RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780610|ref|YP_003065023.1| RNA-pseudouridylate synthase
protein, ribosomal large subunit D [Candidatus Liberibacter asiaticus
str. psy62]
(340 letters)
>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding,
lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB:
2ist_A 1qyu_A 1prz_A
Length = 325
Score = 192 bits (489), Expect = 7e-50
Identities = 120/328 (36%), Positives = 172/328 (52%), Gaps = 21/328 (6%)
Query: 11 IKISLLSDSTAEG-RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGD 69
++++ G R+D+ LA + +SRS +K IL+ + +NG V P KV+ G+
Sbjct: 4 VQLTATVSENQLGQRLDQALAEMFPD-YSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGE 62
Query: 70 SFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHC 129
I ++ ++IPLDI+YED+DII+INKP LVVHP GN GT++N
Sbjct: 63 QVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLN----AL 118
Query: 130 HNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMV 189
+ I V R GIVHRLDKDTTG+MVVAK A +L E Y V
Sbjct: 119 LHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRRE-----ITREYEAV 173
Query: 190 WGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLK 249
+ G ++ P+ R + R AV A+THY+ +E + + + L+
Sbjct: 174 AIGHMTAGGTVDEPISRHPTKRTHMAV----HPMGKPAVTHYRIMEHFRVH-----TRLR 224
Query: 250 CHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSL 309
LETGRTHQIRVHMAH +PL+GDP+YG + + S + RQALHA L
Sbjct: 225 LRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGA-SEAFISTLRKFDRQALHATML 283
Query: 310 SFSHPRNNQDMDFQVPIPEDMLTVIRKL 337
HP + +M++ PIP+DM+ +I +
Sbjct: 284 RLYHPISGIEMEWHAPIPQDMVELIEVM 311
>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine
syntase, RNA binding, lyase; 2.00A {Escherichia coli}
SCOP: d.265.1.3 PDB: 1xpi_A
Length = 228
Score = 162 bits (410), Expect = 1e-40
Identities = 75/246 (30%), Positives = 114/246 (46%), Gaps = 25/246 (10%)
Query: 92 ILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKD 151
I+YEDD I+V+NKP+G VH G G + + +VHRLD+D
Sbjct: 4 IMYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEA--------RFLELVHRLDRD 55
Query: 152 TTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNR 211
T+GV++VAK A + L EQ + G ++ Y A+V G + APL +
Sbjct: 56 TSGVLLVAKKRSALRSLHEQLREKGM----QKDYLALVRGQWQSHVKSVQAPLLKNILQS 111
Query: 212 LRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPL 271
R V+ + + T ++ E Y +L++C TGRTHQIRVH + G+P+
Sbjct: 112 GERIVR--VSQEGKPSETRFKVEERYAFA-----TLVRCSPVTGRTHQIRVHTQYAGHPI 164
Query: 272 IGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPEDML 331
D YG + A L R LHA +L F+HP + M + P+ E +
Sbjct: 165 AFDDRYGDREFDR------QLTEAGTGLNRLFLHAAALKFTHPGTGEVMRIEAPMDEGLK 218
Query: 332 TVIRKL 337
++K+
Sbjct: 219 RCLQKM 224
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA
complex; HET: FOU; 2.05A {Escherichia coli}
Length = 217
Score = 136 bits (342), Expect = 7e-33
Identities = 70/242 (28%), Positives = 101/242 (41%), Gaps = 33/242 (13%)
Query: 86 ENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIV 145
+ L ILY+DD I+V+NKP+GL+ P V + + + V
Sbjct: 8 QEPWLVILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYP---------QAESV 58
Query: 146 HRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLG 205
HRLD T+GV+VVA A ++L QF + + Y A VWG P P G+++ PL
Sbjct: 59 HRLDMATSGVIVVALTKAAERELKRQFREREPKKQ----YVARVWGHPSPAEGLVDLPLI 114
Query: 206 RCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMA 265
NR ++ V K A + + + TGR+HQ+RVHM
Sbjct: 115 CDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTA-------RVVLKPITGRSHQLRVHML 167
