RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13959
(248 letters)
>gnl|CDD|173464 PTZ00180, PTZ00180, 60S ribosomal protein L8; Provisional.
Length = 260
Score = 416 bits (1070), Expect = e-149
Identities = 170/235 (72%), Positives = 196/235 (83%)
Query: 1 MGRVIRAQRKGAGSVFRSHNKHRKGAPKLRSLDFAERHGYLKGVVRDIIHDPGRGAPLAV 60
MGRVIRAQRKG GSVF++H R G KLR LD+AERHGY++GVV+DI HDPGRGAPLA
Sbjct: 1 MGRVIRAQRKGNGSVFKAHGHKRLGPAKLRILDYAERHGYIRGVVKDIEHDPGRGAPLAR 60
Query: 61 VHFRNPYKFKTNKELFIAPEGMYTGQFVYCGKKATLQIGNVMPVGGMPEGTIVCNLEEKT 120
V FR+PYK+K KEL +APEGMYTGQ+VYCG KA L IGNV+P+G +PEGTIVCN+EEK
Sbjct: 61 VEFRDPYKYKRVKELMVAPEGMYTGQYVYCGAKAPLAIGNVLPLGQIPEGTIVCNVEEKP 120
Query: 121 GDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIPSANRAMVGIVAGGGRIDKPIL 180
GDRG LARASG YAT+I H+ D +TR++LPSG KK + S +RAM+GIVAGGGRIDKP+L
Sbjct: 121 GDRGTLARASGCYATIIGHSDDGGKTRIRLPSGQKKTVSSLSRAMIGIVAGGGRIDKPVL 180
Query: 181 KAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGNHQHIGKASTVKRGTSAGRKV 235
KAG A +KY+ KRNCWPKVRGVAMNPVEHPHGGGNHQHIG STV R G+KV
Sbjct: 181 KAGNAFHKYRGKRNCWPKVRGVAMNPVEHPHGGGNHQHIGHPSTVSRHAPPGQKV 235
>gnl|CDD|236589 PRK09612, rpl2p, 50S ribosomal protein L2P; Validated.
Length = 238
Score = 271 bits (696), Expect = 1e-92
Identities = 121/236 (51%), Positives = 155/236 (65%), Gaps = 11/236 (4%)
Query: 1 MGRVIRAQRKGAGS-VFRSHNKHRKGAPKLRSLDFAERHGYLKGVVRDIIHDPGRGAPLA 59
MG+ I +QR+G G+ FRS + KG K LD G L+G V DI+HDPGR AP+A
Sbjct: 1 MGKRIISQRRGRGTPTFRSPSHRYKGPVKYPPLDK---DGTLRGKVVDILHDPGRNAPVA 57
Query: 60 VVHFRNPYKFKTNKELFIAPEGMYTGQFVYCGKKATLQIGNVMPVGGMPEGTIVCNLEEK 119
V F N +F L +APEG+Y GQ + G A ++ GN +P+G +PEGT VCN+E +
Sbjct: 58 KVKFENGEEF-----LILAPEGLYVGQEIEIGPSAEIKPGNTLPLGEIPEGTPVCNIESR 112
Query: 120 TGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIPSANRAMVGIVAGGGRIDKPI 179
GD G+ AR+SG YA V+ H D + V+LPSG K + RA +G+VAGGGR +KP
Sbjct: 113 PGDGGKFARSSGTYALVVGHEGD--KVIVQLPSGKIKELNPRCRATIGVVAGGGRKEKPF 170
Query: 180 LKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGNHQHIGKASTVKRGTSAGRKV 235
LKAG+ ++K KAK WP+VRGVAMN V+HPHGGGNHQH G+ STV R GRKV
Sbjct: 171 LKAGKKYHKMKAKAKKWPRVRGVAMNAVDHPHGGGNHQHPGRPSTVSRNAPPGRKV 226
>gnl|CDD|223168 COG0090, RplB, Ribosomal protein L2 [Translation, ribosomal
structure and biogenesis].
