RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7376
(180 letters)
>gnl|CDD|201649 pfam01189, Nol1_Nop2_Fmu, NOL1/NOP2/sun family.
Length = 277
Score = 84.7 bits (210), Expect = 3e-20
Identities = 38/133 (28%), Positives = 53/133 (39%), Gaps = 40/133 (30%)
Query: 87 FLEASETQRPLTIRTNTLKTRRRDLAQALVNRGVNLDPIGKWSKVGLVIYNSTVPIGATP 146
LEA+ P T+R N LKT+R L QAL GV L+P+G++ L + + IG+ P
Sbjct: 1 ILEANNCSPPGTLRKNVLKTKRWSLLQALELAGVQLEPLGRYPH-ALPVGDLPYSIGSLP 59
Query: 147 EYL---------------------------------------GAALMKNTGVLFANDVSK 167
+ A LMKN G + A D +K
Sbjct: 60 PFENGAVTVQDASSQLDAIALNPQEDEFILDMCAAPGGKTTHIAELMKNEGTVVAVDRNK 119
Query: 168 ERSKAIVGNFHRL 180
+R K + N RL
Sbjct: 120 QRLKRVYANIQRL 132
>gnl|CDD|188051 TIGR00446, nop2p, NOL1/NOP2/sun family putative RNA methylase.
[Protein synthesis, tRNA and rRNA base modification].
Length = 264
Score = 81.7 bits (202), Expect = 3e-19
Identities = 37/121 (30%), Positives = 51/121 (42%), Gaps = 41/121 (33%)
Query: 99 IRTNTLKTRRRDLAQALVNRGVNLDPIGKWSKVGLVIYNSTVPIGATPEYLG-------- 150
IR NTLK DL + L NRGV L+P + + S IG+TPEYL
Sbjct: 1 IRVNTLKINVEDLLERLENRGVVLEPTCEEYFFE--VKESPFSIGSTPEYLFGYYYPQEA 58
Query: 151 -------------------------------AALMKNTGVLFANDVSKERSKAIVGNFHR 179
+ LMKN G + AN++SK R+KA++ N +R
Sbjct: 59 SSMIPPIALEPREDERVLDMAAAPGGKTTQISQLMKNKGCIVANEISKSRTKALISNINR 118
Query: 180 L 180
+
Sbjct: 119 M 119
>gnl|CDD|223222 COG0144, Sun, tRNA and rRNA cytosine-C5-methylases [Translation,
ribosomal structure and biogenesis].
Length = 355
Score = 72.8 bits (179), Expect = 1e-15
Identities = 51/206 (24%), Positives = 73/206 (35%), Gaps = 49/206 (23%)
Query: 15 EEADKVLSIPDVEQRIKDVLMVLGNFKQYRDPARSRCEYTSLLLKDLCTYFSYNEFLMER 74
E + ++ K V VL R RS +L+ Y S+ E+L+E+
Sbjct: 9 ETVEAAKERLGKDRAAKFVNAVL------RRLERSEEALLEEILRPAFRY-SHPEWLVEK 61
Query: 75 IMQIFPLDELMSFLEASETQRPLTIRTNTLKTRRRDLAQALVNRGVNLDPIGKWSKVGLV 134
+ DE + A P ++R NTLK +L +AL GV + L
Sbjct: 62 LPDALGEDEAEAIAAALLRPPPRSLRVNTLKADVEELLEALEEAGVLDEKPW-VLDEVLR 120
Query: 135 IYNSTVPIGATPEYL---------------------------------G------AALMK 155
I S PIG PE+ G A LM+
Sbjct: 121 IEAS-GPIGRLPEFAEGLIYVQDEASQLPALVLDPKPGERVLDLCAAPGGKTTHLAELME 179
Query: 156 NTG-VLFANDVSKERSKAIVGNFHRL 180
N G ++ A DVS +R K + N RL
Sbjct: 180 NEGAIVVAVDVSPKRLKRLRENLKRL 205
>gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional.
Length = 431
Score = 45.6 bits (108), Expect = 4e-06
Identities = 30/161 (18%), Positives = 59/161 (36%), Gaps = 40/161 (24%)
Query: 59 KDLCTYFSYNEFLMERIMQIFPLDELMSFLEASETQRPLTIRTNTLKTRRRDLAQALVNR 118
K+L +S+ ++L+ P + ++ +E ++ P +R N+L R ++ + L
Sbjct: 126 KELHLKYSHPKWLVNYWRSFLPEEAVLRIMEWNQEPLPTMLRVNSLAITREEVIKILAEE 185
Query: 119 GVNLDPIGKWSKVGLVIYNSTVPIGATPEYLG---------------------------- 150
G P GK S L++ V + +
Sbjct: 186 GTEAVP-GKHSPFSLIVRKLGVNMNDSRVIKDGLATVQGESSQIVPLLMELEPGLRVLDT 244
Query: 151 -----------AALMKNTGVLFANDVSKERSKAIVGNFHRL 180
A LMK+ G + A D+S+E+ + + + RL
Sbjct: 245 CAAPGGKTTAIAELMKDQGKILAVDISREKIQLVEKHAKRL 285
>gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF;
Reviewed.
