RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 006372
(648 letters)
>gnl|CDD|223222 COG0144, Sun, tRNA and rRNA cytosine-C5-methylases [Translation,
ribosomal structure and biogenesis].
Length = 355
Score = 158 bits (402), Expect = 4e-43
Identities = 67/198 (33%), Positives = 89/198 (44%), Gaps = 26/198 (13%)
Query: 1 MCAAPGSKTFQLLEIIHQSTNPGALPNGMVIANDLDVQRCNLLIHQTKRMCTANLIVTNH 60
+CAAPG KT L E++ N GA+ V+A D+ +R L KR+ N+IV N
Sbjct: 163 LCAAPGGKTTHLAELME---NEGAI----VVAVDVSPKRLKRLRENLKRLGVRNVIVVNK 215
Query: 61 EAQHFPGCRANKNFSSASDKGIESESNMGQLLFDRVLCDVPCSGDGTLRKAPDIWRKWNV 120
+A+ + E FDR+L D PCSG G +R+ PD+ +
Sbjct: 216 DARRLA------------ELLPGGEK------FDRILLDAPCSGTGVIRRDPDVKWRRTP 257
Query: 121 GLGNGLHSLQVQIAMRGISLLKVGGRIVYSTCSMNPVENEAVVAEILRKCEGSVELVDVS 180
L LQ +I + LLK GG +VYSTCS+ P ENE VV L + EL V
Sbjct: 258 EDIAELAKLQKEILAAALKLLKPGGVLVYSTCSLTPEENEEVVERFLERHPD-FELEPVR 316
Query: 181 NEVPQLIHRPGLRKWKVR 198
L G K R
Sbjct: 317 LPWGPLFEGLGSELGKTR 334
Score = 41.6 bits (98), Expect = 8e-04
Identities = 20/65 (30%), Positives = 26/65 (40%), Gaps = 11/65 (16%)
Query: 245 VNSDEGLQQVEDVLTSADDLEEEVSDLP-----------LERCMRLVPHDQNSGAFFIAV 293
+ +E + VE L D E E LP L + RL PH + FFIA
Sbjct: 291 LTPEENEEVVERFLERHPDFELEPVRLPWGPLFEGLGSELGKTRRLYPHVHGTDGFFIAK 350
Query: 294 LQKVS 298
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 = 118 bits (297), Expect = 8e-30
Identities = 61/184 (33%), Positives = 82/184 (44%), Gaps = 29/184 (15%)
Query: 1 MCAAPGSKTFQLLEIIHQSTNPGALPNGMVIANDLDVQRCNLLIHQTKRMCTANLIVTNH 60
M AAPG KT Q+ +++ N G ++AN++ R LI RM N IV N
Sbjct: 78 MAAAPGGKTTQISQLMK---NKGC-----IVANEISKSRTKALISNINRMGVLNTIVINA 129
Query: 61 EAQHFPGCRANKNFSSASDKGIESESNMGQLLFDRVLCDVPCSGDGTLRKAPDIWRKWNV 120
+ + F L FD +L D PCSG+G +RK P R W+
Sbjct: 130 DGRKFGAYL---------------------LKFDAILLDAPCSGEGVIRKDPSRKRNWSE 168
Query: 121 GLGNGLHSLQVQIAMRGISLLKVGGRIVYSTCSMNPVENEAVVAEILRKCEGSVELVDVS 180
LQ ++ I LK GG +VYSTCS+ ENE V+ ILRK VE +
Sbjct: 169 EDIKYCSLLQKELIDAAIDALKPGGVLVYSTCSLEVEENEEVIDYILRKRPDVVEEIIKG 228
Query: 181 NEVP 184
+E
Sbjct: 229 DEFF 232
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 115 bits (291), Expect = 2e-27
Identities = 63/225 (28%), Positives = 100/225 (44%), Gaps = 45/225 (20%)
Query: 1 MCAAPGSKTFQLLEIIHQSTNPGALPNGMVIANDLDVQRCNLLIHQTKRMCTANLIVTNH 60
CAAPG KT + E++ G V+A D+ + L+ KR L +TN
Sbjct: 257 ACAAPGGKTTHIAELLK--------NTGKVVALDIHEHKLKLIEENAKR-----LGLTNI 303
Query: 61 EAQHFPGCRANKNFSSASDKGIESESNMGQLLFDRVLCDVPCSGDGTLRKAPDIWRKWNV 120
E + + ++ F E FD++L D PCSG G +R+ PDI K+N
Sbjct: 304 ETKALDARKVHEKF-------AEK--------FDKILVDAPCSGLGVIRRKPDI--KYNK 346
Query: 121 GLG--NGLHSLQVQIAMRGISLLKVGGRIVYSTCSMNPVENEAVVAEILRKCEGSVELVD 178
L +Q++I LK GG +VYSTC++ ENE V+ L + ELV
Sbjct: 347 TKEDIESLQEIQLEILESVAQYLKKGGILVYSTCTIEKEENEEVIEAFLEE-HPEFELVP 405
Query: 179 VSNEVPQLIHRPGLRKWKVRDKGIWLASHKH------VRKFRRIG 217
+ +E +P ++V+D + + + + + K R+ G
Sbjct: 406 LQHE------KPDELVYEVKDGYLQILPNDYGTDGFFIAKLRKKG 444
>gnl|CDD|201649 pfam01189, Nol1_Nop2_Fmu, NOL1/NOP2/sun family.
