RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 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)
>1v9k_A Ribosomal large subunit pseudouridine synthase C;
pseudouridine syntase, RNA binding, lyase; 2.00A
{Escherichia coli} (A:)
Length = 228
Score = 179 bits (453), Expect = 7e-46
Identities = 73/251 (29%), Positives = 104/251 (41%), Gaps = 25/251 (9%)
Query: 90 LDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLD 149
I YEDD I+V+NKP+G VH G G + +VHRLD
Sbjct: 2 DVIXYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEAR--------FLELVHRLD 53
Query: 150 KDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKS 209
+DT+GV++VAK A + L EQ + G Y A+V G + APL +
Sbjct: 54 RDTSGVLLVAKKRSALRSLHEQLREKGXQKD----YLALVRGQWQSHVKSVQAPLLKNIL 109
Query: 210 NRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGN 269
R V + + T ++ E Y + +C TGRTHQIRVH + G+
Sbjct: 110 QSGERIV--RVSQEGKPSETRFKVEERYAFATLV-----RCSPVTGRTHQIRVHTQYAGH 162
Query: 270 PLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPED 329
P+ D YG + A L R LHA +L F+HP + + P E
Sbjct: 163 PIAFDDRYGDREFDRQL------TEAGTGLNRLFLHAAALKFTHPGTGEVXRIEAPXDEG 216
Query: 330 MLTVIRKLNEK 340
+ ++K
Sbjct: 217 LKRCLQKXRNA 227
>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA
binding, lyase; 1.70A {Escherichia coli} (A:)
Length = 325
Score = 164 bits (416), Expect = 1e-41
Identities = 114/330 (34%), Positives = 159/330 (48%), Gaps = 21/330 (6%)
Query: 9 SSIKISLLSDSTAEG-RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVP 67
++++ G R+D+ LA + +SRS +K IL+ + +NG V P KV+
Sbjct: 2 QRVQLTATVSENQLGQRLDQALAEMFPD-YSRSRIKEWILDQRVLVNGKVCDKPKEKVLG 60
Query: 68 GDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLY 127
G+ I ++ ++IPLDI+YED+DII+INKP LVVHP GN GT++NALL+
Sbjct: 61 GEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLH 120
Query: 128 HCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYA 187
+ I V R GIVHRLDKDTTG+MVVAK A +L E R Y A
Sbjct: 121 YYPP----IADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREI----TREYEA 172
Query: 188 MVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSL 247
+ G + +
Sbjct: 173 VAIGHMTAGGTVDEPISRHPTKRTHMAVHPM----------GKPAVTHYRIMEHFRVHTR 222
Query: 248 LKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAH 307
L+ LETGRTHQIRVHMAH +PL+GDP+YG + + S + RQALHA
Sbjct: 223 LRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGA-SEAFISTLRKFDRQALHAT 281
Query: 308 SLSFSHPRNNQDMDFQVPIPEDMLTVIRKL 337
L HP + +M++ PIP+DM+ +I +
Sbjct: 282 MLRLYHPISGIEMEWHAPIPQDMVELIEVM 311
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA
complex; HET: FOU; 2.05A {Escherichia coli} (A:)
Length = 217
Score = 158 bits (401), Expect = 8e-40
Identities = 68/242 (28%), Positives = 98/242 (40%), Gaps = 33/242 (13%)
Query: 86 ENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIV 145
+ L ILY+DD I V+NKP+GL+ P V + + + V
Sbjct: 8 QEPWLVILYQDDHIXVVNKPSGLLSVPGRLEEHKDSVXTRIQRDY---------PQAESV 58
Query: 146 HRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLG 205
HRLD T+GV+VVA A ++L QF + K+ Y A VWG P P G+++ PL
Sbjct: 59 HRLDXATSGVIVVALTKAAERELKRQFREREP----KKQYVARVWGHPSPAEGLVDLPLI 114
Query: 206 RCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMA 265
NR ++ V K A + + + TGR+HQ+RVH
Sbjct: 115 CDWPNRPKQKVCYETGKPA--QTEYEVVEYAADNTARV-----VLKPITGRSHQLRVHXL 167
