RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 024947
(260 letters)
>gnl|CDD|173464 PTZ00180, PTZ00180, 60S ribosomal protein L8; Provisional.
Length = 260
Score = 436 bits (1124), Expect = e-157
Identities = 182/260 (70%), Positives = 204/260 (78%)
Query: 1 MGRVIRAQRKGAGSVFKSHTHHRKGPARFRSLDFGERNGYLKGVITEIIHDPGRGAPLAR 60
MGRVIRAQRKG GSVFK+H H R GPA+ R LD+ ER+GY++GV+ +I HDPGRGAPLAR
Sbjct: 1 MGRVIRAQRKGNGSVFKAHGHKRLGPAKLRILDYAERHGYIRGVVKDIEHDPGRGAPLAR 60
Query: 61 VTFRHPFRYQHQKELFVAAEGMYTGQFVYCGRKATLVVGNVLPLRSIPEGAVVCNVEHHV 120
V FR P++Y+ KEL VA EGMYTGQ+VYCG KA L +GNVLPL IPEG +VCNVE
Sbjct: 61 VEFRDPYKYKRVKELMVAPEGMYTGQYVYCGAKAPLAIGNVLPLGQIPEGTIVCNVEEKP 120
Query: 121 GDRGVFARCSGDYAVVISHNPDNDTTRIKLPSGAKKIVPSGCRAMIGQVAGGGRTEKPLL 180
GDRG AR SG YA +I H+ D TRI+LPSG KK V S RAMIG VAGGGR +KP+L
Sbjct: 121 GDRGTLARASGCYATIIGHSDDGGKTRIRLPSGQKKTVSSLSRAMIGIVAGGGRIDKPVL 180
Query: 181 KAGNAYHKFRVKRNCWPKVRGVAMNPVEHPHGGGNHQHIGHASTVRRDAPPGQKVGLIAA 240
KAGNA+HK+R KRNCWPKVRGVAMNPVEHPHGGGNHQHIGH STV R APPGQKVGLIAA
Sbjct: 181 KAGNAFHKYRGKRNCWPKVRGVAMNPVEHPHGGGNHQHIGHPSTVSRHAPPGQKVGLIAA 240
Query: 241 RRTGRLRGQAAATAAKADKA 260
RRTG LRG A +
Sbjct: 241 RRTGLLRGGKKVKGAWHPEE 260
>gnl|CDD|236589 PRK09612, rpl2p, 50S ribosomal protein L2P; Validated.
Length = 238
Score = 298 bits (766), Expect = e-103
Identities = 131/248 (52%), Positives = 165/248 (66%), Gaps = 11/248 (4%)
Query: 1 MGRVIRAQRKGAGS-VFKSHTHHRKGPARFRSLDFGERNGYLKGVITEIIHDPGRGAPLA 59
MG+ I +QR+G G+ F+S +H KGP ++ LD +G L+G + +I+HDPGR AP+A
Sbjct: 1 MGKRIISQRRGRGTPTFRSPSHRYKGPVKYPPLDK---DGTLRGKVVDILHDPGRNAPVA 57
Query: 60 RVTFRHPFRYQHQKELFVAAEGMYTGQFVYCGRKATLVVGNVLPLRSIPEGAVVCNVEHH 119
+V F ++ L +A EG+Y GQ + G A + GN LPL IPEG VCN+E
Sbjct: 58 KVKFE-----NGEEFLILAPEGLYVGQEIEIGPSAEIKPGNTLPLGEIPEGTPVCNIESR 112
Query: 120 VGDRGVFARCSGDYAVVISHNPDNDTTRIKLPSGAKKIVPSGCRAMIGQVAGGGRTEKPL 179
GD G FAR SG YA+V+ H + D ++LPSG K + CRA IG VAGGGR EKP
Sbjct: 113 PGDGGKFARSSGTYALVVGH--EGDKVIVQLPSGKIKELNPRCRATIGVVAGGGRKEKPF 170
Query: 180 LKAGNAYHKFRVKRNCWPKVRGVAMNPVEHPHGGGNHQHIGHASTVRRDAPPGQKVGLIA 239
LKAG YHK + K WP+VRGVAMN V+HPHGGGNHQH G STV R+APPG+KVG IA
Sbjct: 171 LKAGKKYHKMKAKAKKWPRVRGVAMNAVDHPHGGGNHQHPGRPSTVSRNAPPGRKVGHIA 230
Query: 240 ARRTGRLR 247
ARRTGR +
Sbjct: 231 ARRTGRRK 238
>gnl|CDD|223168 COG0090, RplB, Ribosomal protein L2 [Translation, ribosomal
structure and biogenesis].
