RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254780148|ref|YP_003064561.1| transcription antitermination
protein NusG [Candidatus Liberibacter asiaticus str. psy62]
(177 letters)
>2jvv_A Transcription antitermination protein NUSG; transcription
factor, transcription regulation, transcription
termination; NMR {Escherichia coli} PDB: 2k06_A (A:)
Length = 181
Score = 149 bits (377), Expect = 2e-37
Identities = 80/174 (45%), Positives = 118/174 (67%), Gaps = 1/174 (0%)
Query: 3 PRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFP 62
RWY+VQ +S E + S+ + ++ L E+ +P+E VV +R G++ SER+FFP
Sbjct: 7 KRWYVVQAFSGFEGRVATSLREHIKLHNMEDLFGEVMVPTEEVVEIRGGQRRKSERKFFP 66
Query: 63 GYVLIKAVMTDKVYHTIKDTPKVIGFLG-TGENPSPVTDSEIEHIMNQVEAAVQRPVSSV 121
GYVL++ VM D +H ++ P+V+GF+G T + P+P++D E++ IMN+++ +P
Sbjct: 67 GYVLVQMVMNDASWHLVRSVPRVMGFIGGTSDRPAPISDKEVDAIMNRLQQVGDKPRPKT 126
Query: 122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEK 175
FE GE V V+DGPFA FNG+V+ VD EKSR+ V V IFGR TPVEL ++QVEK
Sbjct: 127 LFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELDFSQVEK 180
>1nz8_A Transcription antitermination protein NUSG; transcription
elongation, riken structural genomics/proteomics
initiative, RSGI; NMR {Thermus thermophilus} (A:)
Length = 119
Score = 104 bits (261), Expect = 6e-24
Identities = 34/114 (29%), Positives = 60/114 (52%), Gaps = 6/114 (5%)
Query: 4 RWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRK-GRKVNSERRFFP 62
WY V E+KA ++ R+ GL + ++ IP+E VV +R+ G+K ++ FP
Sbjct: 3 EWYAVHTLVGQEEKAKANLEKRIKAFGLQDKIFQVLIPTEEVVELREGGKKEVVRKKLFP 62
Query: 63 GYVLIKAVMTD-----KVYHTIKDTPKVIGFLGTGENPSPVTDSEIEHIMNQVE 111
GY+ I+ + D + + ++ TP + GF+G G P P++ E+ HI+
Sbjct: 63 GYLFIQMDLGDEEEPNEAWEVVRGTPGITGFVGAGMRPVPLSPDEVRHILEVSG 116
>2oug_A Transcriptional activator RFAH; transcription factor,
virulence, transcription pausing, transcription
elongation; 2.10A {Escherichia coli} (A:1-98)
Length = 98
Score = 97.2 bits (242), Expect = 1e-21
Identities = 19/104 (18%), Positives = 37/104 (35%), Gaps = 9/104 (8%)
Query: 4 RWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPG 63
WY++ ++A E L+ P + + +G++ FP
Sbjct: 3 SWYLLYCKRGQLQRAQEH---------LERQAVNCLAPMITLEKIVRGKRTAVSEPLFPN 53
Query: 64 YVLIKAVMTDKVYHTIKDTPKVIGFLGTGENPSPVTDSEIEHIM 107
Y+ ++ TI T V F+ G +P+ V + I +
Sbjct: 54 YLFVEFDPEVIHTTTINATRGVSHFVRFGASPAIVPSAVIHQLS 97
>1m1h_A Transcription antitermination protein NUSG; transcription
termination, RNP motif, immunoglobulin fold, nucleic
acid interaction; 1.95A {Aquifex aeolicus}
(A:1-49,A:135-168)
Length = 83
Score = 80.4 bits (199), Expect = 1e-16
Identities = 30/92 (32%), Positives = 42/92 (45%), Gaps = 19/92 (20%)
Query: 1 MTPRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRF 60
+ +WY +QV E +A E++ L GL LV E+ +P
Sbjct: 9 LEKKWYALQVEPGKENEAKENLLKVLELEGLKDLVDEVIVP------------------- 49
Query: 61 FPGYVLIKAVMTDKVYHTIKDTPKVIGFLGTG 92
FPGY+LIKA M DK+ I+ TP V + G
Sbjct: 50 FPGYILIKAHMNDKLLMAIEKTPHVFRPVMVG 81
>1nz9_A Transcription antitermination protein NUSG; transcription
elongation, riken structural genomics/proteomics
initiative, RSGI; NMR {Thermus thermophilus} (A:)
Length = 58
Score = 78.5 bits (194), Expect = 5e-16
Identities = 28/57 (49%), Positives = 37/57 (64%)
Query: 119 SSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEK 175