Length = 277
Score = 105 bits (265), Expect = 2e-25
Identities = 66/201 (32%), Positives = 88/201 (43%), Gaps = 33/201 (16%)
Query: 1 MCAAPGSKTFQLLEIIHQSTNPGALPNGMVIANDLDVQRCNLLIHQTKRMCTANLIVTNH 60
MCAAPG KT + E+ G V+A D + QR + +R+ N+IV
Sbjct: 91 MCAAPGGKTTHIAEL--------MKNEGTVVAVDRNKQRLKRVYANIQRLGVFNIIVQEG 142
Query: 61 EAQHFPGCRANKNFSSASDKGIESESNMGQLLFDRVLCDVPCSGDGTLRKAPDIWRKWNV 120
+A+ K + E FDR+L D PCSG G +R+ PDI
Sbjct: 143 DARQ------------IDQKLLGGE-------FDRILLDAPCSGTGVIRRDPDIKWLRRE 183
Query: 121 GLGNGLHSLQVQIAMRGISLLKVGGRIVYSTCSMNPVENEAVVAEILRKCEGSVELVDV- 179
L LQ ++ L+K GG +VYSTCS+ P ENEAV+ L+K VELV
Sbjct: 184 ADIAQLAELQKELLKAAWDLVKPGGVLVYSTCSVLPEENEAVIKYFLQKRP-DVELVPTG 242
Query: 180 -SNEVPQLIHR---PGLRKWK 196
S L R GL+
Sbjct: 243 LSEGKIALAKRIVKGGLQSLP 263
Score = 65.1 bits (159), Expect = 2e-11
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 1/74 (1%)
Query: 96 VLCDVPCSGDGTLRKAPDIWRKWNVGLGNGLHSLQVQIAMRGISLLKVGGRIVYSTCSMN 155
+L CS GTLRK ++W++ L +Q++ R L G + YS S+
Sbjct: 1 ILEANNCSPPGTLRKNVLKTKRWSLLQALELAGVQLEPLGRYPHAL-PVGDLPYSIGSLP 59
Query: 156 PVENEAVVAEILRK 169
P EN AV +
Sbjct: 60 PFENGAVTVQDASS 73
>gnl|CDD|237856 PRK14901, PRK14901, 16S rRNA methyltransferase B; Provisional.