Query: 266 HKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVP 325
G+P++GD Y R LHA L+ +HP F+ P
Sbjct: 168 ALGHPILGDRFYASPEAR-------------AXAPRLLLHAEXLTITHPAYGNSXTFKAP 214
Query: 326 IP 327
Sbjct: 215 AD 216
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF,
ribosome, RNA modifying enzyme, isomerase; 2.60A
{Escherichia coli} (A:)
Length = 237
Score = 145 bits (365), Expect = 9e-36
Identities = 32/263 (12%), Positives = 64/263 (24%), Gaps = 49/263 (18%)
Query: 86 ENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIV 145
+ D +I +NKP G+V G + + H R +
Sbjct: 3 SSHHHHHHGSDLVLIALNKPVGIVSTTEDGERDN--IVDFVNHSK----------RVFPI 50
Query: 146 HRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLG 205
RLDKD+ G++ + + K+ DH ++ Y V + +
Sbjct: 51 GRLDKDSQGLIFLTNHGDLVNKILRAGNDH------EKEYLVTVDKPITEEFIRGXSAGV 104
Query: 206 RCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMA 265
+ F + L G QIR
Sbjct: 105 PILGTV------------------TKKCKVKKEAPFVF-----RITLVQGLNRQIRRXCE 141
Query: 266 HKGNPLIGDPLYGKGFKTKAN--------IVNNNAKSAILSLARQALHAHSLSFSHPRNN 317
H G + + + + ++ + + + + P+
Sbjct: 142 HFGYEVKKLERTRIXNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSEVKPKAKAKPKTA 201
Query: 318 QDMDFQVPIPEDMLTVIRKLNEK 340
V + R +
Sbjct: 202 GIKRPVVKXEKTAEKGGRPASNG 224
>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} (A:64-290)
Length = 227
Score = 138 bits (349), Expect = 7e-34
Identities = 36/251 (14%), Positives = 70/251 (27%), Gaps = 49/251 (19%)
Query: 95 EDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTG 154
ED +I +NKP G+V G +V+ + + KR + RLDKD+ G
Sbjct: 2 EDLVLIALNKPVGIVSTTEDGERD-NIVDFVNHS-----------KRVFPIGRLDKDSQG 49
Query: 155 VMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRR 214
++ + + K+ DH ++ Y V + +
Sbjct: 50 LIFLTNHGDLVNKILRAGNDH------EKEYLVTVDKPITEEFIRGMSAGVPI------- 96
Query: 215 AVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGD 274
T+ K A + + L G QIR H G +
Sbjct: 97 ----------------LGTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKL 140
Query: 275 PLYGKGFKTKAN--------IVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPI 326
+ + + ++ + + + + P+ V +
Sbjct: 141 ERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSEVKPKAKAKPKTAGIKRPVVKM 200
Query: 327 PEDMLTVIRKL 337
+ R
Sbjct: 201 EKTAEKGGRPA 211
>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated
beta sheet, thrombin-cleaved, isomerase; 1.20A
{Escherichia coli} (A:)
Length = 189
Score = 130 bits (328), Expect = 2e-31
Identities = 39/222 (17%), Positives = 60/222 (27%), Gaps = 39/222 (17%)
Query: 87 NIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVH 146
+ + +I+ NKP ++ TL +
Sbjct: 1 STRRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQG------------VYAAG 48
Query: 147 RLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGR 206
RLD+D+ G++V+ N +L++ + YY V GIP D+
Sbjct: 49 RLDRDSEGLLVLTNNGALQARLTQPGKRT------GKIYYVQVEGIPTQDALEALRNGVT 102
Query: 207 CKSNRLRRAVKG-IDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMA 265
A +D+ S K L GR Q+R A
Sbjct: 103 LNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWL-----KITLYEGRNRQVRRMTA 157
Query: 266 HKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAH 307
H G P + Y G SL A
Sbjct: 158 HVGFPTLRLIRYAMGD---------------YSLDNLANGEW 184
