RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17365
(646 letters)
>gnl|CDD|223222 COG0144, Sun, tRNA and rRNA cytosine-C5-methylases [Translation,
ribosomal structure and biogenesis].
Length = 355
Score = 231 bits (591), Expect = 3e-70
Identities = 96/333 (28%), Positives = 147/333 (44%), Gaps = 33/333 (9%)
Query: 22 EQKKANPKTDTRHENYAEIVRENKDFEQYYKAQKICPENEWDSMLETLKKDLPTAFRITN 81
E K D + ++R + E+ + + P S E L + LP A
Sbjct: 12 EAAKERLGKDRAAKFVNAVLRRLERSEEALLEEILRPA-FRYSHPEWLVEKLPDALGE-- 68
Query: 82 CSPEEAKALLSIVESKFFKEL-VNDQETSEEE---KVAPICLPWYPEQMGWQLQLSRRAI 137
+EA+A+ + + + L VN + EE + + W L R I
Sbjct: 69 ---DEAEAIAAALLRPPPRSLRVNTLKADVEELLEALEEAGVLDEKP---WVLDEVLR-I 121
Query: 138 RTSQAFSKLHQFLIMENATGHISRQEAVSMIPPLLLDVQTHHKVLDMCAAPGSKTAQIIE 197
S +L +F A G I Q+ S +P L+LD + +VLD+CAAPG KT + E
Sbjct: 122 EASGPIGRLPEF-----AEGLIYVQDEASQLPALVLDPKPGERVLDLCAAPGGKTTHLAE 176
Query: 198 MIHAADSNPVPSGLVVANDVDNNRCYMLVHQAKRLNSPCAIITNHDASVMPNVLYTDADG 257
++ +VVA DV R L KRL I+ N DA + +L
Sbjct: 177 LME------NEGAIVVAVDVSPKRLKRLRENLKRLGVRNVIVVNKDARRLAELL------ 224
Query: 258 NKVPMKFDRVLCDVPCTGDGTMRKNPDIWTKWTPSNGNNLHGIQYRIVKRGVEMLAVGGK 317
KFDR+L D PC+G G +R++PD+ + TP + L +Q I+ +++L GG
Sbjct: 225 -PGGEKFDRILLDAPCSGTGVIRRDPDVKWRRTPEDIAELAKLQKEILAAALKLLKPGGV 283
Query: 318 IAYSTCSLNPLEDEAVIQRLIVETQGAVQLVDV 350
+ YSTCSL P E+E V++R + +L V
Sbjct: 284 LVYSTCSLTPEENEEVVERFLERHPD-FELEPV 315
>gnl|CDD|188051 TIGR00446, nop2p, NOL1/NOP2/sun family putative RNA methylase.
[Protein synthesis, tRNA and rRNA base modification].
Length = 264
Score = 134 bits (340), Expect = 1e-35
Identities = 62/194 (31%), Positives = 96/194 (49%), Gaps = 17/194 (8%)
Query: 153 ENATGHISRQEAVSMIPPLLLDVQTHHKVLDMCAAPGSKTAQIIEMIHAADSNPVPSGLV 212
E G+ QEA SMIPP+ L+ + +VLDM AAPG KT QI +++ G +
Sbjct: 47 EYLFGYYYPQEASSMIPPIALEPREDERVLDMAAAPGGKTTQISQLMKN-------KGCI 99
Query: 213 VANDVDNNRCYMLVHQAKRLNSPCAIITNHDASVMPNVLYTDADGNKVPMKFDRVLCDVP 272
VAN++ +R L+ R+ I+ N D L +KFD +L D P
Sbjct: 100 VANEISKSRTKALISNINRMGVLNTIVINADGRKFGAYL----------LKFDAILLDAP 149
Query: 273 CTGDGTMRKNPDIWTKWTPSNGNNLHGIQYRIVKRGVEMLAVGGKIAYSTCSLNPLEDEA 332