Query: 266 HKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVP 325
G+P++GD Y A R LHA L+ +HP M F+ P
Sbjct: 168 ALGHPILGDRFYAS-------------PEARAMAPRLLLHAEMLTITHPAYGNSMTFKAP 214
Query: 326 IP 327
Sbjct: 215 AD 216
>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase;
2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB:
1ksl_A 1ksv_A*
Length = 234
Score = 90.6 bits (224), Expect = 5e-19
Identities = 39/249 (15%), Positives = 87/249 (34%), Gaps = 52/249 (20%)
Query: 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNI 83
R+D+++A L SR+ I ++++G + +N K++P +
Sbjct: 5 RLDKFIAQQL--GVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHD------------V 50
Query: 84 AQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPG 143
A + PL ++NKP G V + +
Sbjct: 51 AYDGNPL-AQQHGPRYFMLNKPQGYVCSTDDPDH----------PTVLYFLDEPVAWKLH 99
Query: 144 IVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAP 203
RLD DTTG++++ + +++ ++ Y + P
Sbjct: 100 AAGRLDIDTTGLVLMTDDGQWSHRITSPRHHC------EKTYLVTLES-----------P 142
Query: 204 LGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVH 263
+ + + + V+ ++K +T +E+ + ++ + GR HQ++
Sbjct: 143 VADDTAEQFAKGVQLHNEKD----LTKPAVLEVITP------TQVRLTISEGRYHQVKRM 192
Query: 264 MAHKGNPLI 272
A GN ++
Sbjct: 193 FAAVGNHVV 201
>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding,
unknown function; NMR {Helicobacter pylori}
Length = 92
Score = 73.0 bits (179), Expect = 1e-13
Identities = 17/86 (19%), Positives = 36/86 (41%), Gaps = 3/86 (3%)
Query: 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVP-AAQKLN 82
RID++L + R + G + +NG +K +++V GD+ + ++
Sbjct: 2 RIDKFLQSVGLV-KRRVLATDMCNVGAVWLNGSCAKA-SKEVKAGDTISLHYLKGIEEYT 59
Query: 83 IAQENIPLDILYEDDDIIVINKPAGL 108
I Q ++ +D + + K L
Sbjct: 60 ILQIPALKNVPRKDTHLYIAPKTKEL 85
>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA
complex, S4 domain, alpha/beta protein, isomerase,
RNA-binding, rRNA processing; HET: FHU; 3.00A
{Escherichia coli}
Length = 290
Score = 64.4 bits (156), Expect = 4e-11
Identities = 38/249 (15%), Positives = 74/249 (29%), Gaps = 55/249 (22%)
Query: 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNI 83
R++++++ S SR I G + +NG + +V PGD + V
Sbjct: 8 RLNKYISESG--ICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDV--VKV-------- 54
Query: 84 AQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPG 143
N L E +D+++I + + + + + H KR
Sbjct: 55 ---NGQLIEPREAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHS----------KRVF 101
Query: 144 IVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAP 203
+ RLDKD+ G++ + + K+ ++ P
Sbjct: 102 PIGRLDKDSQGLIFLTNHGDLVNKI-----------------LRAGNDHEKEYLVTVDKP 144
Query: 204 LGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVH 263
+ + V + T + + + L G QIR
Sbjct: 145 ITEEFIRGMSAGVPILGTVTKKCKVKKEAP------------FVFRITLVQGLNRQIRRM 192
Query: 264 MAHKGNPLI 272
H G +
Sbjct: 193 CEHFGYEVK 201
>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta
sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia
coli}
Length = 189
Score = 63.7 bits (154), Expect = 5e-11
Identities = 40/178 (22%), Positives = 63/178 (35%), Gaps = 22/178 (12%)
Query: 95 EDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTG 154
+ +I+ NKP ++ TL + V+ RLD+D+ G
Sbjct: 9 QPTRVILFNKPYDVLPQFTDEAGRKTLKEFI------------PVQGVYAAGRLDRDSEG 56
Query: 155 VMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRR 214
++V+ N +L++ GK YY V GIP D+
Sbjct: 57 LLVLTNNGALQARLTQPGKRTGKI------YYVQVEGIPTQDALEALRNGVTLNDGPTLP 110
Query: 215 AVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLI 272
