RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780345|ref|YP_003064758.1| transcription antitermination
protein NusB [Candidatus Liberibacter asiaticus str. psy62]
(170 letters)
>gnl|CDD|178926 PRK00202, nusB, transcription antitermination protein NusB;
Reviewed.
Length = 137
Score = 135 bits (342), Expect = 6e-33
Identities = 52/143 (36%), Positives = 78/143 (54%), Gaps = 12/143 (8%)
Query: 16 RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHG 75
R AR AAVQALYQ ++ G EII +L E Y D +FR ++ G
Sbjct: 3 RRKAREAAVQALYQWELSGNDIAEIIEA----------QLLEEQ-YDKADPAYFRSLVRG 51
Query: 76 VMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAH 135
V++ + +D LIS L + W+ RLD + +ILR + EL+ VP +V+I+E + +A
Sbjct: 52 VVENQAELDELISPYL-KDWTLERLDPVERAILRLALYELLFRDDVPYKVVINEAIELAK 110
Query: 136 DFFYGDEPKFINAVLDKVSRKEE 158
F D KF+N VLDK++++
Sbjct: 111 KFGDEDSHKFVNGVLDKIAKELR 133
>gnl|CDD|162621 TIGR01951, nusB, transcription antitermination factor NusB. A
transcription antitermination complex active in many
bacteria was designated N-utilization substance (Nus) in
E. coli because of its interaction with phage lambda
protein N. This model represents NusB. Other components
are NusA and NusG. NusE is, in fact, ribosomal protein
S10.
Length = 129
Score = 127 bits (322), Expect = 1e-30
Identities = 56/141 (39%), Positives = 80/141 (56%), Gaps = 12/141 (8%)
Query: 16 RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHG 75
R AR A+QALYQ ++ G EII E F + ELD E D E+F ++ G
Sbjct: 1 RRKARELALQALYQWELSGNDVEEIIEE-----FLEERELDEE------DREYFLELVRG 49
Query: 76 VMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAH 135
V++ ++ ID LIS L + WS RLD + +ILR EL+ VP +V+I+E V +A
Sbjct: 50 VLENQEEIDELISPHL-KDWSLERLDPVDRAILRLAAYELLYRPDVPYKVVINEAVELAK 108
Query: 136 DFFYGDEPKFINAVLDKVSRK 156
F D KF+N VLDK++++
Sbjct: 109 KFGDEDSHKFVNGVLDKIAKE 129
>gnl|CDD|182007 PRK09634, nusB, transcription antitermination protein NusB;
Provisional.
Length = 207
Score = 47.2 bits (113), Expect = 2e-06
Identities = 28/87 (32%), Positives = 43/87 (49%), Gaps = 6/87 (6%)
Query: 72 IIHGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYV 131
I V+ ++ ID L+ + + W RL I ILR V+E++ + P V I+E V
Sbjct: 119 RIGAVIRNRKEIDQLLDTVM-VGWQLKRLPRIDRDILRLAVVEILFL-NTPAAVAINEAV 176
Query: 132 CIAHDFFYGDEP--KFINAVLDKVSRK 156
+A Y DE +FIN VL ++
Sbjct: 177 ELAKR--YSDEQGRRFINGVLRRLQDA 201
>gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional.
Length = 431
Score = 36.8 bits (85), Expect = 0.003
Identities = 31/122 (25%), Positives = 60/122 (49%), Gaps = 8/122 (6%)
Query: 40 IISEYETYRFCADTELD-VESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFS 98
++ +YE +F ++D V S D +F+ ++ GV+ +++ +D I+ L +K
Sbjct: 12 LLRKYEKEKFIFREDVDSVLSFLDDKDRRFFKELVWGVVRKEELLDWYINQLLKKK---- 67
Query: 99 RLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEE 158
+ + LR G +L+ +SVP +SE V + + + K +NAVL ++ E
Sbjct: 68 DIPPAVRVALRMGAYQLLFMNSVPDYAAVSETVKLVKNENF---KKLVNAVLRRLRTVPE 124
Query: 159 IK 160
K
Sbjct: 125 PK 126
>gnl|CDD|184897 PRK14904, PRK14904, 16S rRNA methyltransferase B; Provisional.
