RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780636|ref|YP_003065049.1| ribonuclease D [Candidatus
Liberibacter asiaticus str. psy62]
(207 letters)
>gnl|CDD|128750 smart00474, 35EXOc, 3'-5' exonuclease. 3\' -5' exonuclease
proofreading domain present in DNA polymerase I, Werner
syndrome helicase, RNase D and other enzymes.
Length = 172
Score = 112 bits (283), Expect = 6e-26
Identities = 56/152 (36%), Positives = 81/152 (53%), Gaps = 1/152 (0%)
Query: 20 VDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIF 79
+A+DTET GL +L ++Q+S II A + L +L DE K+
Sbjct: 21 GGEVALDTETTGLNSYSGKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDETITKVG 80
Query: 80 HYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSD 139
H +FD+ VL FG+ + +F T +A+ L ++HGL LKE LG+ + K +Q SD
Sbjct: 81 HNAKFDLHVL-ARFGIELENIFDTMLAAYLLLGGPSKHGLATLLKEYLGVELDKEEQKSD 139
Query: 140 WSADDLSDEQLQYAASDVVHLHALRLQFTEKL 171
W A LS+EQLQYAA D L L + ++L
Sbjct: 140 WGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171
>gnl|CDD|130455 TIGR01388, rnd, ribonuclease D. This model describes ribonuclease
D, a 3'-exonuclease shown to act on tRNA both in vitro
and when overexpressed in vivo. Trusted members of this
family are restricted to the Proteobacteria; Aquifex,
Mycobacterial, and eukaryotic homologs are not
full-length homologs. Ribonuclease D is not essential in
E. coli and is deleterious when overexpressed. Its
precise biological role is still unknown.
Length = 367
Score = 92.5 bits (230), Expect = 7e-20
Identities = 55/194 (28%), Positives = 92/194 (47%), Gaps = 14/194 (7%)
Query: 7 HEGDIPAEC-AARYVDAIAVDTETLGLMPRRDR-----LCIVQLSPGDGTVDIIRIAAGQ 60
+ ++ C A R +A+DTE + R+R L ++Q++ G+ I +
Sbjct: 4 TDDELATVCEAVRTFPFVALDTEFV-----RERTFWPQLGLIQVADGEQLALIDPLVIID 58
Query: 61 KNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLK 120
+ L +L DE K+ H D+ V FG +P+F T+IA+ + G
Sbjct: 59 WSP--LKELLRDESVVKVLHAASEDLEVFLNLFGELPQPLFDTQIAAAFC-GFGMSMGYA 115
Query: 121 DNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLA 180
++E+LG+ + K++ +DW A L+D QL+YAA+DV +L L + E+L+ GR
Sbjct: 116 KLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLEESGRLAWL 175
Query: 181 TSCCNFLMDRAELD 194
C L DR
Sbjct: 176 EEECTLLTDRRTYV 189
>gnl|CDD|182762 PRK10829, PRK10829, ribonuclease D; Provisional.
Length = 373
Score = 57.3 bits (139), Expect = 3e-09
Identities = 50/176 (28%), Positives = 82/176 (46%), Gaps = 5/176 (2%)
Query: 16 AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKR 75
AAR AIA+DTE + +L ++QL G+ + +I +P +L D +
Sbjct: 18 AARAFPAIALDTEFVRTRTYYPQLGLIQLYDGE-QLSLIDPLGITDWSP-FKALLRDPQV 75
Query: 76 EKIFHYGRFDIAVLFYTFGVRVRPVFCTKI-ASRLTRTYTNQHGLKDNLKELLGINISKA 134
K H G D+ V FG +P+ T+I A+ R + G ++E G+ + K+
Sbjct: 76 TKFLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLS--CGFASMVEEYTGVTLDKS 133
Query: 135 QQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDR 190
+ +DW A LS+ Q +YAA+DV +L + + + + G A C L R
Sbjct: 134 ESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGWLPAALDECRLLCQR 189
>gnl|CDD|180237 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 53.2 bits (129), Expect = 5e-08
Identities = 37/161 (22%), Positives = 62/161 (38%), Gaps = 7/161 (4%)
Query: 16 AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNA-PNLVGMLVDEK 74
+ A DTET L P + L + + G I + + L +L D
Sbjct: 311 KLKAAGLFAFDTETTSLDPMQAELVGLSFAVEPGEAAYIPLDQLDREVLAALKPLLEDPA 370
Query: 75 REKIFHYGRFDIAVLFYTFGVRVRPV-FCTKIASRLTRTYTNQHGLKDNLKELLGINISK 133
+K+ ++D+ VL +G+ +R + F T +AS L +HGL + LG
Sbjct: 371 IKKVGQNLKYDLHVL-ARYGIELRGIAFDTMLASYLLDP-GRRHGLDSLAERYLGHKTIS 428
Query: 134 AQQS--SDWSADDLSDEQL-QYAASDVVHLHALRLQFTEKL 171
++ + + E+ +YAA D L KL
Sbjct: 429 FEEVAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKL 469
>gnl|CDD|184938 PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA polymerase;
Provisional.