A + D+ A + E + + S LK L GR Q+R AH G P +
Sbjct: 111 AGAELVDEPAWLWPRNPPIRERKSIPT----SWLKITLYEGRNRQVRRMTAHVGFPTL 164
>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta
sheet, isomerase; 1.60A {Escherichia coli}
Length = 217
Score = 57.1 bits (137), Expect = 5e-09
Identities = 36/179 (20%), Positives = 62/179 (34%), Gaps = 22/179 (12%)
Query: 94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTT 153
+ +I+ NKP ++ TL + V+ RLD+D+
Sbjct: 36 NQPTRVILFNKPYDVLPQFTDEAGRKTLKEFI------------PVQGVYAAGRLDRDSE 83
Query: 154 GVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLR 213
G++V+ N +L++ + YY V GIP D+
Sbjct: 84 GLLVLTNNGALQARLTQPGKRT------GKIYYVQVEGIPTQDALEALRNGVTLNDGPTL 137
Query: 214 RAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLI 272
A + D+ A + E + +++ K L GR Q+R AH G P +
Sbjct: 138 PAGAELVDEPAWLWPRNPPIRERKSIPTSWL----KITLYEGRNRQVRRMTAHVGFPTL 192
>1vio_A Ribosomal small subunit pseudouridine synthase A; structural
genomics, lyase; 1.59A {Haemophilus influenzae} SCOP:
d.265.1.3 d.66.1.5
Length = 243
Score = 56.9 bits (136), Expect = 6e-09
Identities = 35/250 (14%), Positives = 75/250 (30%), Gaps = 52/250 (20%)
Query: 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNI 83
R+D+++A ++ +RS I + ING + K+ + ++ D
Sbjct: 4 RLDKFIAENV--GLTRSQATKAIRQSAVKINGEIVKSGSVQISQED-------------- 47
Query: 84 AQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPG 143
+I +ED+ + I + +++ G Y +
Sbjct: 48 -------EIYFEDELLTWIEEGQYFMLNKPQGCVCSNDDGD--YPTIYQFFDYPLAGKLH 98
Query: 144 IVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAP 203
RLD DTTG++++ + + + + P
Sbjct: 99 SAGRLDVDTTGLVLLTDDGQWSHR-----------------ITSPKHHCEKTYLVTLADP 141
Query: 204 LGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVH 263
+ S + +K + + + GR HQ++
Sbjct: 142 VEENYSAACAEGILLRGEKEPTKPAKLEILDD----------YNVNLTISEGRYHQVKRM 191
Query: 264 MAHKGNPLIG 273
A GN ++G
Sbjct: 192 FAALGNKVVG 201
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 54.2 bits (130), Expect = 5e-08
Identities = 44/254 (17%), Positives = 77/254 (30%), Gaps = 106/254 (41%)
Query: 2 QQTLDNCSSIKISLLSDSTA--EGR------------------IDRWLATSLKEQFSRSY 41
+ +S+ S+L DS EG +++ + L
Sbjct: 311 YEAY-PNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNK-TNSHLPAG---KQ 365
Query: 42 VKI-LILNG---FI------SINGMVS-----KNPN-----------RKVVPGDSFL-IT 74
V+I L+ NG + S+ G+ K P+ RK+ + FL +
Sbjct: 366 VEISLV-NGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVA 424
Query: 75 VP--------AAQKL--NIAQENIPLD-----I-LY-----ED-----DDIIVINKPAGL 108
P A+ + ++ + N+ + I +Y D I +
Sbjct: 425 SPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSIS----ER-I 479
Query: 109 V---VHPAPGNWTGTLVNALLYHC-H------NNLSSINGVKRPGIVHRLDKDTTGVMVV 158
V + P W + H S + GV + HR KD TGV V+
Sbjct: 480 VDCIIR-LPVKWE----TTTQFKATHILDFGPGGASGL-GV----LTHRN-KDGTGVRVI 528
Query: 159 AKNDLAHQKLSEQF 172
L + +
Sbjct: 529 VAGTL-DINPDDDY 541
Score = 44.5 bits (105), Expect = 3e-05
Identities = 55/340 (16%), Positives = 91/340 (26%), Gaps = 137/340 (40%)
Query: 30 ATSLKEQFSRSYVKILILN-GFI--SINGMVSKNPNRKVVPGDSFLITVPAAQKLN---I 83
A S R L L+ G + + +VP SF A +L
Sbjct: 3 AYST-----RP----LTLSHGSLEHVL-----------LVPTASF----FIASQLQEQFN 38
Query: 84 AQENIPLDILYEDDDIIVINKPAGLV----------VHPAPGNWTGTLVNALL------Y 127
P + DD+ PA LV V P+ ++N L Y
Sbjct: 39 KILPEPTEGFAADDEPT---TPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCY 95
Query: 128 HCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYA 187
N++ ++ +L ++ +V K L + Y
Sbjct: 96 LEGNDIHAL--------AAKLLQENDTTLVKTK-------------------ELIKNYIT 128
