RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13418
(159 letters)
>gnl|CDD|223168 COG0090, RplB, Ribosomal protein L2 [Translation, ribosomal
structure and biogenesis].
Length = 275
Score = 81.9 bits (203), Expect = 2e-19
Identities = 50/151 (33%), Positives = 72/151 (47%), Gaps = 14/151 (9%)
Query: 8 GGGIKEDIHWVHDFRRGPTDDSPPLEERVIQIIPSPAPTVRTANLALVGSGDFLK-LILA 66
GGG K + DF+R + +V I P R+A +ALV D K ILA
Sbjct: 55 GGGHKRRYRLI-DFKRNKDG----IPGKVEDIEYDPN---RSAPIALVVYEDGEKRYILA 106
Query: 67 TENMKAGDILKTSMFIPRIPVRAKEGDAYPVGALPMGSIVCCVEKFPGEGAHYARAAGNS 126
E +K GD++ + K G+A P+G +P G+IV VE PG+G AR+AG
Sbjct: 107 PEGLKVGDVI---ESGKDADI--KPGNALPLGNIPEGTIVHNVELKPGDGGQLARSAGTY 161
Query: 127 CTLVRTLHDRVVLQLPSKHEVAVDKHCMAVV 157
+V + V+++LPS V C A +
Sbjct: 162 AQVVGKEGNYVIVRLPSGEMRKVLSECRATI 192
>gnl|CDD|202823 pfam03947, Ribosomal_L2_C, Ribosomal Proteins L2, C-terminal
domain.
Length = 130
Score = 77.2 bits (191), Expect = 5e-19
Identities = 22/70 (31%), Positives = 37/70 (52%)
Query: 90 KEGDAYPVGALPMGSIVCCVEKFPGEGAHYARAAGNSCTLVRTLHDRVVLQLPSKHEVAV 149
K G+A P+ +P+G+++ +E PG+G AR+AG ++ V L+LPS V
Sbjct: 2 KIGNALPLKNIPIGTVIHNIELIPGKGGQLARSAGTYAQIIAKEGKYVTLKLPSGEVRLV 61
Query: 150 DKHCMAVVAQ 159
+C A +
Sbjct: 62 SSNCRATIGV 71
>gnl|CDD|236589 PRK09612, rpl2p, 50S ribosomal protein L2P; Validated.
Length = 238
Score = 73.3 bits (181), Expect = 2e-16
Identities = 40/134 (29%), Positives = 65/134 (48%), Gaps = 9/134 (6%)
Query: 25 PTDDSPPLEERVIQIIPSPAPTVRTANLALVGSGDFLK-LILATENMKAGDILKTSMFIP 83
P D L +V+ I+ P R A +A V + + LILA E + G ++
Sbjct: 32 PLDKDGTLRGKVVDILHDPG---RNAPVAKVKFENGEEFLILAPEGLYVGQEIEIG---- 84
Query: 84 RIPVRAKEGDAYPVGALPMGSIVCCVEKFPGEGAHYARAAGNSCTLVRTLHDRVVLQLPS 143
K G+ P+G +P G+ VC +E PG+G +AR++G +V D+V++QLPS
Sbjct: 85 -PSAEIKPGNTLPLGEIPEGTPVCNIESRPGDGGKFARSSGTYALVVGHEGDKVIVQLPS 143
Query: 144 KHEVAVDKHCMAVV 157
++ C A +
Sbjct: 144 GKIKELNPRCRATI 157
>gnl|CDD|236488 PRK09374, rplB, 50S ribosomal protein L2; Validated.