+ V F G++V V GPFA F G V ++ E+ +V V V IFGR TPVEL ++QV K
Sbjct: 1 AQVAFREGDQVRVVSGPFADFTGTVTEINPERGKVKVMVTIFGRETPVELDFSQVVK 57
>3bbo_W Ribosomal protein L24; large ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea}
(W:1-140)
Length = 140
Score = 29.5 bits (66), Expect = 0.28
Identities = 8/42 (19%), Positives = 17/42 (40%)
Query: 117 PVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVV 158
+ +VG+ V V G G + + + S V ++ +
Sbjct: 63 KLHKRHVKVGDTVKVISGGEKGKIGEISKIHKHNSTVIIKDL 104
>1vq8_T 50S ribosomal protein L24P; ribosome 50S, protein-protein
complex, RNA-RNA complex, protein-RNA complex, peptidyl
transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
2.20A {Haloarcula marismortui} (T:20-120)
Length = 101
Score = 27.7 bits (62), Expect = 0.82
Identities = 16/42 (38%), Positives = 22/42 (52%)
Query: 115 QRPVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE 156
+ +V G+ V V G FA G V NVD +K+ +HVE
Sbjct: 16 EYGQRNVRVNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVE 57
>2zjr_R 50S ribosomal protein L24; ribosome, large ribosomal
subunit, ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} (R:1-87)
Length = 87
Score = 26.6 bits (59), Expect = 2.1
Identities = 10/40 (25%), Positives = 14/40 (35%)
Query: 117 PVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE 156
+ F+ G+ V V G G V +V VE
Sbjct: 10 HNDKLHFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVE 49
>2gc4_D Cytochrome C-L; electron transfer, methylamine
dehydrogenase, blue copper protein, oxidoreductase,
electron transport; HET: TRQ HEM; 1.90A {Paracoccus
denitrificans} (D:1-61,D:108-129)
Length = 83
Score = 26.4 bits (58), Expect = 2.2
Identities = 9/15 (60%), Positives = 9/15 (60%)
Query: 81 DTPKVIGFLGTGENP 95
DT V FL TGEN
Sbjct: 24 DTEAVKHFLETGENV 38
>2d0w_A Cytochrome CL; electron transfer, electron transport; HET:
HEM; 1.98A {Hyphomicrobium denitrificans}
(A:1-63,A:110-130)
Length = 84
Score = 26.4 bits (58), Expect = 2.2
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 81 DTPKVIGFLGTGENP 95
DTP V F+ TG +P
Sbjct: 26 DTPAVKQFMQTGVDP 40
>1ycy_A Conserved hypothetical protein; structural genomics,
southeast collaboratory for structural genomics, secsg,
protein structure initiative; 2.80A {Pyrococcus
furiosus} (A:)
Length = 71
Score = 25.6 bits (56), Expect = 3.9
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 126 GERVCVSDGPFASFNGIVKNVDEE 149
G +V VS G SF G +++ DEE
Sbjct: 16 GHKVAVSVGGDHSFTGTLEDFDEE 39
>2hlv_A Odorant-binding protein; domain swapping, transport protein;
HET: LIK; 1.65A {Bos taurus} PDB: 1gt1_A* 1gt3_A*
1gt4_A* 1gt5_A* 1hn2_A* 1obp_A 1g85_A 1pbo_A* (A:)
Length = 160
Score = 25.6 bits (55), Expect = 4.5
Identities = 11/86 (12%), Positives = 20/86 (23%), Gaps = 10/86 (11%)
Query: 4 RWYIVQVYSNCEKKAVE--------SIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVN 55
W V + S +K E G + + K K +
Sbjct: 16 PWRTVYIGSTNPEKIQENGPFRTYFRELVFDDEKGTVDFYFSVKRDGKCKNVHVKATKQD 75
Query: 56 SERRF--FPGYVLIKAVMTDKVYHTI 79
+ G + K V + +
Sbjct: 76 DGTYVADYEGQNVFKIVSLSRTHLVA 101
>2q5w_E Molybdopterin-converting factor subunit 2; MOCO, MPT
synthase, MOAD, MOAE, transferase, molybdenum cofactor
biosynthesis; 2.00A {Staphylococcus aureus} PDB: 2qie_A*
(E:)
Length = 149
Score = 24.8 bits (54), Expect = 6.1
Identities = 7/46 (15%), Positives = 17/46 (36%), Gaps = 5/46 (10%)
