RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17954
(143 letters)
>gnl|CDD|185404 PTZ00028, PTZ00028, 40S ribosomal protein S6e; Provisional.
Length = 218
Score = 143 bits (362), Expect = 5e-44
Identities = 89/196 (45%), Positives = 105/196 (53%), Gaps = 69/196 (35%)
Query: 1 MKLNISYPATGCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQG 60
MKLNI+ P TG QK +EI DE KL F++KR+G EVP DS+GDE+KGYI +ISGGNDKQG
Sbjct: 1 MKLNIANPFTGLQKCIEIDDEKKLLPFFEKRIGAEVPGDSLGDEFKGYIFKISGGNDKQG 60
Query: 61 FPMKQGEIPGLTDTTI------------PRRLG--------------------------- 81
FPM QG LT+ + PRR G
Sbjct: 61 FPMMQGV---LTNNRVRLLFRKGMKCYRPRRTGEMKRKSVRGCIVGHDLSVLNLVLVKKG 117
Query: 82 -----------------PKRASKIRKLFNLSKEDDVRQYVIKRTLPPKPAKEGKKKVRKL 124
PKRASKIRKLFNLSK DDVR++V++R + EGK K
Sbjct: 118 PQEIPGLTDGERPRRLGPKRASKIRKLFNLSKSDDVRKFVVRRKI------EGKNKT--- 168
Query: 125 YKAPKIQRLITPVTLQ 140
KAPKIQRL+TP LQ
Sbjct: 169 -KAPKIQRLVTPQRLQ 183
>gnl|CDD|110116 pfam01092, Ribosomal_S6e, Ribosomal protein S6e.
Length = 127
Score = 115 bits (289), Expect = 4e-34
Identities = 50/66 (75%), Positives = 60/66 (90%)
Query: 1 MKLNISYPATGCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQG 60
MKLN+S PATGCQKL+E+ DEH+LRVFY+KRMG EV D++GDE KGY++RI+GGNDKQG
Sbjct: 1 MKLNVSDPATGCQKLIEVDDEHRLRVFYEKRMGQEVDGDAVGDELKGYVLRITGGNDKQG 60
Query: 61 FPMKQG 66
FPMKQG
Sbjct: 61 FPMKQG 66
>gnl|CDD|225036 COG2125, RPS6A, Ribosomal protein S6E (S10) [Translation,
ribosomal structure and biogenesis].
Length = 120
Score = 68.1 bits (167), Expect = 8e-16
Identities = 29/70 (41%), Positives = 41/70 (58%), Gaps = 3/70 (4%)
Query: 1 MKLNISYPATGCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQG 60
K+ IS P TG EI DE + R K++G EV +G E+ Y ++I+GG+DK G
Sbjct: 4 FKVVISDPKTGRAYQFEI-DEARARRLIGKKIGDEVDGVIVGLEF-EYKLKITGGSDKDG 61
Query: 61 FPMKQGEIPG 70
FPM+ +PG
Sbjct: 62 FPMRPD-VPG 70
>gnl|CDD|235271 PRK04290, PRK04290, 30S ribosomal protein S6e; Validated.
Length = 115
Score = 41.8 bits (99), Expect = 8e-06
Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 4/69 (5%)
Query: 2 KLNISYPATGCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQGF 61
K+ +S P TG +EI R K++G E+ +G GY ++I+GG+DK GF
Sbjct: 5 KVVVSDPKTGKAYQIEIDGAEANR-LIGKKIGDEIDGSIVG--LDGYKLKITGGSDKSGF 61
Query: 62 PMKQGEIPG 70
PM+ ++PG
Sbjct: 62 PMR-PDVPG 69
>gnl|CDD|215174 PLN02305, PLN02305, lipoxygenase.
Length = 918
Score = 31.0 bits (70), Expect = 0.20
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 75 TIPRRLGPKRASKIRKLFNLSKEDDVRQYVIKRTLPPKPAKEGKKKV 121
++P R +A R +F SK +R I+ +LPP P+ G K V
Sbjct: 501 SLPER----KAYASRTVFFYSKAGALRPIAIELSLPPTPSSPGNKFV 543
>gnl|CDD|225340 COG2719, SpoVR, Uncharacterized conserved protein [Function
unknown].