C+G+G +RK+P W+ + +Q ++ ++ L GG + YSTCSL E+E
Sbjct: 150 CSGEGVIRKDPSRKRNWSEEDIKYCSLLQKELIDAAIDALKPGGVLVYSTCSLEVEENEE 209
Query: 333 VIQRLIVETQGAVQ 346
VI ++ + V+
Sbjct: 210 VIDYILRKRPDVVE 223
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 134 bits (341), Expect = 5e-34
Identities = 76/283 (26%), Positives = 120/283 (42%), Gaps = 63/283 (22%)
Query: 64 SMLETLKKDLPTAFRITN--CSPEEAKALLSIVESKFFKELVNDQETSEEEKVAPICLPW 121
+LE+L + + R+ S EE ++L + EE ++P L
Sbjct: 168 KILESLNEPPKASIRVNTLKISVEELI-----------EKLEEEGYEVEESLLSPEAL-- 214
Query: 122 YPEQMGWQLQLSRRAIRTSQAFSKLHQFLIMENATGHISRQEAVSMIPPLLLDVQTHHKV 181
+ + I + F G I+ Q+ SM+ LD + V
Sbjct: 215 ---------VIEKGNIAGTDLFKD-----------GLITIQDESSMLVAPALDPKGGDTV 254
Query: 182 LDMCAAPGSKTAQIIEMIHAADSNPVPSGLVVANDVDNNRCYMLVHQAKRLNSPCAIITN 241
LD CAAPG KT I E++ +G VVA D+ ++ ++ AKRL +TN
Sbjct: 255 LDACAAPGGKTTHIAELLK-------NTGKVVALDIHEHKLKLIEENAKRLG-----LTN 302
Query: 242 -----HDASVMPNVLYTDADGNKVPMKFDRVLCDVPCTGDGTMRKNPDI-WTKWTPSNGN 295
DA + KFD++L D PC+G G +R+ PDI + K T +
Sbjct: 303 IETKALDARKVHEKFAE---------KFDKILVDAPCSGLGVIRRKPDIKYNK-TKEDIE 352
Query: 296 NLHGIQYRIVKRGVEMLAVGGKIAYSTCSLNPLEDEAVIQRLI 338
+L IQ I++ + L GG + YSTC++ E+E VI+ +
Sbjct: 353 SLQEIQLEILESVAQYLKKGGILVYSTCTIEKEENEEVIEAFL 395
>gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF;
Reviewed.
Length = 470
Score = 113 bits (284), Expect = 1e-26
Identities = 70/199 (35%), Positives = 96/199 (48%), Gaps = 22/199 (11%)
Query: 154 NATGHISR----QEAVSMIPP--LLLDVQTHHKVLDMCAAPGSKTAQIIEMIHAADSNPV 207
N H+S QEA SM+P L D +VLDM AAPGSKT QI AA N
Sbjct: 84 NTAEHLSGLFYIQEASSMLPVAALFADDNAPQRVLDMAAAPGSKTTQI-----AALMNN- 137
Query: 208 PSGLVVANDVDNNRCYMLVHQAKRLNSPCAIITNHDASVMPNVLYTDADGNKVPMKFDRV 267
G +VAN+ +R +L R +T+ D V G +P FD +
Sbjct: 138 -QGAIVANEYSASRVKVLHANISRCGVSNVALTHFDGRVF---------GAALPETFDAI 187
Query: 268 LCDVPCTGDGTMRKNPDIWTKWTPSNGNNLHGIQYRIVKRGVEMLAVGGKIAYSTCSLNP 327
L D PC+G+GT+RK+PD W+P + + Q +++ L GG + YSTC+LN
Sbjct: 188 LLDAPCSGEGTVRKDPDALKNWSPESNLEIAATQRELIESAFHALKPGGTLVYSTCTLNR 247
Query: 328 LEDEAVIQRLIVETQGAVQ 346