Query: 132 SDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKIV 177
G F G V+ + ++E + + +A ++ +I
Sbjct: 25 YQGAVVVFTGHVREWTKGVKTEYLEYEAY-----IPMAEKKLAQIG 65
>2do3_A Transcription elongation factor SPT5; KOW motif, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} (A:)
Length = 69
Score = 25.0 bits (55), Expect = 6.4
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVEL 168
+F++G+ V V G F G++ V+E V++F +T EL
Sbjct: 17 YFKMGDHVKVIAGRFEGDTGLIVRVEEN------FVILFSDLTMHEL 57
>1bj7_A D 2; allergen, lipocalin; 1.80A {Bos taurus} (A:)
Length = 156
Score = 24.8 bits (53), Expect = 6.6
Identities = 7/94 (7%), Positives = 23/94 (24%), Gaps = 10/94 (10%)
Query: 4 RWYIVQVYSNCEKKAVE--------SIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVN 55
W I+ ++ + K VE ++ + + ++ ++
Sbjct: 15 EWRIIYAAADNKDKIVEGGPLRNYYRRIECINDCESLSITFYLKDQGTCLLLTEVAKRQE 74
Query: 56 SERRF--FPGYVLIKAVMTDKVYHTIKDTPKVIG 87
F G ++ + +
Sbjct: 75 GYVYVLEFYGTNTLEVIHVSENMLVTYVENYDGE 108
>1e5p_A Aphrodisin; lipocalin, pheromone, hamster,; HET: MSE;
1.63A {Mesocricetus auratus} (A:)
Length = 151
Score = 24.8 bits (53), Expect = 6.7
Identities = 8/86 (9%), Positives = 19/86 (22%), Gaps = 10/86 (11%)
Query: 4 RWYIVQVYSNCEKKAVESIGGR------LSRSGLDHLVTEITIPSERVVSVRKGRKVNSE 57
+WY + + ++ +K E R + + S
Sbjct: 9 KWYTIVIAADNLEKIEEGGPLRFYFRHIDCYKNCSEXEITFYVITNNQCSKTTVIGYLKG 68
Query: 58 ----RRFFPGYVLIKAVMTDKVYHTI 79
F G + + +
Sbjct: 69 NGTYETQFEGNNIFQPLYITSDKIFF 94
>2j01_Y 50S ribosomal protein L24; ribosome, tRNA, paromomycin,
mRNA, translation; 2.8A {Thermus thermophilus} (Y:1-78)
Length = 78
Score = 24.6 bits (54), Expect = 8.3
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 126 GERVCVSDGPFASFNGIVKNVDEEKSRVHVE 156
G+ V V+ G + G VK V +K V VE
Sbjct: 10 GDTVLVASGKYKGRVGKVKEVLPKKYAVIVE 40
>2j16_A SDP-1, tyrosine-protein phosphatase YIL113W; hydrolase,
hypothetical protein; 2.7A {Saccharomyces cerevisiae}
PDB: 2j17_A* 2j16_B (A:)
Length = 182
Score = 24.4 bits (52), Expect = 8.5
Identities = 6/91 (6%), Positives = 21/91 (23%), Gaps = 3/91 (3%)
Query: 47 SVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKDTPKVIGFLGTGENPSPVTDSEIEHI 106
R + E + + + + + + + P+ + +
Sbjct: 10 LATDERSTDKESPNEDREFVPCSSLDVRRIYPKGPLLVLPEKIYLYSEPTVKELLPFDVV 69
Query: 107 MNQVEAAVQRPVSSVFFEVGERVCVSDGPFA 137
+N A + + E +
Sbjct: 70 IN---VAEEANDLRMQVPAVEYHHYRWEHDS 97
>2byk_B Chrac-14; nucleosome sliding, histone fold, DNA-binding
protein; 2.4A {Drosophila melanogaster} (B:1-79)
Length = 79
Score = 24.3 bits (53), Expect = 8.8
Identities = 6/25 (24%), Positives = 9/25 (36%)
Query: 135 PFASFNGIVKNVDEEKSRVHVEVVI 159
P A ++K E + V E
Sbjct: 11 PNAVIGRLIKEALPESASVSKEARA 35
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 0.136 0.389
Gapped
Lambda K H
0.267 0.0583 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,360,970
Number of extensions: 58995
Number of successful extensions: 216
Number of sequences better than 10.0: 1
Number of HSP's gapped: 211
Number of HSP's successfully gapped: 31
Length of query: 177
Length of database: 4,956,049
Length adjustment: 83
Effective length of query: 94
Effective length of database: 2,150,234
Effective search space: 202121996
Effective search space used: 202121996
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: 52 (24.1 bits)