Query: 188 MVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAI-------THY--QTIEIYN 238
+ P + ++ L RAV + AI Y + ++Y
Sbjct: 129 AR--------IMAKRPFDKKSNSALFRAVG--EGNAQLVAIFGGQGNTDDYFEELRDLYQ 178
Query: 239 KNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDP-----LYGKGFKTKANIVN--NN 291
L+K A + LI ++ +G NI+ N
Sbjct: 179 TYHVLVGDLIKF-------------SAETLSELIRTTLDAEKVFTQGL----NILEWLEN 221
Query: 292 AK---------SA--------ILSLARQALHAHSLSFSHP 314
S ++ LA + A L F P
Sbjct: 222 PSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGF-TP 260
Score = 41.9 bits (98), Expect = 2e-04
Identities = 61/399 (15%), Positives = 106/399 (26%), Gaps = 176/399 (44%)
Query: 14 SLLSD--STAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSF 71
L+ D + + L + + + L + ++ +NP+ P +
Sbjct: 182 VLVGDLIKFSAETLSE-LI-RTTLDAEKVFTQGLNILEWL-------ENPSN--TPDKDY 230
Query: 72 LITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLV--VHPAPGNWTGTLVNALLYHC 129
L+++P + PL I G++ H + T
Sbjct: 231 LLSIPIS---------CPL-I--------------GVIQLAH-----YVVT--------A 253
Query: 130 HN-NLSSINGVKRPGIVHRLDKDTTG-----V--MVVAKNDLAHQKLS-EQFVDHGKST- 179
+ PG + K TG V + +A+ D S E F +
Sbjct: 254 KLLGFT-------PGELRSYLKGATGHSQGLVTAVAIAETD------SWESFFVSVRKAI 300
Query: 180 --------RLKRAY------YAMV-------WGIPLPDSGIINAPLGRCKSNRLRRAVKG 218
R AY +++ G+P P I N + V+
Sbjct: 301 TVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLT---------QEQVQD 351
Query: 219 IDDKT-----ADSAITHYQTIEIYNKNSNFAV-----SL--LKCHLE-----TGRTHQIR 261
+KT A + I + N N V SL L L +G Q R
Sbjct: 352 YVNKTNSHLPAGKQV----EISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSG-LDQSR 406
Query: 262 VHMAHKGNPLIGDPLYGKGF-KTKANIVNN--------------NAKSAILSLARQALHA 306
+ P F + K N A I + L
Sbjct: 407 I-------P----------FSERKLKFSNRFLPVASPFHSHLLVPASDLIN----KDLVK 445
Query: 307 HSLSFS---------HPRNNQDM-DFQVPI-PE--DMLT 332
+++SF+ + D+ I D +
Sbjct: 446 NNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCII 484
>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat
shock proteins, protein-RNA interactions, ribosome,
structural genomics; 2.00A {Escherichia coli} SCOP:
d.66.1.3 PDB: 3bbu_A
Length = 133
Score = 48.5 bits (115), Expect = 2e-06
Identities = 21/137 (15%), Positives = 41/137 (29%), Gaps = 19/137 (13%)
Query: 16 LSDSTAEG-RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLIT 74
+ + A R+D+WL + + +R+ + +I G + NG SK ++ V + +
Sbjct: 1 MKEKPAVEVRLDKWLW-AARFYKTRALAREMIEGGKVHYNGQRSKP-SKIVELNATLTLR 58
Query: 75 VPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLS 134
+ I +PA +
Sbjct: 59 QG------------NDERTVIVKAITEQRRPASEAALLYEETAE----SVEKREKMALAR 102
Query: 135 SINGVKRPGIVHRLDKD 151
+N + P R DK
Sbjct: 103 KLNALTMPHPDRRPDKK 119
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome,
RNA modifying enzyme, isomerase; 2.60A {Escherichia
coli}
Length = 237
Score = 47.4 bits (112), Expect = 5e-06
Identities = 27/174 (15%), Positives = 47/174 (27%), Gaps = 41/174 (23%)
Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158
+I +NKP G+V G + +N KR + RLDKD+ G++ +
Sbjct: 16 LIALNKPVGIVSTTEDGERDNIV------------DFVNHSKRVFPIGRLDKDSQGLIFL 63
Query: 159 AKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKG 218
+ K+ ++ P+ + V
Sbjct: 64 TNHGDLVNKI-----------------LRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPI 106
Query: 219 IDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLI 272
+ T + + L G QIR H G +
Sbjct: 107 LGTVTKKCKVKKEAPFV------------FRITLVQGLNRQIRRMCEHFGYEVK 148
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 34.2 bits (77), Expect = 0.044