E++AV L AV+
Sbjct: 248 EENQAVCLWLKETYPDAVE 266
>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 = 111 bits (279), Expect = 3e-26
Identities = 57/193 (29%), Positives = 84/193 (43%), Gaps = 27/193 (13%)
Query: 155 ATGHISRQEAVSMIPPLLLDVQTHHKVLDMCAAPGSKTAQIIEMIHAADSNPVPSGLVVA 214
G ++ Q+A + L Q +LD CAAPG KT I+E+ P VVA
Sbjct: 216 EEGWVTVQDASAQWVATWLAPQNEETILDACAAPGGKTTHILEL--------APQAQVVA 267
Query: 215 NDVDNNRCYMLVHQAKRLNSPCAIITNHDASVMPNVLYTDADGNKVPM-----KFDRVLC 269
D+ +R + KRL T D DG +FDR+L
Sbjct: 268 LDIHEHRLKRVYENLKRLGLTIKAET------------KDGDGRGPSQWAENEQFDRILL 315
Query: 270 DVPCTGDGTMRKNPDI-WTKWTPSNGNNLHGIQYRIVKRGVEMLAVGGKIAYSTCSLNPL 328
D PC+ G +R++PDI W + P + L +Q I+ +L GG + Y+TCS+ P
Sbjct: 316 DAPCSATGVIRRHPDIKWLR-KPRDIAELAELQSEILDAIWPLLKTGGTLVYATCSVLPE 374
Query: 329 EDEAVIQRLIVET 341
E+ I+ + E
Sbjct: 375 ENSEQIKAFLQEH 387
>gnl|CDD|201649 pfam01189, Nol1_Nop2_Fmu, NOL1/NOP2/sun family.
Length = 277
Score = 107 bits (270), Expect = 5e-26
Identities = 59/180 (32%), Positives = 90/180 (50%), Gaps = 15/180 (8%)
Query: 157 GHISRQEAVSMIPPLLLDVQTHHKVLDMCAAPGSKTAQIIEMIHAADSNPVPSGLVVAND 216
G ++ Q+A S + + L+ Q +LDMCAAPG KT I E+ G VVA D
Sbjct: 64 GAVTVQDASSQLDAIALNPQEDEFILDMCAAPGGKTTHIAEL------MKNE-GTVVAVD 116
Query: 217 VDNNRCYMLVHQAKRLNSPCAIITNHDASVMPNVLYTDADGNKVPMKFDRVLCDVPCTGD 276
+ R + +RL I+ DA D + +FDR+L D PC+G
Sbjct: 117 RNKQRLKRVYANIQRLGVFNIIVQEGDA--------RQIDQKLLGGEFDRILLDAPCSGT 168
Query: 277 GTMRKNPDIWTKWTPSNGNNLHGIQYRIVKRGVEMLAVGGKIAYSTCSLNPLEDEAVIQR 336
G +R++PDI ++ L +Q ++K +++ GG + YSTCS+ P E+EAVI+
Sbjct: 169 GVIRRDPDIKWLRREADIAQLAELQKELLKAAWDLVKPGGVLVYSTCSVLPEENEAVIKY 228
Score = 62.0 bits (151), Expect = 1e-10
Identities = 24/81 (29%), Positives = 34/81 (41%), Gaps = 2/81 (2%)
Query: 267 VLCDVPCTGDGTMRKNPDIWTKWTPSNGNNLHGIQYRIVKRGVEMLAVGGKIAYSTCSLN 326
+L C+ GT+RKN +W+ L G+Q + R L VG YS SL
Sbjct: 1 ILEANNCSPPGTLRKNVLKTKRWSLLQALELAGVQLEPLGRYPHALPVGDLP-YSIGSLP 59
Query: 327 PLEDEAVIQRLIVETQGAVQL 347
P E+ AV + +Q
Sbjct: 60 PFENGAVTVQDA-SSQLDAIA 79
>gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional.
