RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780753|ref|YP_003065166.1| peptide chain release factor 2
[Candidatus Liberibacter asiaticus str. psy62]
(355 letters)
>gnl|CDD|31379 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 373 bits (958), Expect = e-104
Identities = 163/238 (68%), Positives = 187/238 (78%)
Query: 117 AYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPN 176
AYL +HAGAGGTE+QDWA+MLLRMYTRWAE++ FK E L+ DGEEAGIKSATL IKG N
Sbjct: 1 AYLTIHAGAGGTEAQDWASMLLRMYTRWAERKGFKVEVLDTSDGEEAGIKSATLKIKGEN 60
Query: 177 AYGWLKGEQGVHRLVRISPYDSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRAS 236
AYG+LK E GVHRLVRISP+DSN RRHTSF+S+ V+P +D SIEIEI + D RIDTYRAS
Sbjct: 61 AYGYLKTETGVHRLVRISPFDSNGRRHTSFASVEVFPELDISIEIEIPDDDLRIDTYRAS 120
Query: 237 GAGGQHVNTTDSAVRITHIPTGVVVQCQQERSQHKNKAQAWNMLRAKLYELELQKREEIA 296
GAGGQHVN TDSAVR+TH+PTG+VV CQ ERSQH NKA A ML+ KLY L +KR +
Sbjct: 121 GAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALARKMLKGKLYILAQEKRSQEK 180
Query: 297 NIGESSKTEIGWGRQIRSYVLQPYQMVKDLRTNIEKTSPSDVLDGDLDDFMKATLAIK 354
N + K IGWG QIRSYVL PYQ KDLRT +E+ + S VLDGD D F+KA L
Sbjct: 181 NRERALKKLIGWGNQIRSYVLDPYQPTKDLRTGVERRNKSKVLDGDKDGFIKAYLKWD 238
>gnl|CDD|37937 KOG2726, KOG2726, KOG2726, Mitochondrial polypeptide chain release
factor [Translation, ribosomal structure and
biogenesis].
Length = 386
Score = 272 bits (696), Expect = 1e-73
Identities = 121/297 (40%), Positives = 178/297 (59%), Gaps = 3/297 (1%)
Query: 58 FIKEIQDRLCDNLILLELALEEDDCSILQETSDNLQRIKLEVEYKQFESLLSGEADSNDA 117
+K +++ ++ E E+ D +E + + I+ + + L S D+
Sbjct: 79 RMKLVRELKSLKSLIKEGEDEDMDELAEEEAEEISKEIERSLHELELSLLPSDPYDAEAC 138
Query: 118 YLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPNA 177
+EV AGAGG E+Q + L+ MY ++AE+ +K LE GE GIKSATL I+G +A
Sbjct: 139 IIEVRAGAGGQEAQIFTMELVDMYQKYAERLGWKARVLEKAPGESGGIKSATLEIEGESA 198
Query: 178 YGWLKGEQGVHRLVRISPYDSNSRRHTSFSSIWVYPVV-DDSIEIEISESDCRIDTYRAS 236
YG+LK E GVHR+ R+ +++ RRHTS +S+ V P D +++EI E D RI+T+RAS
Sbjct: 199 YGYLKFEAGVHRVQRVPSTETSGRRHTSTASVAVIPQPGRDEVDVEIDEKDLRIETFRAS 258
Query: 237 GAGGQHVNTTDSAVRITHIPTGVVVQCQQERSQHKNKAQAWNMLRAKLYELEL-QKREEI 295
G GGQHVN TDSAVR+THIPTG+VV+CQ+ERSQHKN+A A LRAKL + +K EE
Sbjct: 259 GPGGQHVNKTDSAVRLTHIPTGIVVECQEERSQHKNRALALKRLRAKLAVIYREEKSEEE 318
Query: 296 ANIGESSKTEIGWGRQIRSYVLQPYQMVKDLRTNIEKTSPSDVLDGDLDDFMKATLA 352
++ + +IR+Y + + V D R +E LDG+LD+ ++A L+
Sbjct: 319 KKKRKAQVGSLKRSEKIRTYNFKQDR-VTDHRIGLESHDLESFLDGNLDELIEALLS 374
>gnl|CDD|30565 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 260 bits (665), Expect = 5e-70
Identities = 129/344 (37%), Positives = 194/344 (56%), Gaps = 11/344 (3%)
Query: 17 DNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELA 76
++ ++R L DP + + E + L +E L+ + +E + D E+
Sbjct: 10 ESLLERYEELEALLSDPEVISDPDEYRKLSKEYAELEPIVEKYREYKKAQEDLEDAKEML 69
Query: 77 LEEDDCSILQETSDNLQRIKLEVE--YKQFESLL--SGEADSNDAYLEVHAGAGGTESQD 132
EE D + + + ++ ++ ++E ++ + LL D + LE+ AG GG E+
Sbjct: 70 AEEKDPEMREMAEEEIKELEAKIEELEEELKILLLPKDPNDDKNIILEIRAGTGGDEAAL 129