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 12/34 (35%)
Query: 77 AAQKLNIAQENIPLDILYEDDDIIVINKPAGLVV 110
A +KL Q ++ L Y DD + PA L +
Sbjct: 21 ALKKL---QASLKL---YADD-----SAPA-LAI 42
>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification,
structural genomics, PSI, protein structure initiative;
1.90A {Mycobacterium tuberculosis H37RV} SCOP: b.122.1.1
d.265.1.2
Length = 316
Score = 32.8 bits (74), Expect = 0.13
Identities = 20/80 (25%), Positives = 27/80 (33%), Gaps = 18/80 (22%)
Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158
I+VI+KPAG+ H I +R G LD TGV+V+
Sbjct: 8 IVVIDKPAGMTSH----------------DVVGRCRRIFATRRVGHAGTLDPMATGVLVI 51
Query: 159 AKNDLAHQKLSEQFVDHGKS 178
K+ KS
Sbjct: 52 GIERAT--KILGLLTAAPKS 69
>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop,
lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli}
SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A
Length = 327
Score = 32.0 bits (72), Expect = 0.21
Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 18/80 (22%)
Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158
+++++KP G+ + + I R G LD TG++ +
Sbjct: 27 VLLLDKPQGMSSN----------------DALQKVKRIYNANRAGHTGALDPLATGMLPI 70
Query: 159 AKNDLAHQKLSEQFVDHGKS 178
+ K S+ +D K
Sbjct: 71 CLGEAT--KFSQYLLDSDKR 88
>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation,
lyase/RNA complex; HET: FHU; 2.10A {Thermotoga maritima}
SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A
Length = 309
Score = 32.0 bits (72), Expect = 0.21
Identities = 15/79 (18%), Positives = 26/79 (32%), Gaps = 18/79 (22%)
Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158
I+V KP G H + + ++ G LD GV+++
Sbjct: 5 ILVAYKPKGPTSH----------------DVVDEVRKKLKTRKVGHGGTLDPFACGVLII 48
Query: 159 AKNDLAHQKLSEQFVDHGK 177
N ++ E + D K
Sbjct: 49 GVNQGT--RILEFYKDLKK 65
>3ofo_D 30S ribosomal protein S4; protein biosynthesis, ribosomes, RNA,
tRNA, transfer, eryThr ketolide, macrolide, antibiotic,
EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 1p6g_D
1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D* 2qan_D* 2qb9_D*
2qbb_D* 2qbd_D 2qbf_D 2qbh_D* 2qbj_D* 2qou_D* 2qow_D*
2qoy_D* 2qp0_D* 2vho_D 2vhp_D 2wwl_D* ...
Length = 205
Score = 31.7 bits (72), Expect = 0.22
Identities = 18/91 (19%), Positives = 35/91 (38%), Gaps = 3/91 (3%)
Query: 38 SRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDD 97
+R+ + L+ + I +NG V + +V P D I A+K + + + L E
Sbjct: 109 TRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIR-EKAKKQSRVKAALELAEQREKP 167
Query: 98 DIIVIN--KPAGLVVHPAPGNWTGTLVNALL 126
+ ++ K G + +N L
Sbjct: 168 TWLEVDAGKMEGTFKRKPERSDLSADINEHL 198
>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein,
E.coli, montreal-kingston bacterial structural genomics
initiative, BSGI; NMR {Escherichia coli K12} SCOP:
d.66.1.6
Length = 79
Score = 31.6 bits (72), Expect = 0.24
Identities = 10/32 (31%), Positives = 15/32 (46%)
Query: 38 SRSYVKILILNGFISINGMVSKNPNRKVVPGD 69
S + KI I G + ++G V K+V G
Sbjct: 35 SGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQ 66
>2aus_C Pseudouridine synthase; isomerase, structural protein,
isomerase/structural protein complex; 2.10A {Pyrococcus
abyssi} PDB: 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A
3hjw_A* 3hjy_A
Length = 334
Score = 30.1 bits (67), Expect = 0.78
Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 18/82 (21%)
Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158
+I ++KP G H + I +++ G LD +GV+ V
Sbjct: 48 VINLDKPPGPTSH----------------EVVAWIKRILNLEKAGHGGTLDPKVSGVLPV 91
