RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 027306
(225 letters)
>gnl|CDD|235495 PRK05498, rplF, 50S ribosomal protein L6; Validated.
Length = 178
Score = 285 bits (732), Expect = 3e-99
Identities = 96/177 (54%), Positives = 127/177 (71%)
Query: 47 SRIGKQPIEVPSNVTITLGGQDLKVKGPLGELSLVYPREVKVDREDSFLRVRKTVETRRA 106
SRIGK+PI +P+ V +T+ G + VKGP GELS +V V ED+ + V + ++++A
Sbjct: 2 SRIGKKPIAIPAGVEVTINGNVVTVKGPKGELSRTLNPDVTVKVEDNEITVTRPDDSKKA 61
Query: 107 NQMHGLFRTLTDNMVVGVSKGFEKKLQMVGVGYRAALEGQVLVLSLGFSHPVRMTIPDGI 166
+HG R L +NMVVGV++GFEKKL++VGVGYRA ++G+ L LSLG+SHPV IP+GI
Sbjct: 62 RALHGTTRALINNMVVGVTEGFEKKLEIVGVGYRAQVKGKKLNLSLGYSHPVEYEIPEGI 121
Query: 167 KVNVEENTRITVSGYDKSAIGQFAASIRKWRPPEPYKGKGVKYVDEVIRRKEGKAGK 223
V V + T I V G DK +GQ AA IR +RPPEPYKGKG++Y EV+RRKEGK K
Sbjct: 122 TVEVPKPTEIVVKGIDKQLVGQVAAEIRSYRPPEPYKGKGIRYAGEVVRRKEGKKKK 178
>gnl|CDD|213843 TIGR03654, L6_bact, ribosomal protein L6, bacterial type. [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 175
Score = 276 bits (709), Expect = 1e-95
Identities = 96/175 (54%), Positives = 122/175 (69%)
Query: 47 SRIGKQPIEVPSNVTITLGGQDLKVKGPLGELSLVYPREVKVDREDSFLRVRKTVETRRA 106
SRIGK+PI +P+ V +T+ G + VKGP GELS V V ED L V + +++ A
Sbjct: 1 SRIGKKPIAIPAGVEVTIDGNVVTVKGPKGELSRTLHPGVTVKVEDGQLTVSRPNDSKEA 60
Query: 107 NQMHGLFRTLTDNMVVGVSKGFEKKLQMVGVGYRAALEGQVLVLSLGFSHPVRMTIPDGI 166
+HG R L +NMV+GVS+GFEKKL++VGVGYRA L+G+ L LSLG+SHPV IP+GI
Sbjct: 61 RALHGTTRALINNMVIGVSEGFEKKLEIVGVGYRAQLQGKKLNLSLGYSHPVEYEIPEGI 120
Query: 167 KVNVEENTRITVSGYDKSAIGQFAASIRKWRPPEPYKGKGVKYVDEVIRRKEGKA 221
V V + T I V G DK +GQ AA IR +R PEPYKGKG++Y EV+RRKEGK
Sbjct: 121 TVEVPKPTEIVVKGIDKQLVGQVAAEIRAFRKPEPYKGKGIRYAGEVVRRKEGKK 175
>gnl|CDD|177062 CHL00140, rpl6, ribosomal protein L6; Validated.
Length = 178
Score = 257 bits (658), Expect = 5e-88
Identities = 102/177 (57%), Positives = 135/177 (76%)
Query: 47 SRIGKQPIEVPSNVTITLGGQDLKVKGPLGELSLVYPREVKVDREDSFLRVRKTVETRRA 106
SRIGK PI++P NV +++ Q +KVKGP G LS P + ++ +D+ L V K E+++A
Sbjct: 2 SRIGKLPIKIPDNVNVSIDDQIIKVKGPKGTLSRKIPDLITIEIQDNSLFVSKKDESKKA 61
Query: 107 NQMHGLFRTLTDNMVVGVSKGFEKKLQMVGVGYRAALEGQVLVLSLGFSHPVRMTIPDGI 166
+HGL+RTL +NMV+GVS+GFEKKL++ GVGYRA ++G+ L+L+LG+SHPV++ IP GI
Sbjct: 62 RALHGLYRTLINNMVIGVSEGFEKKLELQGVGYRAQVQGKDLILNLGYSHPVKIKIPPGI 121
Query: 167 KVNVEENTRITVSGYDKSAIGQFAASIRKWRPPEPYKGKGVKYVDEVIRRKEGKAGK 223
V VE NT IT+ G DK +GQFAA IR RPPEPYKGKG++Y EVIRRK GKAGK
Sbjct: 122 SVEVENNTNITIKGIDKELVGQFAAKIRSVRPPEPYKGKGIRYKGEVIRRKAGKAGK 178
>gnl|CDD|223175 COG0097, RplF, Ribosomal protein L6P/L9E [Translation, ribosomal
structure and biogenesis].
