RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 010061
(519 letters)
>gnl|CDD|223222 COG0144, Sun, tRNA and rRNA cytosine-C5-methylases [Translation,
ribosomal structure and biogenesis].
Length = 355
Score = 63.2 bits (154), Expect = 1e-10
Identities = 26/63 (41%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 7 AGISLLKVGGRIVYSTCSMNPVENEAVVAEILRKCEGSVELVDVSNEVPQLIHRPGLRKW 66
A + LLK GG +VYSTCS+ P ENE VV L + EL V L G
Sbjct: 273 AALKLLKPGGVLVYSTCSLTPEENEEVVERFLERHPD-FELEPVRLPWGPLFEGLGSELG 331
Query: 67 KVR 69
K R
Sbjct: 332 KTR 334
Score = 41.2 bits (97), Expect = 9e-04
Identities = 20/65 (30%), Positives = 26/65 (40%), Gaps = 11/65 (16%)
Query: 116 VNSDEGLQQVEDVLTSADDLEEEVSDLP-----------LERCMRLVPHDQNSGAFFIAV 164
+ +E + VE L D E E LP L + RL PH + FFIA
Sbjct: 291 LTPEENEEVVERFLERHPDFELEPVRLPWGPLFEGLGSELGKTRRLYPHVHGTDGFFIAK 350
Query: 165 LQKVS 169
L+K
Sbjct: 351 LRKKR 355
>gnl|CDD|188051 TIGR00446, nop2p, NOL1/NOP2/sun family putative RNA methylase.
[Protein synthesis, tRNA and rRNA base modification].
Length = 264
Score = 56.3 bits (136), Expect = 7e-09
Identities = 23/51 (45%), Positives = 29/51 (56%)
Query: 5 VTAGISLLKVGGRIVYSTCSMNPVENEAVVAEILRKCEGSVELVDVSNEVP 55
+ A I LK GG +VYSTCS+ ENE V+ ILRK VE + +E
Sbjct: 182 IDAAIDALKPGGVLVYSTCSLEVEENEEVIDYILRKRPDVVEEIIKGDEFF 232
>gnl|CDD|201649 pfam01189, Nol1_Nop2_Fmu, NOL1/NOP2/sun family.
Length = 277
Score = 52.0 bits (125), Expect = 2e-07
Identities = 28/66 (42%), Positives = 34/66 (51%), Gaps = 6/66 (9%)
Query: 7 AGISLLKVGGRIVYSTCSMNPVENEAVVAEILRKCEGSVELVDV--SNEVPQLIHR---P 61
A L+K GG +VYSTCS+ P ENEAV+ L+K VELV S L R
Sbjct: 199 AAWDLVKPGGVLVYSTCSVLPEENEAVIKYFLQKRP-DVELVPTGLSEGKIALAKRIVKG 257
Query: 62 GLRKWK 67
GL+
Sbjct: 258 GLQSLP 263
Score = 33.9 bits (78), Expect = 0.14
Identities = 9/40 (22%), Positives = 14/40 (35%)
Query: 1 MVVFVTAGISLLKVGGRIVYSTCSMNPVENEAVVAEILRK 40
+ + G + YS S+ P EN AV +
Sbjct: 34 VQLEPLGRYPHALPVGDLPYSIGSLPPFENGAVTVQDASS 73
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 51.3 bits (124), Expect = 6e-07
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 13/84 (15%)
Query: 11 LLKVGGRIVYSTCSMNPVENEAVVAEILRKCEGSVELVDVSNEVPQLIHRPGLRKWKVRD 70
LK GG +VYSTC++ ENE V+ L + ELV + +E +P ++V+D
Sbjct: 368 YLKKGGILVYSTCTIEKEENEEVIEAFLEE-HPEFELVPLQHE------KPDELVYEVKD 420
Query: 71 KGIWLASHKH------VRKFRRIG 88
+ + + + + K R+ G
Sbjct: 421 GYLQILPNDYGTDGFFIAKLRKKG 444
>gnl|CDD|237856 PRK14901, PRK14901, 16S rRNA methyltransferase B; Provisional.
Length = 434
Score = 50.3 bits (121), Expect = 2e-06
Identities = 15/31 (48%), Positives = 23/31 (74%)
Query: 11 LLKVGGRIVYSTCSMNPVENEAVVAEILRKC 41
LLK GG +VY+TC+++P ENEA + + L +
Sbjct: 373 LLKPGGTLVYATCTLHPAENEAQIEQFLARH 403
>gnl|CDD|237858 PRK14904, PRK14904, 16S rRNA methyltransferase B; Provisional.
