RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 024440
(267 letters)
>gnl|CDD|178791 PRK00010, rplE, 50S ribosomal protein L5; Validated.
Length = 179
Score = 319 bits (821), Expect = e-112
Identities = 106/177 (59%), Positives = 135/177 (76%)
Query: 63 RLKTTYLEKIVPLLREEFSYTNIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALITG 122
RLK Y E+IVP L +EF Y N+ QVPK+EKIV+N G+G+A + K LE A+ DL LITG
Sbjct: 3 RLKEKYKEEIVPALMKEFGYKNVMQVPKLEKIVLNMGVGEAVADKKLLENAVEDLTLITG 62
Query: 123 QRPVKTRARNSIATFKIREGEPLGIAVTLRGNMMYSFLDRLINLGLPRTRDFQGVNPNSF 182
Q+PV T+A+ SIA FK+REG P+G VTLRG MY FLDRLIN+ LPR RDF+G++P SF
Sbjct: 63 QKPVVTKAKKSIAGFKLREGMPIGCKVTLRGERMYEFLDRLINIALPRVRDFRGLSPKSF 122
Query: 183 DGHGNYSIGVKEQSVFPEIRYDALGKPKGIDVCITTTAKTDKEGQRLLALMGMPFRE 239
DG GNY++G+KEQ +FPEI YD + K +G+D+ I TTAKTD+E + LL G PFR+
Sbjct: 123 DGRGNYTLGIKEQIIFPEIDYDKIDKIRGMDITIVTTAKTDEEARALLKAFGFPFRK 179
>gnl|CDD|214356 CHL00078, rpl5, ribosomal protein L5.
Length = 181
Score = 306 bits (787), Expect = e-107
Identities = 109/179 (60%), Positives = 147/179 (82%)
Query: 61 TGRLKTTYLEKIVPLLREEFSYTNIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALI 120
RLK+ Y EKIVP L E+F Y NIHQVPK++KIV+N G+G+A+QN+K LE+++ +L +I
Sbjct: 2 VQRLKSLYKEKIVPKLIEKFLYKNIHQVPKLKKIVINRGLGEASQNSKILESSIKELTII 61
Query: 121 TGQRPVKTRARNSIATFKIREGEPLGIAVTLRGNMMYSFLDRLINLGLPRTRDFQGVNPN 180
TGQ+P+ TRA+ +IA FKIRE P+G++VTLRG+ MY+FLDRLINL LPR RDFQG++P
Sbjct: 62 TGQKPIITRAKKAIAGFKIREKMPVGVSVTLRGDKMYAFLDRLINLALPRIRDFQGLSPK 121
Query: 181 SFDGHGNYSIGVKEQSVFPEIRYDALGKPKGIDVCITTTAKTDKEGQRLLALMGMPFRE 239
SFDGHGNY++G+KEQ +FPEI YD + + +G+D+ I TTAKTD+EG LL +GMPF++
Sbjct: 122 SFDGHGNYNLGLKEQLMFPEIDYDKIDQIRGMDISIVTTAKTDQEGLALLKELGMPFKD 180
>gnl|CDD|223172 COG0094, RplE, Ribosomal protein L5 [Translation, ribosomal
structure and biogenesis].
Length = 180
Score = 270 bits (692), Expect = 2e-92
Identities = 104/178 (58%), Positives = 134/178 (75%)
Query: 63 RLKTTYLEKIVPLLREEFSYTNIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALITG 122
RLK Y ++IVP L ++F Y+N QVP+IEK+VVN G+G+AA + K LE A DL LITG
Sbjct: 3 RLKEKYKDEIVPALIKKFGYSNPMQVPRIEKVVVNMGVGEAAADGKRLEKAAKDLELITG 62
Query: 123 QRPVKTRARNSIATFKIREGEPLGIAVTLRGNMMYSFLDRLINLGLPRTRDFQGVNPNSF 182
Q+PV T+A+ SIA FKIREG P+G+ VTLRG MY FLDRL+N+ LPR RDF+G++P SF
Sbjct: 63 QKPVITKAKKSIAGFKIREGMPIGVKVTLRGERMYEFLDRLLNIALPRVRDFRGLSPKSF 122
Query: 183 DGHGNYSIGVKEQSVFPEIRYDALGKPKGIDVCITTTAKTDKEGQRLLALMGMPFREG 240
DG GNYS G+KEQ +FPEI YD + +G+D+ I TTAK D E + LL+ G+PFR+
Sbjct: 123 DGRGNYSFGIKEQIIFPEIDYDPIIGIRGMDITIVTTAKGDVEARALLSAFGIPFRKR 180
>gnl|CDD|201383 pfam00673, Ribosomal_L5_C, ribosomal L5P family C-terminus. This
region is found associated with pfam00281.