Length = 431
Score = 106 bits (265), Expect = 2e-24
Identities = 59/194 (30%), Positives = 96/194 (49%), Gaps = 17/194 (8%)
Query: 157 GHISRQEAVSMIPPLLLDVQTHHKVLDMCAAPGSKTAQIIEMIHAADSNPVPSGLVVAND 216
G + Q S I PLL++++ +VLD CAAPG KT I E++ G ++A D
Sbjct: 217 GLATVQGESSQIVPLLMELEPGLRVLDTCAAPGGKTTAIAELMK-------DQGKILAVD 269
Query: 217 VDNNRCYMLVHQAKRLNSPCAIITNHDASVMPNVLYTDADGNKVPMKFDRVLCDVPCTGD 276
+ + ++ AKRL I DA + + FDR+L D PCT
Sbjct: 270 ISREKIQLVEKHAKRLKLSSIEIKIADAERLTEYVQD---------TFDRILVDAPCTSL 320
Query: 277 GTMRKNPDIWTKWTPSNGNNLHGIQYRIVKRGVEMLAVGGKIAYSTCSLNPLEDEAVIQR 336
GT R +P++ + + L IQ RIV + ++L GG + YSTC++ E+ V++R
Sbjct: 321 GTARNHPEVLRRVNKEDFKKLSEIQLRIVSQAWKLLEKGGILLYSTCTVTKEENTEVVKR 380
Query: 337 LIVETQGAVQLVDV 350
+ E + +++D+
Sbjct: 381 FVYEQK-DAEVIDI 393
>gnl|CDD|236790 PRK10901, PRK10901, 16S rRNA methyltransferase B; Provisional.
Length = 427
Score = 103 bits (260), Expect = 1e-23
Identities = 63/186 (33%), Positives = 85/186 (45%), Gaps = 37/186 (19%)
Query: 172 LLDVQTHHKVLDMCAAPGSKTAQIIEMIHAADSNPVPSGLVVANDVDNNRCYMLVHQA-K 230
LL Q +VLD CAAPG KTA I+E+ A VVA D+D R V + +
Sbjct: 239 LLAPQNGERVLDACAAPGGKTAHILELAPQAQ--------VVALDIDAQRL-ERVRENLQ 289
Query: 231 RLNSPCAIITNHDASVMPNVLYTDA-------DGNKVPMKFDRVLCDVPCTGDGTMRKNP 283
RL A V+ DA DG FDR+L D PC+ G +R++P
Sbjct: 290 RL--------GLKA----TVIVGDARDPAQWWDG----QPFDRILLDAPCSATGVIRRHP 333
Query: 284 DIWTKWT--PSNGNNLHGIQYRIVKRGVEMLAVGGKIAYSTCSLNPLEDEAVIQRLIVET 341
DI KW P + L +Q I+ +L GG + Y+TCS+ P E+E I+ +
Sbjct: 334 DI--KWLRRPEDIAALAALQSEILDALWPLLKPGGTLLYATCSILPEENEQQIKAFLARH 391
Query: 342 QGAVQL 347
A L
Sbjct: 392 PDAELL 397
>gnl|CDD|237856 PRK14901, PRK14901, 16S rRNA methyltransferase B; Provisional.
Length = 434
Score = 100 bits (252), Expect = 1e-22
Identities = 58/186 (31%), Positives = 90/186 (48%), Gaps = 21/186 (11%)
Query: 157 GHISRQEAVSMIPPLLLDVQTHHKVLDMCAAPGSKTAQIIEMIHAADSNPVPSGLVVAND 216
G + Q+ + + LLD Q +LD CAAPG KT I E++ D G + A D
Sbjct: 232 GWWTVQDRSAQLVAPLLDPQPGEVILDACAAPGGKTTHIAELM--GDQ-----GEIWAVD 284
Query: 217 VDNNRCYMLVHQAKRLNSPCAIITNHDASVMPNVLYTDADGNKVPMK--FDRVLCDVPCT 274
+R L A+RL I D+ + K + FDR+L D PC+
Sbjct: 285 RSASRLKKLQENAQRLGLKSIKILAADS--------RNLLELKPQWRGYFDRILLDAPCS 336
Query: 275 GDGTMRKNPDIWTKW--TPSNGNNLHGIQYRIVKRGVEMLAVGGKIAYSTCSLNPLEDEA 332
G GT+ ++PD +W TP L +Q +++ +L GG + Y+TC+L+P E+EA
Sbjct: 337 GLGTLHRHPDA--RWRQTPEKIQELAPLQAELLESLAPLLKPGGTLVYATCTLHPAENEA 394
Query: 333 VIQRLI 338
I++ +
Sbjct: 395 QIEQFL 400
>gnl|CDD|237858 PRK14904, PRK14904, 16S rRNA methyltransferase B; Provisional.