Length = 445
Score = 42.4 bits (100), Expect = 4e-04
Identities = 16/31 (51%), Positives = 22/31 (70%)
Query: 10 SLLKVGGRIVYSTCSMNPVENEAVVAEILRK 40
SLLK GG +VY+TCS+ P ENE + L++
Sbjct: 365 SLLKPGGVLVYATCSIEPEENELQIEAFLQR 395
>gnl|CDD|236790 PRK10901, PRK10901, 16S rRNA methyltransferase B; Provisional.
Length = 427
Score = 40.9 bits (97), Expect = 0.001
Identities = 20/54 (37%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 11 LLKVGGRIVYSTCSMNPVENEAVVAEILRKCEGSVELVDVSNEVP--QLIHRPG 62
LLK GG ++Y+TCS+ P ENE + L + + L + + P QL+ PG
Sbjct: 361 LLKPGGTLLYATCSILPEENEQQIKAFLARHPDAELLDTGTPQQPGRQLL--PG 412
>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 = 40.6 bits (95), Expect = 0.002
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 11 LLKVGGRIVYSTCSMNPVENEAVV 34
LLK GG +VY+TCS+ P EN +
Sbjct: 357 LLKTGGTLVYATCSVLPEENSEQI 380
>gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF;
Reviewed.
Length = 470
Score = 39.9 bits (94), Expect = 0.003
Identities = 14/23 (60%), Positives = 18/23 (78%)
Query: 12 LKVGGRIVYSTCSMNPVENEAVV 34
LK GG +VYSTC++N EN+AV
Sbjct: 232 LKPGGTLVYSTCTLNREENQAVC 254
>gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional.
Length = 431
Score = 31.8 bits (72), Expect = 1.0
Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 12/64 (18%)
Query: 11 LLKVGGRIVYSTCSMNPVENEAVVAEILRKCEGSVELVDVSNEVPQLIHRPGLRKWKVRD 70
LL+ GG ++YSTC++ EN VV + + + E++D+ R L +++V
Sbjct: 355 LLEKGGILLYSTCTVTKEENTEVVKRFVYE-QKDAEVIDI---------RDKLEEFEV-- 402
Query: 71 KGIW 74
+GIW
Sbjct: 403 EGIW 406
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 31.9 bits (72), Expect = 1.0
Identities = 37/164 (22%), Positives = 65/164 (39%), Gaps = 28/164 (17%)
Query: 102 DATDIEPKHGNVT-DVNSDEGLQQVEDVLTSADDLEEEVSDLP------LERCMRLVPHD 154
+A ++E VT D E + D DL+EEV+D+P L + P++
Sbjct: 3856 EARELESDMNGVTKDSVVSE--NENSDSEEENQDLDEEVNDIPEDLSNSLNEKLWDEPNE 3913
Query: 155 QNSGAFFIAVLQKVSPLPVVQEKHINPEEKMLPRNDDPPKKLQNQDTEEVNG---MEVDL 211
++ + QK E+ E L +D K L+++D +E M D+
Sbjct: 3914 EDL----LETEQK------SNEQSAANNESDLVSKEDDNKALEDKDRQEKEDEEEMSDDV 3963
Query: 212 ADGTDEKDPEG-SLEANSIDNEDGAAVEPDPLTCEKVDSEETEV 254
+ + + +NED P+ L K+D +E +V
Sbjct: 3964 GIDDEIQPDIQENNSQPPPENEDLDL--PEDL---KLDEKEGDV 4002
>gnl|CDD|132528 TIGR03489, cas_csp1, CRISPR-associated protein Cas7/Csp1, subtype
PGING. Members of this protein family are Csp1, a
CRISPR-associated (cas) gene marker for the Pging
subtype of CRISPR/cas system, as found in Porphyromonas
gingivalis W83 and Bacteroides forsythus ATCC 43037.
This protein belongs to the family of DevR (TIGR01875),
a regulator of development in Myxococcus xanthus located
in a cas gene region. A different branch of the DevR
family, Cst2 (TIGR02585), is a marker for the Tneap
subtype of CRISPR/cas system.