Length = 275
Score = 250 bits (642), Expect = 9e-84
Identities = 99/238 (41%), Positives = 133/238 (55%), Gaps = 17/238 (7%)
Query: 1 MGRVIRAQRKGA--GSVFRSHNKHRKGAPKLRSLDFAERHGYLKGVVRDIIHDPGRGAPL 58
MG++I++Q + R K +L DF + G V DI +DP R AP+
Sbjct: 34 MGKLIKSQGRNNRGRITVRHRGGGHKRRYRLI--DFKRNKDGIPGKVEDIEYDPNRSAPI 91
Query: 59 AVVHFRNPYKFKTNKELFIAPEGMYTGQFVYCGKKATLQIGNVMPVGGMPEGTIVCNLEE 118
A+V + + K +APEG+ G + GK A ++ GN +P+G +PEGTIV N+E
Sbjct: 92 ALVVYEDGEKR-----YILAPEGLKVGDVIESGKDADIKPGNALPLGNIPEGTIVHNVEL 146
Query: 119 KTGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIPSANRAMVGIVAGGGRIDKP 178
K GD G+LAR++G YA V+ + V+LPSG + + S RA +G+VA GG I KP
Sbjct: 147 KPGDGGQLARSAGTYAQVVGK--EGNYVIVRLPSGEMRKVLSECRATIGVVANGGHILKP 204
Query: 179 ILKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGNHQHI-GKASTVKRGTSAGRKV 235
+ KAGRA +K K P VRGVAMNPV+HPHGGG QH GK TV G K
Sbjct: 205 LGKAGRARHKGK-----RPTVRGVAMNPVDHPHGGGEGQHPGGKPPTVPWGKPTPGKK 257
>gnl|CDD|202823 pfam03947, Ribosomal_L2_C, Ribosomal Proteins L2, C-terminal
domain.
Length = 130
Score = 154 bits (391), Expect = 8e-48
Identities = 55/133 (41%), Positives = 81/133 (60%), Gaps = 8/133 (6%)
Query: 96 LQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAK 155
++IGN +P+ +P GT++ N+E G G+LAR++G YA +IA + K +KLPSG
Sbjct: 1 IKIGNALPLKNIPIGTVIHNIELIPGKGGQLARSAGTYAQIIAK--EGKYVTLKLPSGEV 58
Query: 156 KVIPSANRAMVGIVAGGGRIDKPILKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGN 215
+++ S RA +G+V+ +KP+ KAGR+ + P VRGVAMNPV+HPHGGG
Sbjct: 59 RLVSSNCRATIGVVSNIDHNNKPLGKAGRSRWLGI-----RPTVRGVAMNPVDHPHGGGE 113
Query: 216 -HQHIGKASTVKR 227
IG+ V
Sbjct: 114 GRTSIGRPPPVSP 126
>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 = 118 bits (298), Expect = 3e-32
Identities = 70/196 (35%), Positives = 107/196 (54%), Gaps = 14/196 (7%)
Query: 21 KHRKGAPK--LRSLDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIA 78
+HR G K R +DF + V I +DP R A +A++H+ + K +A
Sbjct: 50 RHRGGGHKRLYRIIDFKRNKDGIPAKVAAIEYDPNRSARIALLHYAD-----GEKRYILA 104
Query: 79 PEGMYTGQFVYCGKKATLQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIA 138
P+G+ G V G +A ++ GN +P+ +P GT V N+E K G G+LAR++G A ++A
Sbjct: 105 PKGLKVGDTVISGPEAPIKPGNALPLRNIPVGTTVHNIELKPGKGGQLARSAGTSAQILA 164
Query: 139 HNPDTKRTRVKLPSGAKKVIPSANRAMVGIVAGGGRIDKPILKAGRAHYKYKAKRNCWPK 198
+ ++LPSG +++ RA +G V + + KAGR+ ++ R P
Sbjct: 165 K--EGGYVTLRLPSGEMRMVLKECRATIGEVGNEDHNNIVLGKAGRS--RWLGIR---PT 217
Query: 199 VRGVAMNPVEHPHGGG 214
VRGVAMNPV+HPHGGG
Sbjct: 218 VRGVAMNPVDHPHGGG 233
>gnl|CDD|176993 CHL00052, rpl2, ribosomal protein L2.
