RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780751|ref|YP_003065164.1| ribonuclease E [Candidatus
Liberibacter asiaticus str. psy62]
(723 letters)
>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing,
hydrolase, endonuclease; 2.85A {Escherichia coli} PDB:
2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A
Length = 517
Score = 325 bits (835), Expect = 1e-89
Identities = 172/411 (41%), Positives = 255/411 (62%), Gaps = 3/411 (0%)
Query: 159 DVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGET 218
+ I++V++ Q ++VQI KEERGNKGAA+TT++SLAG Y VLMPN +
Sbjct: 86 PANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRA-G 144
Query: 219 ISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVREL 278
+ DR LKE LE+P GMG+I+RTAG ++ ++ D + ++ W+ +++
Sbjct: 145 GISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKA 204
Query: 279 ALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFM-KLLMPSYARIVR 337
A + AP L+++E N+I RA RD +DI EI++ K A+ + L P ++ ++
Sbjct: 205 AESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIK 264
Query: 338 QYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIED 397
Y P+F IE Q++S Q EV LPS G ++I+ TEAL +ID+NS R+TR IE+
Sbjct: 265 LYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARATRGGDIEE 324
Query: 398 TALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVG 457
TA TNLEAA+EIARQLRLRDL GLIV+DFIDM ++ R+VE +L+E++++DRAR+Q+
Sbjct: 325 TAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQIS 384
Query: 458 AISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAH 517
IS FGLLEMSRQR+ S+ ES+ VC C G G +R S++LSILR +EE L+
Sbjct: 385 HISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQ 444
Query: 518 NIIVHTHSDVVLYLLNQKRATIVEYEARF-GVSINVVIGIELADKLFYIEK 567
+ + YLLN+KR+ + E R GV +V ++ +++ +
Sbjct: 445 EVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPHYHVLR 495
Score = 131 bits (330), Expect = 6e-31
Identities = 48/111 (43%), Positives = 66/111 (59%), Gaps = 7/111 (6%)
Query: 3 NKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYG 62
+MLI+A+ EE RV ++ R+ +LD ES +Q K NIY K+TR+EPSL+AAFVDYG
Sbjct: 9 KRMLINATQQEELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDYG 68
Query: 63 GNRHGFLPFLEIHPDYYQIPFSDR-----QALLKESN--IAQTDSEAVADD 106
RHGFLP EI +Y+ +S + +L+E I Q D E +
Sbjct: 69 AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNK 119
>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 = 51.5 bits (123), Expect = 7e-07
Identities = 78/519 (15%), Positives = 151/519 (29%), Gaps = 175/519 (33%)
Query: 19 VLRD-------NRVEELDFESEHKKQIKGNIYLAK-----VTRVEPSLQAAFVD-----Y 61
L++ E + E + + K + VEPS F
Sbjct: 32 QLQEQFNKILPEPTEGFAADDEPTTPAE---LVGKFLGYVSSLVEPSKVGQFDQVLNLCL 88
Query: 62 GGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDHSL- 120
+ +L +IH ++ + L+K + + A + ++ +L
Sbjct: 89 TEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARI--MAKRPFDKKSNSALF 146
Query: 121 -----EEVAPIANFS-Q---ET--EE------------ESIISANNDVVSN-VEDVKGGS 156
+A F Q + EE +I + + +S +
Sbjct: 147 RAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRT----- 201
Query: 157 PEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNK----GAAVT----TYLSLAGRYSV 208
D K F + I E ++N +K ++ + LA Y V
Sbjct: 202 TLDAEKVFTQGLNILEWLENP---------SNTPDKDYLLSIPISCPLIGVIQLA-HYVV 251