Length = 434
Score = 87.3 bits (217), Expect = 3e-18
Identities = 48/173 (27%), Positives = 77/173 (44%), Gaps = 33/173 (19%)
Query: 2 CAAPGSKTFQLLEIIHQSTNPGALPNGMVIANDLDVQRCNLLIHQTKRMCTANLIVTNHE 61
CAAPG KT + E++ G + A D R L +R+ ++ + +
Sbjct: 260 CAAPGGKTTHIAELMGD--------QGEIWAVDRSASRLKKLQENAQRLGLKSIKILAAD 311
Query: 62 AQHFPGCRAN-KNFSSASDKGIESESNMGQLLFDRVLCDVPCSGDGTLRKAPDI-WR--K 117
+++ + + + FDR+L D PCSG GTL + PD WR
Sbjct: 312 SRNLLELKPQWRGY------------------FDRILLDAPCSGLGTLHRHPDARWRQTP 353
Query: 118 WNVGLGNGLHSLQVQIAMRGISLLKVGGRIVYSTCSMNPVENEAVVAEILRKC 170
+ L LQ ++ LLK GG +VY+TC+++P ENEA + + L +
Sbjct: 354 EKI---QELAPLQAELLESLAPLLKPGGTLVYATCTLHPAENEAQIEQFLARH 403
>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 = 86.1 bits (213), Expect = 7e-18
Identities = 51/163 (31%), Positives = 69/163 (42%), Gaps = 29/163 (17%)
Query: 2 CAAPGSKTFQLLEIIHQSTNPGALPNGMVIANDLDVQRCNLLIHQTKRMCTANLIVTNHE 61
CAAPG KT +LE+ P V+A D+ R + KR+ T
Sbjct: 246 CAAPGGKTTHILEL---------APQAQVVALDIHEHRLKRVYENLKRLGLTIKAETKDG 296
Query: 62 AQHFPGCRANKNFSSASDKGIESESNMGQLLFDRVLCDVPCSGDGTLRKAPDI-WRKWNV 120
P + E+E FDR+L D PCS G +R+ PDI W +
Sbjct: 297 DGRGP------------SQWAENE------QFDRILLDAPCSATGVIRRHPDIKWLRKPR 338
Query: 121 GLGNGLHSLQVQIAMRGISLLKVGGRIVYSTCSMNPVENEAVV 163
+ L LQ +I LLK GG +VY+TCS+ P EN +
Sbjct: 339 DIAE-LAELQSEILDAIWPLLKTGGTLVYATCSVLPEENSEQI 380
>gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF;
Reviewed.
Length = 470
Score = 84.6 bits (210), Expect = 3e-17
Identities = 53/168 (31%), Positives = 77/168 (45%), Gaps = 38/168 (22%)
Query: 1 MCAAPGSKTFQLLEIIHQSTNPGALPN--GMVIANDLDVQRCNLLIHQTKRMCTANLIVT 58
M AAPGSKT Q+ AL N G ++AN+ R +L R +N+ +T
Sbjct: 120 MAAAPGSKTTQI----------AALMNNQGAIVANEYSASRVKVLHANISRCGVSNVALT 169
Query: 59 NHEAQHFPGCRANKNFSSASDKGIESESNMGQLL---FDRVLCDVPCSGDGTLRKAPDIW 115
+ + + F G L FD +L D PCSG+GT+RK PD
Sbjct: 170 HFDGRVF-----------------------GAALPETFDAILLDAPCSGEGTVRKDPDAL 206
Query: 116 RKWNVGLGNGLHSLQVQIAMRGISLLKVGGRIVYSTCSMNPVENEAVV 163
+ W+ + + Q ++ LK GG +VYSTC++N EN+AV
Sbjct: 207 KNWSPESNLEIAATQRELIESAFHALKPGGTLVYSTCTLNREENQAVC 254
>gnl|CDD|236790 PRK10901, PRK10901, 16S rRNA methyltransferase B; Provisional.
Length = 427
Score = 79.5 bits (197), Expect = 1e-15
Identities = 57/188 (30%), Positives = 82/188 (43%), Gaps = 55/188 (29%)
Query: 2 CAAPGSKTFQLLEIIHQSTNPGALPNGMVIANDLDVQRCNLLIHQT-KRM-CTANLIVTN 59
CAAPG KT +LE+ Q+ V+A D+D QR + + +R+ A +IV +
Sbjct: 252 CAAPGGKTAHILELAPQAQ---------VVALDIDAQRLER-VRENLQRLGLKATVIVGD 301
Query: 60 HEAQHFPGCRANKNFSSASDKGIESESNMGQL----LFDRVLCDVPCSGDGTLRKAPDIW 115
+ Q FDR+L D PCS G +R+ PDI
Sbjct: 302 A-------------------------RDPAQWWDGQPFDRILLDAPCSATGVIRRHPDI- 335
Query: 116 RKWNVGLG-----NGLHSLQVQI--AMRGISLLKVGGRIVYSTCSMNPVENEAVVAEILR 168
KW L L +LQ +I A+ LLK GG ++Y+TCS+ P ENE + L
Sbjct: 336 -KW---LRRPEDIAALAALQSEILDAL--WPLLKPGGTLLYATCSILPEENEQQIKAFLA 389
Query: 169 KCEGSVEL 176
+ + L
Sbjct: 390 RHPDAELL 397
>gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional.
