RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9430
(255 letters)
>gnl|CDD|240253 PTZ00068, PTZ00068, 60S ribosomal protein L13a; Provisional.
Length = 202
Score = 242 bits (619), Expect = 3e-81
Identities = 96/158 (60%), Positives = 121/158 (76%)
Query: 87 ILIDGRGHLLGRLASIVAKTILNGNRVVVVRAELLNISGNFFRNKLKYLAFLNKRCNVNP 146
I+ID +GHLLGRLAS+VAK +L G ++VVVR E LNISG+ FRNK+KY FL KR N NP
Sbjct: 6 IVIDCKGHLLGRLASVVAKELLLGQKIVVVRCEDLNISGSLFRNKVKYEEFLRKRMNTNP 65
Query: 147 ARGPFHYRAPARIFWKTVRGMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRT 206
RGPFH+RAP+ IFW+TVRGM PHK RGA ALKRLKV+EG+P Y + +R+ +P+ALR
Sbjct: 66 RRGPFHHRAPSDIFWRTVRGMLPHKTKRGAAALKRLKVFEGVPAPYDKVKRVVIPSALRV 125
Query: 207 VCLKPGRSYCSVGRISHEVGWKYKTIVRHLERKRREKS 244
+ LKP R Y +G +S VGWKY +V LE KR+E++
Sbjct: 126 LRLKPERPYTVLGDLSAHVGWKYADVVAKLEEKRKERA 163
Score = 132 bits (335), Expect = 2e-38
Identities = 53/79 (67%), Positives = 64/79 (81%)
Query: 7 KPILIDGRGHLLGRLASIVAKTILNGNRVVVVRAELLNISGNFFRNKLKYLAFLNKRCNV 66
K I+ID +GHLLGRLAS+VAK +L G ++VVVR E LNISG+ FRNK+KY FL KR N
Sbjct: 4 KVIVIDCKGHLLGRLASVVAKELLLGQKIVVVRCEDLNISGSLFRNKVKYEEFLRKRMNT 63
Query: 67 NPARGPFHYRAPARIFWKT 85
NP RGPFH+RAP+ IFW+T
Sbjct: 64 NPRRGPFHHRAPSDIFWRT 82
>gnl|CDD|162192 TIGR01077, L13_A_E, ribosomal protein L13, archaeal/eukaryotic.
This model represents ribosomal protein of L13 from the
Archaea and from the eukaryotic cytosol. Bacterial and
organellar forms are represented by model TIGR01066
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 142
Score = 180 bits (458), Expect = 9e-58
Identities = 85/143 (59%), Positives = 105/143 (73%), Gaps = 1/143 (0%)
Query: 87 ILIDGRGHLLGRLASIVAKTILNGNRVVVVRAELLNISGNFFRNKLKYLAFLNKRCNVNP 146
+IDG GH+LGRLAS+VAK +LNG +VVVV AE + ISGNF+RNKLKY FL KR NP
Sbjct: 1 TVIDGSGHILGRLASVVAKQLLNGEKVVVVNAEKIVISGNFYRNKLKYKEFLRKRTLTNP 60
Query: 147 ARGPFHYRAPARIFWKTVRGMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRT 206
RGPF RAP+RIF +TVRGM PHK RG AL+RLKVY GIPP+ +++R+ VP AL
Sbjct: 61 RRGPFFPRAPSRIFRRTVRGMLPHKTARGRAALRRLKVYVGIPPELDKKKRVVVPEAL-V 119
Query: 207 VCLKPGRSYCSVGRISHEVGWKY 229
L P R Y ++G ++ +GWKY
Sbjct: 120 SRLSPTRKYVTLGELAKFLGWKY 142
Score = 108 bits (272), Expect = 8e-30
Identities = 51/77 (66%), Positives = 60/77 (77%)
Query: 9 ILIDGRGHLLGRLASIVAKTILNGNRVVVVRAELLNISGNFFRNKLKYLAFLNKRCNVNP 68
+IDG GH+LGRLAS+VAK +LNG +VVVV AE + ISGNF+RNKLKY FL KR NP
Sbjct: 1 TVIDGSGHILGRLASVVAKQLLNGEKVVVVNAEKIVISGNFYRNKLKYKEFLRKRTLTNP 60
Query: 69 ARGPFHYRAPARIFWKT 85
RGPF RAP+RIF +T
Sbjct: 61 RRGPFFPRAPSRIFRRT 77
>gnl|CDD|238230 cd00392, Ribosomal_L13, Ribosomal protein L13. Protein L13, a
large ribosomal subunit protein, is one of five proteins