Length = 178
Score = 233 bits (597), Expect = 1e-78
Identities = 98/178 (55%), Positives = 125/178 (70%), Gaps = 2/178 (1%)
Query: 47 SRIGKQPIEVPSNVTITLGGQDLKVKGPLGELSLVYPRE-VKVDREDSFLRVRKTVETRR 105
SRIGK+PI +P+ VT+++ GQ + VKGP GEL+ + VKV+ ED+ L VR V+ +R
Sbjct: 2 SRIGKRPIVIPAGVTVSIEGQVVTVKGPKGELTREFHDNVVKVEVEDNILVVRP-VDGKR 60
Query: 106 ANQMHGLFRTLTDNMVVGVSKGFEKKLQMVGVGYRAALEGQVLVLSLGFSHPVRMTIPDG 165
+HG R L +NMV GV++GFEKKL++VGVGYRA + G L L LG+SHPV + IP+G
Sbjct: 61 KRALHGTVRALINNMVKGVTEGFEKKLEIVGVGYRAQVVGGNLELFLGYSHPVVIEIPEG 120
Query: 166 IKVNVEENTRITVSGYDKSAIGQFAASIRKWRPPEPYKGKGVKYVDEVIRRKEGKAGK 223
I V V T I V G DK +GQ AA+IR R PEPYKGKG++Y E IRRKEGK GK
Sbjct: 121 ITVEVPGPTEIVVEGIDKELVGQVAANIRAARKPEPYKGKGIRYDGEYIRRKEGKTGK 178
>gnl|CDD|215872 pfam00347, Ribosomal_L6, Ribosomal protein L6.
Length = 76
Score = 90.7 bits (226), Expect = 5e-24
Identities = 36/75 (48%), Positives = 45/75 (60%)
Query: 135 VGVGYRAALEGQVLVLSLGFSHPVRMTIPDGIKVNVEENTRITVSGYDKSAIGQFAASIR 194
+ VG R +++G LVL LG + IP G+ V VE+ T I VSG DK +GQFAA I
Sbjct: 1 IPVGVRVSIDGVNLVLVLGPKGELTREIPPGVTVKVEKITVIIVSGIDKEKVGQFAALIG 60
Query: 195 KWRPPEPYKGKGVKY 209
+R P P GKGV Y
Sbjct: 61 TYRAPIPNMGKGVSY 75
Score = 48.0 bits (115), Expect = 8e-08
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 4/76 (5%)
Query: 56 VPSNVTITL-GGQDLKVKGPLGELSLVYPREVKVDREDSFLRVRKTVETRRANQ---MHG 111
+P V +++ G + V GP GEL+ P V V E + + ++ + Q + G
Sbjct: 1 IPVGVRVSIDGVNLVLVLGPKGELTREIPPGVTVKVEKITVIIVSGIDKEKVGQFAALIG 60
Query: 112 LFRTLTDNMVVGVSKG 127
+R NM GVS G
Sbjct: 61 TYRAPIPNMGKGVSYG 76
>gnl|CDD|234296 TIGR03653, arch_L6P, archaeal ribosomal protein L6P. Members of
this protein family are the archaeal ribosomal protein
L6P. The top-scoring proteins not selected by this model
are eukaryotic cytosolic ribosomal protein L9. Bacterial
ribosomal protein L6 scores lower and is described by a
distinct model [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 170
Score = 89.3 bits (222), Expect = 2e-22
Identities = 51/146 (34%), Positives = 84/146 (57%), Gaps = 8/146 (5%)
Query: 54 IEVPSNVTITLGGQDLKVKGPLGELS--LVYPREVKVDREDSFLRVRKTVETRRANQMHG 111
IE+P V++T+ G + VKGP GE++ L YP +++ ED + + ++ M G
Sbjct: 4 IEIPEGVSVTIEGNIVTVKGPKGEVTRELWYP-GIEISVEDGKVVIETDFARKKDKAMVG 62
Query: 112 LFRTLTDNMVVGVSKGFEKKLQMVGVGY--RAALEGQVLVLS--LGFSHPVRMTIPDGIK 167
+R+ NM+ GV++GFE K+++V + + +EG +V+ LG P R IP G+K
Sbjct: 63 TYRSHIKNMIKGVTEGFEYKMKVVYSHFPMQVKVEGNKVVIENFLGEKAPRRAKIPGGVK 122
Query: 168 VNVEENTRITVSGYDKSAIGQFAASI 193
V V+ + V+G DK +GQ AA+I
Sbjct: 123 VKVKGE-EVIVTGIDKEDVGQTAANI 147
>gnl|CDD|235496 PRK05518, rpl6p, 50S ribosomal protein L6P; Reviewed.