Length = 95
Score = 159 bits (405), Expect = 3e-50
Identities = 58/95 (61%), Positives = 71/95 (74%)
Query: 144 PLGIAVTLRGNMMYSFLDRLINLGLPRTRDFQGVNPNSFDGHGNYSIGVKEQSVFPEIRY 203
P+G VTLRG MY FLDRLIN+ LPR RDF+G++P SFDG GNYS G+KE +FPEI+Y
Sbjct: 1 PIGCKVTLRGEKMYEFLDRLINVALPRIRDFRGLSPKSFDGRGNYSFGIKEHIIFPEIKY 60
Query: 204 DALGKPKGIDVCITTTAKTDKEGQRLLALMGMPFR 238
D + G+D+ I TTAKTDKE + LL +GMPF
Sbjct: 61 DPIIGIFGMDITIVTTAKTDKEARALLKELGMPFF 95
>gnl|CDD|235259 PRK04219, rpl5p, 50S ribosomal protein L5P; Reviewed.
Length = 177
Score = 109 bits (274), Expect = 2e-29
Identities = 54/133 (40%), Positives = 78/133 (58%), Gaps = 17/133 (12%)
Query: 89 PKIEKIVVNCGIGDAAQNAKGLEAAMNDLALITGQRPVKTRARNSIATFKIREGEPLGIA 148
P+IEK+VVN G+G++ + L A L +TGQ+PV+TRA+ +I F IR+GEP+G+
Sbjct: 15 PRIEKVVVNIGVGESGER---LTKAEKLLEELTGQKPVRTRAKKTIPDFGIRKGEPIGVK 71
Query: 149 VTLRGNMMYSFLDRLINLGLPRTRDFQGVNPNSFDGHGNYSIGVKEQSVFPEIRYDALGK 208
VTLRG FL + R + +SFD GN S G++E FP ++YD
Sbjct: 72 VTLRGEKAEEFLKTALEAVGNR------LKASSFDETGNVSFGIEEHIDFPGVKYD---- 121
Query: 209 PK----GIDVCIT 217
P+ G+DVC+T
Sbjct: 122 PEIGIFGMDVCVT 134
>gnl|CDD|109342 pfam00281, Ribosomal_L5, Ribosomal protein L5.
Length = 56
Score = 78.1 bits (193), Expect = 4e-19
Identities = 32/57 (56%), Positives = 44/57 (77%), Gaps = 1/57 (1%)
Query: 84 NIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALITGQRPVKTRARNSIATFKIR 140
N+ +VPK+EKIVVN G+G+A N K LE A +L I+GQ+P+ T+A+ SIA+FKIR
Sbjct: 1 NVMEVPKLEKIVVNMGVGEAGDN-KILEKAALELEEISGQKPIITKAKKSIASFKIR 56
>gnl|CDD|185485 PTZ00156, PTZ00156, 60S ribosomal protein L11; Provisional.
Length = 172
Score = 55.4 bits (134), Expect = 2e-09
Identities = 34/105 (32%), Positives = 60/105 (57%), Gaps = 9/105 (8%)
Query: 90 KIEKIVVNCGIGDAAQNAKGLEAAMNDLALITGQRPVKTRARNSIATFKIREGEPLGIAV 149
+IEK+V+N +G++ L A L +TGQ+PV ++AR ++ +F IR E + V
Sbjct: 12 RIEKLVLNICVGESGDR---LTRAAKVLEQLTGQKPVFSKARYTVRSFGIRRNEKIACHV 68
Query: 150 TLRGNMMYSFLDRLINLGLPRTRDFQGVNPNSFDGHGNYSIGVKE 194
T+RG+ L+R GL + ++F+ + +F GN+ G++E
Sbjct: 69 TVRGDKAEEILER----GL-KVKEFE-LKKRNFSDTGNFGFGIQE 107
>gnl|CDD|178930 PRK00211, PRK00211, sulfur relay protein TusC; Validated.
