RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780786|ref|YP_003065199.1| ribosome-binding factor A
[Candidatus Liberibacter asiaticus str. psy62]
(128 letters)
>gnl|CDD|179054 PRK00521, rbfA, ribosome-binding factor A; Validated.
Length = 120
Score = 93.6 bits (234), Expect = 1e-20
Identities = 41/112 (36%), Positives = 67/112 (59%), Gaps = 5/112 (4%)
Query: 6 PKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYIS-LPL 64
S+RALRV E+++ L IL E +D + ++++++V +S DL A VY++ L
Sbjct: 2 MAESQRALRVAEQIQRELA-EILQREIKDPRLG--MVTVTDVEVSPDLAHAKVYVTVLGD 58
Query: 65 DVSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNAL 116
+ + ++AL F+R +G+ LR LRYVPELRF YD SL+ +++ L
Sbjct: 59 EEDKEEALAALKKAAGFLRSELGKRLR-LRYVPELRFVYDESLEYGNRIDEL 109
>gnl|CDD|129191 TIGR00082, rbfA, ribosome-binding factor A. Associates with free
30S ribosomal subunits (but not with 30S subunits that
are part of 70S ribosomes or polysomes). Essential for
efficient processing of 16S rRNA. May interact with the
5'terminal helix region of 16S rRNA. Mutants lacking
rbfA have a cold-sensitive phenotype.
Length = 114
Score = 50.4 bits (121), Expect = 1e-07
Identities = 36/110 (32%), Positives = 58/110 (52%), Gaps = 5/110 (4%)
Query: 8 NSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVS 67
S R RV ++ + IL E +D + ++++++V +S DL+ A V++ D
Sbjct: 2 ASYRKERVESDIIR-EINRILIREIKDPRVG--MLTVTKVEVSKDLQHAKVFVDCYGDEE 58
Query: 68 P-DRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNAL 116
DRV+ ALN FIR +G+++R LR PEL F D SL ++ L
Sbjct: 59 AIDRVVKALNKAKGFIRSLLGQAMR-LRKTPELHFVKDNSLDKGMRIENL 107
>gnl|CDD|172345 PRK13815, PRK13815, ribosome-binding factor A; Provisional.
Length = 122
Score = 47.1 bits (112), Expect = 1e-06
Identities = 26/68 (38%), Positives = 41/68 (60%), Gaps = 2/68 (2%)
Query: 42 ISISEVCMSVDLRVATVYISLPLDVSPDRVISA-LNCNIKFIRGRIGRSLRNLRYVPELR 100
++I+ V ++ DL +AT+Y ++ D + A LN FIR +G+ LR +RY PEL
Sbjct: 32 VTITGVKVTDDLHLATIYFTVIGDDEAKKSTEAGLNSARGFIRKELGKVLR-MRYAPELI 90
Query: 101 FRYDTSLQ 108
F+YD S +
Sbjct: 91 FKYDESQE 98
>gnl|CDD|139879 PRK13817, PRK13817, ribosome-binding factor A; Provisional.
Length = 119
Score = 44.4 bits (104), Expect = 9e-06
Identities = 35/109 (32%), Positives = 61/109 (55%), Gaps = 4/109 (3%)
Query: 9 SRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSP 68
S+R RV + + L +L E +D +S+ IS++ V +S DL+ A V+ SL + +
Sbjct: 2 SQRQQRVADLIHQQLA-ELLKKEVRDSRLSK--ISLTAVSISPDLKQAKVFYSLLENQNE 58
Query: 69 DRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALM 117
V ALN ++R + ++ LRYVP+L F YD S++ +++ L+
Sbjct: 59 KEVQKALNKATGYLRHLLAQATV-LRYVPKLEFVYDESIERAHRISLLI 106
>gnl|CDD|184344 PRK13816, PRK13816, ribosome-binding factor A; Provisional.