Query: 209 LMPNTSK--GETISRKITNPVDRKNLKEIARGLEVPAG--MGVILRTAGASRTKIEIKRD 264
T+K G T P E+ L+ G G++ A A E
Sbjct: 252 ----TAKLLGFT-------P------GELRSYLKGATGHSQGLVTAVAIAETDSWE---S 291
Query: 265 FEYLMR------LWDNVREL---ALNSVAPHLVYE-----EGN----LIKRAIRDLYCKD 306
F +R + VR S+ P ++ + EG L +I +L +
Sbjct: 292 FFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPML---SISNLTQEQ 348
Query: 307 ISEIIVSGEKGYREAKDFMKLLMPSYARIV-------RQY--EDPHPIFFRS--GIEVQL 355
+ + + L P+ ++ + P P +S G+ + L
Sbjct: 349 VQDYV----------NKTNSHL-PAGKQVEISLVNGAKNLVVSGP-P---QSLYGLNLTL 393
Query: 356 ------DSLHQTEVTLPSRGYVIINQTEALVSIDV--NSGRSTREHCIEDTA--LQTNLE 405
L Q+ + R N+ + + +S H + + + +L
Sbjct: 394 RKAKAPSGLDQSRIPFSERKLKFSNR---FLPVASPFHS------HLLVPASDLINKDL- 443
Query: 406 AAEEI---ARQLR-----------LRDLAGLIVVDFIDM 430
+ A+ ++ LR L+G I +D
Sbjct: 444 VKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDC 482
Score = 43.4 bits (102), Expect = 2e-04
Identities = 53/215 (24%), Positives = 82/215 (38%), Gaps = 60/215 (27%)
Query: 10 SHVEET------RVVVLRDNRVE-ELDFESEHKKQIKGNIYLAKV--TRVEPSLQAAFVD 60
+H ++T +V+ +N V + F E K+I+ N Y A + T V+ L+ +
Sbjct: 1651 NHFKDTYGFSILDIVI--NNPVNLTIHFGGEKGKRIREN-YSAMIFETIVDGKLKTEKI- 1706
Query: 61 YGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQ-----TDSEAVADDVTHGDVTIP 115
F EI+ F + LL + Q + A D + G IP
Sbjct: 1707 ----------FKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKG--LIP 1754
Query: 116 ND-----HSLEEVAPIANFSQETEEESIISANNDV---------VSNVEDVKGGS----- 156
D HSL E A +A+ + ES++ +V V+ D G S
Sbjct: 1755 ADATFAGHSLGEYAALASLADVMSIESLV----EVVFYRGMTMQVAVPRDELGRSNYGMI 1810
Query: 157 ---PEDVPKKFKR---QYCIQEVIKNRQILLVQIV 185
P V F + QY ++ V K R LV+IV
Sbjct: 1811 AINPGRVAASFSQEALQYVVERVGK-RTGWLVEIV 1844
Score = 39.5 bits (92), Expect = 0.002
Identities = 47/274 (17%), Positives = 89/274 (32%), Gaps = 101/274 (36%)
Query: 21 RDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSL---QAAFVD-------YGGNRHGFLP 70
+ E++ ++ + N +L +VE SL V YG N
Sbjct: 342 SNLTQEQVQ---DYVNKT--NSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLT---- 392
Query: 71 FL-EI----HPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHG--DVTIPNDHS--LE 121
L + D +IPFS+R+ ++ V P HS L
Sbjct: 393 -LRKAKAPSGLDQSRIPFSERKL-----------------KFSNRFLPVASPF-HSHLLV 433
Query: 122 EVAPIANFSQETEEESI-ISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQIL 180
+ + +++ + ++ +A D+ V D G D ++ + + I
Sbjct: 434 PASDLI--NKDLVKNNVSFNA-KDIQIPVYDTFDG--SD----------LRVLSGS--IS 476
Query: 181 --LVQIVKEERGNKGAAVT---TYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEI 235
+V + T++ G P + G + +T+ +N K+
Sbjct: 477 ERIVDCIIRLPVKWETTTQFKATHILDFG------PGGASG--LGV-LTH----RN-KD- 521
Query: 236 ARGLEVPAGMG--VILRTAGASRTKIEIKRDFEY 267
G G VI+ AG ++I D +Y
Sbjct: 522 --------GTGVRVIV--AGT----LDINPDDDY 541
Score = 38.8 bits (90), Expect = 0.005
Identities = 65/331 (19%), Positives = 124/331 (37%), Gaps = 108/331 (32%)
Query: 244 GMGVIL-RTAGAS-----RTKIEIKRDFEYLMRLWDNVRELALNS---VAPHLVYEEGNL 294
GMG+ L +T+ A+ R K + + ++ ++ +N+ + H E+G
Sbjct: 1630 GMGMDLYKTSKAAQDVWNRADNHFKDTYGF------SILDIVINNPVNLTIHFGGEKG-- 1681
Query: 295 IKRAIRDLYCKDISEIIVSG----EKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRS- 349