required for an early folding intermediate of 23S rRNA
in the assembly of the large subunit. L13 is situated on
the bottom of the large subunit, near the polypeptide
exit site. It interacts with proteins L3 and L6, and
forms an extensive network of interactions with 23S
rRNA. L13 has been identified as a homolog of the human
breast basic conserved protein 1 (BBC1), a protein
identified through its increased expression in breast
cancer. L13 expression is also upregulated in a variety
of human gastrointestinal cancers, suggesting it may
play a role in the etiology of a variety of human
malignancies.
Length = 114
Score = 122 bits (308), Expect = 2e-35
Identities = 52/114 (45%), Positives = 62/114 (54%), Gaps = 13/114 (11%)
Query: 87 ILIDGRGHLLGRLASIVAKTILN------------GNRVVVVRAELLNISGNFFRNKLKY 134
+ID +G +LGRLAS VAK +L G+ VVVV AE + I+G +R K+ Y
Sbjct: 2 HVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVYY 61
Query: 135 LAFLNKRCNVNPARGPFHYRAPARIFWKTVRGMTPHKLDRGAKALKRLKVYEGI 188
NP GP H RAP RI + VRGM P K G ALKRLKVYEG
Sbjct: 62 RHTGYPGGLKNPTAGPLHPRAPERILKRAVRGMLP-KNKLGRAALKRLKVYEGA 114
Score = 91.0 bits (227), Expect = 2e-23
Identities = 35/89 (39%), Positives = 45/89 (50%), Gaps = 12/89 (13%)
Query: 9 ILIDGRGHLLGRLASIVAKTILN------------GNRVVVVRAELLNISGNFFRNKLKY 56
+ID +G +LGRLAS VAK +L G+ VVVV AE + I+G +R K+ Y
Sbjct: 2 HVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVYY 61
Query: 57 LAFLNKRCNVNPARGPFHYRAPARIFWKT 85
NP GP H RAP RI +
Sbjct: 62 RHTGYPGGLKNPTAGPLHPRAPERILKRA 90
>gnl|CDD|223180 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 114 bits (288), Expect = 5e-32
Identities = 48/133 (36%), Positives = 61/133 (45%), Gaps = 18/133 (13%)
Query: 87 ILIDGRGHLLGRLASIVAKTILNGN------------RVVVVRAELLNISGNFFRNKLKY 134
+ID G +LGRLAS VAK + + V+V+ AE + I+G +K Y
Sbjct: 16 YVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTDKKYY 75
Query: 135 LAFLNKRCNVNP-ARGPFHYRAPARIFWKTVRGMTPHKLDRGAKALKRLKVYEGIPPKYA 193
NP GP R P RI + VRGM P G ALKRLKVY GIP +
Sbjct: 76 RHSGYPGGLKNPTRGGPLAPRRPERILERAVRGMLPKN-PLGRAALKRLKVYAGIPHPHE 134
Query: 194 RRQRLCVPTALRT 206
++ P AL
Sbjct: 135 AQK----PEALEL 143
Score = 77.3 bits (191), Expect = 7e-18
Identities = 30/95 (31%), Positives = 41/95 (43%), Gaps = 13/95 (13%)
Query: 4 ISRKPILIDGRGHLLGRLASIVAKTILNGN------------RVVVVRAELLNISGNFFR 51
+ RK +ID G +LGRLAS VAK + + V+V+ AE + I+G
Sbjct: 11 VERKWYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLT 70
Query: 52 NKLKYLAFLNKRCNVNP-ARGPFHYRAPARIFWKT 85
+K Y NP GP R P RI +
Sbjct: 71 DKKYYRHSGYPGGLKNPTRGGPLAPRRPERILERA 105
>gnl|CDD|201314 pfam00572, Ribosomal_L13, Ribosomal protein L13.