Length = 431
Score = 75.3 bits (185), Expect = 2e-14
Identities = 51/202 (25%), Positives = 92/202 (45%), Gaps = 40/202 (19%)
Query: 2 CAAPGSKTFQLLEIIHQSTNPGALPNGMVIANDLDVQRCNLLIHQTKRMCTANLIVTNHE 61
CAAPG KT + E++ ++A D+ ++ L+ KR+ +++ + +
Sbjct: 245 CAAPGGKTTAIAELMKDQGK--------ILAVDISREKIQLVEKHAKRLKLSSIEIKIAD 296
Query: 62 AQHFPGCRANKNFSSASDKGIESESNMGQLLFDRVLCDVPCSGDGTLRKAPDIWRKWNVG 121
A+ + Q FDR+L D PC+ GT R P++ R+ N
Sbjct: 297 AERL--------------------TEYVQDTFDRILVDAPCTSLGTARNHPEVLRRVNKE 336
Query: 122 LGNGLHSLQVQIAMRGISLLKVGGRIVYSTCSMNPVENEAVVAEILRKCEGSVELVDVSN 181
L +Q++I + LL+ GG ++YSTC++ EN VV + + + E++D+
Sbjct: 337 DFKKLSEIQLRIVSQAWKLLEKGGILLYSTCTVTKEENTEVVKRFVYE-QKDAEVIDI-- 393
Query: 182 EVPQLIHRPGLRKWKVRDKGIW 203
R L +++V +GIW
Sbjct: 394 -------RDKLEEFEV--EGIW 406
>gnl|CDD|237858 PRK14904, PRK14904, 16S rRNA methyltransferase B; Provisional.
Length = 445
Score = 70.1 bits (172), Expect = 1e-12
Identities = 42/170 (24%), Positives = 68/170 (40%), Gaps = 32/170 (18%)
Query: 1 MCAAPGSKTFQLLEIIHQSTNPGALPNGMVIANDLDVQRCNLLIHQTKRMCTANLIVTNH 60
+CAAPG K+ + E++ G + A D Q+ + + +
Sbjct: 257 LCAAPGGKSTFMAELMQNR--------GQITAVDRYPQKLEKIRSHASALGITIIETIEG 308
Query: 61 EAQHF-PGCRANKNFSSASDKGIESESNMGQLLFDRVLCDVPCSGDGTLRKAPDIWRKWN 119
+A+ F P + D +L D PC+G G L + ++ K
Sbjct: 309 DARSFSPEEQ-----------------------PDAILLDAPCTGTGVLGRRAELRWKLT 345
Query: 120 VGLGNGLHSLQVQIAMRGISLLKVGGRIVYSTCSMNPVENEAVVAEILRK 169
L LQ ++ SLLK GG +VY+TCS+ P ENE + L++
Sbjct: 346 PEKLAELVGLQAELLDHAASLLKPGGVLVYATCSIEPEENELQIEAFLQR 395
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 33.0 bits (75), Expect = 0.65
Identities = 37/164 (22%), Positives = 65/164 (39%), Gaps = 28/164 (17%)
Query: 231 DATDIEPKHGNVT-DVNSDEGLQQVEDVLTSADDLEEEVSDLP------LERCMRLVPHD 283
+A ++E VT D E + D DL+EEV+D+P L + P++
Sbjct: 3856 EARELESDMNGVTKDSVVSE--NENSDSEEENQDLDEEVNDIPEDLSNSLNEKLWDEPNE 3913
Query: 284 QNSGAFFIAVLQKVSPLPVVQEKHINPEEKMLPRNDDPPKKLQNQDTEEVNG---MEVDL 340
++ + QK E+ E L +D K L+++D +E M D+
Sbjct: 3914 EDL----LETEQK------SNEQSAANNESDLVSKEDDNKALEDKDRQEKEDEEEMSDDV 3963
Query: 341 ADGTDEKDPEG-SLEANSIDNEDGAAVEPDPLTCEKVDSEETEV 383
+ + + +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 = 31.5 bits (71), Expect = 1.2
Identities = 27/83 (32%), Positives = 42/83 (50%), Gaps = 12/83 (14%)
Query: 564 GEALSNPIQIDAST-------IAIGCWKGR--ASLSVM-VTAIDCQELLERLLMRLEIEK 613
G+ +SN I+ID G + R A LSV TA+D E+ LL+R++ +K
Sbjct: 63 GDGISNLIEIDLRADLGGFMHPNKGDYSDRRIAPLSVTPATALDESEIGRDLLVRIKFDK 122
Query: 614 GDLVQENALGTDEVQEE--MNDN 634