Length = 292
Score = 31.2 bits (70), Expect = 1.3
Identities = 27/83 (32%), Positives = 42/83 (50%), Gaps = 12/83 (14%)
Query: 435 GEALSNPIQIDAST-------IAIGCWKGR--ASLSVM-VTAIDCQELLERLLMRLEIEK 484
G+ +SN I+ID G + R A LSV TA+D E+ LL+R++ +K
Sbjct: 63 GDGISNLIEIDLRADLGGFMHPNKGDYSDRRIAPLSVTPATALDESEIGRDLLVRIKFDK 122
Query: 485 GDLVQENALGTDEVQEE--MNDN 505
+ ++ AL T E E+ M+ N
Sbjct: 123 SEDAKDQALATKEFSEQDKMHMN 145
>gnl|CDD|238631 cd01306, PhnM, PhnM is believed to be a subunit of the membrane
associated C-P lyase complex. C-P lyase is thought to
catalyze the direct cleavage of inactivated C-P bonds to
yield inorganic phosphate and the corresponding
hydrocarbons. It is responsible for cleavage of
alkylphosphonates, which are utilized as sole phosphorus
sources by many bacteria.
Length = 325
Score = 29.9 bits (68), Expect = 3.3
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 5/32 (15%)
Query: 69 RDKGIWLASH-----KHVRKFRRIGIVPSMFP 95
R +GI LASH +HV + +G+V S FP
Sbjct: 173 RARGIPLASHDDDTPEHVAEAHELGVVISEFP 204
>gnl|CDD|214726 smart00571, DDT, domain in different transcription and chromosome
remodeling factors.
Length = 63
Score = 27.2 bits (61), Expect = 4.1
Identities = 9/34 (26%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 450 AIGCWKGRASLSVMVTAIDCQE---LLERLLMRL 480
+G RA+L + A+ C++ LL + + L
Sbjct: 20 VLGLSPFRATLEDFIAALKCRDQNGLLTEVHVVL 53
>gnl|CDD|178593 PLN03021, PLN03021, Low-temperature-induced protein; Provisional.
Length = 619
Score = 29.2 bits (64), Expect = 6.3
Identities = 28/93 (30%), Positives = 42/93 (45%), Gaps = 9/93 (9%)
Query: 172 PVVQEKHINPEEKMLPRNDDPPKKLQNQDTEEVNGMEVDLADGT---DEKDPE--GSLEA 226
P E H K+L + + KK++N T+ NG + D+ D DE+DPE G+
Sbjct: 23 PEEDEHHEKGASKVLKKVKEKAKKIKNSLTKHGNGHDHDVEDDDDEYDEQDPEVHGAPVY 82
Query: 227 NSIDNEDGAAVEPDPLTCEKVDSEETEVPVNTE 259
S G +P L+ + ET VP + E
Sbjct: 83 ESSAVRGGVTGKPKSLS----HAGETNVPASEE 111
>gnl|CDD|148632 pfam07136, DUF1385, Protein of unknown function (DUF1385). This
family contains a number of hypothetical bacterial
proteins of unknown function approximately 300 residues
in length. Some family members are predicted to be
metal-dependent.
Length = 235
Score = 28.3 bits (64), Expect = 7.5
Identities = 18/43 (41%), Positives = 22/43 (51%), Gaps = 6/43 (13%)
Query: 389 LYASLVDFKHLLQYKTIKF-ADFVDAEFGEKASKLMMGCCVIV 430
L+ SLV L K + F A+F D E EK SK M VI+
Sbjct: 10 LFESLV-----LGIKALNFSAEFADEEEEEKLSKWEMALTVIL 47
>gnl|CDD|148523 pfam06952, PsiA, PsiA protein. This family consists of several
Enterobacterial PsiA proteins. The function of PsiA is
unknown although it is thought that it may affect the
generation of an SOS signal in Escherichia coli.
Length = 238
Score = 28.2 bits (63), Expect = 8.4
Identities = 27/80 (33%), Positives = 36/80 (45%), Gaps = 14/80 (17%)
Query: 69 RDKGIWLASHKHVRKFRRIGIVPSMFPSGSSHMDATDIEPKHGNVTD-VNSDEGLQQVED 127
R +G L + + R F R+ +GS ++ATD G TD N L+QVE+
Sbjct: 29 RRQGARLPAMPYARAFFRV-------LNGSGRINATDARRIPGLYTDPENRGSSLKQVEE 81
Query: 128 VLTSADDLEE---EVSDLPL 144
L D L E E LPL
Sbjct: 82 AL---DVLIESGGEYCPLPL 98
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
0.314 0.133 0.380
Gapped
Lambda K H
0.267 0.0762 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,127,658
Number of extensions: 2571874
Number of successful extensions: 1554
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1550
Number of HSP's successfully gapped: 28
Length of query: 519
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 418
Effective length of database: 6,457,848
Effective search space: 2699380464
Effective search space used: 2699380464
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: 42 (22.0 bits)
S2: 61 (27.2 bits)