RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254780345|ref|YP_003064758.1| transcription antitermination
protein NusB [Candidatus Liberibacter asiaticus str. psy62]
(170 letters)
>1eyv_A NUSB protein, N-utilizing substance protein B homolog;
helical bundle, structural genomics, PSI, protein
structure initiative; 1.60A {Mycobacterium tuberculosis}
(A:)
Length = 156
Score = 108 bits (272), Expect = 4e-25
Identities = 39/143 (27%), Positives = 60/143 (41%), Gaps = 9/143 (6%)
Query: 16 RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHG 75
R AR AV L++ ++ G S E++ + + G
Sbjct: 10 RHQARKRAVALLFEAEVRGISAAEVVDTRAALA--EAKPDIAR------LHPYTAAVARG 61
Query: 76 VMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAH 135
V + HID LI++ L W+ RL + +ILR V EL+ VP V++ E V +A
Sbjct: 62 VSEHAAHIDDLITAHLR-GWTLDRLPAVDRAILRVSVWELLHAADVPEPVVVDEAVQLAK 120
Query: 136 DFFYGDEPKFINAVLDKVSRKEE 158
+ D P F+N VL +V
Sbjct: 121 ELSTDDSPGFVNGVLGQVMLVTP 143
>2jr0_A Protein NUSB, N utilization substance protein B homolog;
antiterminator, transcription; NMR {Aquifex aeolicus}
(A:)
Length = 148
Score = 106 bits (266), Expect = 1e-24
Identities = 33/143 (23%), Positives = 57/143 (39%), Gaps = 11/143 (7%)
Query: 16 RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHG 75
R AR A LY+ D+ G + E+ E + + + E+ + ++
Sbjct: 4 RKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKD----------AYEYAKKLVDT 53
Query: 76 VMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAH 135
+ + ID +I L + WS RL + + LR GV ELI S + + V +
Sbjct: 54 AVRHIEEIDSIIEKHL-KGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVK 112
Query: 136 DFFYGDEPKFINAVLDKVSRKEE 158
+ KF+N VL + +
Sbjct: 113 KYADEKAGKFVNGVLSAIYKAYI 135
>1tzv_A NUSB protein, N utilization substance protein B homolog;
RNA-protein interaction, transcriptional
antitermination, transcription regulation; 1.35A
{Thermotoga maritima} (A:)
Length = 142
Score = 106 bits (266), Expect = 2e-24
Identities = 44/143 (30%), Positives = 67/143 (46%), Gaps = 12/143 (8%)
Query: 16 RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHG 75
R RLA +AL+Q + E I E D D E R I G
Sbjct: 5 RRRMRLAVFKALFQHEFRRDEDLEQILE-----EILDETYD------KKAKEDARRYIRG 53
Query: 76 VMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAH 135
+ + ID LIS L EKWS +RL ++ ++LR EL+ +P+EV I E + IA
Sbjct: 54 IKENLSMIDDLISRYL-EKWSLNRLSVVDRNVLRLATYELLFEKDIPIEVTIDEAIEIAK 112
Query: 136 DFFYGDEPKFINAVLDKVSRKEE 158
+ + KF+N +LD+++++
Sbjct: 113 RYGTENSGKFVNGILDRIAKEHA 135
>3d3b_A Protein NUSB, N utilization substance protein B; NUSB, NUSE,
NUT site, phage lambda, lambdan antitermination; HET:
NHE; 1.30A {Escherichia coli K12} PDB: 3d3c_A 3imq_A
1ey1_A (A:)
Length = 141
Score = 103 bits (259), Expect = 1e-23
Identities = 40/143 (27%), Positives = 65/143 (45%), Gaps = 13/143 (9%)
Query: 16 RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHG 75
R AR AVQALY + ++ + F A+ ++ VD+ +FR ++ G
Sbjct: 8 RRRARECAVQALYSWQLSQNDIADVEYQ-----FLAEQDVK------DVDVLYFRELLAG 56
Query: 76 VMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAH 135
V ++D L+ L L + ++LR + EL + VP +V I+E + +A
Sbjct: 57 VATNTAYLDGLMKPYL--SRLLEELGQVEKAVLRIALYELSKRSDVPYKVAINEAIELAK 114
Query: 136 DFFYGDEPKFINAVLDKVSRKEE 158
F D KF+N VLDK +
Sbjct: 115 SFGAEDSHKFVNGVLDKAAPVIR 137
