RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4335
(152 letters)
>gnl|CDD|240255 PTZ00070, PTZ00070, 40S ribosomal protein S2; Provisional.
Length = 257
Score = 232 bits (594), Expect = 2e-78
Identities = 88/114 (77%), Positives = 101/114 (88%), Gaps = 1/114 (0%)
Query: 8 RDGKIQSLEQIYLFSLPIKEFEIID-FFIGSSLKDEVLKIMPVQKQTRAGQRTRFKAFVA 66
+ GKI SLE+I+LFS+PIKE++I+D FF S LKDEV+KIMPVQKQT AGQRTRFKAFV
Sbjct: 48 KAGKITSLEEIFLFSIPIKEYQIVDHFFAESKLKDEVMKIMPVQKQTSAGQRTRFKAFVV 107
Query: 67 IGDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVRRGYWGNKIGKPHTVPCK 120
+GD NGHIGLG K +KEVATAIRGAII AKL++VPVRRGYWGNKIG+PHTVP K
Sbjct: 108 VGDGNGHIGLGAKVAKEVATAIRGAIIAAKLNLVPVRRGYWGNKIGEPHTVPMK 161
>gnl|CDD|233235 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 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 212
Score = 178 bits (452), Expect = 1e-57
Identities = 58/115 (50%), Positives = 88/115 (76%), Gaps = 2/115 (1%)
Query: 8 RDGKIQSLEQIYLFSLPIKEFEIIDFFIGSSLKDEVLKIMPVQKQTRAGQRTRFKAFVAI 67
++GKI+S+++I+L +LPIKE EI+D+ + ++EVL + VQ+ T +G+RTRF+AFV +
Sbjct: 19 KEGKIKSIDEIFLRNLPIKEPEIVDYLLPDLNEEEVLDVSLVQRMTDSGRRTRFRAFVVV 78
Query: 68 GDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVRR--GYWGNKIGKPHTVPCK 120
G+ +G++GLG+ +KEVA AIR AII AKL+++PVRR G W G+PH+VP K
Sbjct: 79 GNRDGYVGLGIGKAKEVAPAIRKAIINAKLNIIPVRRGCGSWECGCGRPHSVPFK 133
>gnl|CDD|235213 PRK04044, rps5p, 30S ribosomal protein S5P; Reviewed.
Length = 211
Score = 125 bits (315), Expect = 8e-37
Identities = 52/114 (45%), Positives = 77/114 (67%), Gaps = 3/114 (2%)
Query: 9 DGKIQSLEQIYLFSLPIKEFEIIDFFIGSSLKDEVLKIMPVQKQTRAGQRTRFKAFVAIG 68
+GKI S+++I+ LPIKE EI+D + L+DEVL I VQ+ T +G+R RF+ V +G
Sbjct: 21 EGKITSIDEIFDSGLPIKEPEIVDVLL-PDLEDEVLDINMVQRMTDSGRRVRFRVVVVVG 79
Query: 69 DSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVRR--GYWGNKIGKPHTVPCK 120
+ +G++G+G +K+V AIR AI AKL+++ VRR G W G+PH+VP K
Sbjct: 80 NRDGYVGVGQGKAKQVGPAIRKAIRNAKLNIIKVRRGCGSWECGCGEPHSVPFK 133
>gnl|CDD|144065 pfam00333, Ribosomal_S5, Ribosomal protein S5, N-terminal domain.
Length = 67
Score = 103 bits (259), Expect = 5e-30
Identities = 34/67 (50%), Positives = 46/67 (68%)
Query: 38 SLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKL 97
L+++VL I VQK T+ G+R F+A V +GD NGH+GLG +KEV AIR AI AKL
Sbjct: 1 DLEEKVLVINRVQKVTKGGRRFSFRALVVVGDKNGHVGLGEGKAKEVPGAIRKAIEDAKL 60
Query: 98 SVVPVRR 104
+++ V R
Sbjct: 61 NLIEVPR 67
>gnl|CDD|223176 COG0098, RpsE, Ribosomal protein S5 [Translation, ribosomal
structure and biogenesis].
Length = 181
Score = 100 bits (251), Expect = 2e-27
Identities = 43/112 (38%), Positives = 62/112 (55%), Gaps = 15/112 (13%)
Query: 9 DGKIQSLEQIYLFSLPIKEFEIIDFFIGSSLKDEVLKIMPVQKQTRAGQRTRFKAFVAIG 68
+GKI ++E + LPIKE E+ L ++V+ I V K + G+R RF A V +G
Sbjct: 2 EGKIATIE--FKSGLPIKEPEV------DELLEKVVDINRVSKVVKGGRRFRFSALVVVG 53
Query: 69 DSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVRRGYWGNKIGKPHTVPCK 120
D NG +G G+ +KEV AIR AI AK +++ V R G HT+P +
Sbjct: 54 DRNGRVGFGIGKAKEVPEAIRKAIEDAKKNIIEVPR-------GNGHTIPHE 98
>gnl|CDD|234790 PRK00550, rpsE, 30S ribosomal protein S5; Validated.