Query: 133 WANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPNAYGWLKGEQGVHRLVR 192
+A L RMY+R+AE + +K E L + E G K I G Y LK E GVHR+ R
Sbjct: 130 FAGDLFRMYSRYAESKGWKVEILSASESELGGYKEIIASISGKGVYSRLKFESGVHRVQR 189
Query: 193 ISPYDSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRI 252
+ +S R HTS +++ V P V++ EIEI+ D RIDT+R+SGAGGQHVNTTDSAVRI
Sbjct: 190 VPATESQGRIHTSAATVAVLPEVEEVEEIEINPKDLRIDTFRSSGAGGQHVNTTDSAVRI 249
Query: 253 THIPTGVVVQCQQERSQHKNKAQAWNMLRAKLYELELQKREEIANIGESSKTEIGWG--- 309
TH+PTG+VV+CQ ERSQHKNKA+A +LRA+LY+ E QK + K+++G G
Sbjct: 250 THLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQA--EEASERKSQVGSGDRS 307
Query: 310 RQIRSYVLQPYQMVKDLRTNIEKTSPSDVLD-GDLDDFMKATLA 352
+IR+Y P V D R N+ +V++ G LD+ + A +A
Sbjct: 308 ERIRTYNF-PQNRVTDHRINLTLYKLDEVMEGGKLDEIIDALIA 350
>gnl|CDD|144168 pfam00472, RF-1, RF-1 domain. This domain is found in peptide
chain release factors such as RF-1 and RF-2, and a
number of smaller proteins of unknown function. This
domain contains the peptidyl-tRNA hydrolase activity.
The domain contains a highly conserved motif GGQ, where
the glutamine is thought to coordinate the water that
mediates the hydrolysis.
Length = 114
Score = 172 bits (438), Expect = 2e-43
Identities = 61/114 (53%), Positives = 80/114 (70%), Gaps = 2/114 (1%)
Query: 215 VDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRITHIPTGVVVQCQQERSQHKNKA 274
+D+ +EIEI SD RIDT+R+SG GGQ+VN T+SAVR+TH+PTG+VV+CQ+ERSQHKN+
Sbjct: 2 LDEEVEIEIPPSDLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVVKCQEERSQHKNRE 61
Query: 275 QAWNMLRAKLYELELQKREEIANIGESSKTE-IGWGRQIRSYVLQPYQMVKDLR 327
+A L+AKLYE ELQK+ E S+ +IR+Y P VKD R
Sbjct: 62 KALERLKAKLYEAELQKKREETKPTRKSQVRRGDRKEKIRTY-NFPQGRVKDHR 114
>gnl|CDD|146218 pfam03462, PCRF, PCRF domain. This domain is found in peptide
chain release factors.
Length = 115
Score = 148 bits (377), Expect = 2e-36
Identities = 53/115 (46%), Positives = 74/115 (64%), Gaps = 4/115 (3%)
Query: 74 ELALEEDDCSILQETSDNLQRIKLEVE--YKQFESLL--SGEADSNDAYLEVHAGAGGTE 129
EL EEDD + + + L+ ++ E+E K+ +LL D +A LE+ AGAGGTE
Sbjct: 1 ELLEEEDDPELRELAEEELEELEKELEELEKELLNLLLPLDPYDDKNAILEIRAGAGGTE 60
Query: 130 SQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPNAYGWLKGE 184
+Q +A LLRMY R+AE++ +K E L+ +GEE GIK ATL I+G AYG+LK E
Sbjct: 61 AQLFAEDLLRMYQRYAERKGWKVEVLDYSEGEEGGIKEATLEIEGEGAYGYLKFE 115
>gnl|CDD|38639 KOG3429, KOG3429, KOG3429, Predicted peptidyl-tRNA hydrolase
[Translation, ribosomal structure and biogenesis].
Length = 172
Score = 36.9 bits (85), Expect = 0.009
Identities = 21/80 (26%), Positives = 31/80 (38%), Gaps = 25/80 (31%)
Query: 234 RASGAGGQHVNTTDSAVRIT---------------HIPTG----------VVVQCQQERS 268
R+SG GGQ+VN ++ V + + T +V+ + RS
Sbjct: 48 RSSGPGGQNVNKVNTKVEVRFKVSNAEWIPEFLRNKLLTTEKNRINKDGELVIYSDKTRS 107
Query: 269 QHKNKAQAWNMLRAKLYELE 288
QHKN A LR + E
Sbjct: 108 QHKNIADCLEKLRDIIRAAE 127
>gnl|CDD|37962 KOG2751, KOG2751, KOG2751, Beclin-like protein [Signal transduction
mechanisms].