Length = 445
Score = 32.0 bits (73), Expect = 0.072
Identities = 33/136 (24%), Positives = 59/136 (43%), Gaps = 13/136 (9%)
Query: 19 ARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMD 78
AR A+Q L +++ T E S+ +R + L+ D +++GV+
Sbjct: 4 ARELALQVLQELE-----TGERKSDTLLHRMLERSSLE------RNDRALATELVNGVLR 52
Query: 79 RKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFF 138
+ +D +IS + +L +ILR GV +L+ VP ++E V +A +
Sbjct: 53 YRLQLDFIISRFYHHD--LEKAAPVLKNILRLGVYQLLFLDRVPRWAAVNECVKLARKYK 110
Query: 139 YGDEPKFINAVLDKVS 154
K +N VL +S
Sbjct: 111 GEHMAKLVNGVLRNIS 126
>gnl|CDD|184895 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 29.4 bits (67), Expect = 0.49
Identities = 20/91 (21%), Positives = 40/91 (43%), Gaps = 13/91 (14%)
Query: 72 IIHGVMDRKQHIDLLISSCLT-----EKWSFSRLDMILCSILRAGVLELIECHSVPVEVI 126
+++G + RK +D ++ + + W + +LR + +L+ VP
Sbjct: 47 LVYGTIQRKLTLDYYLAPFIKKRKKLDPW-------VRN-LLRMSLYQLLYLDKVPDHAA 98
Query: 127 ISEYVCIAHDFFYGDEPKFINAVLDKVSRKE 157
++E V IA + KF+N VL + R+
Sbjct: 99 VNEAVEIAKKRGHKGIAKFVNGVLRNILREG 129
>gnl|CDD|152501 pfam12066, DUF3546, Domain of unknown function (DUF3546). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 93 to 114 amino acids in length. This domain has
two completely conserved Y residues that may be
functionally important.
Length = 110
Score = 26.6 bits (59), Expect = 3.8
Identities = 20/95 (21%), Positives = 32/95 (33%), Gaps = 20/95 (21%)
Query: 36 STTEIISEYETYRFCADTELDV----ESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCL 91
S E Y+ Y+ TE + H D EWF+ H + + +
Sbjct: 14 SPAEAEKRYQEYK----TEFQRKQLQDFFDQHKDEEWFKEKYHPE-NLAKRREERRELRK 68
Query: 92 T--EKWSFS---------RLDMILCSILRAGVLEL 115
+ LD+I+ IL GV++L
Sbjct: 69 KRANVFLEDLESGTFDEVSLDIIIEKILDGGVIKL 103
>gnl|CDD|183013 PRK11173, PRK11173, two-component response regulator; Provisional.
Length = 237
Score = 25.4 bits (56), Expect = 8.7
Identities = 11/21 (52%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 36 STTEIISEY--ETYRFCADTE 54
T EII+ E YRFC D E
Sbjct: 217 DTPEIIATIHGEGYRFCGDLE 237
>gnl|CDD|150395 pfam09715, Plasmod_dom_1, Plasmodium protein of unknown function
(Plasmod_dom_1). These sequences represent an
uncharacterized family consisting of a small number of
hypothetical proteins of the malaria parasite Plasmodium
falciparum (isolate 3D7).
Length = 70
Score = 25.1 bits (55), Expect = 9.2
Identities = 16/58 (27%), Positives = 22/58 (37%), Gaps = 6/58 (10%)
Query: 82 HIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFY 139
ID LI S + K SF + D+I L L + I Y+ +FF
Sbjct: 17 FIDKLIDSNIHNKGSFIKEDVI------DNSLSLCTAAIPLTAIPIFSYIAKRINFFT 68
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.325 0.139 0.416
Gapped
Lambda K H
0.267 0.0843 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,743,362
Number of extensions: 166387
Number of successful extensions: 345
Number of sequences better than 10.0: 1
Number of HSP's gapped: 339
Number of HSP's successfully gapped: 16
Length of query: 170
Length of database: 5,994,473
Length adjustment: 87
Effective length of query: 83
Effective length of database: 4,114,577
Effective search space: 341509891
Effective search space used: 341509891
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: 54 (24.4 bits)