Length = 275
Score = 253 bits (649), Expect = 1e-84
Identities = 99/251 (39%), Positives = 130/251 (51%), Gaps = 17/251 (6%)
Query: 1 MGRVIRAQRKGA--GSVFKSHTHHRKGPARFRSLDFGERNGYLKGVITEIIHDPGRGAPL 58
MG++I++Q + + K R DF + G + +I +DP R AP+
Sbjct: 34 MGKLIKSQGRNNRGRITVRHRGGGHKRRYRLI--DFKRNKDGIPGKVEDIEYDPNRSAPI 91
Query: 59 ARVTFRHPFRYQHQKELFVAAEGMYTGQFVYCGRKATLVVGNVLPLRSIPEGAVVCNVEH 118
A V + +K +A EG+ G + G+ A + GN LPL +IPEG +V NVE
Sbjct: 92 ALVVYEDG-----EKRYILAPEGLKVGDVIESGKDADIKPGNALPLGNIPEGTIVHNVEL 146
Query: 119 HVGDRGVFARCSGDYAVVISHNPDNDTTRIKLPSGAKKIVPSGCRAMIGQVAGGGRTEKP 178
GD G AR +G YA V+ + + ++LPSG + V S CRA IG VA GG KP
Sbjct: 147 KPGDGGQLARSAGTYAQVVGK--EGNYVIVRLPSGEMRKVLSECRATIGVVANGGHILKP 204
Query: 179 LLKAGNAYHKFRVKRNCWPKVRGVAMNPVEHPHGGGNHQHI-GHASTVRRDAPPGQKVGL 237
L KAG A HK + P VRGVAMNPV+HPHGGG QH G TV P K
Sbjct: 205 LGKAGRARHKGK-----RPTVRGVAMNPVDHPHGGGEGQHPGGKPPTVPWGKPTPGKKTR 259
Query: 238 IAARRTGRLRG 248
IAA+RTG+
Sbjct: 260 IAAKRTGKFIV 270
>gnl|CDD|202823 pfam03947, Ribosomal_L2_C, Ribosomal Proteins L2, C-terminal
domain.
Length = 130
Score = 155 bits (393), Expect = 6e-48
Identities = 58/137 (42%), Positives = 74/137 (54%), Gaps = 8/137 (5%)
Query: 96 LVVGNVLPLRSIPEGAVVCNVEHHVGDRGVFARCSGDYAVVISHNPDNDTTRIKLPSGAK 155
+ +GN LPL++IP G V+ N+E G G AR +G YA +I+ + +KLPSG
Sbjct: 1 IKIGNALPLKNIPIGTVIHNIELIPGKGGQLARSAGTYAQIIAK--EGKYVTLKLPSGEV 58
Query: 156 KIVPSGCRAMIGQVAGGGRTEKPLLKAGNAYHKFRVKRNCWPKVRGVAMNPVEHPHGGGN 215
++V S CRA IG V+ KPL KAG + P VRGVAMNPV+HPHGGG
Sbjct: 59 RLVSSNCRATIGVVSNIDHNNKPLGKAGRSRWLGI-----RPTVRGVAMNPVDHPHGGGE 113
Query: 216 -HQHIGHASTVRRDAPP 231
IG V P
Sbjct: 114 GRTSIGRPPPVSPWGKP 130
>gnl|CDD|176993 CHL00052, rpl2, ribosomal protein L2.