Length = 445
Score = 95.5 bits (238), Expect = 8e-21
Identities = 58/203 (28%), Positives = 85/203 (41%), Gaps = 28/203 (13%)
Query: 137 IRTSQAFSKLHQFLIMENATGHISRQEAVSMIPPLLLDVQTHHKVLDMCAAPGSKTAQII 196
S+ FS FL G +S Q + LLL+ Q VLD+CAAPG K+ +
Sbjct: 214 FFLSKDFSLFEPFLK----LGLVSVQNPTQALACLLLNPQPGSTVLDLCAAPGGKSTFMA 269
Query: 197 EMIHAADSNPVPSGLVVANDVDNNRCYMLVHQAKRLNSPCAIIT--NHDA-SVMPNVLYT 253
E++ G + A D + + A L II DA S P
Sbjct: 270 ELMQN-------RGQITAVDRYPQKLEKIRSHASALG--ITIIETIEGDARSFSP----- 315
Query: 254 DADGNKVPMKFDRVLCDVPCTGDGTMRKNPDIWTKWTPSNGNNLHGIQYRIVKRGVEMLA 313
+ D +L D PCTG G + + ++ K TP L G+Q ++ +L
Sbjct: 316 -------EEQPDAILLDAPCTGTGVLGRRAELRWKLTPEKLAELVGLQAELLDHAASLLK 368
Query: 314 VGGKIAYSTCSLNPLEDEAVIQR 336
GG + Y+TCS+ P E+E I+
Sbjct: 369 PGGVLVYATCSIEPEENELQIEA 391
>gnl|CDD|222295 pfam13659, Methyltransf_26, Methyltransferase domain. This family
contains methyltransferase domains.
Length = 117
Score = 33.6 bits (77), Expect = 0.088
Identities = 24/148 (16%), Positives = 41/148 (27%), Gaps = 32/148 (21%)
Query: 178 HHKVLDMCAAPGSKTAQIIEMIHAADSNPVPSGLVVANDVDNNRCYMLVHQAKRLN-SPC 236
+VLD A G+ + A P VV ++D + + +P
Sbjct: 1 GDRVLDPGAGSGA----FLLAAARA----GPDARVVGVELDPEAAALARRRLALAGLAPR 52
Query: 237 AIITNHDASVMPNVLYTDADGNKVPMKFDRVLCDVPCTGDGTMRKNPDIWTKWTPSNGNN 296
+ DA + FD VL + P K+
Sbjct: 53 VRVVVGDA-----RELLELPDGS----FDLVLGNPPYGPRAGDPKDNRDLYD-------- 95
Query: 297 LHGIQYRIVKRGVEMLAVGGKIAYSTCS 324
R + + +L GG + T +
Sbjct: 96 ------RFLAAALRLLKPGGVLVVITPA 117
>gnl|CDD|224397 COG1480, COG1480, Predicted membrane-associated HD superfamily
hydrolase [General function prediction only].
Length = 700
Score = 34.3 bits (79), Expect = 0.24
Identities = 16/96 (16%), Positives = 32/96 (33%), Gaps = 7/96 (7%)
Query: 10 RNKSFAQKRREKEQKKANPKTDTRHENYAEIVRE-NKDFEQYYKAQKICPENEWDSM--- 65
++ ++ R+ P E IV+ F+ + ++ ENE ++
Sbjct: 63 EDEKATEEERKAASDSVEPVYKRDAEITQNIVQLYQNFFDAINEVKRSLEENEDENTEYS 122
Query: 66 ---LETLKKDLPTAFRITNCSPEEAKALLSIVESKF 98
++ LK L + S E LL +
Sbjct: 123 LKQVKQLKDRLLRDTNTVDISEERILTLLELDSEDL 158
>gnl|CDD|185280 PRK15382, PRK15382, non-LEE encoded effector protein NleB;
Provisional.