Query: 159 AKNDLAHQKLSEQFVDHGKSTR 180
A ++ + + GK
Sbjct: 92 ALER--ATRVVQALLPAGKEYV 111
>1agj_A Epidermolytic toxin A; hydrolase, serine protease; 1.70A
{Staphylococcus aureus} SCOP: b.47.1.1 PDB: 1dua_A
1exf_A 1due_A
Length = 242
Score = 29.2 bits (64), Expect = 1.5
Identities = 15/68 (22%), Positives = 27/68 (39%)
Query: 272 IGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPEDML 331
I +G + V N+ S I + + + HS SH +++ V I +
Sbjct: 175 IELTTLSRGLRYYGFTVPGNSGSGIFNSNGELVGIHSSKVSHLDREHQINYGVGIGNYVK 234
Query: 332 TVIRKLNE 339
+I + NE
Sbjct: 235 RIINEKNE 242
>3ftb_A Histidinol-phosphate aminotransferase; structural genomics, PSI,
MCSG, protein structure initiative; 2.00A {Clostridium
acetobutylicum}
Length = 361
Score = 28.9 bits (64), Expect = 1.8
Identities = 20/101 (19%), Positives = 34/101 (33%), Gaps = 6/101 (5%)
Query: 30 ATSLKEQFSRSY----VKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQ 85
L + + I++ NG I + + ++ S+ A+K ++
Sbjct: 63 YRRLNKSIENYLKLKDIGIVLGNGASEIIELSISLFEKILIIVPSYAEYEINAKKHGVSV 122
Query: 86 ENIPLDILYEDD--DIIVINKPAGLVVHPAPGNWTGTLVNA 124
LD D DII V+ P N G L+N
Sbjct: 123 VFSYLDENMCIDYEDIISKIDDVDSVIIGNPNNPNGGLINK 163
>3o0m_A HIT family protein; ssgcid, NIH, niaid, SBRI, UW, emerald
biostructures, hydrola structural genomics; HET: AMP;
1.90A {Mycobacterium smegmatis str}
Length = 149
Score = 28.5 bits (63), Expect = 2.3
Identities = 6/21 (28%), Positives = 11/21 (52%)
Query: 82 NIAQENIPLDILYEDDDIIVI 102
I + P +YED++ + I
Sbjct: 11 AIVSGDAPAIRIYEDENFLGI 31
>2f68_X Collagen adhesin; beta barrel, domain SWAP, cell adhesion; 1.95A
{Staphylococcus aureus} PDB: 2f6a_A 1amx_A
Length = 313
Score = 27.8 bits (61), Expect = 3.6
Identities = 6/52 (11%), Positives = 17/52 (32%)
Query: 59 KNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVV 110
+ N K+ GD + P + + I + + + + + +
Sbjct: 40 DDKNGKIQNGDMIKVAWPTSGTVKIEGYSKTVPLTVKGEQVGQAVITPDGAT 91
>3lb5_A HIT-like protein involved in cell-cycle regulation; niaid, seattle
structural genomics center for infectious disease,
ssgcid; 1.90A {Bartonella henselae}
Length = 161
Score = 27.7 bits (61), Expect = 3.7
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 82 NIAQENIPLDILYEDDDIIVI 102
+ + IP +YEDDD+I
Sbjct: 34 KLIRNEIPSVRVYEDDDVIAF 54
>3ksv_A Uncharacterized protein; HIT family, structural genomics,
structural genomics of pathogenic protozoa consortium,
SGPP; 1.90A {Leishmania major}
Length = 149
Score = 27.8 bits (61), Expect = 3.7
Identities = 4/21 (19%), Positives = 8/21 (38%)
Query: 82 NIAQENIPLDILYEDDDIIVI 102
I + +IP + E +
Sbjct: 17 KIIKGDIPCAKVAETSKALAF 37
>1lc5_A COBD, L-threonine-O-3-phosphate decarboxylase; PLP-dependent
decarboxylase, cobalamin, lyase; 1.46A {Salmonella
enterica} SCOP: c.67.1.1 PDB: 1lc7_A* 1lc8_A* 1lkc_A*
Length = 364
Score = 27.5 bits (60), Expect = 4.4
Identities = 19/113 (16%), Positives = 30/113 (26%), Gaps = 10/113 (8%)
Query: 30 ATSLKEQFSRSY----VKILILNGFISINGMVSKN--PNRKVVPGDSFLITVPAAQKLNI 83
L + +R + IL NG V+ P R ++ F A +
Sbjct: 61 YFHLHQALARHHQVPASWILAGNGETESIFTVASGLKPRRAMIVTPGFAEYGRALAQSGC 120
Query: 84 AQENIPLD----ILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNN 132
L D + + + P N TG L L +
Sbjct: 121 EIRRWSLREADGWQLTDAILEALTPDLDCLFLCTPNNPTGLLPERPLLQAIAD 173
>3oj7_A Putative histidine triad family protein; hydrolase, structural
genomics, seattle structural genomics for infectious
disease, ssgcid; 1.40A {Entamoeba histolytica} PDB:
3omf_A*
Length = 117
Score = 27.3 bits (60), Expect = 4.7
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 82 NIAQENIPLDILYEDDDIIVI 102
