RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780244|ref|YP_003064657.1| 30S ribosomal protein S5
[Candidatus Liberibacter asiaticus str. psy62]
(199 letters)
>gnl|CDD|179061 PRK00550, rpsE, 30S ribosomal protein S5; Validated.
Length = 168
Score = 231 bits (591), Expect = 1e-61
Identities = 86/160 (53%), Positives = 117/160 (73%), Gaps = 1/160 (0%)
Query: 13 QNREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVR 72
E+ + +++VAINRV+ + GGRRF+FS LVVVGD K +VGF + AREVPEA+R
Sbjct: 4 MRIEKNKLELEEKVVAINRVTKVVKGGRRFSFSALVVVGDGKGRVGFGYGKAREVPEAIR 63
Query: 73 KATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGM 132
KA E AK+NMI V L+ G T+ H+ +G+ GA KV+++ A GTGVIAGGA+RAV E+ G+
Sbjct: 64 KAVEDAKKNMIKVPLV-GGTIPHEVIGKFGAAKVLLKPASEGTGVIAGGAVRAVLELAGV 122
Query: 133 HDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIK 172
DV+AKS+GS+NP NV+RATF+ L+ P +VA +RG
Sbjct: 123 KDVLAKSLGSNNPINVVRATFDALKQLRSPEEVAAKRGKS 162
>gnl|CDD|130093 TIGR01021, rpsE_bact, ribosomal protein S5, bacterial/organelle
type. This model finds chloroplast ribosomal protein S5
as well as bacterial ribosomal protein S5. A candidate
mitochondrial form (Saccharomyces cerevisiae YBR251W and
its homolog) differs substantially and is not included
in this model.
Length = 154
Score = 182 bits (464), Expect = 6e-47
Identities = 79/147 (53%), Positives = 110/147 (74%), Gaps = 1/147 (0%)
Query: 24 DRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMI 83
+R++A+NRVS + GGRRF+FS LVVVGD K +VGF A+EVP+A++KA E A++N+I
Sbjct: 4 ERLIAVNRVSKVVKGGRRFSFSALVVVGDGKGRVGFGFGKAKEVPDAIKKAVEKARKNLI 63
Query: 84 SVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSS 143
+V L G T+ H+ +G GA KV+++ A GTGVIAGGA+RA+ E+ G+ D++AKS+GS+
Sbjct: 64 NVPLTKG-TIPHEVIGVSGAAKVLLKPASPGTGVIAGGAVRAILELAGVKDILAKSLGSN 122
Query: 144 NPHNVIRATFEVLRSQSHPRDVANRRG 170
NP NV+RATF+ L P DVA RG
Sbjct: 123 NPINVVRATFDALLKLKSPEDVAELRG 149
>gnl|CDD|179727 PRK04044, rps5p, 30S ribosomal protein S5P; Reviewed.
Length = 211
Score = 71.5 bits (176), Expect = 2e-13
Identities = 51/162 (31%), Positives = 79/162 (48%), Gaps = 13/162 (8%)
Query: 22 IVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRN 81
+ D ++ IN V GRR F V+VVVG+ VG A++V A+RKA AK N
Sbjct: 50 LEDEVLDINMVQRMTDSGRRVRFRVVVVVGNRDGYVGVGQGKAKQVGPAIRKAIRNAKLN 109
Query: 82 MISVSLLDG---------RTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGM 132
+I V G ++ G+ G+ +V ++ A G G++AG + V E+ G+
Sbjct: 110 IIKVRRGCGSWECGCGEPHSVPFKVTGKAGSVEVTLKPAPRGLGLVAGDVAKKVLELAGI 169
Query: 133 HDVVAKSIGSS-NPHNVIRATFEVLRSQS---HPRDVANRRG 170
DV ++ G + N +ATF L++ P D A +RG
Sbjct: 170 KDVWTRTFGETRTTVNFAKATFNALKNTYKVRTPPDWAEKRG 211
>gnl|CDD|162160 TIGR01020, rpsE_arch, ribosomal protein S5(archaeal
type)/S2(eukaryote cytosolic type). This model finds
eukaryotic ribosomal protein S2 as well as archaeal
ribosomal protein S5.