Length = 273
Score = 115 bits (291), Expect = 5e-31
Identities = 69/200 (34%), Positives = 95/200 (47%), Gaps = 24/200 (12%)
Query: 22 HRKG--PARFRSLDFGERNGYLKGVITEIIHDPGRGAPLARVTFRHPFRYQH-QKELFVA 78
HR G +R +DF + G I I +DP R A + + Y +K +
Sbjct: 51 HRGGGHKRLYRKIDFRRNKKDIYGRIVTIEYDPNRNAYICLI------HYGDGEKRYILH 104
Query: 79 AEGMYTGQFVYCGRKATLVVGNVLPLRSIPEGAVVCNVEHHVGDRGVFARCSGDYAVVIS 138
G+ G + G +A + +GN LPL +IP G + N+E G G AR +G A +I+
Sbjct: 105 PRGLKIGDTIVSGTEAPIKIGNALPLTNIPLGTAIHNIEITPGKGGQLARAAGAVAKLIA 164
Query: 139 HNPDNDTTRIKLPSGAKKIVPSGCRAMIGQVAGGGRTEKPLLKAGNAYHKFRVKRNCW-- 196
+ + +KLPSG +++ C A IGQV K L KAG W
Sbjct: 165 K--EGKSATLKLPSGEVRLISKNCSATIGQVGNVDVNNKSLGKAG---------SKRWLG 213
Query: 197 --PKVRGVAMNPVEHPHGGG 214
PKVRGV MNPV+HPHGGG
Sbjct: 214 KRPKVRGVVMNPVDHPHGGG 233
>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 = 111 bits (280), Expect = 1e-29
Identities = 69/197 (35%), Positives = 98/197 (49%), Gaps = 14/197 (7%)
Query: 20 THHRKGPA--RFRSLDFGERNGYLKGVITEIIHDPGRGAPLARVTFRHPFRYQHQKELFV 77
+ HR G +R +DF + + I +DP R A +A + + +K +
Sbjct: 49 SRHRGGGHKRLYRIIDFKRNKDGIPAKVAAIEYDPNRSARIALLHYA-----DGEKRYIL 103
Query: 78 AAEGMYTGQFVYCGRKATLVVGNVLPLRSIPEGAVVCNVEHHVGDRGVFARCSGDYAVVI 137
A +G+ G V G +A + GN LPLR+IP G V N+E G G AR +G A ++
Sbjct: 104 APKGLKVGDTVISGPEAPIKPGNALPLRNIPVGTTVHNIELKPGKGGQLARSAGTSAQIL 163
Query: 138 SHNPDNDTTRIKLPSGAKKIVPSGCRAMIGQVAGGGRTEKPLLKAGNAYHKFRVKRNCWP 197
+ + ++LPSG ++V CRA IG+V L KAG + R P
Sbjct: 164 AK--EGGYVTLRLPSGEMRMVLKECRATIGEVGNEDHNNIVLGKAGRSRW--LGIR---P 216
Query: 198 KVRGVAMNPVEHPHGGG 214
VRGVAMNPV+HPHGGG
Sbjct: 217 TVRGVAMNPVDHPHGGG 233
>gnl|CDD|236488 PRK09374, rplB, 50S ribosomal protein L2; Validated.
Length = 276
Score = 107 bits (271), Expect = 4e-28
Identities = 57/145 (39%), Positives = 74/145 (51%), Gaps = 23/145 (15%)
Query: 78 AAEGMYTGQFVYCGRKATLVVGNVLPLRSIPEGAVVCNVEHHVGDRGVFARCSGDYAVVI 137
A +G+ G V G A + GN LPLR+IP G V N+E G G AR +G A ++
Sbjct: 106 APKGLKVGDTVVSGPDADIKPGNALPLRNIPVGTTVHNIELKPGKGGQLARSAGTSAQLV 165
Query: 138 SHNPDNDTTRIKLPSGAKKIVPSGCRAMIGQVAGGGRTEKPLLKAGNAYHKFRV--K--R 193
+ + ++LPSG + V + CRA IG+V GN H K R
Sbjct: 166 AK--EGKYATLRLPSGEVRKVLAECRATIGEV-------------GNEEHSNISLGKAGR 210
Query: 194 NCW----PKVRGVAMNPVEHPHGGG 214
+ W P VRGVAMNPV+HPHGGG
Sbjct: 211 SRWLGIRPTVRGVAMNPVDHPHGGG 235
>gnl|CDD|173329 PTZ00031, PTZ00031, ribosomal protein L2; Provisional.
