWGIALTTEHLSYLADEIYKKPVIIYNYPKELKPFYV 535
Query: 355 SKCPENPALTESVDVLFPNVGEVIGGSMRIWDPEELLAGYKREGIDPAPYYWYTDQRKYG 414
+ ++ + D++ P VG VI GS + L A + G+ Y WY D R++G
Sbjct: 536 -RLNDDGKTVAAFDLVVPKVGTVITGSQNEERMDILNARIEELGLPREQYEWYLDLRRHG 594
Query: 415 STPHGGYGLGLERVLCWLLNQYHVRD 440
+ H G+ LG E ++ + VRD
Sbjct: 595 TVKHSGFSLGFELMVLFATGLPDVRD 620
>gnl|CDD|239766 cd04100, Asp_Lys_Asn_RS_N, Asp_Lys_Asn_RS_N: N-terminal, anticodon
recognition domain of class 2b aminoacyl-tRNA
synthetases (aaRSs). This domain is a beta-barrel domain
(OB fold) involved in binding the tRNA anticodon
stem-loop. Class 2b aaRSs include the homodimeric
aspartyl-, asparaginyl-, and lysyl-tRNA synthetases
(AspRS, AsnRS, and LysRS). aaRSs catalyze the specific
attachment of amino acids (AAs) to their cognate tRNAs
during protein biosynthesis. This 2-step reaction
involves i) the activation of the AA by ATP in the
presence of magnesium ions, followed by ii) the transfer
of the activated AA to the terminal ribose of tRNA. In
the case of the class2b aaRSs, the activated AA is
attached to the 3'OH of the terminal ribose. Eukaryotes
contain 2 sets of aaRSs, both of which are encoded by
the nuclear genome. One set concerns with cytoplasmic
protein synthesis, whereas the other exclusively with
mitochondrial protein synthesis. Included in this group
are archeal and archeal-like AspRSs which are
non-discriminating and can charge both tRNAAsp and
tRNAAsn. E. coli cells have two isoforms of LysRSs (LysS
and LysU) encoded by two distinct genes, which are
differentially regulated. The cytoplasmic and the
mitochondrial isoforms of human LysRS are encoded by a
single gene. Yeast cytoplasmic and mitochondrial LysRSs
participate in mitochondrial import of cytoplasmic
tRNAlysCUU. In addition to their housekeeping role,
human LysRS may function as a signaling molecule that
activates immune cells. Tomato LysRS may participate in
a process possibly connected to conditions of
oxidative-stress conditions or heavy metal uptake. It is
known that human tRNAlys and LysRS are specifically
packaged into HIV-1 suggesting a role for LysRS in tRNA
packaging. AsnRS is immunodominant antigen of the
filarial nematode Brugia malayai and is of interest as a
target for anti-parasitic drug design. Human AsnRS has
been shown to be a pro-inflammatory chemokine which
interacts with CCR3 chemokine receptors on T cells,
immature dendritic cells and macrophages.
Length = 85
Score = 96.5 bits (241), Expect = 3e-24
Identities = 34/85 (40%), Positives = 43/85 (50%), Gaps = 3/85 (3%)
Query: 514 RVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVLADILCQTEHALL--LSTESSVQFRGR 571
VT+ GWVH R G L+F+ LRDGSG +Q V+ L TES V G
Sbjct: 1 EVTLAGWVHSRRDHGG-LIFIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGT 59
Query: 572 IEKVPEGKSAPGGHELKVDYWEVVG 596
+ K PEG A G EL+ + EV+
Sbjct: 60 VVKRPEGNLATGEIELQAEELEVLS 84
Score = 58.7 bits (143), Expect = 6e-11
Identities = 21/57 (36%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 87 KGLMFVTLRDGSGFIQCVLADILCQTEHALL--LSTESSVQFRGRIEKVPEENMKVQ 141
GL+F+ LRDGSG +Q V+ L TES V G + K PE N+
Sbjct: 15 GGLIFIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRPEGNLATG 71
>gnl|CDD|216440 pfam01336, tRNA_anti, OB-fold nucleic acid binding domain. This
family contains OB-fold domains that bind to nucleic
acids. The family includes the anti-codon binding domain
of lysyl, aspartyl, and asparaginyl -tRNA synthetases
(See pfam00152). Aminoacyl-tRNA synthetases catalyze the
addition of an amino acid to the appropriate tRNA
molecule EC:6.1.1.-. This family also includes part of
RecG helicase involved in DNA repair. Replication factor
A is a heterotrimeric complex, that contains a subunit
in this family. This domain is also found at the
C-terminus of bacterial DNA polymerase III alpha chain.
Length = 75
Score = 70.0 bits (172), Expect = 5e-15
Identities = 30/82 (36%), Positives = 43/82 (52%), Gaps = 8/82 (9%)
Query: 515 VTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVL-ADILCQTEHALLLSTESSVQFRGRIE 573
VT+ G V +RR G + F+TLRDG+G IQ VL + + A L V G+++
Sbjct: 1 VTVAGRVTSVRRSGGKVAFLTLRDGTGSIQVVLFKEEA--EKLAKKLKEGDVVLVTGKVK 58
Query: 574 KVPEGKSAPGGHELKVDYWEVV 595
K P G+ EL V+ EV+
Sbjct: 59 KRPGGE-----LELVVEEIEVL 75
Score = 46.5 bits (111), Expect = 9e-07
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 5/62 (8%)
Query: 86 GKGLMFVTLRDGSGFIQCVL-ADILCQTEHALLLSTESSVQFRGRIEKVPEENMKVQLIH 144
G + F+TLRDG+G IQ VL + + A L V G+++K P +++L+
Sbjct: 14 GGKVAFLTLRDGTGSIQVVLFKEEA--EKLAKKLKEGDVVLVTGKVKKRPGG--ELELVV 69
Query: 145 PS 146
Sbjct: 70 EE 71
>gnl|CDD|239814 cd04319, PhAsnRS_like_N, PhAsnRS_like_N: N-terminal, anticodon
recognition domain of the type found in Pyrococcus
horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS).
This domain is a beta-barrel domain (OB fold) involved
in binding the tRNA anticodon stem-loop. The archeal
enzymes in this group are homodimeric class2b
aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the
specific attachment of amino acids (AAs) to their
cognate tRNAs during protein biosynthesis. This 2-step
reaction involves i) the activation of the AA by ATP in
the presence of magnesium ions, followed by ii) the
transfer of the activated AA to the terminal ribose of
tRNA. In the case of the class2b aaRSs, the activated
AA is attached to the 3'OH of the terminal ribose.
Length = 103
Score = 64.5 bits (157), Expect = 9e-13
Identities = 36/111 (32%), Positives = 55/111 (49%), Gaps = 10/111 (9%)
Query: 514 RVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVLADILCQT--EHALLLSTESSVQFRGR 571
+VT+ GWV+R R GK F+ LRD +G +Q V + L + A + ESSV G
Sbjct: 1 KVTLAGWVYRKREVGKKA-FIVLRDSTGIVQAVFSKDLNEEAYREAKKVGIESSVIVEGA 59
Query: 572 IEKVPEGKSAPGGHELKVDYWEVVGLAPAGGADAILNEEALPDVQLDNRHI 622
++ P APGG E+ + E++ + E+A + LD RH+
Sbjct: 60 VKADPR---APGGAEVHGEKLEIIQN----VEFFPITEDASDEFLLDVRHL 103
Score = 32.5 bits (74), Expect = 0.17
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 3/67 (4%)
Query: 91 FVTLRDGSGFIQCVLADILCQT--EHALLLSTESSVQFRGRIEKVPEENMKVQLIHPSSY 148
F+ LRD +G +Q V + L + A + ESSV G ++ P + +H
Sbjct: 19 FIVLRDSTGIVQAVFSKDLNEEAYREAKKVGIESSVIVEGAVKADPRAPGGAE-VHGEKL 77
Query: 149 AIVWLGD 155
I+ +
Sbjct: 78 EIIQNVE 84
>gnl|CDD|239812 cd04317, EcAspRS_like_N, EcAspRS_like_N: N-terminal, anticodon
recognition domain of the type found in Escherichia coli
aspartyl-tRNA synthetase (AspRS), the human
mitochondrial (mt) AspRS-2, the discriminating (D)
Thermus thermophilus AspRS-1, and the nondiscriminating
(ND) Helicobacter pylori AspRS. These homodimeric
enzymes are class2b aminoacyl-tRNA synthetases (aaRSs).
This domain is a beta-barrel domain (OB fold) involved
in binding the tRNA anticodon stem-loop. aaRSs catalyze
the specific attachment of amino acids (AAs) to their
cognate tRNAs during protein biosynthesis. This 2-step
reaction involves i) the activation of the AA by ATP in
the presence of magnesium ions, followed by ii) the
transfer of the activated AA to the terminal ribose of
tRNA. In the case of the class2b aaRSs, the activated
AA is attached to the 3'OH of the terminal ribose.
Eukaryotes contain 2 sets of aaRSs, both of which are
encoded by the nuclear genome. One set concerns with
cytoplasmic synthesis, whereas the other exclusively
with mitochondrial protein synthesis. Human mtAspRS
participates in mitochondrial biosynthesis; this enzyme
been shown to charge E.coli native tRNAsp in addition to
in vitro transcribed human mitochondrial tRNAsp. T.
thermophilus is rare among bacteria in having both a
D_AspRS and a ND_AspRS. H.pylori ND-AspRS can charge
both tRNAASp and tRNAAsn, it is fractionally more
efficient at aminoacylating tRNAAsp over tRNAAsn. The
H.pylori genome does not contain AsnRS.
Length = 135
Score = 63.7 bits (156), Expect = 4e-12
Identities = 33/93 (35%), Positives = 45/93 (48%), Gaps = 6/93 (6%)
Query: 507 GEKYRDKRVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVLA-DILCQTEHALLLSTESS 565
E + + VT+ GWV R R G GL+F+ LRD G +Q V + + E A L ES
Sbjct: 9 RESHVGQEVTLCGWVQRRRDHG-GLIFIDLRDRYGIVQVVFDPEEAPEFELAEKLRNESV 67
Query: 566 VQFRGRIEKVPEG----KSAPGGHELKVDYWEV 594
+Q G++ PEG K G E+ EV
Sbjct: 68 IQVTGKVRARPEGTVNPKLPTGEIEVVASELEV 100
Score = 38.3 bits (90), Expect = 0.003
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 88 GLMFVTLRDGSGFIQCVLA-DILCQTEHALLLSTESSVQFRGRIEKVPEEN 137
GL+F+ LRD G +Q V + + E A L ES +Q G++ PE
Sbjct: 31 GLIFIDLRDRYGIVQVVFDPEEAPEFELAEKLRNESVIQVTGKVRARPEGT 81
>gnl|CDD|223251 COG0173, AspS, Aspartyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 585
Score = 66.4 bits (163), Expect = 2e-11
Identities = 44/158 (27%), Positives = 71/158 (44%), Gaps = 13/158 (8%)
Query: 507 GEKYRDKRVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVLADILCQTEHALL--LSTES 564
E + + VT+ GWVHR R G GL+F+ LRD G +Q V + L E
Sbjct: 10 RESHVGQTVTLSGWVHRRRDHG-GLIFIDLRDREGIVQVVFDPEDSPEAFEVASRLRNEF 68
Query: 565 SVQFRGRIEKVPEGKSAP----GGHELKVDYWEVVGLA---PAGGADAILNEEALPDVQL 617
+Q G + PEG P G E+ + EV+ + P D A +++L
Sbjct: 69 VIQVTGTVRARPEGTINPNLPTGEIEVLAEEIEVLNASKTLPFQIED---ETNASEEIRL 125
Query: 618 DNRHIMIRGENTSRVLLMRSVLLQALRAHFADRNYTEV 655
R++ +R + L +RS + +A+R D+ + E+
Sbjct: 126 KYRYLDLRRPEMQKNLKLRSKVTKAIRNFLDDQGFLEI 163
Score = 43.3 bits (103), Expect = 4e-04
Identities = 33/114 (28%), Positives = 58/114 (50%), Gaps = 18/114 (15%)
Query: 202 LTQSSQLYLETCLPALGDVYC-IAQSYRAENSRTRRHLAEYTHVEAECAFLTFDDLLDKL 260
L QS QL+ + + A D Y IA+ +R E+ R R E+T ++ E +F+ +D+++ +
Sbjct: 193 LPQSPQLFKQLLMVAGFDRYYQIARCFRDEDLRADR-QPEFTQIDLEMSFVDEEDVMELI 251
Query: 261 EDLICDTVDRVMATHGDLVRQMNPNFEPPARPFLRMNYADAIEYLRKHEIRKPD 314
E L+ + +++ E PF RM YA+A+ R++ KPD
Sbjct: 252 EKLLR-----------YVFKEVK-GIELKT-PFPRMTYAEAM---RRYGSDKPD 289
Score = 39.5 bits (93), Expect = 0.006
Identities = 25/69 (36%), Positives = 36/69 (52%), Gaps = 4/69 (5%)
Query: 376 EVIGGSMRIWDPEELLAGYKREGIDPAPYY----WYTDQRKYGSTPHGGYGLGLERVLCW 431
E+ GGS+RI DPE ++ GI P + + KYG+ PHGG GL+R++
Sbjct: 481 ELGGGSIRIHDPEIQEKVFEILGISPEEAEEKFGFLLEAFKYGAPPHGGIAFGLDRLVML 540
Query: 432 LLNQYHVRD 440
L +RD
Sbjct: 541 LTGAESIRD 549
Score = 29.5 bits (67), Expect = 6.1
Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 2/52 (3%)
Query: 88 GLMFVTLRDGSGFIQCVLADILCQTEHALL--LSTESSVQFRGRIEKVPEEN 137
GL+F+ LRD G +Q V + L E +Q G + PE
Sbjct: 32 GLIFIDLRDREGIVQVVFDPEDSPEAFEVASRLRNEFVIQVTGTVRARPEGT 83
>gnl|CDD|238400 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 = 61.8 bits (151), Expect = 2e-10
Identities = 61/254 (24%), Positives = 104/254 (40%), Gaps = 50/254 (19%)
Query: 202 LTQSSQLYLETCLPALGDVYC-IAQSYRAENSRTRRHLAEYTHVEAECAFLTFDDLLDKL 260
L QS QL+ + + + D Y IA+ +R E+ R R E+T ++ E +F+ +D++ +
Sbjct: 53 LPQSPQLFKQLLMVSGFDRYFQIARCFRDEDLRADRQ-PEFTQIDIEMSFVDQEDIMSLI 111
Query: 261 EDLICDTVDRVMATHGDLVRQMNPNFEPPARPFLRMNYADAIEY--LRKHEI-------R 311
E L+ V+ PF RM YA+A+E + I
Sbjct: 112 EGLLKYVFKEVLG-------------VELTTPFPRMTYAEAMERYGFKFLWIVDFPLFEW 158
Query: 312 KPDNTEYEFGEDIPEMPERKMTDQINRPIMLCRFPADIKSFYMSKCPENPALTESVD-VL 370
+ P+ + D + + P D ++ ++ D VL
Sbjct: 159 DEEEGRLVSAHHPFTAPKEEDLDLLEK------DPEDARA-------------QAYDLVL 199
Query: 371 FPNVGEVIGGSMRIWDPEELLAGYKREGIDPAPYY----WYTDQRKYGSTPHGGYGLGLE 426
N E+ GGS+RI DP+ ++ G+ + + KYG+ PHGG LGL+
Sbjct: 200 --NGVELGGGSIRIHDPDIQEKVFEILGLSEEEAEEKFGFLLEAFKYGAPPHGGIALGLD 257
Query: 427 RVLCWLLNQYHVRD 440
R++ L +RD
Sbjct: 258 RLVMLLTGSESIRD 271
>gnl|CDD|232998 TIGR00499, lysS_bact, lysyl-tRNA synthetase, eukaryotic and
non-spirochete bacterial. This model represents the
lysyl-tRNA synthetases that are class II amino-acyl tRNA
synthetases. It includes all eukaryotic and most
bacterial examples of the enzyme, but not archaeal or
spirochete forms [Protein synthesis, tRNA
aminoacylation].