Length = 326
Score = 32.5 bits (74), Expect = 0.64
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 12/64 (18%)
Query: 22 EQKKANPKTDTRHENYAEIVRENKDFEQYYKA-----------QKICPENEWDS-MLETL 69
EQKK + +N I RE+ DF Y K Q+ P +E D+ +L L
Sbjct: 96 EQKKEFLSLENEFQNIKIIYREDVDFSMYDKKLSDIYLENIHEQESYPASERDNYLLGLL 155
Query: 70 KKDL 73
+++L
Sbjct: 156 REEL 159
>gnl|CDD|216666 pfam01728, FtsJ, FtsJ-like methyltransferase. This family consists
of FtsJ from various bacterial and archaeal sources FtsJ
is a methyltransferase, but actually has no effect on
cell division. FtsJ's substrate is the 23S rRNA. The 1.5
A crystal structure of FtsJ in complex with its cofactor
S-adenosylmethionine revealed that FtsJ has a
methyltransferase fold. This family also includes the N
terminus of flaviviral NS5 protein. It has been
hypothesised that the N-terminal domain of NS5 is a
methyltransferase involved in viral RNA capping.
Length = 177
Score = 31.0 bits (71), Expect = 1.2
Identities = 26/108 (24%), Positives = 38/108 (35%), Gaps = 26/108 (24%)
Query: 173 LDVQTHHKVLDMCAAPGSKTAQIIEMIHAADSNPVPSGLVVANDVDNNRCYMLVHQAKRL 232
L VLD+ AAPG + ++E +G VVA D+ V+ R
Sbjct: 18 LKPGKGKTVLDLGAAPGGFSQVLLER--------GGAGKVVAVDLGPMEPIQGVYFL-RG 68
Query: 233 NSPCAIITNHDASVMPNVLYTDAD-GNKVPMKFDRVLCDV--PCTGDG 277
+ IT+ + T +P K D VL D +G
Sbjct: 69 D-----ITDPE---------TLEKLRELLPGKVDLVLSDGAPNVSGIE 102
>gnl|CDD|148622 pfam07120, DUF1376, Protein of unknown function (DUF1376). This
family consists of several hypothetical bacterial
proteins of around 95 residues in length. The function
of this family is unknown.
Length = 88
Score = 29.2 bits (66), Expect = 1.5
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 67 ETLKKDLPTAFRITNCSPEEAKALLSIVESKFFKEL 102
L D R+ CS +E A + V S+FF+EL
Sbjct: 37 GPLPDDDARLARLAGCSTKEWAAAVEFVLSEFFEEL 72
>gnl|CDD|180660 PRK06696, PRK06696, uridine kinase; Validated.
Length = 223
Score = 30.7 bits (70), Expect = 2.0
Identities = 11/38 (28%), Positives = 15/38 (39%)
Query: 312 LAVGGKIAYSTCSLNPLEDEAVIQRLIVETQGAVQLVD 349
L G Y T S + D V ++ AV +VD
Sbjct: 97 LGPNGDRQYRTASHDLKTDIPVHNPPLLAAPNAVLIVD 134
>gnl|CDD|240393 PTZ00383, PTZ00383, malate:quinone oxidoreductase; Provisional.
Length = 497
Score = 30.9 bits (70), Expect = 2.5
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 474 DFYEISPSLPVDCLLTRCLVGKKKIIYFTSPMVKNIIQSNENNLKIINTGVKSFAR 529
D+ ++S S V LV KKI + V NI +SN++ KI + AR
Sbjct: 209 DYQKLSESF-VKHARRDALVPGKKISINLNTEVLNIERSNDSLYKIHTNRGEIRAR 263
>gnl|CDD|238416 cd00801, INT_P4, Bacteriophage P4 integrase. P4-like integrases are
found in temperate bacteriophages, integrative plasmids,
pathogenicity and symbiosis islands, and other mobile
genetic elements. They share the same fold in their
catalytic domain and the overall reaction mechanism with
the superfamily of DNA breaking-rejoining enzymes. The
P4 integrase mediates integrative and excisive
site-specific recombination between two sites, called
attachment sites, located on the phage genome and the
bacterial chromosome. The phage attachment site is often
found adjacent to the integrase gene, while the host
attachment sites are typically situated near tRNA genes.