>1sqg_A SUN protein, FMU protein; rossmann-fold, mixed beta sheet,
methyltransferase-fold, RNA-binding domain; 1.65A
{Escherichia coli} (A:1-142)
Length = 142
Score = 92.6 bits (230), Expect = 3e-20
Identities = 26/143 (18%), Positives = 52/143 (36%), Gaps = 16/143 (11%)
Query: 16 RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHG 75
+ R A QA+ Q+ G S + I+ + ++ + D + + G
Sbjct: 4 QRNLRSMAAQAVEQVVEQGQSLSNILPPLQQ-------KVSDK------DKALLQELCFG 50
Query: 76 VMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAH 135
V+ +D LI+ + + ++ G+ +L +P ++E V A
Sbjct: 51 VLRTLSQLDWLINKL--MARPMTGKQRTVHYLIMVGLYQL-LYTRIPPHAALAETVEGAI 107
Query: 136 DFFYGDEPKFINAVLDKVSRKEE 158
IN VL + R++E
Sbjct: 108 AIKRPQLKGLINGVLRQFQRQQE 130
>1f86_A Transthyretin Thr119Met variant; protein stability, X-RAY
amyloidogenesis, transport protein; HET: T44; 1.10A
{Homo sapiens} (A:)
Length = 115
Score = 27.8 bits (62), Expect = 0.75
Identities = 11/58 (18%), Positives = 20/58 (34%), Gaps = 13/58 (22%)
Query: 46 TYRFCADT-----ELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFS 98
Y+ DT L + + H + + R+ I L+S +S+S
Sbjct: 59 IYKVEIDTKSYWKALGISPFHEHAE---VVFTANDSGPRRYTIAALLSP-----YSYS 108
>2hdv_A SH2-B PH domain containing signaling mediator 1 gamma
isoform; adapter protein, signaling protein; 2.00A {Mus
musculus} PDB: 2hdx_A* 1rpy_A 1rqq_C* (A:)
Length = 111
Score = 28.1 bits (62), Expect = 0.76
Identities = 13/83 (15%), Positives = 22/83 (26%), Gaps = 10/83 (12%)
Query: 63 HVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVP 122
WF HG++ R + L++ F ++ S R G L
Sbjct: 6 LSGYPWF----HGMLSRLKAAQLVLEGGTGSHGVF----LVRQSETRRGECVLTFNFQGK 57
Query: 123 VEVIISEYVCIAHDFFYGDEPKF 145
+ + A F
Sbjct: 58 AKHLRLSL--NAAGQCRVQHLHF 78
>2gr8_A Adhesin; trimeric autotransporter, adhesion, protein
secretion, microbial pathogenesis, membrane protein;
2.00A {Haemophilus influenzae} (A:)
Length = 99
Score = 27.4 bits (61), Expect = 1.1
Identities = 8/35 (22%), Positives = 10/35 (28%), Gaps = 4/35 (11%)
Query: 3 IQDNKKDLKLSHRRGIARLAAVQALYQIDIIGCST 37
+ K G A A L Q + G S
Sbjct: 18 VPRGSKRA----DAGTASALAASQLPQATMPGKSM 48
>1l6j_A Matrix metalloproteinase-9; twisted beta sheet flanked by
helices, hydrolase; 2.50A {Homo sapiens} (A:201-256)
Length = 56
Score = 26.2 bits (58), Expect = 2.3
Identities = 6/20 (30%), Positives = 8/20 (40%)
Query: 35 CSTTEIISEYETYRFCADTE 54
CSTT + + FC
Sbjct: 37 CSTTANYDTDDRFGFCPSER 56
>3cym_A Uncharacterized protein BAD_0989; structural genomics,
unknown function, ribonuclease D, exonuclease; 2.10A
{Bifidobacterium adolescentis ATCC15703} (A:338-440)
Length = 103
Score = 25.9 bits (57), Expect = 3.2
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 108 LRAGVLELIECHSVPVEVIIS 128
+R V ++ E PVE++I
Sbjct: 32 VRKAVSQIAEDTRTPVEIVIK 52
>1ck7_A Protein (gelatinase A); hydrolase (metalloprotease),
FULL-length, metalloproteinase; 2.80A {Homo sapiens}
(A:256-313)
Length = 58
Score = 25.5 bits (56), Expect = 3.9
Identities = 8/24 (33%), Positives = 11/24 (45%)
Query: 35 CSTTEIISEYETYRFCADTELDVE 58
C TTE + Y FC +T +
Sbjct: 33 CGTTEDYDRDKKYGFCPETAMSTV 56
>1n8i_A Probable malate synthase G; glyoxylate pathway, acetyl
coenzyme A, isocitrate lyase, persistence, GLCB,
structural genomics, PSI; 2.10A {Mycobacterium
tuberculosis} (A:1-579)