Length = 553
Score = 52.3 bits (126), Expect = 1e-07
Identities = 26/86 (30%), Positives = 35/86 (40%), Gaps = 3/86 (3%)
Query: 91 YTFGVRVRPVFCTKIASRLTRTYTN--QHGLKDNLKELLGINISKAQQSSDWSADDLSDE 148
GVRV +AS+L L LG + K Q+S S D +E
Sbjct: 63 LAAGVRVERCHDLMLASQLLLGSEGRAGSSLSAAAARALGEGLDKPPQTSALS-DPPDEE 121
Query: 149 QLQYAASDVVHLHALRLQFTEKLQRL 174
QL YAA+D L L ++L R+
Sbjct: 122 QLLYAAADADVLLELYAVLADQLNRI 147
>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated.
Length = 328
Score = 30.4 bits (69), Expect = 0.29
Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 3/62 (4%)
Query: 121 DNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLA 180
D +K+LL S +Q + W L L D H LR Q T+ + LG +D+
Sbjct: 217 DGVKKLLKQQQSASQLAESWLKVPLL--LLFDWFCDWAHD-ILRYQLTQDEEGLGLADMR 273
Query: 181 TS 182
Sbjct: 274 KV 275
>gnl|CDD|179264 PRK01254, PRK01254, hypothetical protein; Provisional.
Length = 707
Score = 28.9 bits (65), Expect = 1.1
Identities = 11/19 (57%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 186 FL-MDRAELDLLGWENVDI 203
FL M R E+D LGW++ DI
Sbjct: 24 FLPMSREEMDQLGWDSCDI 42
>gnl|CDD|149520 pfam08497, Radical_SAM_N, Radical SAM N-terminal. This domain
tends to occur to the N-terminus of the pfam04055 domain
in hypothetical bacterial proteins.
Length = 298
Score = 28.2 bits (64), Expect = 1.7
Identities = 7/19 (36%), Positives = 11/19 (57%), Gaps = 1/19 (5%)
Query: 186 FL-MDRAELDLLGWENVDI 203
FL R E+ GW+ +D+
Sbjct: 1 FLPTSREEMKARGWDQLDV 19
>gnl|CDD|149870 pfam08936, CsoSCA, Carboxysome Shell Carbonic Anhydrase.
Carboxysome Shell Carbonic Anhydrase is a bacterial
carbonic anhydrase localized in the carboxysome, where
it converts bicarbonate ions to carbon dioxide for use
in carbon fixation. It contains three domains, these
being: (1) an N-terminal domain composed primarily of
four alpha-helices; (2) a catalytic domain containing a
tightly bound zinc ion and (3) a C-terminal domain with
weak structural similarity to the catalytic domain.
Length = 459
Score = 27.6 bits (62), Expect = 2.3
Identities = 18/59 (30%), Positives = 24/59 (40%), Gaps = 13/59 (22%)
Query: 4 IRVHEGDIPAE----CAARYVDAIAVDTETLGLMPRRDRLCIVQL------SPGDGTVD 52
IRVH +P R+VD + ETLGL + R I + + G G D
Sbjct: 251 IRVH---VPDADGEVDLDRWVDTADLYRETLGLSAEQARAAIAEAVAADGWAQGPGAPD 306
>gnl|CDD|162979 TIGR02701, shell_carb_anhy, carboxysome shell carbonic anhydrase.
This model describes a carboxysome shell protein that
proves to be a novel class, designated epsilon, of
carbonic anhydrase. It tends to be encoded near genes
for RuBisCo and for other carboxysome shell proteins.