Length = 273
Score = 113 bits (286), Expect = 2e-30
Identities = 70/200 (35%), Positives = 102/200 (51%), Gaps = 22/200 (11%)
Query: 21 KHRKGAPK--LRSLDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIA 78
+HR G K R +DF + G + I +DP R A + ++H+ + K +
Sbjct: 50 RHRGGGHKRLYRKIDFRRNKKDIYGRIVTIEYDPNRNAYICLIHYGD-----GEKRYILH 104
Query: 79 PEGMYTGQFVYCGKKATLQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIA 138
P G+ G + G +A ++IGN +P+ +P GT + N+E G G+LARA+G A +IA
Sbjct: 105 PRGLKIGDTIVSGTEAPIKIGNALPLTNIPLGTAIHNIEITPGKGGQLARAAGAVAKLIA 164
Query: 139 HNPDTKRTRVKLPSGAKKVIPSANRAMVGIVAGGGRIDKPILKAGRAHYKYKAKRNCW-- 196
+ K +KLPSG ++I A +G V +K + KAG W
Sbjct: 165 K--EGKSATLKLPSGEVRLISKNCSATIGQVGNVDVNNKSLGKAG---------SKRWLG 213
Query: 197 --PKVRGVAMNPVEHPHGGG 214
PKVRGV MNPV+HPHGGG
Sbjct: 214 KRPKVRGVVMNPVDHPHGGG 233
>gnl|CDD|236488 PRK09374, rplB, 50S ribosomal protein L2; Validated.
Length = 276
Score = 112 bits (284), Expect = 4e-30
Identities = 64/172 (37%), Positives = 97/172 (56%), Gaps = 12/172 (6%)
Query: 43 GVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIAPEGMYTGQFVYCGKKATLQIGNVM 102
V I +DP R A +A++H+ + K +AP+G+ G V G A ++ GN +
Sbjct: 76 AKVERIEYDPNRSARIALLHYAD-----GEKRYILAPKGLKVGDTVVSGPDADIKPGNAL 130
Query: 103 PVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIPSAN 162
P+ +P GT V N+E K G G+LAR++G A ++A + K ++LPSG + + +
Sbjct: 131 PLRNIPVGTTVHNIELKPGKGGQLARSAGTSAQLVAK--EGKYATLRLPSGEVRKVLAEC 188
Query: 163 RAMVGIVAGGGRIDKPILKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGG 214
RA +G V + + KAGR+ ++ R P VRGVAMNPV+HPHGGG
Sbjct: 189 RATIGEVGNEEHSNISLGKAGRS--RWLGIR---PTVRGVAMNPVDHPHGGG 235
>gnl|CDD|173329 PTZ00031, PTZ00031, ribosomal protein L2; Provisional.