>1vio_A Ribosomal small subunit pseudouridine synthase A; structural
genomics, lyase; 1.59A {Haemophilus influenzae}
(A:58-243)
Length = 186
Score = 125 bits (313), Expect = 1e-29
Identities = 32/222 (14%), Positives = 63/222 (28%), Gaps = 40/222 (18%)
Query: 94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTT 153
E+ ++NKP G V G++ T+ Y + RLD DTT
Sbjct: 2 IEEGQYFMLNKPQGCVCSNDDGDY-PTIYQFFDYPLA---------GKLHSAGRLDVDTT 51
Query: 154 GVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLR 213
G++++ + +++ K+ Y + + A + +
Sbjct: 52 GLVLLTDDGQWSHRITSPKHHCEKT------YLVTLADPVEENYSAACAEGILLRGEK-- 103
Query: 214 RAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIG 273
+ N + GR HQ++ A GN ++G
Sbjct: 104 --------------EPTKPAKLEILDDYNV-----NLTISEGRYHQVKRMFAALGNKVVG 144
Query: 274 DPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPR 315
+ G + + L + + SH
Sbjct: 145 LHRWKIGDVVLD---ESLEEGEYRPLTQSEIEKLVEGGSHHH 183
>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA,
lyase; 2.00A {Escherichia coli} (A:59-234)
Length = 176
Score = 116 bits (291), Expect = 4e-27
Identities = 27/223 (12%), Positives = 58/223 (26%), Gaps = 51/223 (22%)
Query: 94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTT 153
+NKP G V T++ L + RLD DTT
Sbjct: 2 QHGPRYFXLNKPQGYVCSTDDP-DHPTVLYFLDEPV---------AWKLHAAGRLDIDTT 51
Query: 154 GVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLR 213
G+++ + +++ ++ Y + D + +
Sbjct: 52 GLVLXTDDGQWSHRITSPRHHC------EKTYLVTLESPVADD-----------TAEQFA 94
Query: 214 RAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIG 273
+ V+ + + + + + ++ + GR HQ++ A GN ++
Sbjct: 95 KGVQ----------LHNEKDLTKPAVLEVITPTQVRLTISEGRYHQVKRXFAAVGNHVVE 144
Query: 274 DPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRN 316
G T A +
Sbjct: 145 LHRERIGGITLDA--------------DLAPGEYRPLTEEEIA 173
>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated
beta sheet, isomerase; 1.60A {Escherichia coli}
(A:1-102,A:201-217)
Length = 119
Score = 91.9 bits (228), Expect = 1e-19
Identities = 17/133 (12%), Positives = 35/133 (26%), Gaps = 33/133 (24%)
Query: 39 RSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDD 98
R ++ S K + + +
Sbjct: 2 RQFIISENTMQKTSFRNHQVKRFSSQRSTR---------------------RKPENQPTR 40
Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158
+I+ NKP ++ TL + RLD+D+ G++V+
Sbjct: 41 VILFNKPYDVLPQFTDEAGRKTLKEFIPVQ------------GVYAAGRLDRDSEGLLVL 88
Query: 159 AKNDLAHQKLSEQ 171
N +L++
Sbjct: 89 TNNGALQARLTQP 101
>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated
beta sheet, isomerase; 1.60A {Escherichia coli}
(A:103-200)
Length = 98
Score = 85.9 bits (212), Expect = 7e-18
Identities = 24/102 (23%), Positives = 31/102 (30%), Gaps = 6/102 (5%)
Query: 180 RLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRA-VKGIDDKTADSAITHYQTIEIYN 238
R + YY V GIP D+ A + +D+
Sbjct: 2 RTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSI 61
Query: 239 KNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKG 280
S LK L GR Q+R AH G P + Y G
Sbjct: 62 PTS-----WLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMG 98
>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} (A:)
Length = 133
Score = 83.2 bits (205), Expect = 4e-17
Identities = 25/153 (16%), Positives = 49/153 (32%), Gaps = 32/153 (20%)