Length = 168
Score = 50.1 bits (121), Expect = 2e-08
Identities = 26/69 (37%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 39 LKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAK-- 96
L+++V+ I V K + G+R F A V +GD G +G G ++EV AIR A+ AK
Sbjct: 13 LEEKVVAINRVTKVVKGGRRFSFSALVVVGDGKGRVGFGYGKAREVPEAIRKAVEDAKKN 72
Query: 97 LSVVPVRRG 105
+ VP+ G
Sbjct: 73 MIKVPLVGG 81
>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 [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 154
Score = 48.8 bits (117), Expect = 5e-08
Identities = 23/69 (33%), Positives = 40/69 (57%), Gaps = 2/69 (2%)
Query: 39 LKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLS 98
L++ ++ + V K + G+R F A V +GD G +G G +KEV AI+ A+ A+ +
Sbjct: 2 LEERLIAVNRVSKVVKGGRRFSFSALVVVGDGKGRVGFGFGKAKEVPDAIKKAVEAARKN 61
Query: 99 V--VPVRRG 105
+ VP+ +G
Sbjct: 62 LINVPLTKG 70
>gnl|CDD|177060 CHL00138, rps5, ribosomal protein S5; Validated.
Length = 143
Score = 40.7 bits (96), Expect = 4e-05
Identities = 20/54 (37%), Positives = 34/54 (62%)
Query: 43 VLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAK 96
V++I V K + G++ F+A V IG+ NG +G+GV + +V A++ A+ AK
Sbjct: 28 VIQIKRVSKVVKGGKKLSFRAIVVIGNENGWVGVGVGKADDVQNAVKKAVTDAK 81
>gnl|CDD|213797 TIGR03333, salvage_mtnX,
2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate
phosphatase. Members of this family are the methionine
salvage enzyme MnxX, a member of the HAD-superfamily
hydrolases, subfamily IB (see TIGR01488). Members are
found in Bacillus subtilis and related species, paired
with MtnW (TIGR03332). In most species that recycle
methionine from methylthioadenosine, the single protein
MtnC replaces the MtnW/MtnX pair. In B. subtilis, mtnX
was first known as ykrX [Amino acid biosynthesis,
Aspartate family, Central intermediary metabolism,
Sulfur metabolism].
Length = 214
Score = 27.1 bits (60), Expect = 3.3
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 35 IGSSLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNG 72
+ SSLK+E+ + + R G F+ FVA + +G
Sbjct: 53 LPSSLKEEITSFVLETAEIREG----FREFVAFINEHG 86
>gnl|CDD|180780 PRK06965, PRK06965, acetolactate synthase 3 catalytic subunit;
Validated.
Length = 587
Score = 26.7 bits (59), Expect = 5.6
Identities = 11/36 (30%), Positives = 23/36 (63%)
Query: 64 FVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSV 99
FV + ++ GH+G+ ++ + +V A+R A+ L +V
Sbjct: 520 FVKLAEAYGHVGMRIEKTSDVEPALREALRLKDRTV 555
>gnl|CDD|131310 TIGR02257, cobalto_cobN, cobaltochelatase, CobN subunit.
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Heme, porphyrin, and cobalamin].
Length = 1122
Score = 27.0 bits (60), Expect = 5.8
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 38 SLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVK 79
+ DE ++ P+ +TRA R + F G G G G++
Sbjct: 866 AQLDEPDELNPLAARTRAEGRASPRIF---GSKPGAYGAGLQ 904
>gnl|CDD|107203 cd01560, Thr-synth_2, Threonine synthase catalyzes the final step
of threonine biosynthesis. The conversion of
O-phosphohomoserine into threonine and inorganic
phosphate is pyridoxal 5'-phosphate dependent. The
Thr-synth_1 CD includes members from higher plants,
cyanobacteria, archaebacteria and eubacterial groups.
This CD, Thr-synth_2, includes enzymes from fungi and
eubacterial groups, as well as, metazoan threonine
synthase-like proteins.
Length = 460
Score = 26.8 bits (60), Expect = 5.9
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 3/37 (8%)
Query: 14 SLEQIYLFS-LPIKE--FEIIDFFIGSSLKDEVLKIM 47
S E+I +S L +E FE++ FIG + ++ LK +
Sbjct: 38 SAEEIASWSGLSYQELAFEVLSLFIGDEIPEDDLKSL 74
>gnl|CDD|217900 pfam04109, APG9, Autophagy protein Apg9. In yeast, 15 Apg proteins
coordinate the formation of autophagosomes. Autophagy is
a bulk degradation process induced by starvation in
eukaryotic cells. Apg9 plays a direct role in the
formation of the cytoplasm to vacuole targeting and
autophagic vesicles, possibly serving as a marker for a
specialised compartment essential for these
vesicle-mediated alternative targeting pathways.
Length = 365
Score = 26.4 bits (59), Expect = 6.3
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 18 IYLFSLPIKEFEIIDFF 34
I FSLP +IIDFF
Sbjct: 321 ILWFSLPPSSDDIIDFF 337
>gnl|CDD|184633 PRK14338, PRK14338, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 459
Score = 26.3 bits (58), Expect = 8.1
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 22 SLPIKEFEIIDFFIGSSLKDEVLKIMPVQ 50
S+ + ++D F+ S DEV+ + P
Sbjct: 108 SIFAERLPMVDHFVSPSAVDEVVALAPNP 136
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
0.321 0.138 0.406
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,607,966
Number of extensions: 682824
Number of successful extensions: 446
Number of sequences better than 10.0: 1
Number of HSP's gapped: 441
Number of HSP's successfully gapped: 18
Length of query: 152
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 64
Effective length of database: 7,034,450
Effective search space: 450204800
Effective search space used: 450204800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (24.8 bits)