Length = 276
Score = 67.8 bits (167), Expect = 3e-14
Identities = 39/114 (34%), Positives = 59/114 (51%), Gaps = 8/114 (7%)
Query: 48 RTANLALVGSGDFLK-LILATENMKAGDILKTSMFIPRIPVRAKEGDAYPVGALPMGSIV 106
R+A +AL+ D K ILA + +K GD + + P ++ G+A P+ +P+G+ V
Sbjct: 87 RSARIALLHYADGEKRYILAPKGLKVGDTVVSG---PDADIKP--GNALPLRNIPVGTTV 141
Query: 107 CCVEKFPGEGAHYARAAGNSCTLVRTLHDRVVLQLPSKHEV-AVDKHCMAVVAQ 159
+E PG+G AR+AG S LV L+LPS EV V C A + +
Sbjct: 142 HNIELKPGKGGQLARSAGTSAQLVAKEGKYATLRLPSG-EVRKVLAECRATIGE 194
>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 = 61.9 bits (151), Expect = 4e-12
Identities = 49/153 (32%), Positives = 77/153 (50%), Gaps = 14/153 (9%)
Query: 8 GGGIKEDIHWVHDFRRGPTDDSPPLEERVIQIIPSPAPTVRTANLALVGSGDFLK-LILA 66
GGG K ++ + DF+R + + +V I P R+A +AL+ D K ILA
Sbjct: 53 GGGHKR-LYRIIDFKR----NKDGIPAKVAAIEYDPN---RSARIALLHYADGEKRYILA 104
Query: 67 TENMKAGDILKTSMFIPRIPVRAKEGDAYPVGALPMGSIVCCVEKFPGEGAHYARAAGNS 126
+ +K GD + + P P+ K G+A P+ +P+G+ V +E PG+G AR+AG S
Sbjct: 105 PKGLKVGDTV---ISGPEAPI--KPGNALPLRNIPVGTTVHNIELKPGKGGQLARSAGTS 159
Query: 127 CTLVRTLHDRVVLQLPSKHEVAVDKHCMAVVAQ 159
++ V L+LPS V K C A + +
Sbjct: 160 AQILAKEGGYVTLRLPSGEMRMVLKECRATIGE 192
>gnl|CDD|176993 CHL00052, rpl2, ribosomal protein L2.
Length = 273
Score = 60.3 bits (147), Expect = 1e-11
Identities = 44/141 (31%), Positives = 66/141 (46%), Gaps = 13/141 (9%)
Query: 20 DFRRGPTDDSPPLEERVIQIIPSPAPTVRTANLALVGSGDFLK-LILATENMKAGDILKT 78
DFRR D + R++ I P R A + L+ GD K IL +K GD + +
Sbjct: 64 DFRRNKKD----IYGRIVTIEYDPN---RNAYICLIHYGDGEKRYILHPRGLKIGDTIVS 116
Query: 79 SMFIPRIPVRAKEGDAYPVGALPMGSIVCCVEKFPGEGAHYARAAGNSCTLVRTLHDRVV 138
P+ K G+A P+ +P+G+ + +E PG+G ARAAG L+
Sbjct: 117 G---TEAPI--KIGNALPLTNIPLGTAIHNIEITPGKGGQLARAAGAVAKLIAKEGKSAT 171
Query: 139 LQLPSKHEVAVDKHCMAVVAQ 159
L+LPS + K+C A + Q
Sbjct: 172 LKLPSGEVRLISKNCSATIGQ 192
>gnl|CDD|173329 PTZ00031, PTZ00031, ribosomal protein L2; Provisional.
Length = 317
Score = 60.6 bits (147), Expect = 2e-11
Identities = 47/160 (29%), Positives = 73/160 (45%), Gaps = 14/160 (8%)
Query: 1 RVVVAGLGGGIKEDIHWVHDFRRGPTDDSPPLEERVIQIIPSPAPTVRTANLALVGSGD- 59
R+ GGG + + ++ DF+R D + V++I P+ R+A++AL+ D
Sbjct: 79 RITTRHRGGGHVQRLRFI-DFKRSRKD----IYSTVLRIEYDPS---RSAHIALLQYEDG 130
Query: 60 FLKLILATENMKAGDILKTSMFIPRIPVRAKEGDAYPVGALPMGSIVCCVEKFPGEGAHY 119
L ILA ++ GD + S + P G++ P+ +P+GSIV VE PG G
Sbjct: 131 VLSYILAPLLLRPGDKIIASKYANINP-----GNSLPLRNIPVGSIVHNVEMRPGAGGQI 185
Query: 120 ARAAGNSCTLVRTLHDRVVLQLPSKHEVAVDKHCMAVVAQ 159
RA G T+V L+L S C A + Q
Sbjct: 186 IRAGGTYATVVSKDEQFATLKLKSTEIRKFPLDCWATIGQ 225
>gnl|CDD|109247 pfam00181, Ribosomal_L2, Ribosomal Proteins L2, RNA binding
domain.