Length = 496
Score = 62.0 bits (151), Expect = 5e-10
Identities = 57/250 (22%), Positives = 106/250 (42%), Gaps = 36/250 (14%)
Query: 220 VYCIAQSYRAENSRTRRHLAEYTHVEAECAFLTFDDLLDKLEDLICDTVDRVMATHGDLV 279
VY I +++R E T H E+T +E A+ ++DL+D E+L ++ T
Sbjct: 243 VYEIGRNFRNEGVDTT-HNPEFTMIEFYQAYADYEDLMDLTENLFKFLAQELLGTTKITY 301
Query: 280 RQMNPNFEPPARPFLRMNYADAIE---------------------YLRKHEIRKPDNTEY 318
++ +F +PF R+ +AI+ +K I + +
Sbjct: 302 GELEIDF---KKPFKRITMVEAIKKYDMETGIDFDDLKDFETAKALAKKIGIEVAEKS-L 357
Query: 319 EFGEDIPEMPERKMTDQINRPIMLCRFPADIKSFYMSKCPENPALTESVDVLFPNVGEVI 378
G + E+ E+ + + +P + +PA+I S + P NP T+ + LF E+
Sbjct: 358 TLGHILNELFEQFLEHTLIQPTFITHYPAEI-SPLAKRNPSNPEFTDRFE-LFIAGKEIA 415
Query: 379 GGSMRIWDPEELLAGY------KREGIDPAPY--YWYTDQRKYGSTPHGGYGLGLERVLC 430
+ DP + + K G D A + + + +YG P GG G+G++R++
Sbjct: 416 NAFSELNDPLDQRERFEQQVAEKEAGDDEAQFVDEDFVEALEYGMPPTGGLGIGIDRLVM 475
Query: 431 WLLNQYHVRD 440
L + +RD
Sbjct: 476 LLTDSKSIRD 485
Score = 32.0 bits (73), Expect = 1.0
Identities = 40/160 (25%), Positives = 65/160 (40%), Gaps = 26/160 (16%)
Query: 508 EKYRDKRVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVLA-DILCQTEHALLLSTESSV 566
+ ++ V+I G + R GK F+TL+D SG IQ + D L + + +
Sbjct: 49 LEDKNIEVSIAGRIMARRSMGK-ATFITLQDESGQIQLYVNKDDLPE----DFYEFDEYL 103
Query: 567 QFRGRIEKVPEGK-SAPGGHELKVDYWEVVGLAPAGGADAILNEEALPD---------VQ 616
G I V G EL V E+ L A LPD +
Sbjct: 104 LDLGDIIGV-TGYPFKTKTGELSVHVTELQILTKA--------LRPLPDKFHGLTDQETR 154
Query: 617 LDNRHI-MIRGENTSRVLLMRSVLLQALRAHFADRNYTEV 655
R++ +I ++ + L+RS +++A+R DR + EV
Sbjct: 155 YRQRYLDLIVNPDSRQTFLVRSKIIKAIRRFLDDRGFIEV 194
>gnl|CDD|238398 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 = 60.3 bits (147), Expect = 8e-10
Identities = 57/248 (22%), Positives = 98/248 (39%), Gaps = 33/248 (13%)
Query: 220 VYCIAQSYRAENSRTRRHLAEYTHVEAECAFLTFDDLLDKLEDLICDTVDRVMATHGDLV 279
VY I +++R E H E+T +E A+ ++D++D EDL V ++
Sbjct: 79 VYEIGRNFRNE-GIDLTHNPEFTMIEFYEAYADYNDMMDLTEDLFSGLVKKINGKTKIEY 137
Query: 280 RQMNPNFEPPARPFLRMNYADAIE-----YLRKHEIRKPDNTEYEFGEDIPEMPERKMT- 333
+F P PF R+ DA++ + ++ +P+ + I E E+ T
Sbjct: 138 GGKELDFTP---PFKRVTMVDALKEKTGIDFPELDLEQPEELAKLLAKLIKEKIEKPRTL 194
Query: 334 -------------DQINRPIMLCRFPADIKSFYMSKCPENPALTESVDVLFPNVGEVIGG 380
+ +P + P +I S + NP LTE + LF E+
Sbjct: 195 GKLLDKLFEEFVEPTLIQPTFIIDHPVEI-SPLAKRHRSNPGLTERFE-LFICGKEIANA 252
Query: 381 SMRIWDPEELLAGY------KREGIDPAPYYWYTDQR--KYGSTPHGGYGLGLERVLCWL 432
+ DP + + K G D A +YG P GG G+G++R++ L
Sbjct: 253 YTELNDPFDQRERFEEQAKQKEAGDDEAMMMDEDFVTALEYGMPPTGGLGIGIDRLVMLL 312
Query: 433 LNQYHVRD 440
+ +RD
Sbjct: 313 TDSNSIRD 320
>gnl|CDD|234775 PRK00476, aspS, aspartyl-tRNA synthetase; Validated.
Length = 588
Score = 61.2 bits (150), Expect = 1e-09
Identities = 45/167 (26%), Positives = 71/167 (42%), Gaps = 35/167 (20%)
Query: 508 EKYRDKRVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVL---ADILCQTEHALLLSTES 564
E + + VT+ GWVHR R G GL+F+ LRD G +Q V A+ E L +E
Sbjct: 13 ESHVGQTVTLCGWVHRRRDHG-GLIFIDLRDREGIVQVVFDPDAEAFEVAES---LRSEY 68
Query: 565 SVQFRGRIEKVPEG----KSAPGGHELKVDYWEVVGLAPAGGADAILNE-EALP------ 613
+Q G + PEG G E+ E +LN+ + LP
Sbjct: 69 VIQVTGTVRARPEGTVNPNLPTGEIEVLASELE------------VLNKSKTLPFPIDDE 116
Query: 614 -----DVQLDNRHIMIRGENTSRVLLMRSVLLQALRAHFADRNYTEV 655
+++L R++ +R + L +RS + A+R D + E+
Sbjct: 117 EDVSEELRLKYRYLDLRRPEMQKNLKLRSKVTSAIRNFLDDNGFLEI 163
Score = 34.7 bits (81), Expect = 0.19
Identities = 25/74 (33%), Positives = 31/74 (41%), Gaps = 29/74 (39%)
Query: 376 EVIGGSMRIWDPE------ELLAGYKREGIDPAPYYWYTDQR----------KYGSTPHG 419
E+ GGS+RI PE E+L GI + KYG+ PHG
Sbjct: 483 ELGGGSIRIHRPEIQEKVFEIL------GISEE------EAEEKFGFLLDALKYGAPPHG 530
Query: 420 GYGLGLERVLCWLL 433
G GL+R L LL
Sbjct: 531 GIAFGLDR-LVMLL 543
Score = 33.5 bits (78), Expect = 0.40
Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 14/83 (16%)
Query: 221 YCIAQSYRAENSRTRRHLAEYTHVEAECAFLTFDDLLDKLEDLICDTVDRVMATHGDLVR 280
Y IA+ +R E+ R R E+T ++ E +F+T +D++ +E LI V+
Sbjct: 213 YQIARCFRDEDLRADR-QPEFTQIDIEMSFVTQEDVMALMEGLIRHVFKEVL-------- 263
Query: 281 QMNPNFEPPARPFLRMNYADAIE 303
+ P PF RM YA+A+
Sbjct: 264 ----GVDLP-TPFPRMTYAEAMR 281
Score = 32.0 bits (74), Expect = 1.1
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 6/53 (11%)
Query: 88 GLMFVTLRDGSGFIQCVL---ADILCQTEHALLLSTESSVQFRGRIEKVPEEN 137
GL+F+ LRD G +Q V A+ E L +E +Q G + PE
Sbjct: 34 GLIFIDLRDREGIVQVVFDPDAEAFEVAES---LRSEYVIQVTGTVRARPEGT 83
>gnl|CDD|211576 TIGR00459, aspS_bact, aspartyl-tRNA synthetase, bacterial type.
Asparate--tRNA ligases in this family may be
discriminating (6.1.1.12) or nondiscriminating
(6.1.1.23). In a multiple sequence alignment of
representative asparaginyl-tRNA synthetases (asnS),
archaeal/eukaryotic type aspartyl-tRNA synthetases
(aspS_arch), and bacterial type aspartyl-tRNA
synthetases (aspS_bact), there is a striking similarity
between asnS and aspS_arch in gap pattern and in
sequence, and a striking divergence of aspS_bact.
Consequently, a separate model was built for each of the
three groups. This model, aspS_bact, represents
aspartyl-tRNA synthetases from the Bacteria and from
mitochondria. In some species, this enzyme aminoacylates
tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently
transamidated to Asn-tRNA(asn). This model generates
very low scores for the archaeal type of aspS and for
asnS; scores between the trusted and noise cutoffs
represent fragmentary sequences [Protein synthesis, tRNA
aminoacylation].
Length = 583
Score = 60.9 bits (148), Expect = 1e-09
Identities = 41/149 (27%), Positives = 70/149 (46%), Gaps = 10/149 (6%)
Query: 513 KRVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVLADILCQTEHALLLSTESSVQFRGRI 572
+ VT+ GWV+R R G GL+F+ LRD SG +Q V + A L E VQ +G++
Sbjct: 16 QTVTLAGWVNRRRDLG-GLIFIDLRDRSGIVQVVCDPDADALKLAKGLRNEDVVQVKGKV 74
Query: 573 EKVPEGKSAPGGHELKVDYWEVVG-----LAPAGGADAILNE-EALPDVQLDNRHIMIRG 626
PEG L E++ L + I+ + +A +V+L R++ +R
Sbjct: 75 SARPEGNINR---NLDTGEIEILAESITLLNKSKTPPLIIEKTDAEEEVRLKYRYLDLRR 131
Query: 627 ENTSRVLLMRSVLLQALRAHFADRNYTEV 655
+ L +R + +A+R + + E+
Sbjct: 132 PEMQQRLKLRHKVTKAVRNFLDQQGFLEI 160
Score = 48.2 bits (115), Expect = 1e-05
Identities = 65/277 (23%), Positives = 107/277 (38%), Gaps = 72/277 (25%)
Query: 88 GLMFVTLRDGSGFIQCVLADILCQTEHALLLSTESSVQFRGRIEKVPEENMKVQL----- 142
GL+F+ LRD SG +Q V + A L E VQ +G++ PE N+ L
Sbjct: 32 GLIFIDLRDRSGIVQVVCDPDADALKLAKGLRNEDVVQVKGKVSARPEGNINRNLDTGEI 91
Query: 143 -IHPSSYAIVWLGDLKQGGYPP----------------------------------EVSL 167
I S + L + PP +V+
Sbjct: 92 EILAESITL-----LNKSKTPPLIIEKTDAEEEVRLKYRYLDLRRPEMQQRLKLRHKVTK 146
Query: 168 A-------NGIAKVTPPTLVQTQVEGGSTLFSLNFFGEPAY--LTQSSQLYLETCLPALG 218
A G ++ P L ++ EG + + + L QS QL+ + + +
Sbjct: 147 AVRNFLDQQGFLEIETPMLTKSTPEGARDYLVPSRVHKGEFYALPQSPQLFKQLLMVSGV 206
Query: 219 DVYC-IAQSYRAENSRTRRHLAEYTHVEAECAFLTFDDLLDKLEDLICDTVDRVMATHGD 277
D Y IA+ +R E+ R R E+T ++ E +F+T +D+++ +E L+ V D
Sbjct: 207 DRYYQIARCFRDEDLRADRQ-PEFTQIDMEMSFMTQEDVMELIEKLVSHVFLEVKGI--D 263
Query: 278 LVRQMNPNFEPPARPFLRMNYADAIEYLRKHEIRKPD 314
L +PF M YA+A + ++ KPD
Sbjct: 264 L-----------KKPFPVMTYAEA---MERYGSDKPD 286
Score = 47.8 bits (114), Expect = 2e-05
Identities = 33/86 (38%), Positives = 47/86 (54%), Gaps = 7/86 (8%)
Query: 360 NPALTESVDVLFPNVGEVIGGSMRIWDPEELLAGYKREGIDPAP----YYWYTDQRKYGS 415
AL E+ D++ V E+ GGS+RI DPE ++ GIDP + + + KYG+
Sbjct: 463 EEALAEAYDLVLNGV-ELGGGSIRIHDPEVQKKVFEILGIDPEEAREKFGFLLEAFKYGT 521
Query: 416 TPHGGYGLGLERVLCWLLNQYH-VRD 440
PH G+ LGL+R L LL +RD
Sbjct: 522 PPHAGFALGLDR-LMMLLTGTDNIRD 546
>gnl|CDD|239813 cd04318, EcAsnRS_like_N, EcAsnRS_like_N: N-terminal, anticodon
recognition domain of the type found in Escherichia coli
asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis
thaliana and Saccharomyces cerevisiae mitochondrial (mt)
AsnRS. This domain is a beta-barrel domain (OB fold)
involved in binding the tRNA anticodon stem-loop. The
enzymes in this group are homodimeric class2b
aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the
specific attachment of amino acids (AAs) to their
cognate tRNAs during protein biosynthesis. This 2-step
reaction involves i) the activation of the AA by ATP in
the presence of magnesium ions, followed by ii) the
transfer of the activated AA to the terminal ribose of
tRNA. In the case of the class2b aaRSs, the activated
AA is attached to the 3'OH of the terminal ribose.