Query: 17 SDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVP 76
E R+D+WL + +R+ + +I G + NG SK P++ V + +
Sbjct: 3 EKPAVEVRLDKWLWAARFY-KTRALAREMIEGGKVHYNGQRSK-PSKIVELNATLTLRQG 60
Query: 77 AAQKLNIA-------QENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHC 129
++ I + +LYE+ V + +
Sbjct: 61 NDERTVIVKAITEQRRPASEAALLYEETAESVEKREKMALARK----------------- 103
Query: 130 HNNLSSINGVKRPGIVHRLDKDTTGVMVVAKND 162
+N + P R DK ++ K+
Sbjct: 104 ------LNALTMPHPDRRPDKKERRDLLRFKHG 130
>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding,
unknown function; NMR {Helicobacter pylori} (A:)
Length = 92
Score = 78.9 bits (194), Expect = 9e-16
Identities = 18/91 (19%), Positives = 37/91 (40%), Gaps = 3/91 (3%)
Query: 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV-PAAQKLN 82
RID++L + R + G + +NG +K +++V GD+ + ++
Sbjct: 2 RIDKFLQSVGLV-KRRVLATDMCNVGAVWLNGSCAK-ASKEVKAGDTISLHYLKGIEEYT 59
Query: 83 IAQENIPLDILYEDDDIIVINKPAGLVVHPA 113
I Q ++ +D + + K L H
Sbjct: 60 ILQIPALKNVPRKDTHLYIAPKTKELEHHHH 90
>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA,
lyase; 2.00A {Escherichia coli} (A:1-58)
Length = 58
Score = 45.3 bits (108), Expect = 1e-05
Identities = 11/55 (20%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 21 AEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75
+ R+D+++A L SR+ I ++++G + +N K++P +
Sbjct: 2 SHXRLDKFIAQQLG--VSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEH--DVAY 52
>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding
protein, E.coli, montreal-kingston bacterial structural
genomics initiative, BSGI; NMR {Escherichia coli K12}
(A:)
Length = 79
Score = 43.6 bits (103), Expect = 4e-05
Identities = 11/58 (18%), Positives = 19/58 (32%), Gaps = 3/58 (5%)
Query: 18 DSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75
+ L S + KI I G + ++G V K+V G ++
Sbjct: 16 GKHPHVELCDLLK-LEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQ--TVSF 70
>1vio_A Ribosomal small subunit pseudouridine synthase A;
structural genomics, lyase; 1.59A {Haemophilus
influenzae} (A:1-57)
Length = 57
Score = 41.9 bits (99), Expect = 1e-04
Identities = 12/54 (22%), Positives = 25/54 (46%), Gaps = 4/54 (7%)
Query: 22 EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75
R+D+++A ++ +RS I + ING + K+ + ++ D I
Sbjct: 2 SLRLDKFIAENV--GLTRSQATKAIRQSAVKINGEIVKSGSVQISQED--EIYF 51
>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} (A:1-63)
Length = 63
Score = 41.2 bits (97), Expect = 2e-04
Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75
R++++++ S SR I G + +NG + +V PGD ++ V
Sbjct: 8 RLNKYISESG--ICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGD--VVKV 54
>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2,
protein structure initiative; HET: MSE; 1.53A
{Streptococcus thermophilus lmg 18311} (A:1-65)
Length = 65
Score = 35.1 bits (81), Expect = 0.013
Identities = 12/61 (19%), Positives = 22/61 (36%), Gaps = 5/61 (8%)
Query: 17 SDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFI--SINGMVSKNPNRKVVPGDSFLIT 74
S++ + R+D +R K + G + ING P K+ G +
Sbjct: 1 SNAXPKERVDVLAY-KQGLFETREQAKRGVXAGLVVNVINGERYDKPGEKIDDGT--ELK 57
Query: 75 V 75
+
Sbjct: 58 L 58
>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA
synthetase; HET: TYB; 2.0A {Thermus thermophilus}
(A:350-432)
Length = 83