KR IR+ Y I E IV G EK ++E + SY FRS
Sbjct: 1682 -KR-IRENYSAMIFETIVDGKLKTEKIFKEINEHST----SYT-------------FRSE 1722
Query: 350 -GIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVN-SGRSTREHCIEDTALQTNLEAA 407
G+ + Q +TL + +++ L+ D +G S E+ A
Sbjct: 1723 KGL-LSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYA-----------AL 1770
Query: 408 EEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEM 467
+A + + L ++ + M+ ++ +D ++G SN+G++ +
Sbjct: 1771 ASLADVMSIESLVEVVFYRGMTMQ-------------VAVPRD----ELGR-SNYGMIAI 1812
Query: 468 SRQRIRSS--------VLESTTK-------VCTYCKGAGYIRSQSSVALSILRSVEEYLL 512
+ R+ +S V+E K + Y + +Q VA LR+++
Sbjct: 1813 NPGRVAASFSQEALQYVVERVGKRTGWLVEIVNY-----NVENQQYVAAGDLRALD---- 1863
Query: 513 QYTAHNIIVHTHSDVVLYLLNQKRATIVEYE 543
T N VL + ++ I+E +
Sbjct: 1864 --TVTN---------VLNFIKLQKIDIIELQ 1883
Score = 38.0 bits (88), Expect = 0.007
Identities = 32/234 (13%), Positives = 70/234 (29%), Gaps = 89/234 (38%)
Query: 506 SVEEYLLQYTAHNIIVH--------THSDVVLYLLNQKRATIVEYEARF--GVSINVVI- 554
+ E + ++ + + V+ L E+E + G I+ +
Sbjct: 56 TPAELVGKFLGY--VSSLVEPSKVGQFDQVLNLCLT-------EFENCYLEGNDIHALAA 106
Query: 555 ------GIELADKLFYIEKGSPVQALVNTGHKVGSDSQAPSYDKNIECVWQDEALLPIPK 608
L I+ + + A + D ++ S AL
Sbjct: 107 KLLQENDTTLVKTKELIK--NYITARIMAKRP--FDKKSNS------------ALF---- 146
Query: 609 SESLEDIQDNIVS------------EESTGVIRKRRRRRRRRRPATDHHD--AGVVSD-V 653
++ + +V+ EE +R D + +V D +
Sbjct: 147 -RAVGEGNAQLVAIFGGQGNTDDYFEE----LR-------------DLYQTYHVLVGDLI 188
Query: 654 SSIQNVI-------DDSFDMYMEPSDITNHNLLENGAHGFTENYDVSIPPVSTP 700
+ D+ ++ + +I LEN ++ ++Y +SI P+S P
Sbjct: 189 KFSAETLSELIRTTLDAEKVFTQGLNI--LEWLENPSNTPDKDYLLSI-PISCP 239
>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 = 31.5 bits (70), Expect = 0.63
Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 22/50 (44%)
Query: 566 EKGSPVQAL--VNTGHKVGSDSQAPSYDKNIECVWQDEALLPIPKSESLE 613
EK QAL + K+ +D AP+ L I K+ ++E
Sbjct: 18 EK----QALKKLQASLKLYADDSAPA--------------LAI-KA-TME 47
Score = 31.5 bits (70), Expect = 0.75
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 7/24 (29%)
Query: 432 EKKNNRSVEKKLKESLK---KDRA 452
EK+ ++ KKL+ SLK D A
Sbjct: 18 EKQ---AL-KKLQASLKLYADDSA 37
Score = 30.0 bits (66), Expect = 2.2
Identities = 12/65 (18%), Positives = 22/65 (33%), Gaps = 36/65 (55%)
Query: 444 KESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQSSVALSI 503
K++LKK L+++ K+ Y S+ AL+I
Sbjct: 19 KQALKK---------------------------LQASLKL--YA-------DDSAPALAI 42
Query: 504 LRSVE 508
++E
Sbjct: 43 KATME 47
Score = 29.6 bits (65), Expect = 2.9
Identities = 9/31 (29%), Positives = 13/31 (41%), Gaps = 10/31 (32%)
Query: 85 DRQALLKESNIAQTDSEAVADDVTHGDVTIP 115
++QAL K Q + ADD + P
Sbjct: 18 EKQALKK----LQASLKLYADD------SAP 38
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA
degradation, kinase, transferase; 2.60A {Escherichia
coli} PDB: 1sro_A
Length = 723
Score = 30.6 bits (69), Expect = 1.3
Identities = 24/90 (26%), Positives = 34/90 (37%), Gaps = 28/90 (31%)
Query: 23 NRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIP 82
R+EE+ E E G +Y KVTR+ VD+G F+ I
Sbjct: 616 RRIEEITAEIE-----VGRVYTGKVTRI--------VDFGA-------FVAIGG------ 649
Query: 83 FSDRQALLKESNIAQTDSEAVADDVTHGDV 112
++ L+ S IA E V D + G
Sbjct: 650 --GKEGLVHISQIADKRVEKVTDYLQMGQE 677
