RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 007036
(620 letters)
>gnl|CDD|223222 COG0144, Sun, tRNA and rRNA cytosine-C5-methylases [Translation,
ribosomal structure and biogenesis].
Length = 355
Score = 134 bits (338), Expect = 2e-34
Identities = 55/169 (32%), Positives = 73/169 (43%), Gaps = 19/169 (11%)
Query: 2 VIANDLDVQRCNLLIHQTKRMCTANLIVTNHEAQHFPGCRANKNFSSASDKGIESESNMG 61
V+A D+ +R L KR+ N+IV N +A+ + E
Sbjct: 185 VVAVDVSPKRLKRLRENLKRLGVRNVIVVNKDARRLA------------ELLPGGEK--- 229
Query: 62 QLLFDRVLCDVPCSGDGTLRKAPDIWRKWNVGLGNGLHSLQVQIAMRGISLLKVGGRIVY 121
FDR+L D PCSG G +R+ PD+ + L LQ +I + LLK GG +VY
Sbjct: 230 ---FDRILLDAPCSGTGVIRRDPDVKWRRTPEDIAELAKLQKEILAAALKLLKPGGVLVY 286
Query: 122 STCSMNPVENEAVVAEILRKCEGSVELVDVSNEVPQLIHRPGLRKWKVR 170
STCS+ P ENE VV L + EL V L G K R
Sbjct: 287 STCSLTPEENEEVVERFLERHPD-FELEPVRLPWGPLFEGLGSELGKTR 334
Score = 41.6 bits (98), Expect = 9e-04
Identities = 20/65 (30%), Positives = 26/65 (40%), Gaps = 11/65 (16%)
Query: 217 VNSDEGLQQVEDVLTSADDLEEEVSDLP-----------LERCMRLVPHDQNSGAFFIAV 265
+ +E + VE L D E E LP L + RL PH + FFIA
Sbjct: 291 LTPEENEEVVERFLERHPDFELEPVRLPWGPLFEGLGSELGKTRRLYPHVHGTDGFFIAK 350
Query: 266 LQKVS 270
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 = 104 bits (260), Expect = 7e-25
Identities = 51/155 (32%), Positives = 68/155 (43%), Gaps = 21/155 (13%)
Query: 2 VIANDLDVQRCNLLIHQTKRMCTANLIVTNHEAQHFPGCRANKNFSSASDKGIESESNMG 61
++AN++ R LI RM N IV N + + F
Sbjct: 99 IVANEISKSRTKALISNINRMGVLNTIVINADGRKFGAYL-------------------- 138
Query: 62 QLLFDRVLCDVPCSGDGTLRKAPDIWRKWNVGLGNGLHSLQVQIAMRGISLLKVGGRIVY 121
L FD +L D PCSG+G +RK P R W+ LQ ++ I LK GG +VY
Sbjct: 139 -LKFDAILLDAPCSGEGVIRKDPSRKRNWSEEDIKYCSLLQKELIDAAIDALKPGGVLVY 197
Query: 122 STCSMNPVENEAVVAEILRKCEGSVELVDVSNEVP 156
STCS+ ENE V+ ILRK VE + +E
Sbjct: 198 STCSLEVEENEEVIDYILRKRPDVVEEIIKGDEFF 232
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 95.2 bits (238), Expect = 7e-21
Identities = 54/197 (27%), Positives = 88/197 (44%), Gaps = 37/197 (18%)
Query: 1 MVIANDLDVQRCNLLIHQTKRMCTANLIVTNHEAQHFPGCRANKNFSSASDKGIESESNM 60
V+A D+ + L+ KR L +TN E + + ++ F E
Sbjct: 277 KVVALDIHEHKLKLIEENAKR-----LGLTNIETKALDARKVHEKF-------AEK---- 320
Query: 61 GQLLFDRVLCDVPCSGDGTLRKAPDIWRKWNVGLG--NGLHSLQVQIAMRGISLLKVGGR 118
FD++L D PCSG G +R+ PDI K+N L +Q++I LK GG
Sbjct: 321 ----FDKILVDAPCSGLGVIRRKPDI--KYNKTKEDIESLQEIQLEILESVAQYLKKGGI 374
Query: 119 IVYSTCSMNPVENEAVVAEILRKCEGSVELVDVSNEVPQLIHRPGLRKWKVRDKGIWLAS 178
+VYSTC++ ENE V+ L + ELV + +E +P ++V+D + +
Sbjct: 375 LVYSTCTIEKEENEEVIEAFLEE-HPEFELVPLQHE------KPDELVYEVKDGYLQILP 427
Query: 179 HKH------VRKFRRIG 189
+ + + K R+ G
Sbjct: 428 NDYGTDGFFIAKLRKKG 444
>gnl|CDD|201649 pfam01189, Nol1_Nop2_Fmu, NOL1/NOP2/sun family.
