RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11559
(189 letters)
>gnl|CDD|188051 TIGR00446, nop2p, NOL1/NOP2/sun family putative RNA methylase.
[Protein synthesis, tRNA and rRNA base modification].
Length = 264
Score = 121 bits (306), Expect = 2e-34
Identities = 52/138 (37%), Positives = 73/138 (52%), Gaps = 18/138 (13%)
Query: 15 IRTNTLKTRRRDLAQALVNRGVNLDPIGKWSKVGLVIYNSTVPIGATPEYLGGHYILQGA 74
IR NTLK DL + L NRGV L+P + + S IG+TPEYL G+Y Q A
Sbjct: 1 IRVNTLKINVEDLLERLENRGVVLEPTCEEYFFE--VKESPFSIGSTPEYLFGYYYPQEA 58
Query: 75 SKYW---------------ICA-PHRAAKLAAALMKNTGVLFANDVSKERSKAIVGNFHR 118
S + A P + LMKN G + AN++SK R+KA++ N +R
Sbjct: 59 SSMIPPIALEPREDERVLDMAAAPGGKTTQISQLMKNKGCIVANEISKSRTKALISNINR 118
Query: 119 LGVINSVVTCLDGRQYGK 136
+GV+N++V DGR++G
Sbjct: 119 MGVLNTIVINADGRKFGA 136
Score = 34.0 bits (78), Expect = 0.031
Identities = 12/22 (54%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 137 PEENEAVVNYALRKR-DVKLVP 157
EENE V++Y LRKR DV
Sbjct: 204 VEENEEVIDYILRKRPDVVEEI 225
>gnl|CDD|201649 pfam01189, Nol1_Nop2_Fmu, NOL1/NOP2/sun family.
Length = 277
Score = 121 bits (305), Expect = 4e-34
Identities = 51/149 (34%), Positives = 68/149 (45%), Gaps = 17/149 (11%)
Query: 3 FLEASETQRPLTIRTNTLKTRRRDLAQALVNRGVNLDPIGKWSKVGLVIYNSTVPIGATP 62
LEA+ P T+R N LKT+R L QAL GV L+P+G++ L + + IG+ P
Sbjct: 1 ILEANNCSPPGTLRKNVLKTKRWSLLQALELAGVQLEPLGRYPH-ALPVGDLPYSIGSLP 59
Query: 63 EYLGGHYILQGASKYWI----------------CAPHRAAKLAAALMKNTGVLFANDVSK 106
+ G +Q AS AP A LMKN G + A D +K
Sbjct: 60 PFENGAVTVQDASSQLDAIALNPQEDEFILDMCAAPGGKTTHIAELMKNEGTVVAVDRNK 119
Query: 107 ERSKAIVGNFHRLGVINSVVTCLDGRQYG 135
+R K + N RLGV N +V D RQ
Sbjct: 120 QRLKRVYANIQRLGVFNIIVQEGDARQID 148
>gnl|CDD|223222 COG0144, Sun, tRNA and rRNA cytosine-C5-methylases [Translation,
ribosomal structure and biogenesis].
Length = 355
Score = 85.1 bits (211), Expect = 6e-20
Identities = 46/163 (28%), Positives = 63/163 (38%), Gaps = 19/163 (11%)
Query: 3 FLEASETQRPLTIRTNTLKTRRRDLAQALVNRGVNLDPIGKWSKVGLVIYNSTVPIGATP 62
A P ++R NTLK +L +AL GV + L I S PIG P
Sbjct: 74 IAAALLRPPPRSLRVNTLKADVEELLEALEEAGVLDEKPW-VLDEVLRIEAS-GPIGRLP 131
Query: 63 EYLGGHYILQGASKYWI---------------CA-PHRAAKLAAALMKNTG-VLFANDVS 105
E+ G +Q + CA P A LM+N G ++ A DVS
Sbjct: 132 EFAEGLIYVQDEASQLPALVLDPKPGERVLDLCAAPGGKTTHLAELMENEGAIVVAVDVS 191
Query: 106 KERSKAIVGNFHRLGVINSVVTCLDGRQYGKPEENEAVVNYAL 148
+R K + N RLGV N +V D R+ + + L
Sbjct: 192 PKRLKRLRENLKRLGVRNVIVVNKDARRLAELLPGGEKFDRIL 234
Score = 36.2 bits (84), Expect = 0.005
Identities = 13/30 (43%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 137 PEENEAVVNYALRKR-DVKLVPTGLDFGTE 165
PEENE VV L + D +L P L +G
Sbjct: 293 PEENEEVVERFLERHPDFELEPVRLPWGPL 322
>gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF;
Reviewed.