Eukaryotes contain 2 sets of aaRSs, both of which are
encoded by the nuclear genome. One set concerns with
cytoplasmic protein synthesis, whereas the other
exclusively with mitochondrial protein synthesis. S.
cerevisiae mtAsnRS can charge E.coli tRNA with
asparagines. Mutations in the gene for S. cerevisiae
mtAsnRS has been found to induce a "petite" phenotype
typical for a mutation in a nuclear gene that results in
a non-functioning mitochondrial protein synthesis
system.
Length = 82
Score = 54.5 bits (132), Expect = 2e-09
Identities = 31/84 (36%), Positives = 43/84 (51%), Gaps = 6/84 (7%)
Query: 515 VTIFGWVHRLRRQGKGLMFVTLRDGSGF--IQCVLADILCQTEHALLLSTESSVQFRGRI 572
VT+ GWV R R K + F+ L DGS +Q V+ L + L LST SS++ G +
Sbjct: 2 VTVNGWV-RSVRDSKKISFIELNDGSCLKNLQVVVDKELTNFKEILKLSTGSSIRVEGVL 60
Query: 573 EKVPEGKSAPGGHELKVDYWEVVG 596
K P K EL+ + EV+G
Sbjct: 61 VKSPGAKQP---FELQAEKIEVLG 81
Score = 34.1 bits (79), Expect = 0.030
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 87 KGLMFVTLRDGSGF--IQCVLADILCQTEHALLLSTESSVQFRGRIEKVPEENMKVQL 142
K + F+ L DGS +Q V+ L + L LST SS++ G + K P +L
Sbjct: 15 KKISFIELNDGSCLKNLQVVVDKELTNFKEILKLSTGSSIRVEGVLVKSPGAKQPFEL 72
>gnl|CDD|239811 cd04316, ND_PkAspRS_like_N, ND_PkAspRS_like_N: N-terminal,
anticodon recognition domain of the type found in the
homodimeric non-discriminating (ND) Pyrococcus
kodakaraensis aspartyl-tRNA synthetase (AspRS). This
domain is a beta-barrel domain (OB fold) involved in
binding the tRNA anticodon stem-loop. P. kodakaraensis
AspRS is a class 2b aaRS. aaRSs catalyze the specific
attachment of amino acids (AAs) to their cognate tRNAs
during protein biosynthesis. This 2-step reaction
involves i) the activation the AA by ATP in the presence
of magnesium ions, followed by ii) the transfer of the
activated AA to the terminal ribose of tRNA. In the
case of the class2b aaRSs, the activated AA is attached
to the 3'OH of the terminal ribose. P. kodakaraensis
ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of
the enzymes in this group may be discriminating, based
on the presence of homologs of asparaginyl-tRNA
synthetase (AsnRS) in their completed genomes.
Length = 108
Score = 53.1 bits (128), Expect = 9e-09
Identities = 27/78 (34%), Positives = 34/78 (43%), Gaps = 7/78 (8%)
Query: 513 KRVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVLADILCQTE---HALLLSTESSVQFR 569
+ VT+ GWVH +R G G+ FV LRD G +Q E LS ES +
Sbjct: 13 EEVTVAGWVHEIRDLG-GIKFVILRDREGIVQVTAPKKKVDKELFKTVRKLSRESVISVT 71
Query: 570 GRIEKVPEGKSAPGGHEL 587
G V AP G E+
Sbjct: 72 G---TVKAEPKAPNGVEI 86
Score = 30.0 bits (68), Expect = 1.2
Identities = 18/63 (28%), Positives = 25/63 (39%), Gaps = 4/63 (6%)
Query: 88 GLMFVTLRDGSGFIQCVLADILCQTE---HALLLSTESSVQFRGRIEKVPEENMKVQLIH 144
G+ FV LRD G +Q E LS ES + G ++ P+ V+ I
Sbjct: 29 GIKFVILRDREGIVQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAEPKAPNGVE-II 87
Query: 145 PSS 147
P
Sbjct: 88 PEE 90
>gnl|CDD|239815 cd04320, AspRS_cyto_N, AspRS_cyto_N: N-terminal, anticodon
recognition domain of the type found in Saccharomyces
cerevisiae and human cytoplasmic aspartyl-tRNA
synthetase (AspRS). This domain is a beta-barrel domain
(OB fold) involved in binding the tRNA anticodon
stem-loop. The enzymes in this group are homodimeric
class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs
catalyze the specific attachment of amino acids (AAs) to
their cognate tRNAs during protein biosynthesis. This
2-step reaction involves i) the activation of the AA by
ATP in the presence of magnesium ions, followed by ii)
the transfer of the activated AA to the terminal ribose
of tRNA. In the case of the class2b aaRSs, the
activated AA is attached to the 3'OH of the terminal
ribose. Eukaryotes contain 2 sets of aaRSs, both of
which are encoded by the nuclear genome. One set
concerns with cytoplasmic protein synthesis, whereas the
other exclusively with mitochondrial protein synthesis.
Length = 102
Score = 51.8 bits (125), Expect = 2e-08
Identities = 24/71 (33%), Positives = 29/71 (40%), Gaps = 11/71 (15%)
Query: 515 VTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVLA--------DILCQTEHALLLSTESSV 566
V I VH R QG L F+ LR IQ VLA ++ LS ES V
Sbjct: 2 VLIRARVHTSRAQGAKLAFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGS---LSKESIV 58
Query: 567 QFRGRIEKVPE 577
G ++K E
Sbjct: 59 DVEGTVKKPEE 69
Score = 32.2 bits (74), Expect = 0.17
Identities = 18/58 (31%), Positives = 23/58 (39%), Gaps = 11/58 (18%)
Query: 86 GKGLMFVTLRDGSGFIQCVLA--------DILCQTEHALLLSTESSVQFRGRIEKVPE 135
G L F+ LR IQ VLA ++ LS ES V G ++K E
Sbjct: 15 GAKLAFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGS---LSKESIVDVEGTVKKPEE 69
>gnl|CDD|224111 COG1190, LysU, Lysyl-tRNA synthetase (class II) [Translation,
ribosomal structure and biogenesis].
Length = 502
Score = 54.9 bits (133), Expect = 9e-08
Identities = 66/279 (23%), Positives = 112/279 (40%), Gaps = 43/279 (15%)
Query: 194 NFFGEPAYLTQSSQLYLETCLPA-LGDVYCIAQSYRAENSRT-RRHLAEYTHVEAECAFL 251
N YL + +LYL+ + V+ I +++R N H E+T +E A+
Sbjct: 224 NALDMDLYLRIAPELYLKRLIVGGFERVFEIGRNFR--NEGIDTTHNPEFTMLEFYQAYA 281
Query: 252 TFDDLLDKLEDLICDTVDRVMATHGDLVRQMNP---NFEPPARPFLRMNYADAI------ 302
++DL+D E+LI + V +G +F PF R+ DA+
Sbjct: 282 DYEDLMDLTEELIKELAKEV---NGTTKVTYGGQEIDFSK---PFKRITMVDALKEYLGV 335
Query: 303 ------------EYLRKHEIRKPDNTEYEFGEDIPEMPERKMTDQINRPIMLCRFPADIK 350
E +KH I + G + E+ E + ++ +P + P +I
Sbjct: 336 DFDDLFDDEEAKELAKKHGIEVEKYGTWGLGHLLNELFEELVEAKLIQPTFVTDHPVEIS 395
Query: 351 SFYMSKC-PENPALTESVDVLFPNVGEVIGGSMRIWDPEE----LLAGYKRE--GIDPAP 403
+K NP LTE + LF E+ + DP + A + + G D A
Sbjct: 396 PL--AKRHRSNPGLTERFE-LFIGGKEIANAYSELNDPVDQRERFEAQVEEKEAGDDEAM 452
Query: 404 YY--WYTDQRKYGSTPHGGYGLGLERVLCWLLNQYHVRD 440
+ + +YG P GG G+G++R++ L N +RD
Sbjct: 453 ELDEDFVEALEYGMPPTGGLGIGIDRLVMLLTNSPSIRD 491
Score = 32.9 bits (76), Expect = 0.50
Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 11/47 (23%)
Query: 508 EKYRDK----------RVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQ 544
EKY DK V++ G + +R GK F L+DGSG IQ
Sbjct: 47 EKYADKTKEELEALNIEVSVAGRIMTIRNMGK-ASFADLQDGSGKIQ 92
>gnl|CDD|215490 PLN02903, PLN02903, aminoacyl-tRNA ligase.
Length = 652
Score = 53.3 bits (128), Expect = 3e-07
Identities = 41/153 (26%), Positives = 61/153 (39%), Gaps = 20/153 (13%)
Query: 513 KRVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVLADILCQTEHALL--LSTESSVQFRG 570
RVT+ GWV R G GL F+ +RD +G +Q V H L E V G
Sbjct: 73 SRVTLCGWVDLHRDMG-GLTFLDVRDHTGIVQVVTLPDEFPEAHRTANRLRNEYVVAVEG 131
Query: 571 ----RIEKVPEGKSAPGGHEL---KVDYWEVVGLA------PAGGADAILNEEALPDVQL 617
R ++ P K G E+ VD VV + A + EE V+L
Sbjct: 132 TVRSRPQESPNKKMKTGSVEVVAESVDILNVVTKSLPFLVTTADEQKDSIKEE----VRL 187
Query: 618 DNRHIMIRGENTSRVLLMRSVLLQALRAHFADR 650
R + +R + L +R +++ +R + D
Sbjct: 188 RYRVLDLRRPQMNANLRLRHRVVKLIRRYLEDV 220
Score = 47.9 bits (114), Expect = 1e-05
Identities = 35/114 (30%), Positives = 52/114 (45%), Gaps = 18/114 (15%)
Query: 202 LTQSSQLYLETCLPALGD-VYCIAQSYRAENSRTRRHLAEYTHVEAECAFLTFDDLLDKL 260
L QS QL+ + + + D Y IA+ +R E+ R R E+T ++ E AF +D+L
Sbjct: 256 LPQSPQLFKQMLMVSGFDRYYQIARCFRDEDLRADRQ-PEFTQLDMELAFTPLEDMLKLN 314
Query: 261 EDLICDTVDRVMATHGDLVRQMNPNFEPPARPFLRMNYADAIEYLRKHEIRKPD 314
EDLI + L PF R+ YA+A+ K+ KPD
Sbjct: 315 EDLIRQVFKEIKGV--QL-----------PNPFPRLTYAEAMS---KYGSDKPD 352
Score = 35.1 bits (81), Expect = 0.14
Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 22/81 (27%)
Query: 373 NVGEVIGGSMRIWDPEELLAGYKRE---------GIDPA----PYYWYTDQRKYGSTPHG 419
N E+ GGS+RI Y+R+ G+ P + + + G+ PHG
Sbjct: 543 NGVEIGGGSLRI---------YRRDVQQKVLEAIGLSPEEAESKFGYLLEALDMGAPPHG 593
Query: 420 GYGLGLERVLCWLLNQYHVRD 440
G GL+R++ L +RD
Sbjct: 594 GIAYGLDRLVMLLAGAKSIRD 614
>gnl|CDD|239816 cd04321, ScAspRS_mt_like_N, ScAspRS_mt_like_N: N-terminal,
anticodon recognition domain of the type found in
Saccharomyces cerevisiae mitochondrial (mt)
aspartyl-tRNA synthetase (AspRS). This domain is a
beta-barrel domain (OB fold) involved in binding the
tRNA anticodon stem-loop. The enzymes in this fungal
group are homodimeric class2b aminoacyl-tRNA synthetases
(aaRSs). aaRSs catalyze the specific attachment of amino
acids (AAs) to their cognate tRNAs during protein
biosynthesis. This 2-step reaction involves i) the
activation of the AA by ATP in the presence of magnesium
ions, followed by ii) the transfer of the activated AA
to the terminal ribose of tRNA. In the case of the
class2b aaRSs, the activated AA is attached to the 3'OH
of the terminal ribose. Eukaryotes contain 2 sets of
aaRSs, both of which are encoded by the nuclear genome.
One set concerns with cytoplasmic protein synthesis,
whereas the other exclusively with mitochondrial protein
synthesis. Mutations in the gene for S. cerevisiae
mtAspRS result in a "petite" phenotype typical for a
mutation in a nuclear gene that results in a
non-functioning mitochondrial protein synthesis system.
Length = 86
Score = 47.7 bits (114), Expect = 4e-07
Identities = 30/85 (35%), Positives = 42/85 (49%), Gaps = 11/85 (12%)
Query: 514 RVTIFGWVHRLRRQGKGLMFVTLRDGSGF-IQCVLADILCQTEHALL--LSTESSVQFRG 570
+VT+ GW+ R R K L F LRD +G IQ L + +LL ++ ES VQ RG
Sbjct: 1 KVTLNGWIDRKPRIVKKLSFADLRDPNGDIIQ--LVSTAKKDAFSLLKSITAESPVQVRG 58
Query: 571 RIEKVPEGKSAPGGHELKVDYWEVV 595
+++ S K D WE+V
Sbjct: 59 KLQLKEAKSS------EKNDEWELV 77
>gnl|CDD|185588 PTZ00385, PTZ00385, lysyl-tRNA synthetase; Provisional.