Length = 317
Score = 96.8 bits (241), Expect = 9e-24
Identities = 72/222 (32%), Positives = 109/222 (49%), Gaps = 20/222 (9%)
Query: 2 GRVI------RAQRKGAGSVFRSHNKHRKG--APKLRSLDFAERHGYLKGVVRDIIHDPG 53
GRV+ R + G +V R +HR G +LR +DF + V I +DP
Sbjct: 58 GRVVKQLSCRRVKNSGRNNVGRITTRHRGGGHVQRLRFIDFKRSRKDIYSTVLRIEYDPS 117
Query: 54 RGAPLAVVHFRNPYKFKTNKELFIAPEGMYTGQFVYCGKKATLQIGNVMPVGGMPEGTIV 113
R A +A++ + + +AP + G + K A + GN +P+ +P G+IV
Sbjct: 118 RSAHIALLQYEDGVL-----SYILAPLLLRPGDKIIASKYANINPGNSLPLRNIPVGSIV 172
Query: 114 CNLEEKTGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIPSANRAMVGIVAGGG 173
N+E + G G++ RA G YATV++ D + +KL S + P A +G V+
Sbjct: 173 HNVEMRPGAGGQIIRAGGTYATVVSK--DEQFATLKLKSTEIRKFPLDCWATIGQVSNLE 230
Query: 174 RIDKPILKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGN 215
+ + KAG ++ KR P VRGVAMNP +HPHGGG
Sbjct: 231 HHMRILGKAGVN--RWLGKR---PVVRGVAMNPSKHPHGGGT 267
>gnl|CDD|109247 pfam00181, Ribosomal_L2, Ribosomal Proteins L2, RNA binding
domain.
Length = 77
Score = 71.1 bits (175), Expect = 3e-16
Identities = 28/82 (34%), Positives = 40/82 (48%), Gaps = 7/82 (8%)
Query: 11 GAGSVFRSHNKHRKGAPK--LRSLDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYK 68
G + R +HR G K R +DF G +KG V DI +DP R AP+A+V + + K
Sbjct: 1 GRNNPGRITVRHRGGGHKRLYRLIDFKRNKGNIKGKVIDIEYDPNRSAPIALVKYEDGEK 60
Query: 69 FKTNKELFIAPEGMYTGQFVYC 90
+APEG+ G +
Sbjct: 61 R-----YILAPEGLKVGDTIES 77
>gnl|CDD|219286 pfam07072, DUF1342, Protein of unknown function (DUF1342). This
family consists of several hypothetical bacterial
proteins of around 250 residues in length. Members of
this family are often known as YacF after the
Escherichia coli protein. The function of this family is
unknown.
Length = 211
Score = 32.1 bits (74), Expect = 0.18
Identities = 13/56 (23%), Positives = 20/56 (35%), Gaps = 13/56 (23%)
Query: 125 RLARASGNYATVIAHN-------PDTKRT---RVKLPSGAKKVIP--SANRAMVGI 168
RL R SG + A N + R+++P V P S ++ I
Sbjct: 156 RLLRESGQFQPQTARNGFYQQMLEQGRSYQLLRLRIPP-DLGVYPEISGHKYRFAI 210
>gnl|CDD|223685 COG0612, PqqL, Predicted Zn-dependent peptidases [General function
prediction only].
Length = 438
Score = 30.1 bits (68), Expect = 1.2
Identities = 13/57 (22%), Positives = 21/57 (36%), Gaps = 3/57 (5%)
Query: 134 ATVIAHNPDTKRTRVKLPSGAKKVI---PSANRAMVGIVAGGGRIDKPILKAGRAHY 187
A LP+G + + P+A + + G +P KAG AH+
Sbjct: 6 LQPAALPALPGLQVFTLPNGLRVITYPNPTAPTVSLDVWVKAGSRAEPAGKAGIAHF 62
>gnl|CDD|235389 PRK05287, PRK05287, hypothetical protein; Provisional.
Length = 250
Score = 29.4 bits (67), Expect = 1.7
Identities = 12/55 (21%), Positives = 20/55 (36%), Gaps = 12/55 (21%)
Query: 125 RLARASGNYATVIAHNPDTKRT---------RVKLPSGAKKVIP--SANRAMVGI 168
RL R SG + A N ++ R++L + P S ++ I
Sbjct: 173 RLLRESGQFRKQTALNGFYQQNLEGRDAQLLRLRLDL-ELGLYPEISGHKYRFAI 226
>gnl|CDD|143446 cd07128, ALDH_MaoC-N, N-terminal domain of the monoamine oxidase
C dehydratase. The N-terminal domain of the MaoC
dehydratase, a monoamine oxidase regulatory protein.