Score = 32.7 bits (75), Expect = 0.067
Identities = 10/68 (14%), Positives = 22/68 (32%), Gaps = 1/68 (1%)
Query: 6 DNCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKV 65
+ + I + R S + + LI N + ++G V +P +V
Sbjct: 3 EEIPEVTIPASELKEGRIWVARLFT-LAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQV 61
Query: 66 VPGDSFLI 73
++
Sbjct: 62 DLSRPRIL 69
>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} (D:100-193)
Length = 94
Score = 30.6 bits (69), Expect = 0.33
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQK-LN 82
R+D + L SR + L+ +G I++NG P+ +V PGD I V + L
Sbjct: 1 RLDNVVY-RLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGD--EIAVAEKSRNLE 57
Query: 83 IAQENI 88
+ ++N+
Sbjct: 58 LIRQNL 63
>2uxt_A Protein SUFI, SUFI; periplasmic, cupredoxin-like, FTS mutant
suppressor, oxidoreductase; 1.9A {Escherichia coli} PDB:
2uxv_A (A:313-451)
Length = 139
Score = 28.5 bits (63), Expect = 1.2
Identities = 13/112 (11%), Positives = 25/112 (22%), Gaps = 10/112 (8%)
Query: 45 LILNGFISINGMV--SKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVI 102
+ L ING + + G TV A + E + I + +
Sbjct: 17 ISLGDDPGINGQLWDVNRIDVTAQQGTWERWTVRADEPQAFHIEGVMFQIRNVNGAMPFP 76
Query: 103 NKPAGLVVHPAPGN--------WTGTLVNALLYHCHNNLSSINGVKRPGIVH 146
G ++ + G +V+
Sbjct: 77 EDRGWKDTVWVDGQVELLVYFGQPSWAHFPFYFNSQTLEMADRGSIGQLLVN 128
>3i1m_D 30S ribosomal protein S4; ribosome structure, protein-RNA
complex, ribonucleoprotein, ribosomal protein,
RNA-binding, rRNA-binding, antibiotic resistance; 3.19A
{Escherichia coli k-12} PDB: 1vs7_D* 3e1a_R 3e1c_R
1vs5_D 3i1o_D 3i1q_D 3i1s_D 3i1z_D 3i21_D 2qal_D*
1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D* 2qan_D*
2qb9_D* 2qbb_D* 2qbd_D ... (D:97-190)
Length = 94
Score = 28.2 bits (63), Expect = 1.5
Identities = 11/51 (21%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 38 SRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENI 88
+R+ + L+ + I +NG V + +V P D + A+K + + +
Sbjct: 14 TRAEARQLVSHKAIMVNGRVVNIASYQVSPND-VVSIREKAKKQSRVKAAL 63
>1sdd_A Coagulation factor V; copper-binding protein, cofactor,
blood clotting; HET: NAG NDG; 2.80A {Bos taurus}
(A:181-306)
Length = 126
Score = 27.8 bits (61), Expect = 2.0
Identities = 8/102 (7%), Positives = 24/102 (23%), Gaps = 10/102 (9%)
Query: 50 FISINGMVSKNPNRKVVP-GDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGL 108
++NG V+ V D + ++ I + + +
Sbjct: 23 MYTVNGYVNGTMPDITVCAHDHISWHLI-----GMSSGPELFSIHFNGQVLEQNHHKISA 77
Query: 109 VVHPAPGNWTGTLVN----ALLYHCHNNLSSINGVKRPGIVH 146
+ + + T + G++ +
Sbjct: 78 ITLVSATSTTANMTVSPEGRWTIASLIPRHFQAGMQAYIDIK 119
>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA
modification, structural genomics, PSI, protein
structure initiative; 1.90A {Mycobacterium tuberculosis
H37RV} (A:1-60,A:206-232)
Length = 87
Score = 27.8 bits (62), Expect = 2.0
Identities = 17/66 (25%), Positives = 23/66 (34%), Gaps = 16/66 (24%)
Query: 94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTT 153
I+VI+KPAG+ H I +R G LD T
Sbjct: 3 ATGPGIVVIDKPAGMTSH----------------DVVGRCRRIFATRRVGHAGTLDPMAT 46
Query: 154 GVMVVA 159
GV+V+
Sbjct: 47 GVLVIG 52
>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis,
aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine,
RNA-binding, ATP-binding; 2.9A {Mycobacterium
tuberculosis} (A:345-432)