Length = 317
Score = 102 bits (257), Expect = 7e-26
Identities = 76/224 (33%), Positives = 101/224 (45%), Gaps = 24/224 (10%)
Query: 2 GRVI------RAQRKGAGSVFKSHTHHRKGP--ARFRSLDFGERNGYLKGVITEIIHDPG 53
GRV+ R + G +V + T HR G R R +DF + + I +DP
Sbjct: 58 GRVVKQLSCRRVKNSGRNNVGRITTRHRGGGHVQRLRFIDFKRSRKDIYSTVLRIEYDPS 117
Query: 54 RGAPLARVTFRHPFRYQHQKELFVAAEGMYTGQFVYCGRKATLVVGNVLPLRSIPEGAVV 113
R A +A + + +A + G + + A + GN LPLR+IP G++V
Sbjct: 118 RSAHIALLQYEDGVL-----SYILAPLLLRPGDKIIASKYANINPGNSLPLRNIPVGSIV 172
Query: 114 CNVEHHVGDRGVFARCSGDYAVVISHNPDNDTTRIKLPSGAKKIVPSGCRAMIGQVAGGG 173
NVE G G R G YA V+S D +KL S + P C A IGQV+
Sbjct: 173 HNVEMRPGAGGQIIRAGGTYATVVSK--DEQFATLKLKSTEIRKFPLDCWATIGQVSNLE 230
Query: 174 RTEKPLLKAGNAYHKFRVKRNC-W-PKVRGVAMNPVEHPHGGGN 215
+ L KAG V R P VRGVAMNP +HPHGGG
Sbjct: 231 HHMRILGKAG-------VNRWLGKRPVVRGVAMNPSKHPHGGGT 267
>gnl|CDD|109247 pfam00181, Ribosomal_L2, Ribosomal Proteins L2, RNA binding
domain.
Length = 77
Score = 65.3 bits (160), Expect = 4e-14
Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 7/82 (8%)
Query: 11 GAGSVFKSHTHHRKG--PARFRSLDFGERNGYLKGVITEIIHDPGRGAPLARVTFRHPFR 68
G + + HR G +R +DF G +KG + +I +DP R AP+A V +
Sbjct: 1 GRNNPGRITVRHRGGGHKRLYRLIDFKRNKGNIKGKVIDIEYDPNRSAPIALVKYEDG-- 58
Query: 69 YQHQKELFVAAEGMYTGQFVYC 90
+K +A EG+ G +
Sbjct: 59 ---EKRYILAPEGLKVGDTIES 77
>gnl|CDD|219232 pfam06934, CTI, Fatty acid cis/trans isomerase (CTI). This family
consists of several fatty acid cis/trans isomerase
proteins which appear to be found exclusively in
bacteria of the orders Vibrionales and Pseudomonadales.
Cis/trans isomerase (CTI) catalyzes the cis-trans
isomerisation of esterified fatty acids in
phospholipids, mainly cis-oleic acid (C(16:1,9)) and
cis-vaccenic acid (C(18:1,11)), in response to solvents.
The CTI protein has been shown to be involved in solvent
resistance in Pseudomonas putida.
Length = 688
Score = 29.1 bits (66), Expect = 2.8
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 225 VRRDAPPGQKVGLIAARR 242
VR PPGQ + LIA RR
Sbjct: 175 VRSRTPPGQPIDLIATRR 192
>gnl|CDD|225882 COG3345, GalA, Alpha-galactosidase [Carbohydrate transport and
metabolism].
Length = 687
Score = 29.1 bits (65), Expect = 3.1
Identities = 13/53 (24%), Positives = 19/53 (35%), Gaps = 2/53 (3%)
Query: 66 PFRYQHQKELFVAAEGMYTG-QFVYCGRKATLVVGNVLPLRSIPEGAVVCNVE 117
P R Q + F G G Y G A V + P + +G + + E
Sbjct: 193 PERN-LQSDGFTEEAGEVYGFGLTYSGNFAAFVEVHQHPFFRVQDGILPFDGE 244
>gnl|CDD|217402 pfam03170, BcsB, Bacterial cellulose synthase subunit. This family
includes bacterial proteins involved in cellulose
synthesis. Cellulose synthesis has been identified in
several bacteria. In Agrobacterium tumefaciens, for
instance, cellulose has a pathogenic role: it allows the
bacteria to bind tightly to their host plant cells.
While several enzymatic steps are involved in cellulose
synthesis, potentially the only step unique to this
pathway is that catalyzed by cellulose synthase. This
enzyme is a multi subunit complex. This family encodes a
subunit that is thought to bind the positive effector
cyclic di-GMP. This subunit is found in several
different bacterial cellulose synthase enzymes. The
first recognised sequence for this subunit is BcsB. In
the AcsII cellulose synthase, this subunit and the
subunit corresponding to BcsA are found in the same
protein. Indeed, this alignment only includes the
C-terminal half of the AcsAII synthase, which
corresponds to BcsB.