Length = 128
Score = 109 bits (275), Expect = 2e-30
Identities = 44/123 (35%), Positives = 57/123 (46%), Gaps = 13/123 (10%)
Query: 87 ILIDGRGHLLGRLASIVAKTIL------------NGNRVVVVRAELLNISGNFFRNKLKY 134
+ID +G +LGRLAS VAK + G+ VVV+ AE + ++G K Y
Sbjct: 2 HVIDAKGQILGRLASKVAKLLRGKHKPTYTPHVDCGDYVVVINAEKIVLTGKKRDQKKYY 61
Query: 135 LAFLNKRCNVNPARGPFHYRAPARIFWKTVRGMTPHKLDRGAKALKRLKVYEGIPPKYAR 194
NP R P RI + VRGM P G ALKRLKVY G P +A
Sbjct: 62 RHTGYPGGLKNPTAKGPLERKPERILERAVRGMLPKNK-LGRAALKRLKVYAGSPHPHAA 120
Query: 195 RQR 197
++
Sbjct: 121 QKP 123
Score = 72.2 bits (178), Expect = 4e-16
Identities = 27/89 (30%), Positives = 37/89 (41%), Gaps = 12/89 (13%)
Query: 9 ILIDGRGHLLGRLASIVAKTIL------------NGNRVVVVRAELLNISGNFFRNKLKY 56
+ID +G +LGRLAS VAK + G+ VVV+ AE + ++G K Y
Sbjct: 2 HVIDAKGQILGRLASKVAKLLRGKHKPTYTPHVDCGDYVVVINAEKIVLTGKKRDQKKYY 61
Query: 57 LAFLNKRCNVNPARGPFHYRAPARIFWKT 85
NP R P RI +
Sbjct: 62 RHTGYPGGLKNPTAKGPLERKPERILERA 90
>gnl|CDD|235793 PRK06394, rpl13p, 50S ribosomal protein L13P; Reviewed.
Length = 146
Score = 109 bits (276), Expect = 3e-30
Identities = 60/144 (41%), Positives = 84/144 (58%), Gaps = 3/144 (2%)
Query: 87 ILIDGRGHLLGRLASIVAKTILNGNRVVVVRAELLNISGNFFRNKLKYLAFLNKRCNVNP 146
++ID G +LGRLAS VAK +L G VV+V AE I+GN R KY + + NP
Sbjct: 5 VVIDAEGQILGRLASYVAKRLLEGEEVVIVNAEKAVITGNRERVIEKYKQRRERGSHYNP 64
Query: 147 AR-GPFHYRAPARIFWKTVRGMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALR 205
R GP + R P RIF +T+RGM P+K RG +ALKRLKVY G+P + ++ + A
Sbjct: 65 YRNGPKYPRRPDRIFKRTIRGMLPYKKPRGREALKRLKVYVGVPKELEGKEFEVIDEAD- 123
Query: 206 TVCLKPGRSYCSVGRISHEVGWKY 229
+ Y ++G +S E+G K+
Sbjct: 124 -LSRLSTIKYVTLGEVSKELGAKF 146
Score = 64.1 bits (157), Expect = 6e-13
Identities = 36/78 (46%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 9 ILIDGRGHLLGRLASIVAKTILNGNRVVVVRAELLNISGNFFRNKLKYLAFLNKRCNVNP 68
++ID G +LGRLAS VAK +L G VV+V AE I+GN R KY + + NP
Sbjct: 5 VVIDAEGQILGRLASYVAKRLLEGEEVVIVNAEKAVITGNRERVIEKYKQRRERGSHYNP 64
Query: 69 AR-GPFHYRAPARIFWKT 85
R GP + R P RIF +T
Sbjct: 65 YRNGPKYPRRPDRIFKRT 82
>gnl|CDD|181703 PRK09216, rplM, 50S ribosomal protein L13; Reviewed.