Length = 470
Score = 72.6 bits (179), Expect = 2e-15
Identities = 58/166 (34%), Positives = 75/166 (45%), Gaps = 28/166 (16%)
Query: 3 FLEASETQRPL--TIRTNTLKTRRRDLAQALVNRGVNLDPIGKWSKVGLVIYN---STVP 57
F+ A QRPL +IR NTLK D Q + G L PI W + G I +P
Sbjct: 25 FIAAC--QRPLRRSIRVNTLKISVADFLQLMAPYGWTLTPI-PWCEEGFWIERDDEDALP 81
Query: 58 IGATPEYLGGHYILQGASKYW--------ICAPHRAAKLA----------AALMKNTGVL 99
+G T E+L G + +Q AS AP R +A AALM N G +
Sbjct: 82 LGNTAEHLSGLFYIQEASSMLPVAALFADDNAPQRVLDMAAAPGSKTTQIAALMNNQGAI 141
Query: 100 FANDVSKERSKAIVGNFHRLGVINSVVTCLDGRQYGK--PEENEAV 143
AN+ S R K + N R GV N +T DGR +G PE +A+
Sbjct: 142 VANEYSASRVKVLHANISRCGVSNVALTHFDGRVFGAALPETFDAI 187
>gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional.
Length = 431
Score = 54.5 bits (131), Expect = 5e-09
Identities = 33/139 (23%), Positives = 55/139 (39%), Gaps = 19/139 (13%)
Query: 10 QRPL--TIRTNTLKTRRRDLAQALVNRGVNLDPIGKWSKVGLVIYNSTVPIGATPEYLGG 67
Q PL +R N+L R ++ + L G P GK S L++ V + + G
Sbjct: 159 QEPLPTMLRVNSLAITREEVIKILAEEGTEAVP-GKHSPFSLIVRKLGVNMNDSRVIKDG 217
Query: 68 HYILQGASKYWI----------------CAPHRAAKLAAALMKNTGVLFANDVSKERSKA 111
+QG S + AP A LMK+ G + A D+S+E+ +
Sbjct: 218 LATVQGESSQIVPLLMELEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQL 277
Query: 112 IVGNFHRLGVINSVVTCLD 130
+ + RL + + + D
Sbjct: 278 VEKHAKRLKLSSIEIKIAD 296
>gnl|CDD|237856 PRK14901, PRK14901, 16S rRNA methyltransferase B; Provisional.