Length = 659
Score = 51.2 bits (122), Expect = 2e-06
Identities = 67/279 (24%), Positives = 114/279 (40%), Gaps = 46/279 (16%)
Query: 201 YLTQSSQLYLETCL-PALGDVYCIAQSYRAENSRTRRHLAEYTHVEAECAFLTFDDLLDK 259
+L + +L+L+ C+ + +Y I + +R E++ R H E+T E A+ T++DL+
Sbjct: 284 FLRVAPELHLKQCIVGGMERIYEIGKVFRNEDA-DRSHNPEFTSCEFYAAYHTYEDLMPM 342
Query: 260 LEDLICDTVDRVMATHGDLVRQMNPNFEPP----ARPFLRMNYADAIEYLRKHEIRKPDN 315
ED+ RV T + N + P +PF R++ D I+ + E P+
Sbjct: 343 TEDIFRQLAMRVNGTTVVQIYPENAHGNPVTVDLGKPFRRVSVYDEIQRMSGVEFPPPNE 402
Query: 316 TEYEFG----------EDIPEMPER---KM---------TDQINRPIMLCRFPADIKSFY 353
G +IP P R KM TD++ P + P +
Sbjct: 403 LNTPKGIAYMSVVMLRYNIPLPPVRTAAKMFEKLIDFFITDRVVEPTFVMDHP-----LF 457
Query: 354 MSKCPEN----PALTESVDVLFPNVGEVIGGSMRIWDPEELLAGYKREGID-------PA 402
MS + P L E + LF N E + DP E ++++ +D
Sbjct: 458 MSPLAKEQVSRPGLAERFE-LFVNGIEYCNAYSELNDPHEQYHRFQQQLVDRQGGDEEAM 516
Query: 403 PY-YWYTDQRKYGSTPHGGYGLGLERVLCWLLNQYHVRD 440
P + + G P G+G+G++R L L N ++RD
Sbjct: 517 PLDETFLKSLQVGLPPTAGWGMGIDRALMLLTNSSNIRD 555
>gnl|CDD|105955 PRK12820, PRK12820, bifunctional aspartyl-tRNA
synthetase/aspartyl/glutamyl-tRNA amidotransferase
subunit C; Provisional.
Length = 706
Score = 50.4 bits (120), Expect = 3e-06
Identities = 47/169 (27%), Positives = 69/169 (40%), Gaps = 35/169 (20%)
Query: 513 KRVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVL------ADILCQTEHALLLSTESSV 566
+ V + GWV R G L+F+ LRD +GFIQ V AD+ E A L E V
Sbjct: 19 REVCLAGWVDAFRDHG-ELLFIHLRDRNGFIQAVFSPEAAPADVY---ELAASLRAEFCV 74
Query: 567 QFRGRIEKVPEGKSAP----GGHELKVDYWEV----------------VGLAPAGGADAI 606
+G ++K E P G E+ V + A + GADA+
Sbjct: 75 ALQGEVQKRLEETENPHIETGDIEVFVRELSILAASEALPFAISDKAMTAGAGSAGADAV 134
Query: 607 LNEEALPDVQLDNRHIMIRGENTSRVLLMRSVLLQALRAHFADRNYTEV 655
NE D++L R++ IR L R +++ R R + E+
Sbjct: 135 -NE----DLRLQYRYLDIRRPAMQDHLAKRHRIIKCARDFLDSRGFLEI 178
Score = 37.3 bits (86), Expect = 0.026
Identities = 40/149 (26%), Positives = 63/149 (42%), Gaps = 17/149 (11%)
Query: 370 LFPNVGEVIGGSMRIWDPEELLAGYKREGIDPA----PYYWYTDQRKYGSTPHGGYGLGL 425
L N E+ GGS+RI D + L + G+ + ++ + + PHGG LGL
Sbjct: 493 LVVNGEELGGGSIRINDKDIQLRIFAALGLSEEDIEDKFGFFLRAFDFAAPPHGGIALGL 552
Query: 426 ERVLCWLLNQYHVRDKYQLIAKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEA 485
+RV+ +L +R+ A K S A SE +E+ AE +L +A
Sbjct: 553 DRVVSMILQTPSIRE-----VIAFPKNRSAACPLTGAPSEV---AQEQLAELGLLDLGDA 604
Query: 486 KKIVL---KED--PSLPPAVRIKIKDGEK 509
++ KED L RI + E+
Sbjct: 605 DQLPGDAEKEDLIDHLSWVSRIGFAEAER 633
Score = 36.5 bits (84), Expect = 0.045
Identities = 37/141 (26%), Positives = 65/141 (46%), Gaps = 26/141 (18%)
Query: 170 GIAKVTPPTLVQTQVEGG------STLFSLNFFGEPAYLTQSSQLYLETCLPALGDVYC- 222
G ++ P L ++ EG S + F+ P QS QL+ + + A + Y
Sbjct: 174 GFLEIETPILTKSTPEGARDYLVPSRIHPKEFYALP----QSPQLFKQLLMIAGFERYFQ 229
Query: 223 IAQSYRAENSRTRRHLAEYTHVEAECAFLTFDDLLDKLEDLICDTVDRVMATHGDLVRQM 282
+A+ +R E+ R R E+T ++ E +F+ + + + +E+L R+ A G
Sbjct: 230 LARCFRDEDLRPNRQ-PEFTQLDIEASFIDEEFIFELIEELTA----RMFAIGG------ 278
Query: 283 NPNFEPPARPFLRMNYADAIE 303
P RPF RM YA+A++
Sbjct: 279 ---IALP-RPFPRMPYAEAMD 295
Score = 30.3 bits (68), Expect = 3.5
Identities = 21/55 (38%), Positives = 28/55 (50%), Gaps = 9/55 (16%)
Query: 88 GLMFVTLRDGSGFIQCVL------ADILCQTEHALLLSTESSVQFRGRIEKVPEE 136
L+F+ LRD +GFIQ V AD+ E A L E V +G ++K EE
Sbjct: 35 ELLFIHLRDRNGFIQAVFSPEAAPADVY---ELAASLRAEFCVALQGEVQKRLEE 86
>gnl|CDD|173607 PTZ00417, PTZ00417, lysine-tRNA ligase; Provisional.
Length = 585
Score = 48.1 bits (114), Expect = 1e-05
Identities = 65/275 (23%), Positives = 118/275 (42%), Gaps = 39/275 (14%)
Query: 201 YLTQSSQLYLETCL-PALGDVYCIAQSYRAENSRTRRHLAEYTHVEAECAFLTFDDLLDK 259
YL +++L L+ + + VY I + +R E H E+T E A+ F DL+
Sbjct: 304 YLRIATELPLKMLIVGGIDKVYEIGKVFRNEGI-DNTHNPEFTSCEFYWAYADFYDLIKW 362
Query: 260 LEDLICDTVDRVMATHGDLVRQMNPNFEPP----ARPFLRMNYADAIEYLRKHEIRKP-D 314
ED V + T+ L + P +P P+ +++ + +E L ++ +P D
Sbjct: 363 SEDFFSQLVMHLFGTYKILYNKDGPEKDPIEIDFTPPYPKVSIVEELEKLTNTKLEQPFD 422
Query: 315 NTEY------EFGEDIPEMPE----RKMTDQINRPIMLCRFPADIKSFYMSKCPE----- 359
+ E E+ EMP K+ DQ+ + ++P K F++ + P+
Sbjct: 423 SPETINKMINLIKENKIEMPNPPTAAKLLDQLASHFIENKYPN--KPFFIIEHPQIMSPL 480
Query: 360 ------NPALTESVDVLFPNVGEVIGGSMRIWDPEELLAGYK-----REGIDPAPYYW-- 406
P LTE ++ +F EV+ + DP + + RE D + +
Sbjct: 481 AKYHRSKPGLTERLE-MFICGKEVLNAYTELNDPFKQKECFSAQQKDREKGDAEAFQFDA 539
Query: 407 -YTDQRKYGSTPHGGYGLGLERVLCWLLNQYHVRD 440
+ +YG P GG GLG++R+ +L N+ ++D
Sbjct: 540 AFCTSLEYGLPPTGGLGLGIDRITMFLTNKNCIKD 574
Score = 31.1 bits (70), Expect = 2.3
Identities = 57/232 (24%), Positives = 92/232 (39%), Gaps = 23/232 (9%)
Query: 440 DKYQLIAKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKIVLKEDP----- 494
+K + + + + K S A++D K E E R K ++E K + P
Sbjct: 51 EKKEHVMEGEKKVRSVQASKDKKKEEEAEVDPRLYYENRSKFIQEQKAKGINPYPHKFER 110
Query: 495 --SLPPAVRIKIKD---GEKYRDKRVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVLAD 549
++P V K +D GE D + + G + R+ G+ L F L IQ VLA+
Sbjct: 111 TITVPEFVE-KYQDLASGEHLEDTILNVTGRIMRVSASGQKLRFFDLVGDGAKIQ-VLAN 168
Query: 550 ILCQTEHALLLSTESSVQFRGRIEKVP--EGKSAPGGHELKVDYWEVVGLAPAGGADAIL 607
+ RG I + GKS G EL + E + L+P +
Sbjct: 169 FAFHDHTKSNFAECYDKIRRGDIVGIVGFPGKSKKG--ELSIFPKETIILSPC--LHMLP 224
Query: 608 NEEALPDVQLDNRH----IMIRGENTSRVLLMRSVLLQALRAHFADRNYTEV 655
+ L D ++ R +MI E+T + R+ ++ LR DR + EV
Sbjct: 225 MKYGLKDTEIRYRQRYLDLMI-NESTRSTFITRTKIINYLRNFLNDRGFIEV 275
>gnl|CDD|171504 PRK12445, PRK12445, lysyl-tRNA synthetase; Reviewed.
Length = 505
Score = 47.4 bits (112), Expect = 2e-05
Identities = 59/270 (21%), Positives = 112/270 (41%), Gaps = 40/270 (14%)
Query: 201 YLTQSSQLYLET-CLPALGDVYCIAQSYRAENSRTRRHLAEYTHVEAECAFLTFDDLLDK 259
YL + +LYL+ + V+ I +++R E R H E+T +E A+ + DL++
Sbjct: 235 YLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVR-HNPEFTMMELYMAYADYHDLIEL 293
Query: 260 LEDLICDTVDRVMAT----HGDLVRQMNPNFEPPARPFLRMNYADAIEYLR-KHEIRKPD 314
E L V+ T +G+ V +PF ++ +AI+ R + ++ D
Sbjct: 294 TESLFRTLAQEVLGTTKVTYGEHVFDF-------GKPFEKLTMREAIKKYRPETDMADLD 346
Query: 315 NTE----------------YEFGEDIPEMPERKMTDQINRPIMLCRFPADIKSFYMSKCP 358
N + + G + E+ + + +P + +PA++ +
Sbjct: 347 NFDAAKALAESIGITVEKSWGLGRIVTEIFDEVAEAHLIQPTFITEYPAEVSPL-ARRND 405
Query: 359 ENPALTESVDVLFPNVGEVIGGSMRIWDPEELLAGY------KREGIDPAPYYW--YTDQ 410
NP +T+ + F E+ G + D E+ + K G D A +Y Y
Sbjct: 406 VNPEITDRFE-FFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTA 464
Query: 411 RKYGSTPHGGYGLGLERVLCWLLNQYHVRD 440
+YG P G G+G++R++ N + +RD
Sbjct: 465 LEYGLPPTAGLGIGIDRMIMLFTNSHTIRD 494
>gnl|CDD|235095 PRK02983, lysS, lysyl-tRNA synthetase; Provisional.
Length = 1094
Score = 44.2 bits (105), Expect = 2e-04
Identities = 40/158 (25%), Positives = 64/158 (40%), Gaps = 30/158 (18%)
Query: 512 DKRVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQCVLADILCQTE------HALLLSTESS 565
+ V++ G V R+R G G++F LRD SG +Q +L + A+ L
Sbjct: 651 GEEVSVSGRVLRIRDYG-GVLFADLRDWSGELQVLLDASRLEQGSLADFRAAVDLGDLVE 709
Query: 566 VQFRGRIEKVPEGKSAPGGHELKVDYWEVVG--LAP-----AGGADAILNEEALPDVQLD 618
V G + G S G L V W + G L P G D P+ ++
Sbjct: 710 VT--GTM-----GTSRNGTLSLLVTSWRLAGKCLRPLPDKWKGLTD--------PEARVR 754
Query: 619 NRHI-MIRGENTSRVLLMRSVLLQALRAHFADRNYTEV 655
R++ + +L RS +++A+R R + EV
Sbjct: 755 QRYLDLAVNPEARDLLRARSAVVRAVRETLVARGFLEV 792
>gnl|CDD|225178 COG2269, COG2269, Truncated, possibly inactive, lysyl-tRNA
synthetase (class II) [Translation, ribosomal structure
and biogenesis].
Length = 322
Score = 39.2 bits (92), Expect = 0.005
Identities = 43/245 (17%), Positives = 90/245 (36%), Gaps = 32/245 (13%)
Query: 170 GIAKVTPPTLVQTQV-EGGSTLFSLNFFG------EPAYLTQSSQLYLETCLPAL-GDVY 221
G+ +V P L V + F F G +P +L S + +++ L A G ++
Sbjct: 34 GVLEVETPALSVAPVTDIHLHPFETEFLGPGGAKGKPLWLHTSPEYHMKRLLAAGSGPIF 93
Query: 222 CIAQSYRAENSRTRRHLAEYTHVE---AECAFLTFDDLLDKLEDLICDTVDRVMATHGDL 278
+ + +R E R H E+T +E C + + +D L L+ + V+ ++ +
Sbjct: 94 QLGKVFRNE-EMGRLHNPEFTMLEWYRVGCDYYRLMNEVDDLLQLVLECVEAERLSYQEA 152
Query: 279 VRQMNPNFEPPARPFLRMNYADAIEYLRKHEIRKPDNTEYEFGEDIPEMPERKMTDQI-- 336
+P + + E K + + ED + + + +
Sbjct: 153 F-LRYLGIDPLSADKTEL-----REAAAKLGLSAATD------EDWDTLLQLLFVEGVEP 200
Query: 337 ----NRPIMLCRFPADIKSFYMSKCPENPALTESVDVLFPNVGEVIGGSMRIWDPEELLA 392
RP L FPA + +P + E ++ + + E+ G + D E
Sbjct: 201 NLGKERPTFLYHFPASQAAL-AQISTGDPRVAERFELYYKGI-ELANGFHELTDAAEQRR 258
Query: 393 GYKRE 397
++++
Sbjct: 259 RFEQD 263
Score = 29.6 bits (67), Expect = 4.5
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 633 LLMRSVLLQALRAHFADRNYTEV 655
LL R+ ++ A+R FA+R EV
Sbjct: 16 LLKRAAIIAAIRRFFAERGVLEV 38
>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355). This
family of proteins is found in bacteria and viruses.
Proteins in this family are typically between 180 and
214 amino acids in length.