IAQ+ IP I+YEDD+I
Sbjct: 13 KIAQKQIPSTIVYEDDEIFAF 33
>1y23_A HIT, histidine triad protein; HIT protein, PKCI-1, cell-cycle
regulation, NYSGXRC, structural genomics, protein
structure initiative; 2.30A {Bacillus subtilis} SCOP:
d.13.1.1
Length = 145
Score = 27.5 bits (60), Expect = 4.9
Identities = 16/97 (16%), Positives = 31/97 (31%), Gaps = 10/97 (10%)
Query: 82 NIAQENIPLDILYEDDDIIV---INKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSING 138
I +IP +YED+ ++ I++ P N + +
Sbjct: 11 KIIAGDIPSAKVYEDEHVLAFLDISQVTKGHTLVIPKTHI---ENVYEFTDELAKQYFHA 67
Query: 139 VKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDH 175
V + R + + G+ + N + Q V H
Sbjct: 68 VPKIARAIRDEFEPIGLNTLNNNGEK----AGQSVFH 100
>3imi_A HIT family protein; structural genomics, infectious diseases,
center for structural genomics of infectious diseases,
unknown function; 2.01A {Bacillus anthracis str}
Length = 147
Score = 27.5 bits (60), Expect = 4.9
Identities = 10/58 (17%), Positives = 18/58 (31%), Gaps = 6/58 (10%)
Query: 82 NIAQENIPLDILYEDDDIIVI------NKPAGLVVHPAPGNWTGTLVNALLYHCHNNL 133
I I +YED+ ++ K LV+ L + H + +
Sbjct: 15 KIIDGQILCSKVYEDEHVLAFLDISQVTKGHTLVIPKVHKQDIFALTPEIASHIFSVV 72
>1xqu_A HIT family hydrolase; protein structure initiative, PSI, southeast
collaboratory for structural genomics, secsg; 2.30A
{Clostridium thermocellum} SCOP: d.13.1.1
Length = 147
Score = 27.4 bits (60), Expect = 5.0
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 82 NIAQENIPLDILYEDDDIIVI 102
I + +P I YED+ +I I
Sbjct: 41 KIIKRELPSTIYYEDERVIAI 61
>1h76_A Serotransferrin; iron transport, glycoprotein, metal-binding; HET:
NAG; 2.15A {Sus scrofa} SCOP: c.94.1.2 c.94.1.2 PDB:
1jnf_A 2hav_A* 2hau_A* 1suv_E
Length = 696
Score = 27.3 bits (60), Expect = 5.2
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 4/48 (8%)
Query: 214 RAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLK----CHLETGRT 257
+ V D+ THY + + K SNF + L+ CH GR+
Sbjct: 77 KPVVAEFYGQKDNPQTHYYAVAVVKKGSNFQWNQLQGKRSCHTGLGRS 124
>2bp1_A Aflatoxin B1 aldehyde reductase member 2; oxidoreductase, aldo-keto
reductase family 7, SSA reductase, TIM barrel; HET: FLC
NDP; 2.4A {Homo sapiens}
Length = 360
Score = 27.3 bits (59), Expect = 5.4
Identities = 8/58 (13%), Positives = 20/58 (34%), Gaps = 2/58 (3%)
Query: 62 NRKVVPGDSFLITVPAAQKLNIAQENIP-LDILYEDDDII-VINKPAGLVVHPAPGNW 117
+ + G + L ++N+ + + ++ N+ LV H P +
Sbjct: 302 HHSQLQGAHGDAVILGMSSLEQLEQNLAATEEGPLEPAVVDAFNQAWHLVAHECPNYF 359
>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex,
box H/ACA, snoRNP, pseudouridine synthase, RNA
modification; 1.95A {Methanocaldococcus jannaschii}
SCOP: b.122.1.1 d.265.1.2
Length = 357
Score = 27.0 bits (59), Expect = 5.6
Identities = 16/80 (20%), Positives = 25/80 (31%), Gaps = 18/80 (22%)
Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158
++V++KP G H + I + + G LD TGV+ V
Sbjct: 68 VVVVDKPRGPTSH----------------EVSTWVKKILNLDKAGHGGTLDPKVTGVLPV 111
Query: 159 AKNDLAHQKLSEQFVDHGKS 178
A K + K
Sbjct: 112 ALER--ATKTIPMWHIPPKE 129
>2eo4_A 150AA long hypothetical histidine triad nucleotide-binding protein;
HIT family, structural genomics, NPPSFA; 1.80A
{Sulfolobus tokodaii}
Length = 149
Score = 27.2 bits (59), Expect = 6.0
Identities = 5/21 (23%), Positives = 9/21 (42%)
Query: 82 NIAQENIPLDILYEDDDIIVI 102
+I + +YED+ I
Sbjct: 5 SIINRELEGYFVYEDEKFAAI 25
>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET:
TYB; 2.0A {Thermus thermophilus} SCOP: c.26.1.1 d.66.1.4
PDB: 1h3e_A*
Length = 432
Score = 27.1 bits (59), Expect = 6.2