+ ++ 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 = 29.6 bits (67), Expect = 4.7
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 5/32 (15%)
Query: 198 RDKGIWLASH-----KHVRKFRRIGIVPSMFP 224
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 = 4.8
Identities = 9/34 (26%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 579 AIGCWKGRASLSVMVTAIDCQE---LLERLLMRL 609
+G RA+L + A+ C++ LL + + L
Sbjct: 20 VLGLSPFRATLEDFIAALKCRDQNGLLTEVHVVL 53
>gnl|CDD|178593 PLN03021, PLN03021, Low-temperature-induced protein; Provisional.
Length = 619
Score = 29.9 bits (66), Expect = 4.9
Identities = 28/93 (30%), Positives = 42/93 (45%), Gaps = 9/93 (9%)
Query: 301 PVVQEKHINPEEKMLPRNDDPPKKLQNQDTEEVNGMEVDLADGT---DEKDPE--GSLEA 355
P E H K+L + + KK++N T+ NG + D+ D DE+DPE G+
Sbjct: 23 PEEDEHHEKGASKVLKKVKEKAKKIKNSLTKHGNGHDHDVEDDDDEYDEQDPEVHGAPVY 82
Query: 356 NSIDNEDGAAVEPDPLTCEKVDSEETEVPVNTE 388
S G +P L+ + ET VP + E
Sbjct: 83 ESSAVRGGVTGKPKSLS----HAGETNVPASEE 111
>gnl|CDD|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid).
Members of this family are bacterial proteins with a
conserved motif [KR]FYDLN, sometimes flanked by a pair
of CXXC motifs, followed by a long region of low
complexity sequence in which roughly half the residues
are Asp and Glu, including multiple runs of five or more
acidic residues. The function of members of this family
is unknown.
Length = 104
Score = 27.7 bits (62), Expect = 6.7
Identities = 12/67 (17%), Positives = 28/67 (41%)
Query: 303 VQEKHINPEEKMLPRNDDPPKKLQNQDTEEVNGMEVDLADGTDEKDPEGSLEANSIDNED 362
+ +D KK ++++ E+ ++ D D D+ P+ + +D++D
Sbjct: 35 EVPPEVAKSRAPAADAEDAAKKDEDEEDEDDVVLDDDDDDDDDDDLPDLDDDDVDLDDDD 94
Query: 363 GAAVEPD 369
+E D
Sbjct: 95 DDFLEDD 101
>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 = 28.7 bits (65), Expect = 7.9
Identities = 18/43 (41%), Positives = 22/43 (51%), Gaps = 6/43 (13%)
Query: 518 LYASLVDFKHLLQYKTIKF-ADFVDAEFGEKASKLMMGCCVIV 559
L+ SLV L K + F A+F D E EK SK M VI+
Sbjct: 10 LFESLV-----LGIKALNFSAEFADEEEEEKLSKWEMALTVIL 47
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
0.316 0.134 0.388
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: 32,280,995
Number of extensions: 3159153
Number of successful extensions: 2398
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2370
Number of HSP's successfully gapped: 29
Length of query: 648
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 545
Effective length of database: 6,369,140
Effective search space: 3471181300
Effective search space used: 3471181300
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 (21.6 bits)
S2: 62 (27.6 bits)