Length = 180
Score = 89.1 bits (222), Expect = 3e-22
Identities = 52/149 (34%), Positives = 78/149 (52%), Gaps = 14/149 (9%)
Query: 54 IEVPSNVTITLGGQDLKVKGPLGELS--LVYPREVKVDREDSFLRVRKTVETRRANQMHG 111
IE+P VT+ + G + VKGP GEL+ YP V + ED + + ++ M G
Sbjct: 10 IEIPEGVTVEIEGLVVTVKGPKGELTRDFWYP-GVTISVEDGKVVIETEFARKKTKAMVG 68
Query: 112 LFRTLTDNMVVGVSKGFEKKLQMVGVGY-----RAALEGQVLVLS--LGFSHPVRMTIPD 164
F + NM+ GV++GFE KL++V Y + ++G +V+ LG P R I
Sbjct: 69 TFASHIKNMIKGVTEGFEYKLKIV---YSHFPMQVKVQGNEVVIENFLGEKSPRRAKILG 125
Query: 165 GIKVNVEENTRITVSGYDKSAIGQFAASI 193
G+KV V+ + V G DK +GQ AA+I
Sbjct: 126 GVKVKVKGE-DVIVEGIDKEDVGQTAANI 153
>gnl|CDD|240234 PTZ00027, PTZ00027, 60S ribosomal protein L6; Provisional.
Length = 190
Score = 36.3 bits (84), Expect = 0.005
Identities = 24/90 (26%), Positives = 47/90 (52%), Gaps = 9/90 (10%)
Query: 52 QPIEVPSNVTITLGGQDLKVKGPLGELSLVY---PREVKVDREDSFLRVRKTVETRRANQ 108
+ I +P VT+T+ + + V G GEL+ + P ++K+ ++ +++V T
Sbjct: 8 EKIRIPEGVTVTVKSRKVTVTGKYGELTRSFRHLPVDIKLSKDGKYIKVEMWFGTPS--- 64
Query: 109 MHGLFRTL---TDNMVVGVSKGFEKKLQMV 135
RT+ NM+ GV+K F+ K+++V
Sbjct: 65 HLACIRTVCSHIKNMMTGVTKKFQYKMRLV 94
>gnl|CDD|140206 PTZ00179, PTZ00179, 60S ribosomal protein L9; Provisional.
Length = 189
Score = 33.0 bits (75), Expect = 0.061
Identities = 28/122 (22%), Positives = 60/122 (49%), Gaps = 7/122 (5%)
Query: 54 IEVPSNVTITLGGQDLKVKGPLGELS--LVYPR-EVKVDREDSFLRVRKTVETRRANQMH 110
I +P +VT+++ + + VKG G L+ L + + + +V++++ + ++ N
Sbjct: 9 ITIPEDVTVSVKDRIVTVKGKRGTLTKDLRHLQLDFRVNKKNRTFTAVRWFGSKIPNSTI 68
Query: 111 GLFRTLTDNMVVGVSKGFEKKLQMVGVGY--RAALEGQVLVLS--LGFSHPVRMTIPDGI 166
+ NM+ GV+KGF K++ + ++E Q++ + LG R + D +
Sbjct: 69 NTALSHVRNMITGVTKGFRFKVRFAYAHFPISVSVENQLVEIRNFLGEKRVRRQVVADTV 128
Query: 167 KV 168
KV
Sbjct: 129 KV 130
>gnl|CDD|233187 TIGR00921, 2A067, The (Largely Archaeal Putative)
Hydrophobe/Amphiphile Efflux-3 (HAE3) Family.
Characterized members of the RND superfamily all
probably catalyze substrate efflux via an H+ antiport
mechanism. These proteins are found ubiquitously in
bacteria, archaea and eukaryotes. They fall into seven
phylogenetic families, this family (2.A.6.7) consists of
uncharacterised putative transporters, largely in the
Archaea [Transport and binding proteins, Unknown
substrate].
Length = 719
Score = 29.0 bits (65), Expect = 2.4
Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 7/75 (9%)
Query: 91 EDSFLRVRKTVETRRANQMHGLFRTLTDNMVVGVSKGFEKKLQMVGVGYRAALEG--QVL 148
+ V +++E R N G F +T + ++ E++ +G A+ G VL
Sbjct: 154 VPIYNDVERSLE--RTNPPSGKFLDVTGSP--AINYDIEREFGK-DMGTTMAISGILVVL 208
Query: 149 VLSLGFSHPVRMTIP 163
VL L F R +P
Sbjct: 209 VLLLDFKRWWRPLLP 223
>gnl|CDD|235749 PRK06225, PRK06225, aspartate aminotransferase; Provisional.