>1iru_N 20S proteasome; cell cycle, immune response, proteolysis,
ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
Length = 219
Score = 28.9 bits (64), Expect = 4.4
Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 6/62 (9%)
Query: 285 PHLVYEEG-NLIKRAIRDLYCKDIS-----EIIVSGEKGYREAKDFMKLLMPSYARIVRQ 338
P L E +L++R +R LY +D + EKG A ++
Sbjct: 158 PVLSQTEARDLVERCMRVLYYRDARSYNRFQTATVTEKGVEIEGPLSTETNWDIAHMISG 217
Query: 339 YE 340
+E
Sbjct: 218 FE 219
>2epj_A Glutamate-1-semialdehyde 2,1-aminomutase; PLP enzyme, GSA,
structural genomics, NPPSFA; HET: PMP; 1.70A {Aeropyrum
pernix K1} PDB: 2zsl_A* 2zsm_A*
Length = 434
Score = 28.8 bits (63), Expect = 5.0
Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 6/45 (13%)
Query: 309 EIIVSGEKG---YREAKDFMKLLMPSYARIVRQYEDPHPIFFRSG 350
+++ SGEK + K+ + S VR P+P + + G
Sbjct: 4 DVLASGEKSRMLFERTKELFPGGVNSP---VRAAVKPYPFYVKRG 45
>2pe4_A Hyaluronidase-1; hyaluronan, EGF-like domain, alternative splicing,
hydrolase; HET: NAG BMA MAN; 2.00A {Homo sapiens}
Length = 424
Score = 28.2 bits (63), Expect = 6.9
Identities = 8/29 (27%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 400 LQTNLE-AAEEIARQLRLRDLAGLIVVDF 427
L +L ++I + D +GL V+D+
Sbjct: 83 LIAHLARTFQDILAAIPAPDFSGLAVIDW 111
>1knv_A BSE634I restriction endonuclease; APO-enzyme, hydrolase; 2.17A
{Geobacillus stearothermophilus} SCOP: c.52.1.7
Length = 293
Score = 28.0 bits (62), Expect = 7.2
Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 262 KRDFEYLMRLWDNV---RELALNSVAPHLVYEEGNLIKRAIRDLY 303
K +F+Y + V + AL + A H + + +RA+ D++
Sbjct: 231 KAEFKYYGASSEPVSKADDDALQTAATHTIVNVNSTPERAVDDIF 275
>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide
transferase, ATP-GTP diphosphotransferase RNA
processing, RNA degradation; 2.5A {Streptomyces
antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4
d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A
Length = 757
Score = 27.8 bits (62), Expect = 7.6
Identities = 9/35 (25%), Positives = 12/35 (34%), Gaps = 2/35 (5%)
Query: 40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI 74
G L V + AFV + G L +I
Sbjct: 668 GERILGSVVKTTTF--GAFVSLLPGKDGLLHISQI 700
>1d6t_A Ribonuclease P, RNAse P protein; endonuclease, subunit; NMR
{Staphylococcus aureus} SCOP: d.14.1.2
Length = 117
Score = 27.8 bits (62), Expect = 9.3
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 7/63 (11%)
Query: 216 GETISRKITNPVDRKNLKEIARGLEVPAGMG-------VILRTAGASRTKIEIKRDFEYL 268
G ++S+K+ N V R +K R VI R T ++I+ E++
Sbjct: 46 GISVSKKLGNAVLRNKIKRAIRENFKVHKSHILAKDIIVIARQPAKDMTTLQIQNSLEHV 105
Query: 269 MRL 271
+++
Sbjct: 106 LKI 108
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
0.316 0.132 0.369
Gapped
Lambda K H
0.267 0.0664 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 6,130,040
Number of extensions: 295659
Number of successful extensions: 1256
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1235
Number of HSP's successfully gapped: 32
Length of query: 723
Length of database: 5,693,230
Length adjustment: 99
Effective length of query: 624
Effective length of database: 3,293,074
Effective search space: 2054878176
Effective search space used: 2054878176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 60 (27.0 bits)