RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 045484
(179 letters)
>gnl|CDD|236488 PRK09374, rplB, 50S ribosomal protein L2; Validated.
Length = 276
Score = 93.6 bits (234), Expect = 1e-23
Identities = 43/77 (55%), Positives = 50/77 (64%), Gaps = 6/77 (7%)
Query: 97 HEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWGKPCKW 156
H L KAG+S WLG RP +RGV MNPVDHP G GEGR +SG GR +TPWGKP K
Sbjct: 200 HSNISLGKAGRSRWLGIRPTVRGVAMNPVDHPHGGGEGR--TSG--GRHPVTPWGKPTKG 255
Query: 157 CKTASRKKKRKFSCLII 173
KT RKK ++ I+
Sbjct: 256 YKT--RKKNKRSDKFIV 270
>gnl|CDD|162234 TIGR01171, rplB_bact, ribosomal protein L2, bacterial/organellar.
This model distinguishes bacterial and organellar
ribosomal protein L2 from its counterparts in the
archaea nad in the eukaryotic cytosol. Plant
mitochondrial examples tend to have long, variable
inserts [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 273
Score = 92.8 bits (231), Expect = 2e-23
Identities = 43/77 (55%), Positives = 48/77 (62%), Gaps = 6/77 (7%)
Query: 97 HEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWGKPCKW 156
H VL KAG+S WLG RP +RGV MNPVDHP G GEGR GR +TPWGKP K
Sbjct: 198 HNNIVLGKAGRSRWLGIRPTVRGVAMNPVDHPHGGGEGRTPG----GRHPVTPWGKPTKG 253
Query: 157 CKTASRKKKRKFSCLII 173
KT RKKK+ I+
Sbjct: 254 YKT--RKKKKYSDKFIV 268
>gnl|CDD|176993 CHL00052, rpl2, ribosomal protein L2.
Length = 273
Score = 86.5 bits (215), Expect = 5e-21
Identities = 41/81 (50%), Positives = 48/81 (59%), Gaps = 12/81 (14%)
Query: 97 HEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGR---GKSSGNHGRCSLTPWGKP 153
K L KAG WLG+RP +RGV MNPVDHP G GEGR G+ +TPWGKP
Sbjct: 198 VNNKSLGKAGSKRWLGKRPKVRGVVMNPVDHPHGGGEGRAPIGRKK------PVTPWGKP 251
Query: 154 CKWCKTASRKKKRKFSCLIIL 174
KT RK+K K+S +IL
Sbjct: 252 ALGRKT--RKRK-KYSDNLIL 269
>gnl|CDD|202823 pfam03947, Ribosomal_L2_C, Ribosomal Proteins L2, C-terminal
domain.
Length = 130
Score = 79.5 bits (197), Expect = 1e-19
Identities = 32/57 (56%), Positives = 36/57 (63%), Gaps = 3/57 (5%)
Query: 97 HEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWGKP 153
H K L KAG+S WLG RP +RGV MNPVDHP G GEGR ++PWGKP
Sbjct: 77 HNNKPLGKAGRSRWLGIRPTVRGVAMNPVDHPHGGGEGRTSIGRPP---PVSPWGKP 130
>gnl|CDD|223168 COG0090, RplB, Ribosomal protein L2 [Translation, ribosomal
structure and biogenesis].
Length = 275
Score = 80.7 bits (200), Expect = 7e-19
Identities = 33/77 (42%), Positives = 42/77 (54%), Gaps = 6/77 (7%)
Query: 97 HEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWGKPCKW 156
H K L KAG++ G+RP +RGV MNPVDHP G GEG+ G+ PWGKP
Sbjct: 200 HILKPLGKAGRARHKGKRPTVRGVAMNPVDHPHGGGEGQHPG----GKPPTVPWGKPTPG 255
Query: 157 CKTASRKKKRKFSCLII 173
KT R ++ I+
Sbjct: 256 KKT--RIAAKRTGKFIV 270
>gnl|CDD|173329 PTZ00031, PTZ00031, ribosomal protein L2; Provisional.
Length = 317
Score = 70.3 bits (172), Expect = 9e-15
Identities = 33/72 (45%), Positives = 41/72 (56%), Gaps = 4/72 (5%)
Query: 93 TTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWGK 152
+ L H ++L KAG + WLG+RPV+RGV MNP HP G G K +CSL WG
Sbjct: 227 SNLEHHMRILGKAGVNRWLGKRPVVRGVAMNPSKHPHGGGT--SKKGTKRPKCSL--WGI 282
Query: 153 PCKWCKTASRKK 164
KT S+KK
Sbjct: 283 CRDGYKTRSKKK 294
>gnl|CDD|173464 PTZ00180, PTZ00180, 60S ribosomal protein L8; Provisional.
Length = 260
Score = 38.6 bits (90), Expect = 7e-04
Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 5/38 (13%)
Query: 100 KVLRKAGQSH--WLGQR---PVIRGVPMNPVDHPRGRG 132
K + KAG + + G+R P +RGV MNPV+HP G G
Sbjct: 177 KPVLKAGNAFHKYRGKRNCWPKVRGVAMNPVEHPHGGG 214
>gnl|CDD|236589 PRK09612, rpl2p, 50S ribosomal protein L2P; Validated.