Length = 119
Score = 29.1 bits (66), Expect = 1.0
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 117 LALITGQRPVKTRARNSIATFKI 139
L+ GQ+P AR+ IATFK+
Sbjct: 45 FQLLPGQQPDAILARDYIATFKL 67
>gnl|CDD|221472 pfam12228, DUF3604, Protein of unknown function (DUF3604). This
family of proteins is found in bacteria. Proteins in
this family are typically between 621 and 693 amino
acids in length.
Length = 592
Score = 29.5 bits (67), Expect = 2.1
Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 5/51 (9%)
Query: 8 HSSASS-----FHGRFPALSSSSYVRPTYPNPINVNGVVSVKAAAGGIVLV 53
H+ +S F G+F AL + R P+ + A G+ V
Sbjct: 331 HTGLASVEEDNFFGKFGALDEPAEKRGRIPDGGEGTDQSGWEMGASGLAAV 381
>gnl|CDD|79056 PRK12581, PRK12581, oxaloacetate decarboxylase; Provisional.
Length = 468
Score = 28.9 bits (64), Expect = 3.5
Identities = 23/83 (27%), Positives = 35/83 (42%), Gaps = 8/83 (9%)
Query: 162 RLINLGLPRTRDFQGVNPNSFDGHGNYS-------IGVKEQSVFPEIR-YDALGKPKGID 213
R + GLP TR + + G+ +Y+ I + Q+ R +DAL P+ I
Sbjct: 76 RTLKKGLPNTRLQMLLRGQNLLGYRHYADDIVDKFISLSAQNGIDVFRIFDALNDPRNIQ 135
Query: 214 VCITTTAKTDKEGQRLLALMGMP 236
+ KT KE Q +A P
Sbjct: 136 QALRAVKKTGKEAQLCIAYTTSP 158
>gnl|CDD|131404 TIGR02351, thiH, thiazole biosynthesis protein ThiH. Members this
protein family are the ThiH protein of thiamine
biosynthesis, a homolog of the BioB protein of biotin
biosynthesis. Genes for the this protein generally are
found in operons with other thiamin biosynthesis genes
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Thiamine].
Length = 366
Score = 28.5 bits (64), Expect = 3.6
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 3/37 (8%)
Query: 68 YLEKIVPLLREEFSYTNIHQVPKIE---KIVVNCGIG 101
Y+ + + L RE FS I P E K +V G+
Sbjct: 138 YIAEAIKLAREYFSSLAIEVQPLNEEEYKKLVEAGLD 174
>gnl|CDD|172177 PRK13619, psbV, cytochrome c-550; Provisional.
Length = 160
Score = 27.5 bits (61), Expect = 5.4
Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 3/28 (10%)
Query: 178 NPNSFDGHGNYS---IGVKEQSVFPEIR 202
+P S+DG +YS V +FPE+R
Sbjct: 103 HPTSYDGEDDYSELHPNVSRPDIFPELR 130
>gnl|CDD|239390 cd03116, MobB, Molybdenum is an essential trace element in the
form of molybdenum cofactor (Moco) which is associated
with the metabolism of nitrogen, carbon and sulfur by
redox active enzymes. In E. coli, the synthesis of Moco
involves genes from several loci: moa, mob, mod, moe
and mog. The mob locus contains mobA and mobB genes.
MobB catalyzes the attachment of the guanine
dinucleotide to molybdopterin.