Length = 212
Score = 65.6 bits (160), Expect = 8e-12
Identities = 42/145 (28%), Positives = 68/145 (46%), Gaps = 10/145 (6%)
Query: 24 DRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMI 83
+ ++ ++ V GRR F VVVG+ VG A+EV A+RKA AK N+I
Sbjct: 52 EEVLDVSLVQRMTDSGRRTRFRAFVVVGNRDGYVGLGIGKAKEVAPAIRKAIINAKLNII 111
Query: 84 SVSLLDG---------RTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHD 134
V G ++ G+ G+ +V + A G G++AG + V + G+ D
Sbjct: 112 PVRRGCGSWECGCGRPHSVPFKVTGKCGSVRVRLIPAPRGLGLVAGDVAKKVLRLAGIDD 171
Query: 135 VVAKSIGSSNP-HNVIRATFEVLRS 158
V ++ G + N +ATF+ L+
Sbjct: 172 VWTQTRGETRTTVNFAKATFDALKK 196
>gnl|CDD|185425 PTZ00070, PTZ00070, 40S ribosomal protein S2; Provisional.
Length = 257
Score = 55.9 bits (135), Expect = 7e-09
Identities = 44/149 (29%), Positives = 70/149 (46%), Gaps = 8/149 (5%)
Query: 18 RDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEA 77
++ + D ++ I V G+R F VVVGD +G A+EV A+R A A
Sbjct: 76 AESKLKDEVMKIMPVQKQTSAGQRTRFKAFVVVGDGNGHIGLGAKVAKEVATAIRGAIIA 135
Query: 78 AKRNMISV-------SLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVL 130
AK N++ V + + T+ G+ G+ +V + A GTG++A + + E
Sbjct: 136 AKLNLVPVRRGYWGNKIGEPHTVPMKVTGKCGSVRVRLVPAPRGTGIVAAPTPKKILEFA 195
Query: 131 GMHDVVAKSIGSSNPH-NVIRATFEVLRS 158
G+ DV S G + N ++ATF LR
Sbjct: 196 GVEDVFTSSRGKTRTRGNFLKATFYALRK 224
>gnl|CDD|183859 PRK13103, secA, preprotein translocase subunit SecA; Reviewed.
Length = 913
Score = 30.7 bits (69), Expect = 0.24
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 12/76 (15%)
Query: 54 KSKVGFAHSTAREVPEAVRKATEAAKRNM----ISVSLLDGRTLHHDGVG--RHGAGKVI 107
K+++ + + +PEA A EA KR M V L+ G TLH + R G GK +
Sbjct: 51 KARLAKGETLDQLLPEAFAVAREAGKRVMGMRHFDVQLIGGMTLHEGKIAEMRTGEGKTL 110
Query: 108 MRS------AMAGTGV 117
+ + A++G GV
Sbjct: 111 VGTLAVYLNALSGKGV 126
>gnl|CDD|183164 PRK11504, tynA, tyramine oxidase; Provisional.
Length = 647
Score = 29.1 bits (66), Expect = 0.74
Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 2/41 (4%)
Query: 132 MHDVVAKSIGSSNPH-NVIRATFEVLRSQSH-PRDVANRRG 170
+ V +G NPH N +L ++S RD G
Sbjct: 458 EVNSVPVPMGPDNPHGNAFYTRETLLETESEAARDADPSTG 498
>gnl|CDD|149298 pfam08161, NUC173, NUC173 domain. This is the central domain of of
novel family of hypothetical nucleolar proteins.
Length = 198
Score = 29.1 bits (66), Expect = 0.87
Identities = 8/38 (21%), Positives = 16/38 (42%), Gaps = 8/38 (21%)
Query: 141 GSSNPH--NVIRATFEVLRSQSHP------RDVANRRG 170
++ V+ A FE L +S+P + + + R
Sbjct: 14 QAAWKEVLQVLSALFEKLGERSNPLLLKVLKTLGDLRT 51
>gnl|CDD|178689 PLN03144, PLN03144, Carbon catabolite repressor protein 4 homolog;
Provisional.