Length = 125
Score = 36.5 bits (85), Expect = 0.010
Identities = 13/52 (25%), Positives = 28/52 (53%)
Query: 440 DKYQLIAKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKIVLK 491
+K Q K++ +K++K++A + A+ E + ++E + + E E K K
Sbjct: 25 EKKQEEKKSEAEKLAKMSAEEKAEYELEKLEKELEELEAELARRELKAEAKK 76
>gnl|CDD|218336 pfam04935, SURF6, Surfeit locus protein 6. The surfeit locus
protein SURF-6 is shown to be a component of the
nucleolar matrix and has a strong binding capacity for
nucleic acids.
Length = 206
Score = 37.7 bits (88), Expect = 0.011
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 446 AKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKIVLKEDPSLPPAVRIKIK 505
K LKK+ + E KA + EE EK K L +A+ + +K+D L ++ +K
Sbjct: 94 YKQLLKKLEARKKKLEELDEDKAAEIEEK-EKWTKALAKAEGVKVKDDEKL---LKKALK 149
Query: 506 DGEKYRDKR 514
EK + K
Sbjct: 150 RKEKQKKKS 158
Score = 30.4 bits (69), Expect = 2.1
Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 456 LAARDNAKSESKAKKEEEDAEKREKNLEEAKKIVLKEDPSLPPAVRIKIKD 506
L R + + KA+K+++ E ++K E+A+K +E + + K
Sbjct: 8 LEQRRRKREQRKARKKQKRKEAKKK--EDAQKSEAEEVKNEENKSKKKAAP 56
>gnl|CDD|232984 TIGR00462, genX, EF-P lysine aminoacylase GenX. Many Gram-negative
bacteria have a protein closely homologous to the
C-terminal region of lysyl-tRNA synthetase (LysS).
Multiple sequence alignment of these proteins with the
homologous regions of collected LysS proteins shows that
these proteins form a distinct set rather than just
similar truncations of LysS. The protein is termed GenX
after its designation in E. coli. Interestingly, genX
often is located near a homolog of
lysine-2,3-aminomutase. Its function is unknown [Unknown
function, General].
Length = 290
Score = 37.9 bits (89), Expect = 0.011
Identities = 38/189 (20%), Positives = 66/189 (34%), Gaps = 60/189 (31%)
Query: 191 FSLNFFGEPAYLTQSSQLYLET----CLPAL-----GDVYCIAQSYRAENSRTRRHLAEY 241
F+ F G Q LYL+T + L G ++ I + +R R RRH E+
Sbjct: 28 FATEFVGPDG---QGRPLYLQTSPEYAMKRLLAAGSGPIFQICKVFRNG-ERGRRHNPEF 83
Query: 242 THVEAECAFLTFDDLLDKLEDLICDTVDRVMATHGDLVRQMNPNFEPPARPFLRMNYADA 301
T +E + DL+D++E L+ + P P R++Y +A
Sbjct: 84 TMLEWYRPGFDYHDLMDEVEALLQEL------------------LGDPFAPAERLSYQEA 125
Query: 302 -----------------IEYLRKHEIRKPDNTEYEFGEDIPEMPERKMTDQI------NR 338
H IR + +D ++ + ++++ R
Sbjct: 126 FLRYAGIDPLTASLAELQAAAAAHGIRASE------EDDRDDLLDLLFSEKVEPHLGFGR 179
Query: 339 PIMLCRFPA 347
P L +PA
Sbjct: 180 PTFLYDYPA 188
>gnl|CDD|239817 cd04322, LysRS_N, LysRS_N: N-terminal, anticodon recognition domain
of lysyl-tRNA synthetases (LysRS). These enzymes are
homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs).
This domain is a beta-barrel domain (OB fold) involved
in binding the tRNA anticodon stem-loop. aaRSs catalyze
the specific attachment of amino acids (AAs) to their
cognate tRNAs during protein biosynthesis. This 2-step
reaction involves i) the activation of the AA by ATP in
the presence of magnesium ions, followed by ii) the
transfer of the activated AA to the terminal ribose of
tRNA. In the case of the class2b aaRSs, the activated
AA is attached to the 3'OH of the terminal ribose.
Included in this group are E. coli LysS and LysU. These
two isoforms of LysRS are encoded by distinct genes
which are differently regulated. Eukaryotes contain 2
sets of aaRSs, both of which encoded by the nuclear
genome. One set concerns with cytoplasmic protein
synthesis, whereas the other exclusively with
mitochondrial protein synthesis. Saccharomyces
cerevisiae cytoplasmic and mitochondrial LysRSs have
been shown to participate in the mitochondrial import of
the only nuclear-encoded tRNA of S. cerevisiae
(tRNAlysCUU). The gene for human LysRS encodes both the
cytoplasmic and the mitochondrial isoforms of LysRS. In
addition to their housekeeping role, human lysRS may
function as a signaling molecule that activates immune
cells and tomato LysRS may participate in a
root-specific process possibly connected to conditions
of oxidative-stress conditions or heavy metal uptake. It
is known that human tRNAlys and LysRS are specifically
packaged into HIV-1 suggesting a role for LysRS in tRNA
packaging.
Length = 108
Score = 34.0 bits (79), Expect = 0.052
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 514 RVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQ 544
V++ G + R GK L F L+D SG IQ
Sbjct: 1 EVSVAGRIMSKRGSGK-LSFADLQDESGKIQ 30
>gnl|CDD|215278 PLN02502, PLN02502, lysyl-tRNA synthetase.
Length = 553
Score = 35.4 bits (82), Expect = 0.12
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 220 VYCIAQSYRAENSRTRRHLAEYTHVEAECAFLTFDDLLDKLEDLICDTVDRVMATHGDLV 279
VY I + +R E TR H E+T E A+ ++D+++ E+++ V G
Sbjct: 300 VYEIGRQFRNEGISTR-HNPEFTTCEFYQAYADYNDMMELTEEMVSGM---VKELTGSYK 355
Query: 280 RQMNP---NFEPPAR 291
+ + +F PP R
Sbjct: 356 IKYHGIEIDFTPPFR 370
Score = 35.0 bits (81), Expect = 0.12
Identities = 33/136 (24%), Positives = 49/136 (36%), Gaps = 36/136 (26%)
Query: 446 AKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKIVLKEDPSLPPAVRIK-- 503
A + K + AK E+KA A+ R + A + DP+ A R+K
Sbjct: 12 ALKKRLKAKQAEEEKAAKEEAKAAAAAAAAKGRSRKSAAADDETM--DPTQYRANRLKKV 69
Query: 504 ------------------------------IKDGEKYRDKRVTIFGWVHRLRRQGKGLMF 533
+++GE+ D V++ G + R GK L F
Sbjct: 70 EALRAKGVEPYPYKFDVTHTAPELQEKYGSLENGEELEDVSVSVAGRIMAKRAFGK-LAF 128
Query: 534 VTLRDGSGFIQCVLAD 549
LRD G IQ + AD
Sbjct: 129 YDLRDDGGKIQ-LYAD 143
>gnl|CDD|240314 PTZ00208, PTZ00208, 65 kDa invariant surface glycoprotein;
Provisional.
Length = 436
Score = 34.9 bits (80), Expect = 0.13
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 419 GGYGLGLERVLCWLL---NQYHVRDKYQLIAKAQLKKVSKL--AARDNAKSE-SKAKKEE 472
G L+R+ WL H D Y ++ + +KV ++ A+D + +AKK
Sbjct: 69 GYIEFELDRLDYWLEKLNGPKHSNDGYAKLSDSDTEKVKEIFEKAKDGIAKQLPEAKKAG 128
Query: 473 EDAEKREKNLEEAKK 487
E+AEK + +++A K
Sbjct: 129 EEAEKLHQEVKKAAK 143
>gnl|CDD|234778 PRK00484, lysS, lysyl-tRNA synthetase; Reviewed.
Length = 491
Score = 35.1 bits (82), Expect = 0.13
Identities = 35/155 (22%), Positives = 60/155 (38%), Gaps = 37/155 (23%)
Query: 235 RRHLAEYTHVEAECAFLTFDDLLDKLEDLICDTVDRVMATHGDLVRQMNP---NFEPPAR 291
RH E+T +E A+ ++D++D E+LI V G +F P
Sbjct: 257 TRHNPEFTMLEFYQAYADYNDMMDLTEELIRHLAQAV---LGTTKVTYQGTEIDFGP--- 310
Query: 292 PFLRMNYADAI-----------------EYLRKHEIRKPDNTEYEFGEDIPEMPERKMTD 334
PF R+ DAI ++ I + + G+ I E+ E +
Sbjct: 311 PFKRLTMVDAIKEYTGVDFDDMTDEEARALAKELGIEVEKS--WGLGKLINELFEEFVEP 368
Query: 335 QINRPIMLCRFPADIKSFYMS----KCPENPALTE 365
++ +P + +P +I S + E+P LTE
Sbjct: 369 KLIQPTFITDYPVEI-----SPLAKRHREDPGLTE 398
Score = 33.9 bits (79), Expect = 0.28
Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 503 KIKDGEKYRDKRVTIFGWVHRLRRQGKGLMFVTLRDGSGFIQ 544
K K+ + + V++ G V R GK F TL+DGSG IQ
Sbjct: 45 KEKEELEELEIEVSVAGRVMLKRVMGK-ASFATLQDGSGRIQ 85
>gnl|CDD|218896 pfam06098, Radial_spoke_3, Radial spoke protein 3. This family
consists of several radial spoke protein 3 (RSP3)
sequences. Eukaryotic cilia and flagella present in
diverse types of cells perform motile, sensory, and
developmental functions in organisms from protists to
humans. They are centred by precisely organised,
microtubule-based structures, the axonemes. The axoneme
consists of two central singlet microtubules, called the
central pair, and nine outer doublet microtubules. These
structures are well-conserved during evolution. The
outer doublet microtubules, each composed of A and B
sub-fibres, are connected to each other by nexin links,
while the central pair is held at the centre of the
axoneme by radial spokes. The radial spokes are T-shaped
structures extending from the A-tubule of each outer
doublet microtubule to the centre of the axoneme. Radial
spoke protein 3 (RSP3), is present at the proximal end
of the spoke stalk and helps in anchoring the radial
spoke to the outer doublet. It is thought that radial
spokes regulate the activity of inner arm dynein through
protein phosphorylation and dephosphorylation.
Length = 288
Score = 33.1 bits (76), Expect = 0.35
Identities = 11/51 (21%), Positives = 30/51 (58%)
Query: 439 RDKYQLIAKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKIV 489
+ +++ A+L + +L + + E K +++++D E++++ E A+KI
Sbjct: 161 QRQFEQRRNAELAETQRLEEAERRRREEKERRKKQDKERKQREKETAEKIA 211
>gnl|CDD|217843 pfam04012, PspA_IM30, PspA/IM30 family. This family includes PspA
a protein that suppresses sigma54-dependent
transcription. The PspA protein, a negative regulator of
the Escherichia coli phage shock psp operon, is produced
when virulence factors are exported through secretins in
many Gram-negative pathogenic bacteria and its homologue
in plants, VIPP1, plays a critical role in thylakoid
biogenesis, essential for photosynthesis. Activation of
transcription by the enhancer-dependent bacterial
sigma(54) containing RNA polymerase occurs through ATP
hydrolysis-driven protein conformational changes enabled
by activator proteins that belong to the large AAA(+)
mechanochemical protein family. It has been shown that
PspA directly and specifically acts upon and binds to
the AAA(+) domain of the PspF transcription activator.
Length = 220
Score = 32.7 bits (75), Expect = 0.40
Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 12/81 (14%)
Query: 432 LLNQYHVRDKYQLIAKAQLKKVSKLAAR---DNAKSESKAKKEEEDAEKREKNLEEAKKI 488
+L Q +RD +++L K + A+ + E K ++++E A+K E A
Sbjct: 27 MLEQA-IRD-----MQSELGKARQALAQVIARQKQLERKLEEQKEQAKKLENKARAA--- 77
Query: 489 VLKEDPSLPPAVRIKIKDGEK 509
+ K + L +I EK
Sbjct: 78 LTKGNEELAREALAEIATLEK 98
>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding
[General function prediction only].
Length = 239
Score = 32.7 bits (75), Expect = 0.42
Identities = 26/124 (20%), Positives = 44/124 (35%), Gaps = 30/124 (24%)
Query: 437 HVRDKYQLIAKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKI-VLKEDPS 495
+ ++ + + K +L + +E++A+ EEE AE RE+ E + K LKE
Sbjct: 114 ELMEEIEKLEKEIEDLKERLERLEKNLAEAEARLEEEVAEIREEGQELSSKREELKEK-- 171
Query: 496 LPPAVRIKIKDGEKYRDKRVTIFGWVHRLRRQGKGLMFVTLRD----------GSGFIQC 545
L P + R+R+ KG+ V L S +
Sbjct: 172 LDPEL-----------------LSEYERIRKNKKGVGVVPLEGRVCGGCHMKLPSQTLSK 214
Query: 546 VLAD 549
V
Sbjct: 215 VRKK 218
>gnl|CDD|225368 COG2811, NtpF, Archaeal/vacuolar-type H+-ATPase subunit H [Energy
production and conversion].
Length = 108
Score = 31.2 bits (71), Expect = 0.48
Identities = 13/46 (28%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 446 AKAQLKKVSKLAARDNAKSESKAKKEEED--AEKREKNLEEAKKIV 489
A+ +K+ + A ++E +A+K ++ E RE+ EEA++I+
Sbjct: 30 AEQIIKEAREEAREIIEEAEEEAEKLAQEILEEAREEAEEEAEEIL 75
>gnl|CDD|222649 pfam14284, PcfJ, PcfJ-like protein. The PcfJ-like protein family
includes the E. faecalis PcfJ protein, which is
functionally uncharacterized. It is found in bacteria
and viruses, and is typically between 159 and 170 amino
acids in length. There is a conserved HCV sequence
motif.
Length = 169
Score = 31.9 bits (73), Expect = 0.61
Identities = 16/37 (43%), Positives = 22/37 (59%)
Query: 457 AARDNAKSESKAKKEEEDAEKREKNLEEAKKIVLKED 493
AA D A ++ +AKKE+E AEK K E +KI +
Sbjct: 29 AAHDRAVAKYQAKKEKEKAEKMRKRYPELEKIFRELK 65
>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein
TolA; Provisional.