Length = 77
Score = 44.5 bits (106), Expect = 5e-07
Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 9/79 (11%)
Query: 1 RVVVAGLGGGIKEDIHWVHDFRRGPTDDSPPLEERVIQIIPSPAPTVRTANLALVGSGDF 60
R+ V GGG K + DF+R + ++ +VI I P R+A +ALV D
Sbjct: 7 RITVRHRGGGHKRLYRLI-DFKRNKGN----IKGKVIDIEYDPN---RSAPIALVKYEDG 58
Query: 61 LK-LILATENMKAGDILKT 78
K ILA E +K GD +++
Sbjct: 59 EKRYILAPEGLKVGDTIES 77
>gnl|CDD|173464 PTZ00180, PTZ00180, 60S ribosomal protein L8; Provisional.
Length = 260
Score = 47.0 bits (112), Expect = 6e-07
Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 92 GDAYPVGALPMGSIVCCVEKFPGEGAHYARAAGNSCTLVRTLHD--RVVLQLPSKHEVAV 149
G+ P+G +P G+IVC VE+ PG+ ARA+G T++ D + ++LPS + V
Sbjct: 99 GNVLPLGQIPEGTIVCNVEEKPGDRGTLARASGCYATIIGHSDDGGKTRIRLPSGQKKTV 158
Query: 150 DKHCMAVV 157
A++
Sbjct: 159 SSLSRAMI 166
>gnl|CDD|233722 TIGR02093, P_ylase, glycogen/starch/alpha-glucan phosphorylases.
This family consists of phosphorylases. Members use
phosphate to break alpha 1,4 linkages between pairs of
glucose residues at the end of long glucose polymers,
releasing alpha-D-glucose 1-phosphate. The nomenclature
convention is to preface the name according to the
natural substrate, as in glycogen phosphorylase, starch
phosphorylase, maltodextrin phosphorylase, etc. Name
differences among these substrates reflect differences
in patterns of branching with alpha 1,6 linkages.
Members include allosterically regulated and unregulated
forms. A related family, TIGR02094, contains examples
known to act well on particularly small alpha 1,4
glucans, as may be found after import from exogenous
sources [Energy metabolism, Biosynthesis and degradation
of polysaccharides].
Length = 794
Score = 27.2 bits (61), Expect = 4.9
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 19 HDFRRGPTDDSPPLEERV--IQIIP-SPAPTVRTANLALVGS 57
F P E ++ + II + VR ANLA+VGS
Sbjct: 374 RRFLAELAAKGPGDEAKIRRMSIIEEGQSKRVRMANLAIVGS 415
>gnl|CDD|197958 smart00890, EKR, Domain of unknown function. EKR is a short, 33
residue, domain found in bacterial and some lower
eukaryotic species which lies between a POR (pyruvate
ferredoxin/flavodoxin oxidoreductase) and the 4Fe-4S
binding domain Fer4. It contains a characteristic EKR
sequence motif. The exact function of this domain is not
known.
Length = 57
Score = 24.9 bits (55), Expect = 7.1
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 2/23 (8%)
Query: 81 FIPRI--PVRAKEGDAYPVGALP 101
F+ + P+ A EGD PV A P
Sbjct: 16 FVKNVVAPMNAGEGDDLPVSAFP 38
>gnl|CDD|184471 PRK14039, PRK14039, ADP-dependent glucokinase; Provisional.
Length = 453
Score = 26.3 bits (58), Expect = 8.3
Identities = 13/32 (40%), Positives = 15/32 (46%), Gaps = 6/32 (18%)
Query: 12 KEDIHWVHDFRRGPTDDSP------PLEERVI 37
+E IH+V DFR G T P E R I
Sbjct: 153 QEPIHFVFDFREGETFSLYGTRIRAPRENRFI 184
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 0.139 0.422
Gapped
Lambda K H
0.267 0.0770 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,309,108
Number of extensions: 762685
Number of successful extensions: 577
Number of sequences better than 10.0: 1
Number of HSP's gapped: 570
Number of HSP's successfully gapped: 22
Length of query: 159
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 70
Effective length of database: 6,990,096
Effective search space: 489306720
Effective search space used: 489306720
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 (24.9 bits)