Length = 606
Score = 28.9 bits (65), Expect = 0.91
Identities = 21/59 (35%), Positives = 27/59 (45%), Gaps = 8/59 (13%)
Query: 44 FSVLVVVGDTKSKVGFAHS--TAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGVGR 100
F +VV +T VG S T+R +P A R +I V+ LDG H D GR
Sbjct: 196 FECVVVDAETGLPVGHPQSILTSRVIP-----APSPTPRRLIQVNGLDG-MGHLDLDGR 248
>gnl|CDD|134348 PRK00694, PRK00694, 4-hydroxy-3-methylbut-2-en-1-yl diphosphate
synthase; Validated.
Length = 606
Score = 28.7 bits (64), Expect = 0.94
Identities = 13/27 (48%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 125 AVCEVLGMHDVVAKSIGSSNPHNVIRA 151
VCE L DVV S+ SSNP ++ A
Sbjct: 194 EVCEKLDYRDVVF-SMKSSNPKVMVAA 219
>gnl|CDD|130763 TIGR01702, CO_DH_cata, carbon-monoxide dehydrogenase, catalytic
subunit. This model represents the carbon-monoxide
dehydrogenase catalytic subunit. This protein is related
to prismane (also called hybrid cluster protein), a
complex whose activity is not yet fully described; the
two share similar sets of ligands to unusual
metal-containing clusters.
Length = 621
Score = 28.2 bits (63), Expect = 1.6
Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 14/90 (15%)
Query: 47 LVVVGDTKSKVGFAH-STAREVPE---AVRKATEAAKRNMISVSLLDGRTLHHDGVGRHG 102
+ G K V S + + V E KRN++ ++ G
Sbjct: 425 AIASGKIKGVVLVVGCSNLKNGGQDSSTVTLTKELIKRNILVLAT---------GCSNGA 475
Query: 103 AGKVIMRSAMAGTGVIAGGAIRAVCEVLGM 132
K + + +AG ++ VC+ LG+
Sbjct: 476 LEKAGLMT-PEAAEELAGEGLKGVCKALGI 504
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 28.0 bits (63), Expect = 1.6
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 8/42 (19%)
Query: 46 VLVVVGDTKS-------KVGFAHST-AREVPEAVRKATEAAK 79
L+++G+T K GF + A + EAV+KA E AK
Sbjct: 375 KLILLGETAQEIAEAARKYGFDNILFAETLEEAVKKAYEIAK 416
>gnl|CDD|117463 pfam08896, DUF1842, Domain of unknown function (DUF1842). This
domain is found at the N-terminus of proteins that are
functionally uncharacterized.
Length = 114
Score = 27.2 bits (61), Expect = 2.5
Identities = 14/33 (42%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 31 RVSTALPGGRRFAFSVLVVVGDTKSKVGFAHST 63
RV T LPG ++LV D KS G A T
Sbjct: 9 RVGTGLPGAPVLTLNLLVYTPD-KSVSGTAVIT 40
>gnl|CDD|180524 PRK06309, PRK06309, DNA polymerase III subunit epsilon; Validated.
Length = 232
Score = 26.7 bits (59), Expect = 4.1
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 116 GVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPR 163
G A RA+ +V+ +H V + +G +P V +++L HPR
Sbjct: 139 GFEENQAHRALDDVITLHRVFSALVGDLSPQQV----YDLLNESCHPR 182
>gnl|CDD|163120 TIGR03055, photo_alph_chp2, putative photosynthetic complex
assembly protein 2. This uncharacterized protein family
was identified, by the method of partial phylogenetic
profiling, as having a matching phylogenetic
distribution to that of the photosynthetic reaction
center of the alpha-proteobacterial type. It is nearly
always encoded near other photosynthesis-related genes,
including puhA.
Length = 245
Score = 26.3 bits (58), Expect = 6.0
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 4/31 (12%)
Query: 93 LHHDGVGRHGAGKVIMRSAMAGTGVIAGGAI 123
D +GR +RS +AG ++ GG
Sbjct: 19 WLLDSLGRS----THLRSVVAGLPLLTGGLW 45
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
0.316 0.129 0.359
Gapped
Lambda K H
0.267 0.0656 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,140,817
Number of extensions: 196882
Number of successful extensions: 465
Number of sequences better than 10.0: 1
Number of HSP's gapped: 461
Number of HSP's successfully gapped: 26
Length of query: 199
Length of database: 5,994,473
Length adjustment: 89
Effective length of query: 110
Effective length of database: 4,071,361
Effective search space: 447849710
Effective search space used: 447849710
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.1 bits)