Length = 434
Score = 51.5 bits (124), Expect = 5e-08
Identities = 39/155 (25%), Positives = 56/155 (36%), Gaps = 21/155 (13%)
Query: 12 PLTIRTNTLKTRRRDLAQALVNRGVNLDPIGKWSKVGLVIYNSTVPIGATPEYLGGHYIL 71
L +R N L+T ++ AL G+ PI + GL + + I P Y G + +
Sbjct: 178 SLDLRINPLRTSLEEVQAALAEAGITATPIPGLPQ-GLRLTGNPGSIRQLPGYEEGWWTV 236
Query: 72 QGASKYWIC----------------APHRAAKLAAALMKNTGVLFANDVSKERSKAIVGN 115
Q S + AP A LM + G ++A D S R K + N
Sbjct: 237 QDRSAQLVAPLLDPQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQEN 296
Query: 116 FHRLGVINSVVTCL-DGRQYGKPEENEAVVNYALR 149
RLG + S+ D R E Y R
Sbjct: 297 AQRLG-LKSIKILAADSRNL--LELKPQWRGYFDR 328
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 46.3 bits (111), Expect = 2e-06
Identities = 42/154 (27%), Positives = 59/154 (38%), Gaps = 29/154 (18%)
Query: 4 LEASETQRPLTIRTNTLKTRRRDLAQALVNRGVNLDPIGKWSKVGLVIYNSTVPIGATPE 63
LE+ +IR NTLK +L + L G ++ S LVI I T
Sbjct: 170 LESLNEPPKASIRVNTLKISVEELIEKLEEEGYEVEE-SLLSPEALVIEKG--NIAGTDL 226
Query: 64 YLGGHYILQGASKYWI---------------C-AP-----HRAAKLAAALMKNTGVLFAN 102
+ G +Q S + C AP H A L+KNTG + A
Sbjct: 227 FKDGLITIQDESSMLVAPALDPKGGDTVLDACAAPGGKTTH-----IAELLKNTGKVVAL 281
Query: 103 DVSKERSKAIVGNFHRLGVINSVVTCLDGRQYGK 136
D+ + + K I N RLG+ N LD R+ +
Sbjct: 282 DIHEHKLKLIEENAKRLGLTNIETKALDARKVHE 315
>gnl|CDD|233025 TIGR00563, rsmB, ribosomal RNA small subunit methyltransferase
RsmB. This protein is also known as sun protein. The
reading frame was originally interpreted as two reading
frames, fmu and fmv. The recombinant protein from E.
coli was shown to methylate only C967 of small subunit
(16S) ribosomal RNA and to produce only m5C at that
position. The seed alignment is built from bacterial
sequences only. Eukaryotic homologs include Nop2, a
protein required for processing pre-rRNA, that is likely
also a rRNA methyltransferase, although the fine
specificity may differ. Cutoff scores are set to avoid
treating archaeal and eukaroytic homologs automatically
as functionally equivalent, although they may have very
similar roles [Protein synthesis, tRNA and rRNA base
modification].
Length = 426
Score = 40.2 bits (94), Expect = 3e-04
Identities = 38/159 (23%), Positives = 56/159 (35%), Gaps = 20/159 (12%)
Query: 2 SFLEASETQRPLTIRTNTLKTRRRDLAQALVNRGVNLDPIGKWSKVGLVIYNSTVPIGAT 61
S EA+ + P+ +R N K R + L G+ P V + + A
Sbjct: 155 SICEANNQRPPMWLRINRTKHSRDEWLALLAEAGMKGFPHDLAPDA--VRLETPAAVHAL 212
Query: 62 PEYLGGHYILQGASKYWI---------------C-APHRAAKLAAALMKNTGVLFANDVS 105
P + G +Q AS W+ C AP L + A D+
Sbjct: 213 PGFEEGWVTVQDASAQWVATWLAPQNEETILDACAAPGGKTTHILELAPQ-AQVVALDIH 271
Query: 106 KERSKAIVGNFHRLGV-INSVVTCLDGRQYGKPEENEAV 143
+ R K + N RLG+ I + DGR + ENE
Sbjct: 272 EHRLKRVYENLKRLGLTIKAETKDGDGRGPSQWAENEQF 310
>gnl|CDD|227824 COG5537, IRR1, Cohesin [Cell division and chromosome partitioning].
Length = 740
Score = 30.6 bits (69), Expect = 0.55
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 1 MSFLEASETQRPLTIRTNTLKTRRRDLAQALVNRGVNLDPIGKWSKVGLVIYNSTV 56
+S L + L + K R RD+ Q R + ++ + +W V + I+NS+
Sbjct: 153 LSILRGKGFEVVLYLYDENFKVRFRDVYQDFNIRALLVEFVSEWV-VSVGIFNSSC 207
>gnl|CDD|224158 COG1237, COG1237, Metal-dependent hydrolases of the beta-lactamase
superfamily II [General function prediction only].