Length = 450
Score = 26.3 bits (58), Expect = 5.3
Identities = 17/44 (38%), Positives = 19/44 (43%), Gaps = 7/44 (15%)
Query: 4 IRVHEGDIPAE----CAARYVDAIAVDTETLGLMPRRDRLCIVQ 43
IRVH IP RYVD + ETLGL R I +
Sbjct: 252 IRVH---IPDADGFVNLYRYVDNTVLYAETLGLTADEARQHIAE 292
>gnl|CDD|181529 PRK08662, PRK08662, nicotinate phosphoribosyltransferase; Reviewed.
Length = 343
Score = 26.4 bits (59), Expect = 5.6
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 190 RAELDLLGWENVDIF 204
R LD+ G+E+V IF
Sbjct: 251 RWTLDIRGYEHVKIF 265
>gnl|CDD|178146 PLN02531, PLN02531, GTP cyclohydrolase I.
Length = 469
Score = 26.3 bits (58), Expect = 6.1
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 157 VVHLHALRLQFTEKLQR 173
+VH + RLQ E+L R
Sbjct: 385 IVHFYGFRLQVQERLTR 401
>gnl|CDD|181680 PRK09182, PRK09182, DNA polymerase III subunit epsilon;
Validated.
Length = 294
Score = 26.1 bits (58), Expect = 7.2
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 22 AIAVDTETLGLMPRRD 37
+ +DTET GL PR+D
Sbjct: 39 GVILDTETTGLDPRKD 54
>gnl|CDD|181671 PRK09145, PRK09145, DNA polymerase III subunit epsilon;
Validated.
Length = 202
Score = 25.6 bits (57), Expect = 8.4
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 23 IAVDTETLGLMPRRDRL 39
+A+D ET GL PRR +
Sbjct: 32 VALDCETTGLDPRRAEI 48
>gnl|CDD|181551 PRK08769, PRK08769, DNA polymerase III subunit delta'; Validated.
Length = 319
Score = 25.7 bits (56), Expect = 8.8
Identities = 24/98 (24%), Positives = 38/98 (38%), Gaps = 27/98 (27%)
Query: 122 NLKELLGINISKAQQSSDWSADDLSDEQLQYAA-----------SDVVHLHALRLQF--- 167
+L+++ + W+ D +D++L++AA +D LH L F
Sbjct: 223 DLEQIASGRAGAVDVAQRWTNDGQADQRLRHAADLALAQASAGLTDPSRLHKLATWFDAA 282
Query: 168 --TEKLQRLG-RSDLATSCCNFLMDRAELDLLGWENVD 202
T L R R+DLA EL LL W +
Sbjct: 283 NRTRDLLRTTVRADLAV---------TEL-LLAWREGE 310
>gnl|CDD|179566 PRK03354, PRK03354, crotonobetainyl-CoA dehydrogenase; Validated.
Length = 380
Score = 25.6 bits (56), Expect = 8.9
Identities = 15/35 (42%), Positives = 18/35 (51%), Gaps = 7/35 (20%)
Query: 169 EKLQRLG-RSDLATSCCNFLMDRAEL---DLLGWE 199
KL++LG R D SCC D EL D+ G E
Sbjct: 195 TKLEKLGLRMD---SCCEITFDDVELDEKDMFGRE 226
>gnl|CDD|147901 pfam05992, SbmA_BacA, SbmA/BacA-like family. The Rhizobium
meliloti bacA gene encodes a function that is essential
for bacterial differentiation into bacteroids within
plant cells in the symbiosis between R. meliloti and
alfalfa. An Escherichia coli homolog of BacA, SbmA, is
implicated in the uptake of microcins and bleomycin.
This family is likely to be a subfamily of the ABC
transporter family.
Length = 315
Score = 25.8 bits (57), Expect = 9.3
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 79 FHYGRFDIAVLFY 91
FHY F+IA +FY
Sbjct: 235 FHYLYFNIARIFY 247
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
0.323 0.137 0.408
Gapped
Lambda K H
0.267 0.0645 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,427,955
Number of extensions: 215210
Number of successful extensions: 407
Number of sequences better than 10.0: 1
Number of HSP's gapped: 399
Number of HSP's successfully gapped: 25
Length of query: 207
Length of database: 5,994,473
Length adjustment: 89
Effective length of query: 118
Effective length of database: 4,071,361
Effective search space: 480420598
Effective search space used: 480420598
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (25.1 bits)