Length = 495
Score = 28.9 bits (65), Expect = 1.0
Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 3/61 (4%)
Query: 71 LTDTTIPRRLGPKRAS--KIRKLFNLSKEDDVRQYV-IKRTLPPKPAKEGKKKVRKLYKA 127
+ + + R PK+ S + R +E Q + RTLP KP + K R+
Sbjct: 168 IMEYGVDRYKRPKKISSEEERARQEEREEYLQSQVNDLWRTLPKKPGEAAVKDARRFPSE 227
Query: 128 P 128
P
Sbjct: 228 P 228
>gnl|CDD|217010 pfam02387, IncFII_repA, IncFII RepA protein family. This protein
is plasmid encoded and found to be essential for plasmid
replication.
Length = 279
Score = 28.5 bits (64), Expect = 1.3
Identities = 17/49 (34%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 75 TIPRRLGPKRASKIRKLFNLSKEDDVRQYVIKRTLPPKPAKEGKKKVRK 123
T P+ G KR IR + E DV ++ + TL PK K G R
Sbjct: 16 TPPKN-GKKRPPFIRYAMKKASEIDVARHELNYTLLPKDPKTGNILPRF 63
>gnl|CDD|235169 PRK03879, PRK03879, ribonuclease P protein component 1; Validated.
Length = 96
Score = 26.8 bits (60), Expect = 2.3
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 82 PKRASKIRKLFNLSKEDDVRQYVIKRTLPPKPAKEGKKKVRKLY 125
PK + F L ++D V+ V R L +P KKK++KL
Sbjct: 55 PKDGATFE--FELGRDDVVKVKVDGRLLVGRPEDRLKKKIKKLR 96
>gnl|CDD|178001 PLN02373, PLN02373, soluble inorganic pyrophosphatase.
Length = 188
Score = 27.0 bits (60), Expect = 3.6
Identities = 14/54 (25%), Positives = 27/54 (50%)
Query: 80 LGPKRASKIRKLFNLSKEDDVRQYVIKRTLPPKPAKEGKKKVRKLYKAPKIQRL 133
L P R ++IR+ F K+++ ++ + LP + A E + LY ++ L
Sbjct: 133 LPPHRLAEIRRFFEDYKKNENKEVAVNDFLPAEAAIEAIQYSMDLYAEYIVESL 186
>gnl|CDD|212038 cd10328, SLC5sbd_YidK, uncharacterized SLC5 subfamily, Escherichia
coli YidK-like; solute binding domain. Uncharacterized
subfamily of the solute binding domain of the solute
carrier 5 (SLC5) transporter family (also called the
sodium/glucose cotransporter family or solute sodium
symporter family) that co-transports Na+ with sugars,
amino acids, inorganic ions or vitamins. One member of
the SLC5 family, human SGLT3, has been characterized as
a glucose sensor and not a transporter. This subfamily
includes the uncharacterized Escherichia coli YidK
protein, and belongs to the solute carrier 5 (SLC5)
transporter family.
Length = 472
Score = 27.1 bits (61), Expect = 4.0
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 102 QYVIKRTLPPKPAKEGKKKVRKLYKAPKIQRLITPVTLQVSG 143
Q +++R L K KEG+K V L +L+ P+ L + G
Sbjct: 255 QAIVQRALGAKNLKEGQKGV--LLAG--FFKLLVPLILVLPG 292
>gnl|CDD|216261 pfam01041, DegT_DnrJ_EryC1, DegT/DnrJ/EryC1/StrS aminotransferase
family. The members of this family are probably all
pyridoxal-phosphate-dependent aminotransferase enzymes
with a variety of molecular functions. The family
includes StsA, StsC and StsS. The aminotransferase
activity was demonstrated for purified StsC protein as
the L-glutamine:scyllo-inosose aminotransferase
EC:2.6.1.50, which catalyzes the first amino transfer in
the biosynthesis of the streptidine subunit of
streptomycin.