Length = 159
Score = 26.8 bits (60), Expect = 7.5
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 65 KTTYLEKIVPLLREE 79
KTT LEK++P L
Sbjct: 14 KTTLLEKLIPALSAR 28
>gnl|CDD|200229 TIGR03010, sulf_tusC_dsrF, sulfur relay protein TusC/DsrF. The
three proteins TusB, TusC, and TusD form a heterohexamer
responsible for a sulfur relay reaction. In large
numbers of proteobacterial species, this complex acts on
a Cys-derived persulfide moiety, delivered by the
cysteine desulfurase IscS to TusA, then to TusBCD. The
activated sulfur group is then transferred to TusE
(DsrC), then by MnmA (TrmU) for modification of an
anticodon nucleotide in tRNAs for Glu, Lys, and Gln. The
sulfur relay complex TusBCD is also found, under the
designation DsrEFH, in phototrophic and chemotrophic
sulfur bacteria, such as Chromatium vinosum. In these
organisms, it seems the primary purpose is related to
sulfur flux, such as oxidation from sulfide to molecular
sulfur to sulfate [Protein synthesis, tRNA and rRNA base
modification].
Length = 116
Score = 26.3 bits (59), Expect = 7.9
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 117 LALITGQRPVKTRARNSIATFKI 139
L L+ Q+P ++ IATFK
Sbjct: 43 LQLLKNQQPELILQKDYIATFKA 65
>gnl|CDD|222606 pfam14224, DUF4331, Domain of unknown function (DUF4331). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 223 and 526 amino
acids in length. There is a conserved FPY sequence
motif.
Length = 348
Score = 27.5 bits (61), Expect = 8.6
Identities = 17/107 (15%), Positives = 32/107 (29%), Gaps = 8/107 (7%)
Query: 131 RNSIATFKIREGEPLGIAVTLRGNMMYSFLDRLINLGLPRTRDFQGVNPNSFDGHGNYSI 190
+ + + R + + L + +L ++ G SI
Sbjct: 110 ADGAVSSDGTTPGGGRVFAGQRDDPFFFDLGEVFDLVALLGGRTPDAARDTLAGKNVTSI 169
Query: 191 GVKEQSVFPEIRYDALG-KPKGIDVCITTTAKTDKEGQRLLALMGMP 236
+ E+ LG I V TT+ T+ G + +G P
Sbjct: 170 AL-------EVPTSCLGGGNPVIGVWATTSRATNGGGWVQVDRLGRP 209
>gnl|CDD|226753 COG4303, EutB, Ethanolamine ammonia-lyase, large subunit [Amino
acid transport and metabolism].
Length = 453
Score = 27.4 bits (61), Expect = 9.2
Identities = 12/41 (29%), Positives = 15/41 (36%), Gaps = 10/41 (24%)
Query: 206 LGKPKGIDVCITTTAKTDKEGQRLLA----------LMGMP 236
G G D C T AK D+ L +MG+P
Sbjct: 355 SGISMGCDCCYTNHAKADQNDNENLMTLLAAAGCNYIMGIP 395
>gnl|CDD|217421 pfam03200, Glyco_hydro_63, Mannosyl oligosaccharide glucosidase.
This is a family of eukaryotic enzymes belonging to
glycosyl hydrolase family 63. They catalyze the specific
cleavage of the non-reducing terminal glucose residue
from Glc(3)Man(9)GlcNAc(2). Mannosyl oligosaccharide
glucosidase EC:3.2.1.106 is the first enzyme in the
N-linked oligosaccharide processing pathway.
Length = 775
Score = 27.3 bits (61), Expect = 9.8
Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 4/45 (8%)
Query: 52 LVEKSEAEK----TGRLKTTYLEKIVPLLREEFSYTNIHQVPKIE 92
L+E AE ++L++ P L+ F + N Q +E
Sbjct: 469 LLESIRAEGFYNNENEKILSFLKRAYPRLKTWFEWFNTTQSGPLE 513
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.135 0.387
Gapped
Lambda K H
0.267 0.0615 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,634,471
Number of extensions: 1323091
Number of successful extensions: 1067
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1063
Number of HSP's successfully gapped: 24
Length of query: 267
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 172
Effective length of database: 6,723,972
Effective search space: 1156523184
Effective search space used: 1156523184
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 (21.6 bits)
S2: 58 (26.4 bits)