Length = 277
Score = 92.1 bits (229), Expect = 1e-20
Identities = 58/174 (33%), Positives = 79/174 (45%), Gaps = 29/174 (16%)
Query: 2 VIANDLDVQRCNLLIHQTKRMCTANLIVTNHEAQHFPGCRANKNFSSASDKGIESESNMG 61
V+A D + QR + +R+ N+IV +A+ K + E
Sbjct: 112 VVAVDRNKQRLKRVYANIQRLGVFNIIVQEGDARQ------------IDQKLLGGE---- 155
Query: 62 QLLFDRVLCDVPCSGDGTLRKAPDIWRKWNVGLGNG--LHSLQVQIAMRGISLLKVGGRI 119
FDR+L D PCSG G +R+ PDI KW + L LQ ++ L+K GG +
Sbjct: 156 ---FDRILLDAPCSGTGVIRRDPDI--KWLRREADIAQLAELQKELLKAAWDLVKPGGVL 210
Query: 120 VYSTCSMNPVENEAVVAEILRKCEGSVELVDV--SNEVPQLIHR---PGLRKWK 168
VYSTCS+ P ENEAV+ L+K VELV S L R GL+
Sbjct: 211 VYSTCSVLPEENEAVIKYFLQKRP-DVELVPTGLSEGKIALAKRIVKGGLQSLP 263
Score = 65.1 bits (159), Expect = 2e-11
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 1/74 (1%)
Query: 68 VLCDVPCSGDGTLRKAPDIWRKWNVGLGNGLHSLQVQIAMRGISLLKVGGRIVYSTCSMN 127
+L CS GTLRK ++W++ L +Q++ R L G + YS S+
Sbjct: 1 ILEANNCSPPGTLRKNVLKTKRWSLLQALELAGVQLEPLGRYPHAL-PVGDLPYSIGSLP 59
Query: 128 PVENEAVVAEILRK 141
P EN AV +
Sbjct: 60 PFENGAVTVQDASS 73
>gnl|CDD|237856 PRK14901, PRK14901, 16S rRNA methyltransferase B; Provisional.
Length = 434
Score = 84.2 bits (209), Expect = 3e-17
Identities = 34/82 (41%), Positives = 47/82 (57%), Gaps = 6/82 (7%)
Query: 64 LFDRVLCDVPCSGDGTLRKAPDI-WR--KWNVGLGNGLHSLQVQIAMRGISLLKVGGRIV 120
FDR+L D PCSG GTL + PD WR + L LQ ++ LLK GG +V
Sbjct: 325 YFDRILLDAPCSGLGTLHRHPDARWRQTPEKI---QELAPLQAELLESLAPLLKPGGTLV 381
Query: 121 YSTCSMNPVENEAVVAEILRKC 142
Y+TC+++P ENEA + + L +
Sbjct: 382 YATCTLHPAENEAQIEQFLARH 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 = 72.2 bits (177), Expect = 2e-13
Identities = 31/73 (42%), Positives = 41/73 (56%), Gaps = 2/73 (2%)
Query: 64 LFDRVLCDVPCSGDGTLRKAPDI-WRKWNVGLGNGLHSLQVQIAMRGISLLKVGGRIVYS 122
FDR+L D PCS G +R+ PDI W + + L LQ +I LLK GG +VY+
Sbjct: 309 QFDRILLDAPCSATGVIRRHPDIKWLRKPRDIAE-LAELQSEILDAIWPLLKTGGTLVYA 367
Query: 123 TCSMNPVENEAVV 135
TCS+ P EN +
Sbjct: 368 TCSVLPEENSEQI 380
>gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF;
Reviewed.