Length = 88
Score = 27.8 bits (62), Expect = 2.1
Identities = 7/32 (21%), Positives = 12/32 (37%)
Query: 38 SRSYVKILILNGFISINGMVSKNPNRKVVPGD 69
S+ + I G +S+N + N D
Sbjct: 26 SKGAARRTIHEGGVSVNNIRVDNEEWVPQSSD 57
>1cb6_A Protein (lactoferrin); iron transport, apolactoferrin,
conformational change; 2.00A {Homo sapiens}
(A:90-242,A:317-333)
Length = 170
Score = 27.6 bits (61), Expect = 2.4
Identities = 11/42 (26%), Positives = 18/42 (42%), Gaps = 4/42 (9%)
Query: 229 THYQTIEIYNKNSNFAVSLLK----CHLETGRTHQIRVHMAH 266
THY + + K +F ++ L+ CH RT V +
Sbjct: 1 THYYAVAVVKKGGSFQLNELQGLKSCHTGLRRTAGWNVPIGT 42
>2apo_A Probable tRNA pseudouridine synthase B; protein-protein
complex, box H/ACA, snoRNP, pseudouridine synthase, RNA
modification; 1.95A {Methanocaldococcus jannaschii}
(A:51-266)
Length = 216
Score = 27.4 bits (60), Expect = 2.5
Identities = 13/61 (21%), Positives = 21/61 (34%), Gaps = 16/61 (26%)
Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158
++V++KP G H + + + G LD TGV+ V
Sbjct: 18 VVVVDKPRGPTSHEV--------STWVKKIL--------NLDKAGHGGTLDPKVTGVLPV 61
Query: 159 A 159
A
Sbjct: 62 A 62
>1jil_A Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer;
truncation, structure based inhibitor design, ligase;
HET: 485; 2.20A {Staphylococcus aureus} (A:247-420)
Length = 174
Score = 27.3 bits (60), Expect = 2.6
Identities = 10/43 (23%), Positives = 17/43 (39%)
Query: 29 LATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSF 71
+ S+ + + NG I ING ++ N + P D
Sbjct: 112 VLIETGISPSKRQAREDVNNGAIYINGERQQDVNYALAPEDKI 154
>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T
stem-loop, lyase/RNA complex; HET: FHU; 1.85A
{Escherichia coli} (A:1-79,A:225-253)
Length = 108
Score = 27.1 bits (60), Expect = 3.1
Identities = 10/66 (15%), Positives = 23/66 (34%), Gaps = 16/66 (24%)
Query: 94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTT 153
+ + +++++KP G+ + + I R G LD T
Sbjct: 22 MDINGVLLLDKPQGMSSN----------------DALQKVKRIYNANRAGHTGALDPLAT 65
Query: 154 GVMVVA 159
G++ +
Sbjct: 66 GMLPIC 71
>3cvz_A S-layer protein; surface layer protein, protein binding,
structural protein; 2.40A {Clostridium difficile}
(A:94-236)
Length = 143
Score = 27.2 bits (60), Expect = 3.2
Identities = 11/39 (28%), Positives = 14/39 (35%), Gaps = 2/39 (5%)
Query: 36 QFSRSYVKILILNGFISINGMVSK--NPNRKVVPGDSFL 72
+ + K LI GMVSK + K V L
Sbjct: 13 KLNSLNEKTLIDIATKDTFGMVSKTQDSEGKNVAATKAL 51
>2r7e_B Coagulation factor VIII; ceruloplasmin fold, cupper protein
fold, C2 domain fold, acute phase, blood coagulation,
calcium, disease mutation; HET: NAG BMA MAN; 3.70A {Homo
sapiens} PDB: 3cdz_B* (B:305-458)
Length = 154
Score = 26.8 bits (58), Expect = 4.0
Identities = 10/105 (9%), Positives = 26/105 (24%), Gaps = 9/105 (8%)
Query: 48 NGFISINGMVSKNPNRKVVP-GDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPA 106
F +ING + V+ + + + + + +
Sbjct: 50 YRFHAINGYIMDTLPGLVMAQDQRIRWYL---LSMGSNENIHSIHFSGHVFTVRKKEEYK 106
Query: 107 GLVVHPAPGNWTGTLVNA-----LLYHCHNNLSSINGVKRPGIVH 146
+ + PG + + C G+ +V+
Sbjct: 107 MALYNLYPGVFETVEMLPSKAGIWRVECLIGEHLHAGMSTLFLVY 151
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3
homolog; S4 domain, structural genomics, NPPSFA; NMR
{Homo sapiens} (A:)
Length = 71
Score = 26.9 bits (60), Expect = 4.3