Identities = 8/38 (21%), Positives = 17/38 (44%)
Query: 38 SRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75
S + + LI N + ++G V +P +V ++
Sbjct: 383 SNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRILQR 420
>3o1c_A Histidine triad nucleotide-binding protein 1; hydrolase, HINT
protein, HIT protein, adenosine 5'- monophosphoramidase;
HET: ADN; 1.08A {Oryctolagus cuniculus} PDB: 3llj_A*
1rzy_A* 3o1z_A 3o1x_A* 1kpe_B* 1kpb_A* 1kpf_A* 1kpa_A
1kpc_A 1av5_A* 1kpe_A* 4rhn_A* 3rhn_A* 5rhn_A* 6rhn_A
Length = 126
Score = 26.9 bits (59), Expect = 6.9
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 82 NIAQENIPLDILYEDDDIIVI 102
I ++ IP I++EDD +
Sbjct: 21 KIIRKEIPAKIIFEDDQALAF 41
>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin
helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB:
2nrv_A 2nrw_A 2nrx_A 2nrz_A
Length = 220
Score = 26.6 bits (58), Expect = 7.5
Identities = 22/154 (14%), Positives = 49/154 (31%), Gaps = 13/154 (8%)
Query: 144 IVHRLDKDTTGVMVVAKNDLA----HQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGI 199
I H K T +VV ++ +++ + ++ PLP+
Sbjct: 30 ISHLQGKYTVASLVVFEDGFPKKGDYRRYKIEQDHPDDYESIRTVVKRRYSKHPLPNLLF 89
Query: 200 INAPLGRC----KSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLL-----KC 250
++ +G+ ++ + + ++ EI+ + + + LL +
Sbjct: 90 VDGGIGQVNAAIEALKEIGKDCPVVGLAKKEETVVFENREIHLPHDHPVLRLLVQIRDET 149
Query: 251 HLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTK 284
H H+ R + L P G K K
Sbjct: 150 HRFAVSYHRKRREKESLRSVLDNVPGIGPIRKKK 183
>2gi4_A Possible phosphotyrosine protein phosphatase; low molecular weight,
protein tyrosine phosphatase, bacterial phosphatase; NMR
{Campylobacter jejuni}
Length = 156
Score = 26.8 bits (58), Expect = 7.6
Identities = 14/66 (21%), Positives = 24/66 (36%)
Query: 236 IYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSA 295
I NSNF L + +I + DP Y F I++ K+
Sbjct: 86 ITMDNSNFKNVLKNFTNTQNKVLKITDFSPSLNYDEVPDPWYSGNFDETYKILSLACKNL 145
Query: 296 ILSLAR 301
++ L++
Sbjct: 146 LVFLSK 151
>3n1s_A HIT-like protein HINT; histidine triad nucleotide binding protein,
GMP, hydro; HET: 5GP; 1.45A {Escherichia coli} PDB:
3n1t_A*
Length = 119
Score = 26.8 bits (59), Expect = 7.8
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 82 NIAQENIPLDILYEDDDIIVI 102
I + IP DI+Y+DD +
Sbjct: 9 KIIRREIPSDIVYQDDLVTAF 29
>1cb6_A Protein (lactoferrin); iron transport, apolactoferrin,
conformational change; 2.00A {Homo sapiens} SCOP:
c.94.1.2 c.94.1.2 PDB: 1bka_A 1b0l_A 1lfi_A* 1fck_A
1lcf_A* 2bjj_X* 1lfh_A 1n76_A 1lfg_A* 1sqy_A* 1b1x_A
1b7u_A 1b7z_A 1i6b_A 1qjm_A 3cr9_A* 1f9b_A* 1dtz_A
1i6q_A 1jw1_A ...
Length = 691
Score = 26.6 bits (58), Expect = 9.3
Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 6/53 (11%)
Query: 229 THYQTIEIYNKNSNFAVSLLK----CHLETGRTH--QIRVHMAHKGNPLIGDP 275
THY + + K +F ++ L+ CH RT + + G P
Sbjct: 90 THYYAVAVVKKGGSFQLNELQGLKSCHTGLRRTAGWNVPIGTLRPFLNWTGPP 142
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.318 0.134 0.395
Gapped
Lambda K H
0.267 0.0499 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,889,258
Number of extensions: 129811
Number of successful extensions: 450
Number of sequences better than 10.0: 1
Number of HSP's gapped: 424
Number of HSP's successfully gapped: 55
Length of query: 340
Length of database: 5,693,230
Length adjustment: 93
Effective length of query: 247
Effective length of database: 3,438,538
Effective search space: 849318886
Effective search space used: 849318886
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: 57 (26.3 bits)