Length = 387
Score = 32.5 bits (74), Expect = 0.70
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 446 AKAQLKKVSKLAARDNAK-SESKAKKEEEDAEKREKNLEEAKK 487
A A+ +K A AK + + AKK +A+K+ + EA K
Sbjct: 137 AAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAE--AEAAK 177
Score = 32.5 bits (74), Expect = 0.75
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 446 AKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKK 487
A A+ KK ++ A A +E+K K E E A K EAKK
Sbjct: 163 AAAEAKKKAEAEAAKKAAAEAKKKAEAEAAAKAA---AEAKK 201
Score = 32.5 bits (74), Expect = 0.80
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 446 AKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKK 487
A A+ KK ++ A+ A +E+K K E K EAK
Sbjct: 195 AAAEAKKKAEAEAKKKAAAEAKKKAAAEAKAAAAKAAAEAKA 236
Score = 30.5 bits (69), Expect = 2.5
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 5/47 (10%)
Query: 446 AKAQLKKVSKLAARDNAKSESKAKKEEE-----DAEKREKNLEEAKK 487
A A+ KK ++ A A +E+K K E E AE ++K EAK
Sbjct: 179 AAAEAKKKAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKKAAAEAKA 225
Score = 30.2 bits (68), Expect = 3.3
Identities = 18/42 (42%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 446 AKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKK 487
AKA+ + +K AA K+ ++AKK+ E AE +K EAKK
Sbjct: 145 AKAKAEAEAKRAAAAAKKAAAEAKKKAE-AEAAKKAAAEAKK 185
Score = 30.2 bits (68), Expect = 3.4
Identities = 12/42 (28%), Positives = 21/42 (50%)
Query: 446 AKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKK 487
A+A+ KK + A+ A +E+KA + AE + + A
Sbjct: 203 AEAEAKKKAAAEAKKKAAAEAKAAAAKAAAEAKAAAEKAAAA 244
>gnl|CDD|201130 pfam00280, potato_inhibit, Potato inhibitor I family.
Length = 63
Score = 29.1 bits (66), Expect = 0.87
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 7/43 (16%)
Query: 480 KNLEEAKKIVLKEDPSLPPAVRIKIKDGEK----YRDKRVTIF 518
K EEAK I+ KE+P + V + +G +R RV +F
Sbjct: 10 KTGEEAKAIIEKENPDVDVVV---LPEGSPVTADFRCNRVRVF 49
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 32.2 bits (74), Expect = 0.90
Identities = 12/44 (27%), Positives = 19/44 (43%)
Query: 446 AKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKIV 489
+ + + L+ + K K +K E+ AEK E AKK
Sbjct: 396 GEEEEGENGNLSPAERKKLRKKQRKAEKKAEKEEAEKAAAKKKA 439
Score = 32.2 bits (74), Expect = 0.93
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 5/54 (9%)
Query: 447 KAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKIVLKEDPSLPPAV 500
A+ KK+ K K+E KA+KEE + +K E A K K V
Sbjct: 408 PAERKKLRKKQR----KAEKKAEKEEAEKAAAKKKAEAAAK-KAKGPDGETKKV 456
>gnl|CDD|224755 COG1842, PspA, Phage shock protein A (IM30), suppresses
sigma54-dependent transcription [Transcription / Signal
transduction mechanisms].
Length = 225
Score = 31.5 bits (72), Expect = 0.99
Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 12/81 (14%)
Query: 432 LLNQYHVRDKYQLIAKAQLKKVSKLAARDNA---KSESKAKKEEEDAEKREKNLEEAKKI 488
+L Q +RD +++L K + A+ A + E K ++ + AEK E+ E A
Sbjct: 28 MLEQA-IRD-----MESELAKARQALAQAIARQKQLERKLEEAQARAEKLEEKAELA--- 78
Query: 489 VLKEDPSLPPAVRIKIKDGEK 509
+ + L + + E
Sbjct: 79 LQAGNEDLAREALEEKQSLED 99
>gnl|CDD|198139 smart01071, CDC37_N, Cdc37 N terminal kinase binding. Cdc37 is a
molecular chaperone required for the activity of
numerous eukaryotic protein kinases. This domain
corresponds to the N terminal domain which binds
predominantly to protein kinases.and is found N terminal
to the Hsp (Heat shocked protein) 90-binding domain.
Expression of a construct consisting of only the
N-terminal domain of Saccharomyces pombe Cdc37 results
in cellular viability. This indicates that interactions
with the cochaperone Hsp90 may not be essential for
Cdc37 function.
Length = 154
Score = 30.8 bits (70), Expect = 1.0
Identities = 14/55 (25%), Positives = 24/55 (43%)
Query: 449 QLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKIVLKEDPSLPPAVRIK 503
QLKK + A D+ + KK + +K +K L + + KE+ +V
Sbjct: 94 QLKKELEEANGDSEGLLEELKKHRDKLKKEQKELRKKLDELEKEEKKKIWSVDTH 148
>gnl|CDD|224032 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains
DnaJ-type Zn finger domain [DNA replication,
recombination, and repair].
Length = 715
Score = 32.4 bits (74), Expect = 1.0
Identities = 19/71 (26%), Positives = 29/71 (40%), Gaps = 1/71 (1%)
Query: 475 AEKREKNLEEAKKIVLKEDPSLPPAVRIKIKDGEKYRDKRVTIFGWVHRLRRQGKGLMFV 534
EK E + E +E R I D ++ K V I G V ++++ +F
Sbjct: 176 PEKGEIDFEPVGLDRYREVQVEKELPRTLIDDLDEMIGKTVRIEGEVTQIKQTSGPTVF- 234
Query: 535 TLRDGSGFIQC 545
TL D +G I
Sbjct: 235 TLTDETGAIWA 245
>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 = 31.3 bits (71), Expect = 1.1
Identities = 19/92 (20%), Positives = 32/92 (34%), Gaps = 6/92 (6%)
Query: 176 PPTLVQTQVEGGSTLFSLNFFGEPAYLTQSSQLYLET----CLPALGD-VYCIAQSYRAE 230
P L + E L E YL + + L + L + I ++R E
Sbjct: 29 EPLLEKAGHEPKDLLPVGAENEEDLYLRPTLEPGLVRLFVSHIRKLPLRLAEIGPAFRNE 88
Query: 231 NSRTR-RHLAEYTHVEAECAFLTFDDLLDKLE 261
R R + E+T +E E ++ + E
Sbjct: 89 GGRRGLRRVREFTQLEGEVFGEDGEEASEFEE 120
>gnl|CDD|110537 pfam01540, Lipoprotein_7, Adhesin lipoprotein. This family
consists of the p50 and variable adherence-associated
antigen (Vaa) adhesins from Mycoplasma hominis. M.
hominis is a mycoplasma associated with human urogenital
diseases, pneumonia, and septic arthritis. An adhesin is
a cell surface molecule that mediates adhesion to other
cells or to the surrounding surface or substrate. The
Vaa antigen is a 50-kDa surface lipoprotein that has
four tandem repetitive DNA sequences encoding a periodic
peptide structure, and is highly immunogenic in the
human host. p50 is also a 50-kDa lipoprotein, having
three repeats A,B and C, that may be a tetramer of
191-kDa in its native environment.
Length = 353
Score = 32.0 bits (72), Expect = 1.1
Identities = 26/67 (38%), Positives = 33/67 (49%), Gaps = 11/67 (16%)
Query: 453 VSKL-AARDNAKSESK---------AKKEEEDAEKREKNLEEAKKIVLKEDPSLPPAVRI 502
+SKL AA +NAK+E K AK+ E K + N+EE KKI E L V
Sbjct: 92 ISKLSAAVENAKNEKKAIDDKNAQIAKELAERNAKIQSNIEELKKIN-NEAFELSKTVNK 150
Query: 503 KIKDGEK 509
I + EK
Sbjct: 151 TIAEVEK 157
>gnl|CDD|204918 pfam12436, USP7, Ubiquitin-specific protease 7. This domain family
is found in eukaryotes, and is approximately 40 amino
acids in length. The family is found in association with
pfam00443, pfam00917. USP7 regulates the turnover of
p53.
Length = 35
Score = 27.9 bits (63), Expect = 1.3
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 467 KAKKEEEDAEKREKNLEEA 485
+ ++E E+ E+R K EEA
Sbjct: 12 RLEEEREERERRRKEREEA 30
>gnl|CDD|203462 pfam06476, DUF1090, Protein of unknown function (DUF1090). This
family consists of several bacterial proteins of unknown
function and is known as YqjC in E. coli.
Length = 115
Score = 29.9 bits (68), Expect = 1.3
Identities = 13/47 (27%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 441 KYQLIAKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKK 487
+ + AK + K+ ++A R+ E++AK + + EK+++ L EA+
Sbjct: 65 RAERQAKVEEKE-QEVAEREQELKEAQAKGDADKIEKKQRKLAEAQA 110
>gnl|CDD|239931 cd04485, DnaE_OBF, DnaE_OBF: A subfamily of OB folds corresponding
to the C-terminal OB-fold nucleic acid binding domain of
Thermus aquaticus and Escherichia coli type C
replicative DNA polymerase III alpha subunit (DnaE). The
DNA polymerase holoenzyme of E. coli contains two copies
of this replicative polymerase, each of which copies a
different DNA strand. This group also contains Bacillus
subtilis DnaE. Replication in B. subtilis and
Staphylococcus aureus requires two different type C
polymerases, polC and DnaE, both of which are thought to
be included in the DNA polymerase holoenzyme. At the B.
subtilis replication fork, polC appears to be involved
in leading strand synthesis and DnaE in lagging strand
synthesis.
Length = 84
Score = 29.4 bits (67), Expect = 1.4
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 7/64 (10%)
Query: 516 TIFGWVHRLRR----QGKGLMFVTLRDGSGFIQCVL-ADILCQTEHALLLSTESSVQFRG 570
T+ G V +RR +GK + FVTL D +G I+ V+ + + LL ++ + G
Sbjct: 1 TVAGLVTSVRRRRTKKGKRMAFVTLEDLTGSIEVVVFPETYEKYRD--LLKEDALLLVEG 58
Query: 571 RIEK 574
++E+
Sbjct: 59 KVER 62
Score = 28.2 bits (64), Expect = 3.0
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 6/59 (10%)
Query: 86 GKGLMFVTLRDGSGFIQCVL-ADILCQTEHALLLSTESSVQFRGRIEKVPEENMKVQLI 143
GK + FVTL D +G I+ V+ + + LL ++ + G++E + ++LI
Sbjct: 17 GKRMAFVTLEDLTGSIEVVVFPETYEKYRD--LLKEDALLLVEGKVE---RRDGGLRLI 70
>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
subunit. This is a family of proteins which are
subunits of the eukaryotic translation initiation factor
3 (eIF3). In yeast it is called Hcr1. The Saccharomyces
cerevisiae protein eIF3j (HCR1) has been shown to be
required for processing of 20S pre-rRNA and binds to 18S
rRNA and eIF3 subunits Rpg1p and Prt1p.
Length = 242
Score = 31.2 bits (71), Expect = 1.5
Identities = 17/51 (33%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 451 KKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKIVLKEDPSLPPAVR 501
++ +K+AA+ AK KAK EE++ KREK E+ + + ++ P A +
Sbjct: 47 EEKAKVAAKAKAKKALKAKIEEKEKAKREK-EEKGLRELEEDTPEDELAEK 96
Score = 29.6 bits (67), Expect = 4.2
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 446 AKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNL-----EEAKKIVLKE 492
AK K +K A + + + KAK+E+E+ RE E A+K+ L++
Sbjct: 50 AKVAAKAKAKKALKAKIEEKEKAKREKEEKGLRELEEDTPEDELAEKLRLRK 101
>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell
envelope biogenesis, outer membrane].
Length = 387
Score = 31.1 bits (70), Expect = 2.1
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 441 KYQLIAKAQ---LKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKK 487
K + AKA K AA+ A++E+KA E+ AE K E K
Sbjct: 172 KAEEAAKAAEEAKAKAEAAAAKKKAEAEAKAAAEKAKAEAEAKAKAEKKA 221
>gnl|CDD|205206 pfam13025, DUF3886, Protein of unknown function (DUF3886). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 90 amino acids in length.
There are two completely conserved L residues that may
be functionally important.
Length = 70
Score = 28.5 bits (64), Expect = 2.1
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 446 AKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAK 486
A+LK A + K+E + ++EEE+A KRE+ E K
Sbjct: 18 LLAKLK-----AKKKELKAEEEKREEEEEARKREERKEREK 53
>gnl|CDD|222665 pfam14303, NAM-associated, No apical meristem-associated C-terminal
domain. This domain is found in a number of different
types of plant proteins including NAM-like proteins.
Length = 147
Score = 30.0 bits (68), Expect = 2.1
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 446 AKAQLKKVSKLAARDNA----KSESKAKKEEEDAEKREKNLEEAKKIVLKE 492
AK +L++ A ++ A + E + K +AEK LE+ KK K
Sbjct: 68 AKEKLRRDKLKAKKEEAEKEKEKEERFMKALAEAEKERAELEK-KKAEAKL 117
>gnl|CDD|235554 PRK05673, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1135
Score = 31.2 bits (72), Expect = 2.2
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 511 RDKRVTIFGWVHRLRR----QGKGLMFVTLRDGSGFIQCVL-ADILCQTEHALLLSTESS 565
VT+ G V +RR +G + VTL D SG I+ +L ++ L + LL +
Sbjct: 976 GGSVVTVAGLVVSVRRRVTKRGNKMAIVTLEDLSGRIEVMLFSEALEKYRD--LLEEDRI 1033
Query: 566 VQFRGRIEKVPEG 578
V +G++ G
Sbjct: 1034 VVVKGQVSFDDGG 1046
>gnl|CDD|129200 TIGR00092, TIGR00092, GTP-binding protein YchF. This predicted
GTP-binding protein is found in a single copy in every
complete bacterial genome, and is found in Eukaryotes. A
more distantly related protein, separated from this
model, is found in the archaea. It is known to bind GTP
and double-stranded nucleic acid. It is suggested to
belong to a nucleoprotein complex and act as a
translation factor [Unknown function, General].
Length = 368
Score = 30.9 bits (70), Expect = 2.3
Identities = 15/63 (23%), Positives = 21/63 (33%), Gaps = 3/63 (4%)
Query: 444 LIAKAQLKKVSKLAARDNAKSESKAKKEEEDA-EKREKNLEEAKKIVLKEDPSLPPAVRI 502
+ KA V K R +E K+EE + L ++ D L I
Sbjct: 132 ELLKADEFLVEKRIGRSKKSAEGGKDKKEELLLLEIILPLLNGGQMARHVD--LSKEELI 189
Query: 503 KIK 505
IK
Sbjct: 190 LIK 192
>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal. This
domain is found to the N-terminus of bacterial signal
peptidases of the S49 family (pfam01343).