Length = 470
Score = 45.3 bits (108), Expect = 5e-06
Identities = 43/161 (26%), Positives = 58/161 (36%), Gaps = 57/161 (35%)
Query: 69 EFLMERIMQIFP----LDELMSFLEASETQRPL--TIRTNTLKTRRRDLAQALVNRGVNL 122
FL ++ + P +D+ F+ A QRPL +IR NTLK D Q + G L
Sbjct: 7 AFL-TQMREAMPSHLSMDD---FIAAC--QRPLRRSIRVNTLKISVADFLQLMAPYGWTL 60
Query: 123 DPIGKWSKVGLVIYN---STVPIGATPEYLG----------------------------- 150
PI W + G I +P+G T E+L
Sbjct: 61 TPI-PWCEEGFWIERDDEDALPLGNTAEHLSGLFYIQEASSMLPVAALFADDNAPQRVLD 119
Query: 151 ------------AALMKNTGVLFANDVSKERSKAIVGNFHR 179
AALM N G + AN+ S R K + N R
Sbjct: 120 MAAAPGSKTTQIAALMNNQGAIVANEYSASRVKVLHANISR 160
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 42.5 bits (101), Expect = 4e-05
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 1/77 (1%)
Query: 59 KDLCTYFSYNEFLMERIMQIFPLDELMSFLEASETQRPLTIRTNTLKTRRRDLAQALVNR 118
K L +S+ +L++R + + ++ LE+ +IR NTLK +L + L
Sbjct: 141 KRLSIKYSHPVWLVKRWIDQYGEEKAEKILESLNEPPKASIRVNTLKISVEELIEKLEEE 200
Query: 119 GVNLDPIGKWSKVGLVI 135
G ++ S LVI
Sbjct: 201 GYEVEE-SLLSPEALVI 216
>gnl|CDD|131247 TIGR02192, HtrL_YibB, protein YibB. The protein from this rare,
uncharacterized protein family is designated HtrL or
YibB in E. coli, where its gene is found in a region of
LPS core biosynthesis genes. Homologs are found in
Shigella flexneri, Campylobacter jejuni, and
Caenorhabditis elegans only. The htrL gene may represent
an insertion to the LPS core biosynthesis region, rather
than an LPS biosynthetic protein [Hypothetical proteins,
Conserved].
Length = 270
Score = 33.7 bits (77), Expect = 0.034
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 59 KDLCTYFSYNEFL--MERIMQIFPLDELMSFLEASETQRPLTIRTNTLKTRRRDL 111
+ L TY SY E L +E M IF + F+ + T+ L +T +K DL
Sbjct: 24 RPLDTYHSYFETLATLENNMIIFTDESSKDFVVKTRTKLGLMDKTIVIKKTLDDL 78
>gnl|CDD|237856 PRK14901, PRK14901, 16S rRNA methyltransferase B; Provisional.
Length = 434
Score = 31.1 bits (71), Expect = 0.28
Identities = 14/61 (22%), Positives = 28/61 (45%)
Query: 65 FSYNEFLMERIMQIFPLDELMSFLEASETQRPLTIRTNTLKTRRRDLAQALVNRGVNLDP 124
S+ ++L++ ++ L+E + L +R N L+T ++ AL G+ P
Sbjct: 147 HSFPDWLVKLWLEWLGLEEAEQLCKWFNQPPSLDLRINPLRTSLEEVQAALAEAGITATP 206
Query: 125 I 125
I
Sbjct: 207 I 207
>gnl|CDD|223749 COG0677, WecC, UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell
envelope biogenesis, outer membrane].
Length = 436
Score = 29.9 bits (68), Expect = 0.64
Identities = 19/50 (38%), Positives = 23/50 (46%), Gaps = 5/50 (10%)
Query: 125 IGKWSKVG-LVIYNSTVPIGATPEYLGAALMKNTGVLFANDV----SKER 169
I K G LVI ST P G T E + L + +G+ F D S ER
Sbjct: 114 IAPVLKKGDLVILESTTPPGTTEEVVKPLLEERSGLKFGEDFYLAYSPER 163
>gnl|CDD|227140 COG4803, COG4803, Predicted membrane protein [Function unknown].
Length = 170
Score = 29.3 bits (66), Expect = 0.84
Identities = 11/39 (28%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 1 MNIADHEVFAFPSEEEADKVLSIPDVEQRIKDVLMVLGN 39
+N++D V AF E++A++V + + K+ L+ L +
Sbjct: 1 LNMSDLIVIAFDDEDKAEEVRER--LNELQKEYLITLED 37
>gnl|CDD|183093 PRK11346, PRK11346, hypothetical protein; Provisional.