Length = 470
Score = 67.6 bits (166), Expect = 7e-12
Identities = 40/138 (28%), Positives = 63/138 (45%), Gaps = 26/138 (18%)
Query: 1 MVIANDLDVQRCNLLIHQTKRMCTANLIVTNHEAQHFPGCRANKNFSSASDKGIESESNM 60
++AN+ R +L R +N+ +T+ + + F
Sbjct: 140 AIVANEYSASRVKVLHANISRCGVSNVALTHFDGRVF----------------------- 176
Query: 61 GQLL---FDRVLCDVPCSGDGTLRKAPDIWRKWNVGLGNGLHSLQVQIAMRGISLLKVGG 117
G L FD +L D PCSG+GT+RK PD + W+ + + Q ++ LK GG
Sbjct: 177 GAALPETFDAILLDAPCSGEGTVRKDPDALKNWSPESNLEIAATQRELIESAFHALKPGG 236
Query: 118 RIVYSTCSMNPVENEAVV 135
+VYSTC++N EN+AV
Sbjct: 237 TLVYSTCTLNREENQAVC 254
>gnl|CDD|236790 PRK10901, PRK10901, 16S rRNA methyltransferase B; Provisional.
Length = 427
Score = 67.1 bits (165), Expect = 7e-12
Identities = 36/92 (39%), Positives = 49/92 (53%), Gaps = 14/92 (15%)
Query: 64 LFDRVLCDVPCSGDGTLRKAPDIWRKWNVGLG-----NGLHSLQVQI--AMRGISLLKVG 116
FDR+L D PCS G +R+ PDI KW L L +LQ +I A+ LLK G
Sbjct: 313 PFDRILLDAPCSATGVIRRHPDI--KW---LRRPEDIAALAALQSEILDAL--WPLLKPG 365
Query: 117 GRIVYSTCSMNPVENEAVVAEILRKCEGSVEL 148
G ++Y+TCS+ P ENE + L + + L
Sbjct: 366 GTLLYATCSILPEENEQQIKAFLARHPDAELL 397
>gnl|CDD|237858 PRK14904, PRK14904, 16S rRNA methyltransferase B; Provisional.
Length = 445
Score = 63.9 bits (156), Expect = 9e-11
Identities = 28/77 (36%), Positives = 41/77 (53%)
Query: 65 FDRVLCDVPCSGDGTLRKAPDIWRKWNVGLGNGLHSLQVQIAMRGISLLKVGGRIVYSTC 124
D +L D PC+G G L + ++ K L LQ ++ SLLK GG +VY+TC
Sbjct: 319 PDAILLDAPCTGTGVLGRRAELRWKLTPEKLAELVGLQAELLDHAASLLKPGGVLVYATC 378
Query: 125 SMNPVENEAVVAEILRK 141
S+ P ENE + L++
Sbjct: 379 SIEPEENELQIEAFLQR 395
>gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional.
Length = 431
Score = 61.0 bits (148), Expect = 7e-10
Identities = 43/174 (24%), Positives = 81/174 (46%), Gaps = 32/174 (18%)
Query: 2 VIANDLDVQRCNLLIHQTKRMCTANLIVTNHEAQHFPGCRANKNFSSASDKGIESESNMG 61
++A D+ ++ L+ KR+ +++ + +A+ +
Sbjct: 265 ILAVDISREKIQLVEKHAKRLKLSSIEIKIADAERL--------------------TEYV 304
Query: 62 QLLFDRVLCDVPCSGDGTLRKAPDIWRKWNVGLGNGLHSLQVQIAMRGISLLKVGGRIVY 121
Q FDR+L D PC+ GT R P++ R+ N L +Q++I + LL+ GG ++Y
Sbjct: 305 QDTFDRILVDAPCTSLGTARNHPEVLRRVNKEDFKKLSEIQLRIVSQAWKLLEKGGILLY 364
Query: 122 STCSMNPVENEAVVAEILRKCEGSVELVDVSNEVPQLIHRPGLRKWKVRDKGIW 175
STC++ EN VV + + + E++D+ R L +++V +GIW
Sbjct: 365 STCTVTKEENTEVVKRFVYE-QKDAEVIDI---------RDKLEEFEV--EGIW 406
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 32.7 bits (74), Expect = 0.77
Identities = 37/164 (22%), Positives = 65/164 (39%), Gaps = 28/164 (17%)
Query: 203 DATDIEPKHGNVT-DVNSDEGLQQVEDVLTSADDLEEEVSDLP------LERCMRLVPHD 255
+A ++E VT D E + D DL+EEV+D+P L + P++
Sbjct: 3856 EARELESDMNGVTKDSVVSE--NENSDSEEENQDLDEEVNDIPEDLSNSLNEKLWDEPNE 3913
Query: 256 QNSGAFFIAVLQKVSPLPVVQEKHINPEEKMLPRNDDPPKKLQNQDTEEVNG---MEVDL 312
++ + QK E+ E L +D K L+++D +E M D+