Identities = 9/59 (15%), Positives = 17/59 (28%), Gaps = 1/59 (1%)
Query: 22 EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQK 80
R+ L L+ + G + + V +P V +T + K
Sbjct: 7 GRRLPTVLL-KLRMAQHLQAAVAFVEQGHVRVGPDVVTDPAFLVTRSMEDFVTWVDSSK 64
>1r3e_A TRNA pseudouridine synthase B; RNA modification,
pseudouridylation, lyase/RNA complex; HET: FHU; 2.10A
{Thermotoga maritima} (A:1-57,A:190-224)
Length = 92
Score = 26.7 bits (59), Expect = 4.8
Identities = 11/61 (18%), Positives = 19/61 (31%), Gaps = 16/61 (26%)
Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158
I+V KP G H + + ++ G LD GV+++
Sbjct: 5 ILVAYKPKGPTSH----------------DVVDEVRKKLKTRKVGHGGTLDPFACGVLII 48
Query: 159 A 159
Sbjct: 49 G 49
>2cvl_A TTHA0137, protein translation initiation inhibitor;
structural genomics, NPPSFA; 1.65A {Thermus
thermophilus} (A:)
Length = 124
Score = 26.4 bits (58), Expect = 6.2
Identities = 8/29 (27%), Positives = 16/29 (55%)
Query: 41 YVKILILNGFISINGMVSKNPNRKVVPGD 69
Y + + GF+ ++G + P+ +V GD
Sbjct: 16 YAQAVKAGGFVFVSGQIPLAPDGSLVEGD 44
>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea}
(D:82-201)
Length = 120
Score = 26.4 bits (58), Expect = 6.4
Identities = 19/91 (20%), Positives = 37/91 (40%), Gaps = 3/91 (3%)
Query: 38 SRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDD 97
+ + L+ + I +NG + P+ + P D+ + + + + Q ++ L E
Sbjct: 22 TIPGARQLVNHRHILVNGRIVDIPSYRCKPQDTIMAR-DEQKSIALIQNSLDLSPREELP 80
Query: 98 DIIVINKPA--GLVVHPAPGNWTGTLVNALL 126
+ +N GLV W G +N LL
Sbjct: 81 KHLTLNPFPYKGLVNQIIDSKWVGLKINELL 111
>3lb5_A HIT-like protein involved in cell-cycle regulation; niaid,
seattle structural genomics center for infectious
disease, ssgcid; 1.90A {Bartonella henselae} (A:)
Length = 161
Score = 26.2 bits (57), Expect = 6.6
Identities = 12/41 (29%), Positives = 17/41 (41%), Gaps = 7/41 (17%)
Query: 82 NIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLV 122
+ + IP +YEDDD+I + P TLV
Sbjct: 34 KLIRNEIPSVRVYEDDDVIAF-------MDIMPQAPGHTLV 67
>3g5w_A Multicopper oxidase type 1; two domain, laccase, nitrifier,
metal binding protein; 1.90A {Nitrosomonas europaea}
(A:131-290)
Length = 160
Score = 26.0 bits (56), Expect = 7.9
Identities = 16/104 (15%), Positives = 29/104 (27%), Gaps = 7/104 (6%)
Query: 50 FISINGMVSKN-PNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGL 108
+ +IN +V GD + + A A D ++KP
Sbjct: 36 YYTINAKSFPETQPIRVKKGDVIRLRLIGAGDHVHAIHTHGHISQIAFKDGFPLDKPIKG 95
Query: 109 VVHPAPGNWTGTLVN------ALLYHCHNNLSSINGVKRPGIVH 146
++ + H H + + NG K G +
Sbjct: 96 DTVLIGPGERYDVILNMDNPGLWMIHDHVDTHTTNGDKPDGGIM 139
>3i7t_A RV2704, putative uncharacterized protein; siras,
YJGF/YER057C/UK114, homotrimer, quick SOAK NAI
derivative, unknown function; 1.93A {Mycobacterium
tuberculosis} (A:)
Length = 149
Score = 25.7 bits (56), Expect = 8.6
Identities = 3/13 (23%), Positives = 4/13 (30%)
Query: 301 RQALHAHSLSFSH 313
+ A L H
Sbjct: 134 KDPSPAGGLEHHH 146
>2f68_X Collagen adhesin; beta barrel, domain SWAP, cell adhesion;
1.95A {Staphylococcus aureus} PDB: 2f6a_A 1amx_A
(X:1-147,X:299-313)
Length = 162
Score = 25.6 bits (56), Expect = 8.7
Identities = 7/41 (17%), Positives = 14/41 (34%), Gaps = 2/41 (4%)
Query: 61 PNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIV 101
N K+ GD + P + + I + + + V
Sbjct: 42 KNGKIQNGDMIKVAWPTSGTVKIEGYSKTVPL--TVKGEQV 80