Length = 154
Score = 29.8 bits (68), Expect = 2.3
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 12/61 (19%)
Query: 433 LNQYHVRDKYQLIA----KAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKI 488
LN+ + K L A K +LK K+E KA+K + AEK++ EE K
Sbjct: 47 LNEEYKDLKESLEAALLDKKELKAW--------EKAEKKAEKAKAKAEKKKAKKEEPKPR 98
Query: 489 V 489
+
Sbjct: 99 L 99
>gnl|CDD|239935 cd04489, ExoVII_LU_OBF, ExoVII_LU_OBF: A subfamily of OB folds
corresponding to the N-terminal OB-fold domain of
Escherichia coli exodeoxyribonuclease VII (ExoVII) large
subunit. E. coli ExoVII is composed of two non-identical
subunits. E. coli ExoVII is a single-strand-specific
exonuclease which degrades ssDNA from both 3-prime and
5-prime ends. ExoVII plays a role in methyl-directed
mismatch repair in vivo. ExoVII may also guard the
genome from mutagenesis by removing excess ssDNA, since
the build up of ssDNA would lead to SOS induction and
PolIV-dependent mutagenesis.
Length = 78
Score = 28.3 bits (64), Expect = 2.4
Identities = 21/97 (21%), Positives = 35/97 (36%), Gaps = 42/97 (43%)
Query: 70 ITNINIPAIPGPPAIPGKGLMFVTLRDGSGFIQCVLADILCQTEHALLLSTESSVQFRGR 129
I+N+ P+ G ++ TL+D I+CV+ +R
Sbjct: 8 ISNLKRPS---------SGHLYFTLKDEDASIRCVM--------------------WRSN 38
Query: 130 IEKV---PEENMKVQLIH--PSSYAIVWLGDLKQGGY 161
++ EE M+V L+ S Y +GGY
Sbjct: 39 ARRLGFPLEEGMEV-LVRGKVSFYE-------PRGGY 67
>gnl|CDD|225651 COG3109, ProQ, Activator of osmoprotectant transporter ProP [Signal
transduction mechanisms].
Length = 208
Score = 30.2 bits (68), Expect = 2.5
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 464 SESKAKKEEEDAEKREKNLEEAKKIVLKEDPSLP-PAVRIKIKDGEKYRDKRVT 516
+E+KA+ + + AE++ K EEA K P A R K K + V+
Sbjct: 104 AEAKARVQAQRAEQQAKKREEAPAAGEKPTAERPATAARPKPKAPREEVHTPVS 157
>gnl|CDD|214727 smart00573, HSA, domain in helicases and associated with SANT
domains.
Length = 73
Score = 28.1 bits (63), Expect = 2.5
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 3/53 (5%)
Query: 429 LCWLLNQYHVRDKYQLIAKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKN 481
+ W + K+ A KK++K + E + ++ EE EKR
Sbjct: 20 MIWHAKDFKEEHKW---KIAAAKKMAKAVMDYHQNKEKEEERREEKNEKRRLR 69
>gnl|CDD|173863 cd08498, PBP2_NikA_DppA_OppA_like_2, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains 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
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 481
Score = 30.6 bits (70), Expect = 2.6
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 472 EEDAEKREKNLEEAKKIVLKEDPSLP 497
E D KR L+EA++IV + +P
Sbjct: 435 EMDPAKRAALLQEAQEIVADDAAYIP 460
>gnl|CDD|131972 TIGR02926, AhaH, ATP synthase archaeal, H subunit. he A1/A0 ATP
synthase is homologous to the V-type (V1/V0, vacuolar)
ATPase, but functions in the ATP synthetic direction as
does the F1/F0 ATPase of bacteria. The hydrophilic A1
"stalk" complex (AhaABCDEFG) is the site of ATP
generation and is coupled to the membrane-embedded
proton translocating A0 complex. It is unclear precisely
where AhaH fits into these complexes.
Length = 85
Score = 28.3 bits (63), Expect = 2.9
Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 4/69 (5%)
Query: 445 IAKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKIV---LKEDPSLPPAVR 501
I KA+ + + + + A+ EE E E+ EEA K+ +KE
Sbjct: 4 IKKAEEDAEELIEEAEEERKQRIAEAREEARELLEEAEEEASKLGEEIIKEAEEEIEKEA 63
Query: 502 IKI-KDGEK 509
KI ++GEK
Sbjct: 64 EKIREEGEK 72
>gnl|CDD|189017 cd09610, M3B_PepF_5, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 472
Score = 30.7 bits (70), Expect = 2.9
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 12/57 (21%)
Query: 238 LAEYTHVEAECAFLTFDDLLDKLED------LICDTVDRVMATHGDLVRQMN-PNFE 287
LAE V E L FD LL++L D L+ ++ + AT + RQ+ FE
Sbjct: 300 LAETASVFGE--MLVFDRLLERLSDPEERLALLAGKIEDIFAT---VFRQIAFTRFE 351
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 30.9 bits (70), Expect = 3.0
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 440 DKYQLIA--KAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKK 487
D L+ + +LK++ KL + E + ++E E E+R LEE K+
Sbjct: 200 DIEDLLEALEEELKELKKLEEIQEEQEEEELEQEIEALEERLAELEEEKE 249
>gnl|CDD|189027 cd09857, PIN_EXO1, PIN domain of Exonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Exonuclease-1 (EXO1) is involved
in multiple, eukaryotic DNA metabolic pathways,
including DNA replication processes (5' flap DNA
endonuclease activity and double stranded DNA
5'-exonuclease activity), DNA repair processes (DNA
mismatch repair (MMR) and post-replication repair
(PRR)), recombination, and telomere integrity. EXO1
functions in the MMS2 error-free branch of the PRR
pathway in the maintenance and repair of stalled
replication forks. Studies also suggest that EXO1 plays
both structural and catalytic roles during MMR-mediated
mutation avoidance. EXO1 belongs to the FEN1-EXO1-like
family of structure-specific, 5' nucleases. These
nucleases contain a PIN (PilT N terminus) domain with a
helical arch/clamp region (I domain) of variable length
(approximately 43 residues in EXO1 PIN domains) and a
H3TH (helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+). EXO1 nucleases also have
C-terminal Mlh1- and Msh2-binding domains which allow
interaction with MMR and PRR proteins, respectively.
Length = 210
Score = 29.8 bits (68), Expect = 3.1
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 466 SKAKKEEEDAEKREKNLEEAKK 487
SK EEE E+RE+NLE+A +
Sbjct: 84 SKKGTEEERRERREENLEKALE 105
>gnl|CDD|241344 cd13190, FERM_C_FAK1, Focal Adhesion Kinase 1 and 2 FERM domain
C-lobe. FAK1 (also called FRNK/Focal adhesion
kinase-related nonkinase;
p125FAK/pp125FAK;PTK2/Protein-tyrosine kinase 2 protein
tyrosine kinase 2 (PTK2) is a non-receptor tyrosine
kinase that localizes to focal adhesions in adherent
cells. It has been implicated in diverse cellular roles
including cell locomotion, mitogen response and cell
survival. The N-terminal region of FAK1 contains a FERM
domain, a linker, a kinase domain, and a C-terminal FRNK
(FAK-related-non-kinase) domain. Three subdomains of
FERM (FERM_N, FERM_M, FERM_C/N, alpha-, and
C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3) form a clover
leaf fold, similar to those of known FERM structures
despite the low sequence conservation. The C-lobe/F3
within the FERM domain is part of the PH domain family.
The phosphoinositide-binding site found in ERM family
proteins is not present in the FERM domain of FAK1. The
adjacent Src SH3 and SH2 binding sites in the linker of
FAK1 associates with the F3 and F1 lobes and are thought
to be involved in regulation. The FERM domain of FAK1
can inhibit enzymatic activity and repress FAK
signaling. In an inactive state of FAK1, the FERM domain
is thought to interact with the catalytic domain of FAK1
to repress its activity. Upon activation this
interaction is disrupted and its kinase activity
restored. The FRNK domain is thought to function as a
negative regulator of kinase activity. The C-lobe/F3 is
the third structural domain within the FERM domain. The
FERM domain is found in the cytoskeletal-associated
proteins such as ezrin, moesin, radixin, 4.1R, and
merlin. These proteins provide a link between the
membrane and cytoskeleton and are involved in signal
transduction pathways. The FERM domain is also found in
protein tyrosine phosphatases (PTPs) , the tyrosine
kinases FAK and JAK, in addition to other proteins
involved in signaling. This domain is structurally
similar to the PH and PTB domains and consequently is
capable of binding to both peptides and phospholipids at
different sites.
Length = 111
Score = 28.7 bits (65), Expect = 3.2
Identities = 6/20 (30%), Positives = 9/20 (45%)
Query: 226 SYRAENSRTRRHLAEYTHVE 245
SY E HLA++ +
Sbjct: 28 SYLTEKGSAPTHLADFKQIR 47
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 30.3 bits (69), Expect = 3.3
Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 9/78 (11%)
Query: 441 KYQLIAKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKIVLKEDPSLPPAV 500
+++ KA+ K+ + + K K+EEE+ EK +K +E
Sbjct: 412 IKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKE---------EEKEEEEEEA 462
Query: 501 RIKIKDGEKYRDKRVTIF 518
+ ++ E+ + K+ T+F
Sbjct: 463 EEEKEEEEEKKKKQATLF 480
>gnl|CDD|132364 TIGR03321, alt_F1F0_F0_B, alternate F1F0 ATPase, F0 subunit B. A
small number of taxonomically diverse prokaryotic
species, including Methanosarcina barkeri, have what
appears to be a second ATP synthase, in addition to the
normal F1F0 ATPase in bacteria and A1A0 ATPase in
archaea. These enzymes use ion gradients to synthesize
ATP, CC and in principle may run in either direction.
This model represents the F0 subunit B of this apparent
second ATP synthase.
Length = 246
Score = 30.0 bits (68), Expect = 3.4
Identities = 29/110 (26%), Positives = 48/110 (43%), Gaps = 15/110 (13%)
Query: 428 VLCWLLNQYHVRDKYQLIAKAQLKKVSKLAARDNAKSESKA------KKEEEDAEKREKN 481
+L WLL ++ R + + K +LA D K E++ +K EE ++RE
Sbjct: 17 ILVWLLKRFLYRPILDAMDAREKKIAGELADADTKKREAEQERREYEEKNEELDQQREVL 76
Query: 482 LEEAKKIVLKEDPSLPPAVRIKIKDGEKYRDKRVTIFGWVHRLRRQGKGL 531
L +AK+ E L R ++ ++ R+K W LRR+ L
Sbjct: 77 LTKAKEEAQAERQRLLDEAR---EEADEIREK------WQEALRREQAAL 117
>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742).
This is a family of fungal proteins of unknown function.
Length = 182
Score = 29.3 bits (66), Expect = 4.1
Identities = 13/50 (26%), Positives = 25/50 (50%)
Query: 438 VRDKYQLIAKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKK 487
V+ +Y+ K + KK +D K + KK+++ +K EK E+ +
Sbjct: 74 VKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAEDKLE 123
>gnl|CDD|224308 COG1390, NtpE, Archaeal/vacuolar-type H+-ATPase subunit E [Energy
production and conversion].
Length = 194
Score = 29.3 bits (66), Expect = 4.4
Identities = 12/56 (21%), Positives = 28/56 (50%), Gaps = 5/56 (8%)
Query: 438 VRDKYQLIAKAQLKKVSKLAARDNAKSESKAKKEEEDAEKR-EKNLEEAKKIVLKE 492
+ + I + ++ + + A+ E A+K +E+A++ E+ +EE + KE
Sbjct: 4 LEKLIKKILREAEEEAEE--ILEEAREE--AEKIKEEAKREAEEAIEEILRKAEKE 55
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 30.1 bits (67), Expect = 4.6
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 8/48 (16%)
Query: 445 IAKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNL----EEAKKI 488
I A+ K A ++ K +AKK EED +K + L EEAKK
Sbjct: 1661 IKAAEEAK----KAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKA 1704
Score = 29.7 bits (66), Expect = 6.2
Identities = 15/37 (40%), Positives = 21/37 (56%)
Query: 451 KKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKK 487
KK ++ A + + +A+ EE AE EK EEAKK
Sbjct: 1342 KKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKK 1378
Score = 29.7 bits (66), Expect = 7.1
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 447 KAQLKKVSKLAARDNAK-SESKAKKEEEDAEKREKNLEEAKK 487
A+ K AA D A+ +E KA+ E+ E+ +K + AKK
Sbjct: 1344 AAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKK 1385
Score = 29.3 bits (65), Expect = 9.3
Identities = 16/40 (40%), Positives = 21/40 (52%)
Query: 449 QLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKI 488
+LKK +L + K +AKK EED + EEAKK
Sbjct: 1550 ELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKA 1589
>gnl|CDD|177625 PHA03389, polh, polyhedrin; Provisional.
Length = 246
Score = 29.7 bits (67), Expect = 4.6
Identities = 15/39 (38%), Positives = 21/39 (53%)
Query: 466 SKAKKEEEDAEKREKNLEEAKKIVLKEDPSLPPAVRIKI 504
+K KK + EK EK L+ K ++ EDP L P K+
Sbjct: 32 AKRKKHLLEHEKEEKELDPLDKYLVAEDPFLGPGKNQKL 70
>gnl|CDD|190741 pfam03763, Remorin_C, Remorin, C-terminal region. Remorins are
plant-specific plasma membrane-associated proteins. In
tobacco remorin co-purifies with lipid rafts. Most
remorins have a variable, proline-rich C-half and a more
conserved N-half that is predicted to form coiled coils.
Consistent with this, circular dichroism studies have
demonstrated that much of the protein is alpha-helical.
Remorins exist in plasma membrane preparations as
oligomeric structures and form filaments in vitro. The
proteins can bind polyanions including the extracellular
matrix component oligogalacturonic acid (OGA). In vitro,
remorin in plasma membrane preparations is
phosphorylated (principally on threonine residues) in
the presence of OGA and thus co-purifies with a protein
kinases(s). The biological functions of remorins are
unknown but roles as components of the
membrane/cytoskeleton are possible.