Length = 579
Score = 25.3 bits (55), Expect = 4.6
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 62 LHVDLEWFRVIIHGVMDRKQHIDLLISSCLT 92
LH+++ G DR D+++ S +T
Sbjct: 237 LHIEILIDPESQVGTTDRAGVKDVILESAIT 267
>1v8d_A Hypothetical protein (TT1679); X-RAY craytallography,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; 2.16A {Thermus
thermophilus} (A:1-213)
Length = 213
Score = 25.1 bits (55), Expect = 5.4
Identities = 5/15 (33%), Positives = 11/15 (73%)
Query: 29 QIDIIGCSTTEIISE 43
+ ++G ST+E++ E
Sbjct: 64 SLFVLGGSTSEVLGE 78
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase,
translation termination, ATP-binding, cytoplasm,
hydrolase, membrane; 2.80A {Schizosaccharomyces pombe}
(A:1-326)
Length = 326
Score = 25.1 bits (54), Expect = 6.0
Identities = 12/154 (7%), Positives = 36/154 (23%), Gaps = 31/154 (20%)
Query: 31 DIIGCSTT----------EIISEYETYRF------CADTELDVESVYLHV-DLEWFRVII 73
++IG S + ++S + A + + V ++ + +
Sbjct: 160 NMIGQSQSGTGKTAAFALTMLSRVDASVPKPQAICLAPSRELARQIMDVVTEMGKYTEVK 219
Query: 74 HGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCI 133
+ + + ++ L+ + V V+ +
Sbjct: 220 TAFGIKDSVPKGAKIDAQIVIGTPGTVMDLMKR----RQLDARDIK---VFVLDEADNML 272
Query: 134 AHDFFYGDEPKFINAVLDKVSRKEEIKRSGCVSA 167
+ + R + SA
Sbjct: 273 DQQGLGDQ----SMRIKHLLPRN---TQIVLFSA 299
>1j7m_A Matrix metalloproteinase 2; beta sheet, alpha helix,
hydrolase; NMR {Homo sapiens} (A:)
Length = 72
Score = 24.8 bits (54), Expect = 6.0
Identities = 6/21 (28%), Positives = 9/21 (42%)
Query: 35 CSTTEIISEYETYRFCADTEL 55
C+TT + + FC D
Sbjct: 49 CATTANYDDDRKWGFCPDQGW 69
>1ck7_A Protein (gelatinase A); hydrolase (metalloprotease),
FULL-length, metalloproteinase; 2.80A {Homo sapiens}
(A:194-255)
Length = 62
Score = 24.7 bits (54), Expect = 6.5
Identities = 8/21 (38%), Positives = 9/21 (42%)
Query: 35 CSTTEIISEYETYRFCADTEL 55
CSTT + Y FC L
Sbjct: 37 CSTTYNFEKDGKYGFCPHEAL 57
>1v5u_A SBF1, SET binding factor 1; MTMR5, the pleckstrin homology
domain, structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus musculus}
(A:)
Length = 117
Score = 24.4 bits (52), Expect = 9.2
Identities = 6/34 (17%), Positives = 11/34 (32%), Gaps = 8/34 (23%)
Query: 39 EIISEYETYRFCADTELDVESVYLHVDLEWFRVI 72
++ + Y FCA + +W I
Sbjct: 81 DVKTTRRVYNFCAQDVPSAQ--------QWVDRI 106
>2fl7_A Regulatory protein SIR3; ORC, silencing, chromatin,
transcription; 1.85A {Saccharomyces cerevisiae} PDB:
2fvu_A (A:56-232)
Length = 177
Score = 24.5 bits (53), Expect = 9.4
Identities = 5/33 (15%), Positives = 11/33 (33%)
Query: 128 SEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIK 160
+ V + H+ + + R E+K
Sbjct: 13 TYSVYLIHEIRLNTLNNVVEIWVFSYLRWFELK 45
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
0.325 0.139 0.416
Gapped
Lambda K H
0.267 0.0499 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,315,157
Number of extensions: 56660
Number of successful extensions: 206
Number of sequences better than 10.0: 1
Number of HSP's gapped: 200
Number of HSP's successfully gapped: 35
Length of query: 170
Length of database: 4,956,049
Length adjustment: 82
Effective length of query: 88
Effective length of database: 2,184,039
Effective search space: 192195432
Effective search space used: 192195432
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.0 bits)