Length = 357
Score = 30.7 bits (70), Expect = 2.6
Identities = 31/197 (15%), Positives = 59/197 (29%), Gaps = 57/197 (28%)
Query: 15 AQKRREKEQKKANPKTDTRHENYAEIVRENKDFEQYYKAQKI-CPENEWDSMLETLKKDL 73
+++ EK K + T +AE+ E + A+K E TL+K +
Sbjct: 57 EERKEEKAAKLSAANT------FAEVAEE------WLAAKKPRWSEKHARQWRRTLEKHV 104
Query: 74 PTAF---RITNCSPEEAKALLSIVESKFFKELVNDQETSEEEKVAPICLPWYPEQMGWQL 130
IT + + +L +E++ E
Sbjct: 105 LPVLGKKPITEITARDLLDVLRRIEAR-----------------------GALETARRVR 141
Query: 131 QLSRRAIRTSQAFSKLHQFLIMENATGHISRQEAVSMIPPLLLDVQTHHKVLDMCAAPGS 190
Q ++ R + I A G I A + + H + L
Sbjct: 142 QRLKQVFR----------YAI---ARGLIEANPAADLRGADGAPKKQHDRAL-----SPD 183
Query: 191 KTAQIIEMIHAADSNPV 207
+ + ++ + AA +PV
Sbjct: 184 ELPEFLQALDAASGSPV 200
>gnl|CDD|238946 cd01988, Na_H_Antiporter_C, The C-terminal domain of a subfamily of
Na+ /H+ antiporter existed in bacteria and archea .
Na+/H+ exchange proteins eject protons from cells,
effectively eliminating excess acid from actively
metabolising cells. Na+ /H+ exchange activity is also
crucial for the regulation of cell volume, and for the
reabsorption of NaCl across renal, intestinal, and other
epithelia. These antiports exchange Na+ for H+ in an
electroneutral manner, and this activity is carried out
by a family of Na+ /H+ exchangers, or NHEs, which are
known to be present in both prokaryotic and eukaryotic
cells. These exchangers are highly-regulated
(glyco)phosphoproteins, which, based on their primary
structure, appear to contain 10-12 membrane-spanning
regions (M) at the N-terminus and a large cytoplasmic
region at the C-terminus. The transmembrane regions
M3-M12 share identity wit h other members of the family.
The M6 and M7 regions are highly conserved. Thus, this
is thought to be the region that is involved in the
transport of sodium and hydrogen ions. The cytoplasmic
region or C-terminal has homology with a family
universal stress protein.Usp is a small cytoplasmic
bacterial protein whose expression is enhanced when the
cell is exposed to stress agents. Usp enhances the rate
of cell survival during prolonged exposure to such
conditions, and may provide a general "stress endurance"
activity.
Length = 132
Score = 29.2 bits (66), Expect = 3.0
Identities = 22/104 (21%), Positives = 39/104 (37%), Gaps = 16/104 (15%)
Query: 543 QEGLSSMKAFIGEKRKVRVNREELITILNNSTPEQPTDL-----ELLRPETR-------- 589
L + A + + + +I + N+S+P Q +LLR R
Sbjct: 12 ARDLLELAAALARAQNGEIIPLNVIEVPNHSSPSQLEVNVQRARKLLRQAERIAASLGVP 71
Query: 590 -QTLTREGFGVGSCLLELQDDLPLSLV--GWRGKSSVRAYISGS 630
T+ R + S +L + L+ GW G +S+R + G
Sbjct: 72 VHTIIRIDHDIASGILRTAKERQADLIIMGWHGSTSLRDRLFGG 115
>gnl|CDD|219987 pfam08719, DUF1768, Domain of unknown function (DUF1768). This is
a domain of unknown function. It is alpha helical in
structure. The GO annotation for this protein suggests
it is involved in nematode larval development and has a
positive regulation on growth rate.