Sbjct: 3914 EDL----LETEQK------SNEQSAANNESDLVSKEDDNKALEDKDRQEKEDEEEMSDDV 3963
Query: 313 ADGTDEKDPEG-SLEANSIDNEDGAAVEPDPLTCEKVDSEETEV 355
+ + + +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 = 1.3
Identities = 27/83 (32%), Positives = 42/83 (50%), Gaps = 12/83 (14%)
Query: 536 GEALSNPIQIDAST-------IAIGCWKGR--ASLSVM-VTAIDCQELLERLLMRLEIEK 585
G+ +SN I+ID G + R A LSV TA+D E+ LL+R++ +K
Sbjct: 63 GDGISNLIEIDLRADLGGFMHPNKGDYSDRRIAPLSVTPATALDESEIGRDLLVRIKFDK 122
Query: 586 GDLVQENALGTDEVQEE--MNDN 606
+ ++ 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 = 4.4
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 5/32 (15%)
Query: 170 RDKGIWLASH-----KHVRKFRRIGIVPSMFP 196
R +GI LASH +HV + +G+V S FP
Sbjct: 173 RARGIPLASHDDDTPEHVAEAHELGVVISEFP 204
>gnl|CDD|178593 PLN03021, PLN03021, Low-temperature-induced protein; Provisional.
Length = 619
Score = 29.9 bits (66), Expect = 4.6
Identities = 28/93 (30%), Positives = 42/93 (45%), Gaps = 9/93 (9%)
Query: 273 PVVQEKHINPEEKMLPRNDDPPKKLQNQDTEEVNGMEVDLADGT---DEKDPE--GSLEA 327
P E H K+L + + KK++N T+ NG + D+ D DE+DPE G+
Sbjct: 23 PEEDEHHEKGASKVLKKVKEKAKKIKNSLTKHGNGHDHDVEDDDDEYDEQDPEVHGAPVY 82
Query: 328 NSIDNEDGAAVEPDPLTCEKVDSEETEVPVNTE 360
S G +P L+ + ET VP + E
Sbjct: 83 ESSAVRGGVTGKPKSLS----HAGETNVPASEE 111
>gnl|CDD|214726 smart00571, DDT, domain in different transcription and chromosome
remodeling factors.
Length = 63
Score = 27.2 bits (61), Expect = 4.9
Identities = 9/34 (26%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 551 AIGCWKGRASLSVMVTAIDCQE---LLERLLMRL 581
+G RA+L + A+ C++ LL + + L
Sbjct: 20 VLGLSPFRATLEDFIAALKCRDQNGLLTEVHVVL 53
>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 = 7.5
Identities = 18/43 (41%), Positives = 22/43 (51%), Gaps = 6/43 (13%)
Query: 490 LYASLVDFKHLLQYKTIKF-ADFVDAEFGEKASKLMMGCCVIV 531
L+ SLV L K + F A+F D E EK SK M VI+
Sbjct: 10 LFESLV-----LGIKALNFSAEFADEEEEEKLSKWEMALTVIL 47
>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 = 27.3 bits (61), Expect = 8.2
Identities = 12/67 (17%), Positives = 28/67 (41%)
Query: 275 VQEKHINPEEKMLPRNDDPPKKLQNQDTEEVNGMEVDLADGTDEKDPEGSLEANSIDNED 334
+ +D KK ++++ E+ ++ D D D+ P+ + +D++D
Sbjct: 35 EVPPEVAKSRAPAADAEDAAKKDEDEEDEDDVVLDDDDDDDDDDDLPDLDDDDVDLDDDD 94
Query: 335 GAAVEPD 341
+E D
Sbjct: 95 DDFLEDD 101
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: 30,873,849
Number of extensions: 3026939
Number of successful extensions: 2319
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2300
Number of HSP's successfully gapped: 27
Length of query: 620
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 517
Effective length of database: 6,369,140
Effective search space: 3292845380
Effective search space used: 3292845380
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)