Length = 238
Score = 37.9 bits (89), Expect = 0.001
Identities = 24/68 (35%), Positives = 29/68 (42%), Gaps = 22/68 (32%)
Query: 100 KVLRKAGQS-HWLGQR----PVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWGKPC 154
K KAG+ H + + P +RGV MN VDHP G GNH G+P
Sbjct: 168 KPFLKAGKKYHKMKAKAKKWPRVRGVAMNAVDHPHG--------GGNHQHP-----GRP- 213
Query: 155 KWCKTASR 162
T SR
Sbjct: 214 ---STVSR 218
>gnl|CDD|132871 cd07044, CofD_YvcK, Family of CofD-like proteins and proteins
related to YvcK. CofD is a 2-phospho-L-lactate
transferase that catalyzes the last step in the
biosynthesis of coenzyme F(420)-0 (F(420) without
polyglutamate) by transferring the lactyl phosphate
moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to
7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0).
F420 is a hydride carrier, important for energy
metabolism of methanogenic archaea, as well as for the
biosynthesis of other natural products, like
tetracycline in Streptomyces. F420 and some of its
precursors are also utilized as cofactors for enzymes,
like DNA photolyase in Mycobacterium tuberculosis. YvcK
from Bacillus subtilis is a member of a family of mostly
uncharacterized proteins and has been proposed to play a
role in carbon metabolism, since its function is
essential for growth on intermediates of the Krebs cycle
and pentose phosphate pathway. Both families appear to
have a conserved phosphate binding site, but have
different substrate binding residues conserved within
each family.
Length = 309
Score = 29.9 bits (67), Expect = 0.66
Identities = 7/24 (29%), Positives = 9/24 (37%)
Query: 105 AGQSHWLGQRPVIRGVPMNPVDHP 128
G+S I V + PVD
Sbjct: 139 HGESFIPKGEKKIDRVFLTPVDEA 162
>gnl|CDD|215453 PLN02844, PLN02844, oxidoreductase/ferric-chelate reductase.
Length = 722
Score = 28.3 bits (63), Expect = 2.4
Identities = 14/28 (50%), Positives = 16/28 (57%)
Query: 52 FSTITLLNAISPVKLNQLVMTLILKLEV 79
I LLN IS + LNQ L LKL+V
Sbjct: 468 SQDICLLNPISSLLLNQSSNQLNLKLKV 495
>gnl|CDD|197713 smart00418, HTH_ARSR, helix_turn_helix, Arsenical Resistance Operon
Repressor.
Length = 66
Score = 26.0 bits (58), Expect = 3.0
Identities = 14/37 (37%), Positives = 23/37 (62%)
Query: 70 VMTLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKAG 106
++ L+ + E+ L +LG S +T+SH K LR+AG
Sbjct: 2 ILKLLAEGELCVCELAEILGLSQSTVSHHLKKLREAG 38
>gnl|CDD|234070 TIGR02956, TMAO_torS, TMAO reductase sytem sensor TorS. This
protein, TorS, is part of a regulatory system for the
torCAD operon that encodes the pterin molybdenum
cofactor-containing enzyme trimethylamine-N-oxide (TMAO)
reductase (TorA), a cognate chaperone (TorD), and a
penta-haem cytochrome (TorC). TorS works together with
the inducer-binding protein TorT and the response
regulator TorR. TorS contains histidine kinase ATPase
(pfam02518), HAMP (pfam00672), phosphoacceptor
(pfam00512), and phosphotransfer (pfam01627) domains and
a response regulator receiver domain (pfam00072) [Signal
transduction, Two-component systems].
Length = 968
Score = 27.8 bits (62), Expect = 3.6
Identities = 25/89 (28%), Positives = 30/89 (33%), Gaps = 8/89 (8%)
Query: 17 QNLGNRDTERDRQ---KWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKLNQLVMTL 73
Q L N D ER RQ K L + L HS LPF+ L VK ++ TL
Sbjct: 64 QLLSNVDDERQRQAIGKKLTLQSETLL-HSLKALGELPFNEDLLARLEVLVK--DIIDTL 120
Query: 74 ILKLEVACHLLVCMLGPSSTTLSHEAKVL 102
+ L LS E
Sbjct: 121 AQLGLSVGERIT--LQAQLQQLSRELSEA 147
>gnl|CDD|237133 PRK12553, PRK12553, ATP-dependent Clp protease proteolytic subunit;
Reviewed.
Length = 207
Score = 26.5 bits (59), Expect = 7.3
Identities = 10/17 (58%), Positives = 12/17 (70%), Gaps = 2/17 (11%)
Query: 21 NRDTERDRQKWLGAEYA 37
+DT+RD KWL AE A
Sbjct: 176 RKDTDRD--KWLTAEEA 190
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
0.322 0.135 0.438
Gapped
Lambda K H
0.267 0.0782 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,591,631
Number of extensions: 739601
Number of successful extensions: 571
Number of sequences better than 10.0: 1
Number of HSP's gapped: 565
Number of HSP's successfully gapped: 17
Length of query: 179
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 88
Effective length of database: 6,901,388
Effective search space: 607322144
Effective search space used: 607322144
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 (22.0 bits)
S2: 56 (25.2 bits)