Length = 362
Score = 26.4 bits (59), Expect = 5.6
Identities = 11/35 (31%), Positives = 14/35 (40%), Gaps = 7/35 (20%)
Query: 13 QKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKG 47
+ IA EH L V D A + G +KG
Sbjct: 129 DAIRAIAAEHGLPVIEDA-------AHAHGATYKG 156
>gnl|CDD|99740 cd00616, AHBA_syn, 3-amino-5-hydroxybenzoic acid synthase family
(AHBA_syn). AHBA_syn family belongs to pyridoxal
phosphate (PLP)-dependent aspartate aminotransferase
superfamily (fold I). The members of this CD are
involved in various biosynthetic pathways for secondary
metabolites. Some well studied proteins in this CD are
AHBA_synthase, protein product of pleiotropic regulatory
gene degT, Arnb aminotransferase and pilin
glycosylation protein. The prototype of this family, the
AHBA_synthase, is a dimeric PLP dependent enzyme.
AHBA_syn is the terminal enzyme of
3-amino-5-hydroxybenzoic acid (AHBA) formation which is
involved in the biosynthesis of ansamycin antibiotics,
including rifamycin B. Some members of this CD are
involved in 4-amino-6-deoxy-monosaccharide D-perosamine
synthesis. Perosamine is an important element in the
glycosylation of several cell products, such as
antibiotics and lipopolysaccharides of gram-positive and
gram-negative bacteria. The pilin glycosylation protein
encoded by gene pglA, is a galactosyltransferase
involved in pilin glycosylation. Additionally, this CD
consists of ArnB (PmrH) aminotransferase, a
4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying
enzyme. This CD also consists of several predicted
pyridoxal phosphate-dependent enzymes apparently
involved in regulation of cell wall biogenesis. The
catalytic lysine which is present in all characterized
PLP dependent enzymes is replaced by histidine in some
members of this CD.
Length = 352
Score = 26.3 bits (59), Expect = 6.2
Identities = 10/35 (28%), Positives = 15/35 (42%), Gaps = 7/35 (20%)
Query: 13 QKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKG 47
++ IA H L V D A ++G +KG
Sbjct: 123 DAIMAIAKRHGLPVIEDA-------AQALGATYKG 150
>gnl|CDD|181738 PRK09265, PRK09265, aminotransferase AlaT; Validated.
Length = 404
Score = 26.3 bits (59), Expect = 6.9
Identities = 10/22 (45%), Positives = 15/22 (68%), Gaps = 4/22 (18%)
Query: 13 QKLVEIADEHKLRVF----YDK 30
+++VEIA +H L +F YDK
Sbjct: 191 EEIVEIARQHNLIIFADEIYDK 212
>gnl|CDD|235648 PRK05932, PRK05932, RNA polymerase factor sigma-54; Reviewed.
Length = 455
Score = 26.3 bits (59), Expect = 7.3
Identities = 9/31 (29%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 87 KIRKLFNLSKEDDVRQYV-IKRTLPPKPAKE 116
+ K + KE+D+++ + + R+L PKP
Sbjct: 213 TLAKKLGV-KEEDLQEALDLIRSLDPKPGAG 242
>gnl|CDD|223476 COG0399, WecE, Predicted pyridoxal phosphate-dependent enzyme
apparently involved in regulation of cell wall
biogenesis [Cell envelope biogenesis, outer membrane].
Length = 374
Score = 26.1 bits (58), Expect = 8.9
Identities = 9/35 (25%), Positives = 14/35 (40%), Gaps = 7/35 (20%)
Query: 13 QKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKG 47
++ +A H L V D A + G +KG
Sbjct: 139 DAIMALAKRHGLPVIEDA-------AQAHGATYKG 166
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 0.138 0.402
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,393,298
Number of extensions: 669009
Number of successful extensions: 749
Number of sequences better than 10.0: 1
Number of HSP's gapped: 745
Number of HSP's successfully gapped: 40
Length of query: 143
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 56
Effective length of database: 7,078,804
Effective search space: 396413024
Effective search space used: 396413024
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: 54 (24.5 bits)