Length = 447
Score = 33.1 bits (75), Expect = 0.13
Identities = 21/102 (20%), Positives = 38/102 (37%), Gaps = 13/102 (12%)
Query: 15 DWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLE 74
+ D L L + +D + E K L E + L + +++ + L L LE
Sbjct: 158 EVDTYKACLQRLEQQNQDVSEEDLLKELKNLKEEEERLLQQLEELEKEEAELDHQLKELE 217
Query: 75 L---ALEEDDCSILQE----------TSDNLQRIKLEVEYKQ 103
L E++ +E D L ++ ++EY Q
Sbjct: 218 FKAERLNEEEDQYWREYNNFQRQLIEHQDELDSLEAQIEYSQ 259
>gnl|CDD|110607 pfam01617, Surface_Ag_2, Surface antigen. This family includes a
number of bacterial surface antigens expressed on the
surface of pathogens.
Length = 279
Score = 29.0 bits (65), Expect = 1.9
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 94 RIKLEVEYKQFESLLSGEADSNDAY 118
R++LEV Y++F+ G NDA+
Sbjct: 115 RVELEVSYERFDVKNQGNNYKNDAH 139
>gnl|CDD|37423 KOG2212, KOG2212, KOG2212, Alpha-amylase [Carbohydrate transport
and metabolism].
Length = 504
Score = 28.8 bits (64), Expect = 2.5
Identities = 11/56 (19%), Positives = 23/56 (41%), Gaps = 3/56 (5%)
Query: 293 EEIANIGESSKTEIGWGRQIRSYVL---QPYQMVKDLRTNIEKTSPSDVLDGDLDD 345
N ++ +I +GR R ++ + L+T + + DV+ GD +
Sbjct: 412 TPFTNWYDNGSNQIAFGRGNRGFIAFNNDDWDFSLTLQTGLPAGTYCDVISGDKIN 467
>gnl|CDD|35580 KOG0359, KOG0359, KOG0359, Chaperonin complex component, TCP-1 zeta
subunit (CCT6) [Posttranslational modification, protein
turnover, chaperones].
Length = 520
Score = 27.6 bits (61), Expect = 5.3
Identities = 30/145 (20%), Positives = 59/145 (40%), Gaps = 34/145 (23%)
Query: 43 KMLMRERQHLDNAISFIKEIQDRLCDNLIL---------LELALEEDDCSILQETSDNLQ 93
+++ ER+ +D + I E++ ++C+ +++ L+ + ++ + N++
Sbjct: 255 VLVLAERKFIDQRVRKIIELKRKVCEFVVINQKGIDPTSLDSLAKSGILALRRAKRRNME 314
Query: 94 RIKLEVEYKQFESLLSGEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTE 153
R+ L + S+ D YL +AG L+ YT EK F +
Sbjct: 315 RLVLACGGEAVNSV----DDLTPDYLG-YAG------------LVYEYTLGEEKFTFIEK 357
Query: 154 ALEIHDGEEAGIKSATLLIKGPNAY 178
S T+LIKGPN +
Sbjct: 358 C--------NNPSSVTILIKGPNKH 374
>gnl|CDD|35327 KOG0104, KOG0104, KOG0104, Molecular chaperones GRP170/SIL1, HSP70
superfamily [Posttranslational modification, protein
turnover, chaperones].
Length = 902
Score = 27.7 bits (61), Expect = 5.5
Identities = 21/75 (28%), Positives = 29/75 (38%), Gaps = 2/75 (2%)
Query: 16 WDNAVQRLSFLNTKTEDPHLWQNVIEAKM--LMRERQHLDNAISFIKEIQDRLCDNLILL 73
W N L KTEDP L IE K L RE +L N + K + + +
Sbjct: 793 WLNDRLDLFEKKAKTEDPVLKVKEIEEKAKSLDREVLYLLNKLKIRKPRKQKKKEKKKKT 852
Query: 74 ELALEEDDCSILQET 88
+ EE + + E
Sbjct: 853 KEEKEESESNDETEE 867
>gnl|CDD|36652 KOG1439, KOG1439, KOG1439, RAB proteins geranylgeranyltransferase
component A (RAB escort protein) [Posttranslational
modification, protein turnover, chaperones].
Length = 440
Score = 27.2 bits (60), Expect = 8.3
Identities = 28/91 (30%), Positives = 39/91 (42%), Gaps = 11/91 (12%)
Query: 12 GLFDWDNAVQRLSF-LNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEI-QDRLCDN 69
GLF+ ++ L F LN EDP WQ +K MRE F+ + +
Sbjct: 133 GLFEKRRVMKFLKFVLNYDEEDPKTWQGYDLSKDTMRE---------FLGKFGLLEGTID 183
Query: 70 LILLELALEEDDCSILQETSDNLQRIKLEVE 100
I +AL DD + Q + L+RI L V
Sbjct: 184 FIGHAIALLCDDSYLDQPAKETLERILLYVR 214
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.316 0.132 0.385
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,142,013
Number of extensions: 206910
Number of successful extensions: 484
Number of sequences better than 10.0: 1
Number of HSP's gapped: 477
Number of HSP's successfully gapped: 16
Length of query: 355
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 260
Effective length of database: 4,210,882
Effective search space: 1094829320
Effective search space used: 1094829320
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: 58 (26.2 bits)