Length = 259
Score = 29.7 bits (67), Expect = 0.83
Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 15/62 (24%)
Query: 98 VLFANDVSKERSKAIVGNFHRLGVINSVVTCLDGRQYGKPEENEAVVNYALRKRDVKLVP 157
V +A + S +R KA++G FH +G E E V +Y L++ V+ +
Sbjct: 183 VEWAKERSGDRVKAVIGGFHLIGA--------------SEERLEEVADY-LKELGVEKIY 227
Query: 158 TG 159
Sbjct: 228 PC 229
>gnl|CDD|224812 COG1900, COG1900, Uncharacterized conserved protein [Function
unknown].
Length = 365
Score = 28.9 bits (65), Expect = 1.6
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 9/47 (19%)
Query: 143 VVNYALRKRDVKLVPTGLDFGTEGFVNYRQNKSYRPEMQEKQERVSP 189
VV+Y++R+RD + +V+Y + +S R E++ K R SP
Sbjct: 291 VVDYSIRRRDRPEI---------TYVDYWELRSGRIEIEGKTVRTSP 328
>gnl|CDD|181020 PRK07533, PRK07533, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 258
Score = 28.4 bits (64), Expect = 2.2
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 84 RAAKLAAALMKNTGVLFANDVSKERSKAIVGNFHRLGVI 122
R A+LA LM N G L +S ++ +V N++ +G +
Sbjct: 129 RMARLAEPLMTNGGSLLT--MSYYGAEKVVENYNLMGPV 165
>gnl|CDD|198447 cd10479, EphR_LBD_A1, Ligand Binding Domain of Ephrin type-A
Receptor 1. Ephrin receptors (EphRs) comprise the
largest subfamily of receptor tyrosine kinases (RTKs).
Class EphA receptors bind GPI-anchored ephrin-A ligands.
There are ten vertebrate EphA receptors (EphA1-10),
which display promiscuous interactions with six ephrin-A
ligands. EphA1 is downregulated in some advanced
colorectal and myeloid cancers and upregulated in
neuroblasoma and glioblastoma. EphRs contain a ligand
binding domain and two fibronectin repeats
extracellularly, a transmembrane segment, and a
cytoplasmic tyrosine kinase domain. Binding of the
ephrin ligand to EphR requires cell-cell contact since
both are anchored to the plasma membrane. The resulting
downstream signals occur bidirectionally in both
EphR-expressing cells (forward signaling) and
ephrin-expressing cells (reverse signaling). Ephrin/EphR
interaction mainly results in cell-cell repulsion or
adhesion.
Length = 177
Score = 26.9 bits (59), Expect = 4.8
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 10 QRPLTIRTNTLKTRR----RDLAQALVNRGVNLDPIGKWSKVGL 49
+RPL + T+ + RDLA V V +GK ++ GL
Sbjct: 112 RRPLFQKVTTVAADQSFTIRDLASGSVKLNVERCSLGKLTRRGL 155
>gnl|CDD|202278 pfam02545, Maf, Maf-like protein. Maf is a putative inhibitor of
septum formation in eukaryotes, bacteria, and archaea.
Length = 193
Score = 26.9 bits (60), Expect = 6.0
Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 6/66 (9%)
Query: 100 FANDVSKERSKAIVGNFHR---LGVINSVVTCLDGRQYGKPEENEAVVNY--ALRKRDVK 154
+ D++ E++ A V L + V L GR GKP++ E L
Sbjct: 44 YVVDLACEKALAKVAQLAPDNALIIGADTVVILGGRILGKPKDKEEAREMLRKLSGNVHS 103
Query: 155 LVPTGL 160
+ TGL
Sbjct: 104 VY-TGL 108
>gnl|CDD|227148 COG4811, COG4811, Predicted membrane protein [Function unknown].