>3jq1_A SUSD superfamily protein; structural genomics, joint center
for structural genomics, JCSG, protein structure
initiative, PSI-2; HET: MSE; 1.55A {Bacteroides vulgatus
atcc 8482} (A:1-21,A:67-217,A:462-481)
Length = 192
Score = 25.7 bits (56), Expect = 8.9
Identities = 5/22 (22%), Positives = 9/22 (40%)
Query: 13 ISLLSDSTAEGRIDRWLATSLK 34
SLL + G+ + A +
Sbjct: 120 ASLLPITNKIGKPTQGAAYAAL 141
>1n67_A Clumping factor; DEV-IGG, IGG, immunoglobulin, IGSF,
fibrinongen-binding, cell adhesion; 1.90A
{Staphylococcus aureus} (A:1-169)
Length = 169
Score = 25.6 bits (56), Expect = 9.0
Identities = 11/37 (29%), Positives = 16/37 (43%)
Query: 64 KVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDII 100
V GD+F ITVP LN + + D ++
Sbjct: 67 SAVKGDTFKITVPKELNLNGVTSTAKVPPIMAGDQVL 103
>2wdq_D Succinate dehydrogenase hydrophobic membrane anchor subunit;
succinate dehydrogenase activity, cell inner membrane,
tricarboxylic acid cycle; HET: FAD HEM CBE; 2.40A
{Escherichia coli} PDB: 1nen_D* 2acz_D* 1nek_D* 2wdr_D*
2wdv_D* (D:)
Length = 115
Score = 25.8 bits (57), Expect = 9.2
Identities = 4/31 (12%), Positives = 10/31 (32%)
Query: 106 AGLVVHPAPGNWTGTLVNALLYHCHNNLSSI 136
G +T + ++L H + +
Sbjct: 49 IGFFASAFTKVFTLLALFSILIHAWIGMWQV 79
>2eo4_A 150AA long hypothetical histidine triad nucleotide-binding
protein; HIT family, structural genomics, NPPSFA; 1.80A
{Sulfolobus tokodaii} (A:)
Length = 149
Score = 25.9 bits (56), Expect = 9.2
Identities = 9/41 (21%), Positives = 15/41 (36%), Gaps = 7/41 (17%)
Query: 82 NIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLV 122
+I + +YED+ I + P + TLV
Sbjct: 5 SIINRELEGYFVYEDEKFAAI-------LDKYPVSLGHTLV 38
>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 (C:31-245)
Length = 215
Score = 25.8 bits (56), Expect = 9.2
Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 18/79 (22%)
Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158
+I ++KP G H +V + + +++ G LD +GV+ V
Sbjct: 18 VINLDKPPGPTSH--------EVVAWIKRILN--------LEKAGHGGTLDPKVSGVLPV 61
Query: 159 AKNDLAHQKLSEQFVDHGK 177
A ++ + + GK
Sbjct: 62 ALER--ATRVVQALLPAGK 78
>2hd9_A UPF0310 protein PH1033; structural genomics, NPPSFA,
national project on protein structural and functional
analyses; HET: CIT; 1.35A {Pyrococcus horikoshii OT3}
(A:)
Length = 145
Score = 25.5 bits (56), Expect = 9.2
Identities = 10/49 (20%), Positives = 20/49 (40%), Gaps = 6/49 (12%)
Query: 28 WLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVP 76
W+ + +R +++ + + KN +V PGD +I V
Sbjct: 4 WICIT-----NRENWEVIKRHNVWGVP-KKHKNTLSRVKPGDKLVIYVR 46
Database: mmdb70
Posted date: Jun 20, 2010 3:12 AM
Number of letters in database: 4,956,049
Number of sequences in database: 33,805
Lambda K H
0.318 0.134 0.395
Gapped
Lambda K H
0.267 0.0542 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 2,544,006
Number of extensions: 111789
Number of successful extensions: 387
Number of sequences better than 10.0: 1
Number of HSP's gapped: 353
Number of HSP's successfully gapped: 54
Length of query: 340
Length of database: 4,956,049
Length adjustment: 89
Effective length of query: 251
Effective length of database: 1,947,404
Effective search space: 488798404
Effective search space used: 488798404
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: 55 (25.4 bits)