Length = 614
Score = 28.5 bits (64), Expect = 4.0
Identities = 14/62 (22%), Positives = 19/62 (30%), Gaps = 6/62 (9%)
Query: 44 VITEIIHDPGRGAPLARVTFRHPFRYQHQKELFVAAEGMYTGQFVYCGRKATLVVGNVLP 103
+ I + L VT R P +L AA + G G +V L
Sbjct: 235 TLAVIDNPADPYGKLLLVTGRDP------ADLRTAARALALGNAALAGASVLVVRVVQLA 288
Query: 104 LR 105
R
Sbjct: 289 PR 290
>gnl|CDD|199819 cd00050, MH2, C-terminal Mad Homology 2 (MH2) domain. The MH2
domain is found in the SMAD (small mothers against
decapentaplegic) family of proteins and is responsible
for type I receptor interactions,
phosphorylation-triggered homo- and
hetero-oligomerization, and transactivation. It is
negatively regulated by the N-terminal MH1 domain which
prevents it from forming a complex with SMAD4. The MH2
domain is multifunctional and provides SMADs with their
specificity and selectivity, as well as transcriptional
activity. Several transcriptional co-activators and
repressors have also been reported to regulate SMAD
signaling by interacting with the MH2 domain. Mutations
in the MH2 domains of SMAD2 and especially SMAD4 have
been detected in colorectal and other human cancers.
Length = 170
Score = 27.6 bits (61), Expect = 4.6
Identities = 21/102 (20%), Positives = 38/102 (37%), Gaps = 6/102 (5%)
Query: 159 PSGCRAMIGQVAGGGRT---EKPLLKAGNAYHKFRVKRNCWPKVRGVAMNPVEHPHGGGN 215
+G R +GQ++ R E+ G H + V W + V+ + +
Sbjct: 33 SNGDRFCLGQLSNVNRNETIERTRRHIGKGVHLYYVGGEVWAECLSDHAIFVQSRNL--D 90
Query: 216 HQHIGHASTVRRDAPPGQKVGLIAARRTGRLRGQAAATAAKA 257
+ H H TV PPG + + + +L Q+ T +
Sbjct: 91 YPHGRHPLTVC-KIPPGCSIKVFDNQEFAQLLHQSVNTGFEG 131
>gnl|CDD|163469 TIGR03757, conj_TIGR03757, integrating conjugative element
protein, PFL_4709 family. Members of this protein
belong to extended genomic regions that appear to be
spread by conjugative transfer [Mobile and
extrachromosomal element functions, Plasmid functions].
Length = 113
Score = 26.5 bits (59), Expect = 6.9
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 51 DPGRGAPLARVTFRHPFRYQHQKELFVAAEGM 82
DP + A AR + P + Q+ L A +G+
Sbjct: 43 DPQQAAAQARQRLQSPDWARLQRRLAQAYQGV 74
>gnl|CDD|153101 cd01042, DMQH, Demethoxyubiquinone hydroxylase, ferritin-like
diiron-binding domain. Demethoxyubiquinone hydroxylases
(DMQH) are members of the ferritin-like,
diiron-carboxylate family which are present in
eukaryotes (the CLK-1/CAT5 family) and prokaryotes (the
Coq7 family). DMQH participates in one of the last steps
of ubiquinone biosysnthesis and is responsible for DMQ
hydroxylation, resulting in the formation of
hydroxyubiquinone, a precursor of ubiquinone. CLK-1 is a
mitochondrial inner membrane protein and Coq7 is a
proposed interfacial integral membrane protein.
Mutations in the Caenorhabditis elegans gene clk-1
affect biological timing and extend longevity. The
conserved residues of a diiron center are present in
this domain.
Length = 165
Score = 26.7 bits (60), Expect = 8.8
Identities = 5/25 (20%), Positives = 12/25 (48%)
Query: 142 DNDTTRIKLPSGAKKIVPSGCRAMI 166
+ + L + K ++ +GC+ I
Sbjct: 136 ELGAEKAPLYALLKALIKAGCKVAI 160
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 0.138 0.429
Gapped
Lambda K H
0.267 0.0659 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,572,353
Number of extensions: 1314399
Number of successful extensions: 1011
Number of sequences better than 10.0: 1
Number of HSP's gapped: 988
Number of HSP's successfully gapped: 23
Length of query: 260
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 165
Effective length of database: 6,723,972
Effective search space: 1109455380
Effective search space used: 1109455380
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: 58 (26.3 bits)