Length = 144
Score = 52.4 bits (127), Expect = 9e-09
Identities = 38/123 (30%), Positives = 53/123 (43%), Gaps = 33/123 (26%)
Query: 87 ILIDGRGHLLGRLASIVAKTIL-------------NGNRVVVVRAELLNISGNFFRNKLK 133
+ID G +LGRLAS VA +IL G+ V+V+ AE + ++G +K+
Sbjct: 16 YVIDAEGKVLGRLASEVA-SILRGKHKPTFTPHVDTGDFVIVINAEKVKLTGKKLTDKIY 74
Query: 134 Y--------LAFLNKRCNVNPARGPFHYRAPARIFWKTVRGMTPH-KLDRGAKALKRLKV 184
Y L K + P R+ K V+GM P L G K+LKV
Sbjct: 75 YRHSGYPGGL----KEITFGELLA----KKPERVIEKAVKGMLPKNPL--GRAMFKKLKV 124
Query: 185 YEG 187
Y G
Sbjct: 125 YAG 127
Score = 38.5 bits (91), Expect = 8e-04
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 14/66 (21%)
Query: 4 ISRKPILIDGRGHLLGRLASIVAKTIL-------------NGNRVVVVRAELLNISGNFF 50
+ RK +ID G +LGRLAS VA +IL G+ V+V+ AE + ++G
Sbjct: 11 VERKWYVIDAEGKVLGRLASEVA-SILRGKHKPTFTPHVDTGDFVIVINAEKVKLTGKKL 69
Query: 51 RNKLKY 56
+K+ Y
Sbjct: 70 TDKIYY 75
>gnl|CDD|177072 CHL00159, rpl13, ribosomal protein L13; Validated.
Length = 143
Score = 51.5 bits (124), Expect = 2e-08
Identities = 35/121 (28%), Positives = 52/121 (42%), Gaps = 31/121 (25%)
Query: 88 LIDGRGHLLGRLASIVAKTIL------------NGNRVVVVRAELLNISGNFFRNKLKYL 135
+ID + LGRLA+ +A + G+ V+V+ AE + ++GN + K+
Sbjct: 18 IIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVINAEKIKVTGN--KTSQKFY 75
Query: 136 AFLNKRCNVNPAR-GPFHY--------RAPARIFWKTVRGMTPHKLDRGAKALKRLKVYE 186
+ R G R P RI K V+GM P K G K +LKVY+
Sbjct: 76 VR-------HSGRPGGLKIETFEELQNRLPNRIIEKAVKGMLP-KGPLGRKLFTKLKVYK 127
Query: 187 G 187
G
Sbjct: 128 G 128
Score = 37.3 bits (87), Expect = 0.002
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 12/56 (21%)
Query: 5 SRKPILIDGRGHLLGRLASIVAKTIL------------NGNRVVVVRAELLNISGN 48
+RK +ID + LGRLA+ +A + G+ V+V+ AE + ++GN
Sbjct: 13 NRKWYIIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVINAEKIKVTGN 68
>gnl|CDD|162186 TIGR01066, rplM_bact, ribosomal protein L13, bacterial type. This
model distinguishes ribosomal protein L13 of bacteria
and organelles from its eukarytotic and archaeal
counterparts [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 140
Score = 40.4 bits (95), Expect = 2e-04
Identities = 34/122 (27%), Positives = 49/122 (40%), Gaps = 33/122 (27%)
Query: 88 LIDGRGHLLGRLASIVAKTILN------------GNRVVVVRAELLNISGNFFRNKLKY- 134
++D G LGRLAS VA+ + G+ V+V+ AE + ++G K+ Y
Sbjct: 15 VVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQKVYYR 74
Query: 135 ---------LAFLNKRCNVNPARGPFHYRAPARIFWKTVRGMTPHKLDRGAKALKRLKVY 185
+ R P R+ V+GM P K G K K+LKVY
Sbjct: 75 HSGYPGGLKSRTFEEMIA----------RKPERVLEHAVKGMLP-KNRLGRKLFKKLKVY 123
Query: 186 EG 187
G
Sbjct: 124 AG 125