Length = 380
Score = 28.6 bits (64), Expect = 3.3
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 10/47 (21%)
Query: 159 RMTIPDGIKVNVEENTRITV---------SGYDKSAIGQFAASIRKW 196
++T P+ +K N++ENTR+ S Y + I +FA R
Sbjct: 144 KLT-PELVKENMDENTRLIYLIDPLNPLGSSYTEEEIKEFAEIARDN 189
>gnl|CDD|132372 TIGR03329, Phn_aa_oxid, putative aminophosphonate oxidoreductase.
This clade of sequences are members of the pfam01266
family of FAD-dependent oxidoreductases. Characterized
proteins within this family include glycerol-3-phosphate
dehydrogenase (1.1.99.5), sarcosine oxidase beta subunit
(1.5.3.1) and a number of deaminating amino acid
oxidases (1.4.-.-). These genes have been consistently
observed in a genomic context including genes for the
import and catabolism of 2-aminoethylphosphonate (AEP).
If the substrate of this oxidoreductase is AEP itself,
then it is probably acting in the manner of a
deaminating oxidase, resulting in the same product
(phosphonoacetaldehyde) as the transaminase PhnW
(TIGR02326), but releasing ammonia instead of coupling
to pyruvate:alanine. Alternatively, it is reasonable to
suppose that the various ABC cassette transporters which
are also associated with these loci allow the import of
phosphonates closely related to AEP which may not be
substrates for PhnW.
Length = 460
Score = 28.2 bits (63), Expect = 3.5
Identities = 16/42 (38%), Positives = 18/42 (42%), Gaps = 8/42 (19%)
Query: 177 TVSGYDKSAIGQFAASIRKWRPPEPYKGKGVKYVDEVIRRKE 218
T S K +G F PPEP + G V IRRKE
Sbjct: 399 TRSPLVKGPLGYF--------PPEPIRYLGALVVRNAIRRKE 432
>gnl|CDD|191688 pfam07107, WI12, Wound-induced protein WI12. This family consists
of several plant wound-induced protein sequences related
to WI12 from Mesembryanthemum crystallinum. Wounding,
methyl jasmonate, and pathogen infection is known to
induce local WI12 expression. WI12 expression is also
thought to be developmentally controlled in the placenta
and developing seeds. WI12 preferentially accumulates in
the cell wall and it has been suggested that it plays a
role in the reinforcement of cell wall composition after
wounding and during plant development. This family seems
partly related to the NTF2-like superfamily.
Length = 109
Score = 26.0 bits (57), Expect = 7.8
Identities = 12/43 (27%), Positives = 17/43 (39%), Gaps = 2/43 (4%)
Query: 161 TIPDGIKVNVEE--NTRITVSGYDKSAIGQFAASIRKWRPPEP 201
T+ DG+ V E NT +TV+ A G A +
Sbjct: 46 TVGDGVITQVREYFNTSLTVTRLGLGAAGWDATASAPCSHCCS 88
>gnl|CDD|216366 pfam01208, URO-D, Uroporphyrinogen decarboxylase (URO-D).
Length = 338
Score = 27.2 bits (61), Expect = 7.9
Identities = 12/59 (20%), Positives = 23/59 (38%), Gaps = 7/59 (11%)
Query: 160 MTIPD--GIKVNVEENTRITVSGYDKSAIGQFAASIRKWRPPEPYKGKGVKYVDEVIRR 216
+ + G +V+ E V ++ + K P+P + + + YV E IR
Sbjct: 75 LVEAEAMGCEVDFGEGEGPVVENPIRTP-----EDVEKLEVPDPLEDERLPYVLEAIRI 128
>gnl|CDD|236261 PRK08412, flgL, flagellar hook-associated protein FlgL; Validated.
Length = 827
Score = 27.1 bits (60), Expect = 9.3
Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 5/60 (8%)
Query: 139 YRAALEGQVLVLSLGFSHPVRMTIPDGIKVNVEENTRITVSGYDKSAIGQFAASIRKWRP 198
Y L+ +S+ + ++ I D N+ NT++ YD A F+ ++ +P
Sbjct: 633 YINLLKQAKGNVSVNLNEQGKLIIQD----NMHSNTKMQFMLYDSDA-NDFSQALHSDKP 687
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 0.381
Gapped
Lambda K H
0.267 0.0613 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,216,996
Number of extensions: 1039486
Number of successful extensions: 814
Number of sequences better than 10.0: 1
Number of HSP's gapped: 791
Number of HSP's successfully gapped: 19
Length of query: 225
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 132
Effective length of database: 6,812,680
Effective search space: 899273760
Effective search space used: 899273760
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: 57 (26.0 bits)