Length = 131
Score = 35.2 bits (81), Expect = 0.004
Identities = 30/105 (28%), Positives = 52/105 (49%), Gaps = 13/105 (12%)
Query: 9 SRRALRVGEEVRSALMWVILNNEFQD-RLISRDVISISEVCMSVDLRVATVYISL----- 62
++R R+ + V+ L ++ E +D RL +++IS V +S DL A VY+++
Sbjct: 2 NQRLKRMADSVQRELS-ELIRQELKDPRLGG--LVTISSVKVSPDLGYADVYVTVMGREL 58
Query: 63 ---PLDVSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYD 104
+V+ + LN F+R + R ++ R P LRF YD
Sbjct: 59 SDDQNEVAHRETLDVLNKASGFLRTELSRRIKT-RITPRLRFHYD 102
>gnl|CDD|184345 PRK13818, PRK13818, ribosome-binding factor A; Provisional.
Length = 121
Score = 28.4 bits (63), Expect = 0.53
Identities = 28/93 (30%), Positives = 45/93 (48%), Gaps = 5/93 (5%)
Query: 27 ILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLD--VSPDRVISALNCNIKFIRG 84
IL +D +S ++I+ V + DL ATVY SL + V L +R
Sbjct: 19 ILRKNIRDPRLSD--VTITAVECTNDLSYATVYYSLLTEDEAKEKEVQEGLEKAKGMMRH 76
Query: 85 RIGRSLRNLRYVPELRFRYDTSLQSYWKLNALM 117
+G++L + VPEL F+ D S+ K++ L+
Sbjct: 77 LLGQTL-TVYKVPELIFKRDNSVAYGSKIDRLI 108
>gnl|CDD|163109 TIGR03023, WcaJ_sugtrans, Undecaprenyl-phosphate glucose
phosphotransferase. Colanic acid biosynthesis utilizes
a glucose-undecaprenyl carrier, knockout of EpsB
abolishes incorporation of UDP-glucose into the lipid
phase and the C-terminal portion of GumD has been shown
to be responsible for the glucosyl-1-transferase
activity.
Length = 451
Score = 27.9 bits (63), Expect = 0.80
Identities = 26/117 (22%), Positives = 37/117 (31%), Gaps = 28/117 (23%)
Query: 8 NSRRALRVGEEVRSALMWVILNNE----------FQDRLISRDVISISEVCMSVD----- 52
N RR L VG + L F DR +R + V +D
Sbjct: 127 NLRRVLIVGAGELGRRLAERLARNPELGYRVVGFFDDRPDARTGVRGVPVLGKLDDLEEL 186
Query: 53 ---LRVATVYISLPLDVSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTS 106
V VYI+LPL I + + ++R VP+L F +
Sbjct: 187 IREGEVDEVYIALPLAAEDR---------ILELLDALEDLTVDVRLVPDL-FDFALL 233
>gnl|CDD|184036 PRK13407, bchI, magnesium chelatase subunit I; Provisional.
Length = 334
Score = 26.4 bits (58), Expect = 2.3
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 57 TVYISLPLDVSPDRVISALNCNIKFIRGR-------IGRSLRNLRYVPELRFRYD 104
T + LPL V+ DRV+ AL+ RG + R+ R Y+ E+ D
Sbjct: 88 TPVVDLPLGVTEDRVVGALDIERALTRGEKAFEPGLLARANRGYLYIDEVNLLED 142
>gnl|CDD|172578 PRK14088, dnaA, chromosomal replication initiation protein;
Provisional.
Length = 440
Score = 25.2 bits (55), Expect = 4.6
Identities = 17/66 (25%), Positives = 33/66 (50%), Gaps = 10/66 (15%)
Query: 30 NEFQDRLISRDVISI--------SEVCMSVDLRVATV-YISLPLDVSPDRVISALNCNIK 80
+EFQDRL+SR + + E + ++ + + LP +V + V ++ N++
Sbjct: 242 SEFQDRLVSRFQMGLVAKLEPPDEETRKKIARKMLEIEHGELPEEVL-NFVAENVDDNLR 300
Query: 81 FIRGRI 86
+RG I
Sbjct: 301 RLRGAI 306
>gnl|CDD|183046 PRK11234, nfrB, bacteriophage N4 adsorption protein B; Provisional.