Length = 152
Score = 26.6 bits (59), Expect = 6.4
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 8/57 (14%)
Query: 47 VGLVIYNSTVPIGA-TPEYLGGHYILQGASKYWICAPHRAAKLAAALMKNTGVLFAN 102
+ ++IYN+ GA +L L G ++I R K+ + K G FAN
Sbjct: 54 IVILIYNNVTNHGALITTWLLSALALLGFYIFFI----RVPKI---IFKEKGFFFAN 103
>gnl|CDD|216817 pfam01969, DUF111, Protein of unknown function DUF111. This
prokaryotic family has no known function.
Length = 381
Score = 26.7 bits (60), Expect = 7.6
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 79 ICAPHRAAKLAAALMKNTGVL 99
+C P A LA L + T L
Sbjct: 298 LCKPEDAEALARILFRETTTL 318
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 27.0 bits (59), Expect = 7.8
Identities = 16/41 (39%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 142 AVVNYALRKRDVKLVPTGLDFGTEGFVNYRQNKSYRPEMQE 182
AVV+YALR+R + F T F N+ NK P E
Sbjct: 340 AVVDYALRRR-FSFIDIEPGFDTPQFRNFLLNKKAEPSFVE 379
>gnl|CDD|223749 COG0677, WecC, UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell
envelope biogenesis, outer membrane].
Length = 436
Score = 26.9 bits (60), Expect = 8.3
Identities = 12/24 (50%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 41 IGKWSKVG-LVIYNSTVPIGATPE 63
I K G LVI ST P G T E
Sbjct: 114 IAPVLKKGDLVILESTTPPGTTEE 137
>gnl|CDD|129276 TIGR00172, maf, MAF protein. This nonessential gene causes
inhibition of septation when overexpressed. A member of
the family is found in the Archaeon Pyrococcus
horikoshii and another in the round worm Caenorhabditis
elegans [Cellular processes, Cell division].
Length = 183
Score = 26.2 bits (58), Expect = 9.0
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 103 DVSKERSKAIVGNFHRLGVINS-VVTCLDGRQYGKPEENEAVVNYALRK 150
++KE+++A+ +I + V LDG YGKP +++ LRK
Sbjct: 48 RLAKEKAQAVAELLADALIIGADTVVILDGEIYGKP-KDKEEAAEFLRK 95
>gnl|CDD|223501 COG0424, Maf, Nucleotide-binding protein implicated in inhibition
of septum formation [Cell division and chromosome
partitioning].
Length = 193
Score = 26.3 bits (59), Expect = 9.2
Identities = 12/25 (48%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 126 VTCLDGRQYGKPEENEAVVNYALRK 150
V LDGR GKP ++E LRK
Sbjct: 73 VVVLDGRILGKP-KDEEEAREMLRK 96
>gnl|CDD|223006 PHA03179, PHA03179, UL43 envelope protein; Provisional.
Length = 387
Score = 26.4 bits (58), Expect = 9.4
Identities = 19/74 (25%), Positives = 27/74 (36%), Gaps = 5/74 (6%)
Query: 65 LGGHYILQGASKYWICAPHRAAKLAAALMKNTGVLFANDVSKERSKAIVGNFHRLGVINS 124
+ G + ++++W AA LAAAL+ G A D A HR G +
Sbjct: 150 VAGGFAAGASARFWWIGGRGAAALAAALVAGLGASSARDRFSAACPA-----HRRGCVIG 204
Query: 125 VVTCLDGRQYGKPE 138
L R E
Sbjct: 205 AGESLSRRPPEDAE 218
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 0.134 0.392
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,544,412
Number of extensions: 877454
Number of successful extensions: 778
Number of sequences better than 10.0: 1
Number of HSP's gapped: 766
Number of HSP's successfully gapped: 38
Length of query: 189
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 98
Effective length of database: 6,901,388
Effective search space: 676336024
Effective search space used: 676336024
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 (21.7 bits)
S2: 56 (25.3 bits)