Length = 285
Score = 29.5 bits (66), Expect = 0.89
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 2/68 (2%)
Query: 44 RDPARSRCEYTSLLLKDLCTYFSYNEFL--MERIMQIFPLDELMSFLEASETQRPLTIRT 101
R + + L + + YFSY E L +E M IF +L +EA +P T+
Sbjct: 16 RGDWTANKGFREKLARSVDVYFSYFERLAALENEMIIFTSPDLKERVEAIRNGKPTTVIV 75
Query: 102 NTLKTRRR 109
+K + R
Sbjct: 76 IDIKKKFR 83
>gnl|CDD|218872 pfam06048, DUF927, Domain of unknown function (DUF927). Family of
bacterial proteins of unknown function. The C-terminal
half of this family contains a P-loop motif.
Length = 284
Score = 29.2 bits (66), Expect = 0.97
Identities = 13/63 (20%), Positives = 23/63 (36%), Gaps = 2/63 (3%)
Query: 6 HEVFAFPSEE--EADKVLSIPDVEQRIKDVLMVLGNFKQYRDPARSRCEYTSLLLKDLCT 63
VF P + + I E +I+D L G ++R + C LL+ +
Sbjct: 118 GGVFVLPDQVIGSDGEKQIIAQDEGKIEDGLSQKGTLDEWRRQVAALCVGNPLLILAVSA 177
Query: 64 YFS 66
+
Sbjct: 178 ALA 180
>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 = 29.4 bits (66), Expect = 1.0
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 61 LCTYFSYNEFLMERIMQIFPLDELMSFLEASETQRPLTIRTNTLKTRRRDLAQALVNRGV 120
L + + E+L++R+ + +P S EA+ + P+ +R N K R + L G+
Sbjct: 131 LDARYLHPEWLVKRLQKAYPGQW-QSICEANNQRPPMWLRINRTKHSRDEWLALLAEAGM 189
Query: 121 NLDP 124
P
Sbjct: 190 KGFP 193
>gnl|CDD|184685 PRK14453, PRK14453, chloramphenicol/florfenicol resistance protein;
Provisional.
Length = 347
Score = 28.6 bits (64), Expect = 1.7
Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 7/78 (8%)
Query: 79 FPLDELMSFLEA--SETQRPLTIRTNTLK--TRRRDLAQALVNRGVNLDPIGKWSKVGLV 134
FPL+E+M L+ T R + I L+ ++ A+A+V N V L+
Sbjct: 229 FPLNEVMKTLDEHIRHTGRKVYIAYIMLEGVNDSKEHAEAVVGLLRNRGSWEHLYHVNLI 288
Query: 135 IYNSTVPIGATPEYLGAA 152
YNST TP ++
Sbjct: 289 PYNSTD---KTPFKFQSS 303
>gnl|CDD|227824 COG5537, IRR1, Cohesin [Cell division and chromosome partitioning].
Length = 740
Score = 28.3 bits (63), Expect = 2.5
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 85 MSFLEASETQRPLTIRTNTLKTRRRDLAQALVNRGVNLDPIGKWSKVGLVIYNSTV 140
+S L + L + K R RD+ Q R + ++ + +W V + I+NS+
Sbjct: 153 LSILRGKGFEVVLYLYDENFKVRFRDVYQDFNIRALLVEFVSEWV-VSVGIFNSSC 207
>gnl|CDD|217692 pfam03721, UDPG_MGDP_dh_N, UDP-glucose/GDP-mannose dehydrogenase
family, NAD binding domain. The UDP-glucose/GDP-mannose
dehydrogenaseses are a small group of enzymes which
possesses the ability to catalyze the NAD-dependent
2-fold oxidation of an alcohol to an acid without the
release of an aldehyde intermediate.
Length = 188
Score = 27.6 bits (62), Expect = 2.9
Identities = 17/42 (40%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 125 IGKWSKVG-LVIYNSTVPIGATPEYLGAALMKNTGVLFANDV 165
IG K G +V+ STVP G T E + L K +G F D
Sbjct: 107 IGPVLKKGKVVVVKSTVPPGTTEEVVKPILEKRSGKKFGVDF 148
>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 = 27.3 bits (60), Expect = 3.7
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 94 QRPLTIRTNTLKTRR----RDLAQALVNRGVNLDPIGKWSKVGL 133
+RPL + T+ + RDLA V V +GK ++ GL
Sbjct: 112 RRPLFQKVTTVAADQSFTIRDLASGSVKLNVERCSLGKLTRRGL 155
>gnl|CDD|223499 COG0422, ThiC, Thiamine biosynthesis protein ThiC [Coenzyme
metabolism].
Length = 432
Score = 26.4 bits (59), Expect = 9.3
Identities = 13/47 (27%), Positives = 18/47 (38%), Gaps = 5/47 (10%)
Query: 119 GVNLDPIGKWSKVGLVIYNSTVPIGATPEYLGAALMKNTGVLFANDV 165
G +L I +W +I NS VP+G P Y + D
Sbjct: 101 GGDLHEIREW-----IIRNSPVPVGTVPIYQALEEVNGKVEDLTEDD 142
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 0.136 0.391
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,258,500
Number of extensions: 854670
Number of successful extensions: 801
Number of sequences better than 10.0: 1
Number of HSP's gapped: 798
Number of HSP's successfully gapped: 34
Length of query: 180
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 89
Effective length of database: 6,901,388
Effective search space: 614223532
Effective search space used: 614223532
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: 56 (25.3 bits)