Length = 727
Score = 25.1 bits (55), Expect = 5.5
Identities = 32/124 (25%), Positives = 45/124 (36%), Gaps = 32/124 (25%)
Query: 8 NSRRALRVG-----------EEVRSAL------MWVILNNEFQD-RLISRDVISISEVCM 49
N R LR+G E++ AL W L+ LI+
Sbjct: 505 NRVRGLRLGQSLLMQGLISAEQLAQALAEQNGVAWESLDPWQIPSSLIAE---------- 554
Query: 50 SVDLRVATVYISLPLDVSPDRVISALNCNIKFIR-GRIGRSL-RNLRYVPELRFRYDTSL 107
+ VA Y LPL D +I A I + + R L R +RYV R + T L
Sbjct: 555 -MPASVALHYAVLPLREEGDELIVASEDGISPVSLAALTRKLGRKVRYVIVPRGQVTTGL 613
Query: 108 QSYW 111
+ +W
Sbjct: 614 R-HW 616
>gnl|CDD|152576 pfam12141, DUF3589, Protein of unknown function (DUF3589). This
family of proteins is found in eukaryotes. Proteins in
this family are typically between 541 and 717 amino
acids in length. The function of this family is not
known,.
Length = 488
Score = 25.0 bits (55), Expect = 6.4
Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 5/54 (9%)
Query: 58 VYISLPLDVSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELR--FRYDTSLQS 109
+ ++VS + LN ++K I + + L Y EL+ F+ D Q
Sbjct: 6 LEFEDSVEVSKSK---NLNADLKKILDTLLKQLSTDPYYKELKPFFQPDLPEQL 56
>gnl|CDD|178166 PLN02551, PLN02551, aspartokinase.
Length = 521
Score = 24.7 bits (54), Expect = 6.6
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 31 EFQDRLISRDVISISEVCMSVDL 53
F+D IS DV++ SEV +S+ L
Sbjct: 389 TFEDLGISVDVVATSEVSISLTL 411
>gnl|CDD|150832 pfam10220, DUF2146, Uncharacterized conserved protein (DUF2146).
This is a family of proteins conserved from plants to
humans. In Dictyostelium it is annotated as Mss11p but
this could not be confirmed. Mss11p is required for the
activation of pseudo-hyphal and invasive growth by
Ste12p in yeast.
Length = 890
Score = 24.4 bits (53), Expect = 8.0
Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 13/64 (20%)
Query: 65 DVSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELR-FRYDTSLQSYWKLNALMCLPKIP 123
D+S R+ AL SLR + + LR D + S K +C P++
Sbjct: 130 DLSYIRLFKALK------------SLREKKVLQFLRDMLKDCPVGSEMKSEGRLCPPRLL 177
Query: 124 VALE 127
+
Sbjct: 178 FLFQ 181
>gnl|CDD|151003 pfam10423, AMNp_N, Bacterial AMP nucleoside phosphorylase
N-terminus. This is the N-terminal domain of bacterial
AMP nucleoside phosphorylase (AMNp). The N- and
C-termini form distinct domains which intertwine with
each other to form a stable monomer which associates
with five other monomers to yield the active hexamer.
The N-terminus consists of a long helix and a
four-stranded sheet with a novel topology. The
C-terminus binds the nucleoside whereas the N-terminus
acts as the enzymatic regulatory domain. AMNp
(EC:3.2.2.4) catalyses the hydrolysis of AMP to form
adenine and ribose 5-phosphate. thereby regulating
intracellular AMP levels.
Length = 160
Score = 24.4 bits (54), Expect = 9.1
Identities = 8/35 (22%), Positives = 10/35 (28%), Gaps = 7/35 (20%)
Query: 78 NIKFIRGRIGRSLRNLR-------YVPELRFRYDT 105
F+R L + PELR D
Sbjct: 14 ATAFLRDAFQAYLDGGLPDARVRAFYPELRVTTDG 48
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 0.138 0.406
Gapped
Lambda K H
0.267 0.0792 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,066,498
Number of extensions: 118075
Number of successful extensions: 325
Number of sequences better than 10.0: 1
Number of HSP's gapped: 316
Number of HSP's successfully gapped: 27
Length of query: 128
Length of database: 5,994,473
Length adjustment: 82
Effective length of query: 46
Effective length of database: 4,222,617
Effective search space: 194240382
Effective search space used: 194240382
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 (23.3 bits)