Orthologs of MaoC include PaaZ (Escherichia coli) and
PaaN (Pseudomonas putida), which are putative
ring-opening enzymes of the aerobic phenylacetic acid
(PA) catabolic pathway. The C-terminal domain of MaoC
has sequence similarity to enoyl-CoA hydratase. Also
included in this CD is a novel Burkholderia xenovorans
LB400 ALDH of the aerobic benzoate oxidation (box)
pathway. This pathway involves first the synthesis of a
CoA thio-esterified aromatic acid, with subsequent
dihydroxylation and cleavage steps, yielding the CoA
thio-esterified aliphatic aldehyde,
3,4-dehydroadipyl-CoA semialdehyde, which is further
converted into its corresponding CoA acid by the
Burkholderia LB400 ALDH.
Length = 513
Score = 29.2 bits (66), Expect = 2.2
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 23 RKGAPKLRSLDFAERHGYLKGVVR 46
KG P LR+L F ER LK + +
Sbjct: 47 EKGGPALRALTFHERAAMLKALAK 70
>gnl|CDD|223403 COG0326, HtpG, Molecular chaperone, HSP90 family [Posttranslational
modification, protein turnover, chaperones].
Length = 623
Score = 28.4 bits (64), Expect = 4.6
Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 8/42 (19%)
Query: 57 PLAVVHFRNPYKFKTNKELFI---APEGMYT-----GQFVYC 90
PL +H + + + LFI AP ++ G +Y
Sbjct: 257 PLLWIHNKVEGRLEYTALLFIPSKAPFDLFRRDRKRGLKLYV 298
>gnl|CDD|176201 cd08239, THR_DH_like, L-threonine dehydrogenase (TDH)-like.
MDR/AHD-like proteins, including a protein annotated as
a threonine dehydrogenase. L-threonine dehydrogenase
(TDH) catalyzes the zinc-dependent formation of
2-amino-3-ketobutyrate from L-threonine via
NAD(H)-dependent oxidation. The zinc-dependent alcohol
dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent
interconversion of alcohols to aldehydes or ketones.
Zinc-dependent ADHs are medium chain
dehydrogenase/reductase type proteins (MDRs) and have a
NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. In addition to alcohol
dehydrogenases, this group includes quinone reductase,
sorbitol dehydrogenase, formaldehyde dehydrogenase,
butanediol DH, ketose reductase, cinnamyl reductase, and
numerous others. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 339
Score = 28.1 bits (63), Expect = 4.8
Identities = 19/63 (30%), Positives = 25/63 (39%), Gaps = 3/63 (4%)
Query: 126 LARASGNYATVIAHNPDTKRTRVKLPSGAKKVIPSANRAMVGI--VAGGGRIDKPILKAG 183
LARA G VI +P +R + GA VI S + I + G D I +G
Sbjct: 182 LARALG-AEDVIGVDPSPERLELAKALGADFVINSGQDDVQEIRELTSGAGADVAIECSG 240
Query: 184 RAH 186
Sbjct: 241 NTA 243
>gnl|CDD|227435 COG5104, PRP40, Splicing factor [RNA processing and modification].
Length = 590
Score = 27.7 bits (61), Expect = 6.0
Identities = 13/51 (25%), Positives = 20/51 (39%)
Query: 136 VIAHNPDTKRTRVKLPSGAKKVIPSANRAMVGIVAGGGRIDKPILKAGRAH 186
V +N T+ +R K+P KKV P A + GG + +
Sbjct: 68 VYYYNSITRESRWKIPPERKKVEPIAEQKHDERSMIGGNGNDMAITDHETS 118
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
0.320 0.137 0.416
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,821,128
Number of extensions: 1233182
Number of successful extensions: 898
Number of sequences better than 10.0: 1
Number of HSP's gapped: 874
Number of HSP's successfully gapped: 21
Length of query: 248
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 154
Effective length of database: 6,768,326
Effective search space: 1042322204
Effective search space used: 1042322204
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 (21.8 bits)
S2: 58 (26.0 bits)