Length = 112
Score = 28.5 bits (64), Expect = 4.7
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 445 IAKAQLKKVSKLAARDN---AKSESKAKKEEEDAE-KREKNLEEAKK 487
K Q ++ +K+ A +N AK+E++ KK E E K+ + E+ K
Sbjct: 22 NNKYQ-REEAKIQAWENKKKAKAEAELKKIERKLEKKKAEAAEKLKN 67
>gnl|CDD|227560 COG5235, RFA2, Single-stranded DNA-binding replication protein A
(RPA), medium (30 kD) subunit [DNA replication,
recombination, and repair].
Length = 258
Score = 29.6 bits (66), Expect = 4.7
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 1/31 (3%)
Query: 515 VTIFGWVHRLRRQGKGLMFVTLRDGSGFIQC 545
V G V ++ MF + DG+G I+
Sbjct: 69 VQFVGVVRNIKTSTTNSMF-VIEDGTGSIEV 98
>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed.
Length = 158
Score = 29.0 bits (65), Expect = 5.3
Identities = 9/42 (21%), Positives = 21/42 (50%), Gaps = 3/42 (7%)
Query: 451 KKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKIVLKE 492
+K K + ++E K + + +K +K + A+K+ K+
Sbjct: 96 EKEQKEVS---KETEEKEAIKAKKEKKEKKEKKVAEKLAKKK 134
>gnl|CDD|239786 cd04253, AAK_UMPK-PyrH-Pf, AAK_UMPK-PyrH-Pf: UMP kinase (UMPK)-Pf,
the mostly archaeal uridine monophosphate kinase
(uridylate kinase) enzymes that catalyze UMP
phosphorylation and play a key role in pyrimidine
nucleotide biosynthesis; regulation of this process is
via feed-back control and via gene repression of
carbamoyl phosphate synthetase (the first enzyme of the
pyrimidine biosynthesis pathway). The UMP kinase of
Pyrococcus furiosus (Pf) is known to function as a
homohexamer, with GTP and UTP being allosteric
effectors. Like other related enzymes (carbamate kinase,
aspartokinase, and N-acetylglutamate kinase) the E. coli
and most bacterial UMPKs have a conserved, N-terminal,
lysine residue proposed to function in the catalysis of
the phosphoryl group transfer, whereas most archaeal
UMPKs (this CD) appear to lack this residue and the
Pyrococcus furiosus structure has an additional Mg ion
bound to the ATP molecule which is proposed to function
as the catalysis instead. Members of this CD belong to
the Amino Acid Kinase Superfamily (AAK).
Length = 221
Score = 29.1 bits (66), Expect = 5.4
Identities = 11/41 (26%), Positives = 22/41 (53%)
Query: 271 VMATHGDLVRQMNPNFEPPARPFLRMNYADAIEYLRKHEIR 311
+ AT+ D V +P +P A+ F R++ + I+ + K +
Sbjct: 134 INATNVDGVYSKDPRKDPDAKKFDRLSADELIDIVGKSSWK 174
>gnl|CDD|240134 cd04864, LigD_Pol_like_1, LigD_Pol_like_1: Polymerase (Pol) domain
of mostly bacterial LigD proteins similar to Pseudomonas
aeruginosa (Pae) LigD, subgroup 1. The LigD Pol domain
belongs to the archaeal/eukaryal primase (AEP)
superfamily. In prokaryotes, LigD along with Ku is
required for non-homologous end joining (NHEJ)-mediated
repair of DNA double-strand breaks (DSB). NHEJ-mediated
DNA DSB repair is error-prone. It has been suggested
that LigD Pol contributes to NHEJ-mediated DNA DSB
repair in vivo, by filling in short 5'-overhangs with
ribonucleotides; the filled in termini would then be
sealed by the associated LigD ligase domain, resulting
in short stretches of RNA incorporated into the genomic
DNA. The Pol domains of PaeLigD and Mycobacterium
tuberculosis (Mt)LigD are stimulated by manganese, are
error-prone, and prefer adding rNTPs to dNTPs in vitro;
however PaeLigD and MtLigD belong to other subgroups,
proteins in this subgroup await functional
characterization.
Length = 228
Score = 29.4 bits (66), Expect = 5.5
Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 338 RPIMLCRFPADI--KSFYMSKCPEN-PALTESVDV 369
RPI L RFP I FY + PE+ P E V+V
Sbjct: 22 RPITLERFPDGIGKPGFYQKEAPEHFPDWIERVEV 56
>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein. TolA couples the inner
membrane complex of itself with TolQ and TolR to the
outer membrane complex of TolB and OprL (also called
Pal). Most of the length of the protein consists of
low-complexity sequence that may differ in both length
and composition from one species to another,
complicating efforts to discriminate TolA (the most
divergent gene in the tol-pal system) from paralogs such
as TonB. Selection of members of the seed alignment and
criteria for setting scoring cutoffs are based largely
conserved operon struction. //The Tol-Pal complex is
required for maintaining outer membrane integrity. Also
involved in transport (uptake) of colicins and
filamentous DNA, and implicated in pathogenesis.
Transport is energized by the proton motive force. TolA
is an inner membrane protein that interacts with
periplasmic TolB and with outer membrane porins ompC,
phoE and lamB [Transport and binding proteins, Other,
Cellular processes, Pathogenesis].
Length = 346
Score = 29.4 bits (66), Expect = 5.5
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 6/53 (11%)
Query: 446 AKAQLKKVSKLAARDNAKSESKAKKEE------EDAEKREKNLEEAKKIVLKE 492
AKA+ + K ++E +AK + + AE ++K EAK +
Sbjct: 134 AKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAKAEAK 186
Score = 28.6 bits (64), Expect = 9.4
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 6/47 (12%)
Query: 447 KAQLKKVS-KLAARDNAKSESKAKKEEED-----AEKREKNLEEAKK 487
+A+ K++ + AA AK +A K+ E+ E + K EAK
Sbjct: 88 QARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKA 134
>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein. This family
consists of several Borrelia P83/P100 antigen proteins.
Length = 489
Score = 29.6 bits (66), Expect = 5.9
Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 8/69 (11%)
Query: 447 KAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKIVLKEDPSLPPAVRIKIKD 506
QLK+ D K++ KA +++A+K+ + + +E +LP
Sbjct: 215 AQQLKEELDKKQIDADKAQQKADFAQDNADKQRDEVRQK----QQEAKNLPKPADTS--- 267
Query: 507 GEKYRDKRV 515
DK+V
Sbjct: 268 -SPKEDKQV 275
>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit
RPA34.5. This is a family of proteins conserved from
yeasts to human. Subunit A34.5 of RNA polymerase I is a
non-essential subunit which is thought to help Pol I
overcome topological constraints imposed on ribosomal
DNA during the process of transcription.
Length = 193
Score = 28.9 bits (65), Expect = 6.0
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 445 IAKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKIVLKE 492
+ K + + K E K KK+E EK+EK ++ K + K
Sbjct: 136 EKETTAKVEKEAEVEEEEKKE-KKKKKEVKKEKKEKKDKKEKMVEPKG 182
>gnl|CDD|235322 PRK04950, PRK04950, ProP expression regulator; Provisional.
Length = 213
Score = 29.1 bits (66), Expect = 6.0
Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 9/42 (21%)
Query: 446 AKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKK 487
A+ QL++ AK++ +A++ E+ A+KRE E+ K
Sbjct: 99 ARKQLEE---------AKAKVQAQRAEQQAKKREAAGEKEKA 131
>gnl|CDD|185429 PTZ00074, PTZ00074, 60S ribosomal protein L34; Provisional.
Length = 135
Score = 28.5 bits (64), Expect = 6.1
Identities = 28/98 (28%), Positives = 41/98 (41%), Gaps = 21/98 (21%)
Query: 391 LAGYKREGIDPAPYYWYTDQRKYGSTPHGGYGLGLERVLCWLLNQYHVRDKY-------- 442
LAG K + P Y + + + S +GG VLC VRD+
Sbjct: 51 LAGIKA--LRPTEYKQLSRRERTVSRAYGG-------VLC----HKCVRDRIVRAFLVEE 97
Query: 443 QLIAKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREK 480
Q I K LK+ +K + K + K KK + A K++K
Sbjct: 98 QKIVKQVLKEKAKQKKQKKKKKKKKKKKTSKKAAKKKK 135
>gnl|CDD|223660 COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication,
recombination, and repair].
Length = 1139
Score = 29.9 bits (68), Expect = 6.1
Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 500 VRIKIKDGEKYRDKRVTIFGWV----HRLRRQGKGLMFVTLRDGSGFIQCVL 547
I++ D + + V G V + +G + F+TL D +G ++ V+
Sbjct: 965 TPIRLLDLVEDGRRVVLAGGIVAVRQRPTKAKGNKMAFLTLEDETGILEVVV 1016
>gnl|CDD|218899 pfam06102, DUF947, Domain of unknown function (DUF947). Family of
eukaryotic proteins with unknown function.
Length = 168
Score = 28.4 bits (64), Expect = 7.9
Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 12/57 (21%)
Query: 447 KAQLKKV-SKLAARDNAKSESKAKKEEEDAEKREKNLE----------EAKKIVLKE 492
K L+ + S+L N E + KE + EK E E E KK+VLK+
Sbjct: 85 KRTLQSMKSRLKTLKNKDREREILKEHKKQEK-ELIKEGKKPYYLKKSEIKKLVLKK 140
>gnl|CDD|153282 cd07598, BAR_FAM92, The Bin/Amphiphysin/Rvs (BAR) domain of Family
with sequence similarity 92 (FAM92). BAR domains are
dimerization, lipid binding and curvature sensing
modules found in many different proteins with diverse
functions including organelle biogenesis, membrane
trafficking or remodeling, and cell division and
migration. This group is composed of proteins from the
family with sequence similarity 92 (FAM92), which were
originally identified by the presence of the unknown
domain DUF1208. This domain shows similarity to the BAR
domains of sorting nexins. Mammals contain at least two
member types, FAM92A and FAM92B, which may exist in many
variants. The Xenopus homolog of FAM92A1, xVAP019, is
essential for embryo survival and cell differentiation.
FAM92A1 may be involved in regulating cell proliferation
and apoptosis. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 211
Score = 28.4 bits (64), Expect = 8.8
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 438 VRDKYQLIAKAQLKKVSKLAARDN---AKSESKAKKEEEDAEKREKNLEE 484
R+K +L QL+K+ + D +++ES+ +K DA + K LEE
Sbjct: 112 ARNK-ELKQLKQLEKLRQKNPSDRQIISQAESELQKASVDANRSTKELEE 160
>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis). This nucleolar
family of proteins are involved in 60S ribosomal
biogenesis. They are specifically involved in the
processing beyond the 27S stage of 25S rRNA maturation.
This family contains sequences that bear similarity to
the glioma tumour suppressor candidate region gene 2
protein (p60). This protein has been found to interact
with herpes simplex type 1 regulatory proteins.
Length = 387
Score = 28.9 bits (65), Expect = 8.9
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 443 QLIAKAQLKKVSKLAARDNAKSESK--AKKEEEDAEKREKNLEEAKKIVLK 491
+ + QLKK KLA K +K A+KE+ A K+E+ E +K LK
Sbjct: 295 EAKEEKQLKK--KLAQLARLKEIAKEVAQKEKARARKKEQRKERGEKKKLK 343
>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207). This
family is found in eukaryotes; it has several conserved
tryptophan residues. The function is not known.
Length = 261
Score = 28.5 bits (64), Expect = 9.2
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 438 VRDKYQLIAKAQLKKVSKLAARDNAKSESKAKKEE--EDAEKREKNLEEAKKIVLKED 493
R K Q AK + K K AA + S S + K E E+ +K L+E + LK+
Sbjct: 138 CRQKAQQAAKQRTPKHKKEAAESASSSLSGSAKPERNVSQEEAKKRLQEWELKKLKQQ 195
>gnl|CDD|176962 CHL00019, atpF, ATP synthase CF0 B subunit.
Length = 184
Score = 28.3 bits (64), Expect = 9.2
Identities = 11/46 (23%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 446 AKAQLKKVSKLAARDNAKSESKAKKEEED----AEKREKNLEEAKK 487
A+A+L++ A S+ ++E+E+ A++ + LE K
Sbjct: 81 ARARLRQAELEADEIRVNGYSEIEREKENLINQAKEDLERLENYKN 126
>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 28.8 bits (65), Expect = 9.3
Identities = 9/36 (25%), Positives = 17/36 (47%)
Query: 445 IAKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREK 480
K + KK + A E + K EE++ +K+ +
Sbjct: 286 EKKEEKKKEEREAKLAKLSPEEQRKLEEKERKKQAR 321
>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional.
Length = 413
Score = 28.9 bits (65), Expect = 9.9
Identities = 14/51 (27%), Positives = 28/51 (54%)
Query: 445 IAKAQLKKVSKLAARDNAKSESKAKKEEEDAEKREKNLEEAKKIVLKEDPS 495
++K L S+ + S K KKE+++ E ++K+ ++ KK K++P
Sbjct: 34 LSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKKKKEKKEPK 84
>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3. This
protein, which interacts with both microtubules and
TRAF3 (tumour necrosis factor receptor-associated factor
3), is conserved from worms to humans. The N-terminal
region is the microtubule binding domain and is
well-conserved; the C-terminal 100 residues, also
well-conserved, constitute the coiled-coil region which
binds to TRAF3. The central region of the protein is
rich in lysine and glutamic acid and carries KKE motifs
which may also be necessary for tubulin-binding, but
this region is the least well-conserved.
Length = 506
Score = 29.1 bits (65), Expect = 10.0
Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 9/81 (11%)
Query: 443 QLIAKAQLKKVSKLAA-RDNAKSESKAK-------KEEEDAEKREKNLEEAKKIVLKEDP 494
Q +AK K+S A + K SK KE ++ +E+ E+ + K+
Sbjct: 61 QALAKCAESKLSSDEAVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKK 120
Query: 495 SLPPAVRIKI-KDGEKYRDKR 514
P K K E+ ++KR
Sbjct: 121 KEKPKEEPKDRKPKEEAKEKR 141
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.138 0.416
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 34,708,505
Number of extensions: 3518501
Number of successful extensions: 4791
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4579
Number of HSP's successfully gapped: 209
Length of query: 658
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 555
Effective length of database: 6,369,140
Effective search space: 3534872700
Effective search space used: 3534872700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 62 (27.8 bits)