Score = 31.5 bits (72), Expect = 0.18
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 12/65 (18%)
Query: 4 ISRKPILIDGRGHLLGRLASIVAKTILN------------GNRVVVVRAELLNISGNFFR 51
RK ++D G LGRLAS VA+ + G+ V+V+ AE + ++G
Sbjct: 9 KKRKWYVVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLE 68
Query: 52 NKLKY 56
K+ Y
Sbjct: 69 QKVYY 73
>gnl|CDD|235843 PRK06635, PRK06635, aspartate kinase; Reviewed.
Length = 404
Score = 28.2 bits (64), Expect = 4.4
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 20 RLASIVAKTILNGNRVVVV 38
R+A V + G++VVVV
Sbjct: 21 RVAERVKAEVEAGHQVVVV 39
Score = 28.2 bits (64), Expect = 4.4
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 98 RLASIVAKTILNGNRVVVV 116
R+A V + G++VVVV
Sbjct: 21 RVAERVKAEVEAGHQVVVV 39
>gnl|CDD|183276 PRK11688, PRK11688, hypothetical protein; Provisional.
Length = 154
Score = 27.5 bits (62), Expect = 5.1
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 32 GNRVVVVRAELLNISG 47
GN+V V R EL N G
Sbjct: 126 GNKVAVARMELHNEQG 141
Score = 27.5 bits (62), Expect = 5.1
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 110 GNRVVVVRAELLNISG 125
GN+V V R EL N G
Sbjct: 126 GNKVAVARMELHNEQG 141
>gnl|CDD|222072 pfam13360, PQQ_2, PQQ-like domain. This domain contains several
repeats of the PQQ repeat.
Length = 234
Score = 27.4 bits (61), Expect = 8.0
Identities = 9/34 (26%), Positives = 15/34 (44%)
Query: 83 WKTPILIDGRGHLLGRLASIVAKTILNGNRVVVV 116
W+ P+ G + RL I +++G RV
Sbjct: 143 WEAPVAAPRGGSEIERLVDITGTPVVDGGRVYAS 176
>gnl|CDD|224049 COG1124, DppF, ABC-type dipeptide/oligopeptide/nickel transport
system, ATPase component [Amino acid transport and
metabolism / Inorganic ion transport and metabolism].
Length = 252
Score = 27.2 bits (61), Expect = 8.2
Identities = 14/66 (21%), Positives = 25/66 (37%), Gaps = 18/66 (27%)
Query: 161 WKTVR-----GMTPHKLDRGAKALKRLKVYEGIPPKYARR----------QRLCVPTALR 205
+TV + PH L + + + L G+PP + R QR+ + R
Sbjct: 98 RRTVGRILSEPLRPHGLSKSQQRIAELLDQVGLPPSFLDRRPHELSGGQRQRIAI---AR 154
Query: 206 TVCLKP 211
+ +P
Sbjct: 155 ALIPEP 160
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
0.327 0.142 0.442
Gapped
Lambda K H
0.267 0.0686 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,543,428
Number of extensions: 1316669
Number of successful extensions: 1414
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1389
Number of HSP's successfully gapped: 37
Length of query: 255
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 160
Effective length of database: 6,723,972
Effective search space: 1075835520
Effective search space used: 1075835520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 58 (26.2 bits)