Length = 146
Score = 29.1 bits (66), Expect = 4.1
Identities = 19/59 (32%), Positives = 23/59 (38%), Gaps = 14/59 (23%)
Query: 48 EQYYKAQKICPENEWDSMLETLKKDLPTAFRITNC-SPEEAKALLSIVESKFFKELVND 105
E Y++AQK L D A +I SP EAK L V + F E D
Sbjct: 32 EHYFQAQKFR-----------LFGDREIAAKILAAKSPAEAKKLGRKV--RNFDEARKD 77
>gnl|CDD|219863 pfam08490, DUF1744, Domain of unknown function (DUF1744). This
domain is found on the epsilon catalytic subunit of DNA
polymerase. It is found C terminal to pfam03104 and
pfam00136.
Length = 396
Score = 30.0 bits (68), Expect = 4.2
Identities = 17/58 (29%), Positives = 24/58 (41%), Gaps = 5/58 (8%)
Query: 85 EEAKALLSIVESKFFKELVNDQETSEEEKVAPICL----PWYPEQMGWQLQLSRRAIR 138
E++ L ++S F L EE I + P +GWQ QL+RR I
Sbjct: 57 EKSGPTLLALQSPFPSRLKKKIPILEEFPCVQIHINDDESSLP-ALGWQRQLARRLIN 113
>gnl|CDD|238939 cd01981, Pchlide_reductase_B, Pchlide_reductase_B: B protein of the
NB protein complex of Protochlorophyllide
(Pchlide)_reductase. Pchlide reductase catalyzes the
reductive formation of chlorophyllide (chlide) from
protochlorophyllide (pchlide) during biosynthesis of
chlorophylls and bacteriochlorophylls. This group
contains both the light-independent Pchlide reductase
(DPOR) and light-dependent Pchlide reductase (LPOR).
Angiosperms contain only LPOR, cyanobacteria, algae and
gymnosperms contain both DPOR and LPOR, primitive
anoxygenic photosynthetic bacteria contain only DPOR. NB
is structurally similar to the FeMo protein of
nitrogenase, forming an N2B2 heterotetramer. N and B are
homologous to the FeMo alpha and beta subunits
respectively. Also in common with nitrogenase in vitro
DPOR activity requires ATP hydrolysis and dithoionite or
ferredoxin as electron donor. The NB protein complex may
serve as a catalytic site for Pchlide reduction similar
to MoFe for nitrogen reduction.
Length = 430
Score = 29.7 bits (67), Expect = 5.5
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 6/39 (15%)
Query: 224 MLVHQAKRLNSPCAIIT------NHDASVMPNVLYTDAD 256
M H KRL+ PCA+I+ N P + Y +
Sbjct: 379 MERHIGKRLDIPCAVISAPVHIQNFPLGYRPFLGYEGTN 417
>gnl|CDD|164910 PHA02335, PHA02335, hypothetical protein.
Length = 118
Score = 28.2 bits (63), Expect = 5.6
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 8/38 (21%)
Query: 458 PFVFFNTDEAVWPPIRDF------YEISPSLPVD--CL 487
P +F+ + WP I+ F I P+ VD CL
Sbjct: 75 PLLFYKLEAEYWPAIKSFLLFLNRLPIFPNEEVDQECL 112
>gnl|CDD|226732 COG4282, SMI1, Protein involved in beta-1,3-glucan synthesis
[Carbohydrate transport and metabolism].
Length = 191
Score = 28.7 bits (64), Expect = 6.3
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 6/61 (9%)
Query: 170 PLLLDVQTHHKVLDMCAAPGSKTAQIIEMIHAADSNPV--PSG----LVVANDVDNNRCY 223
PL D + +H +D+ P QII D+ PV S +ANDV+ R
Sbjct: 122 PLFGDPRGNHICIDLAPGPTGGYGQIIWFGRDEDTKPVVAQSWAEFLSRIANDVETGRWL 181
Query: 224 M 224
+
Sbjct: 182 L 182
>gnl|CDD|237493 PRK13762, PRK13762, tRNA-modifying enzyme; Provisional.
Length = 322
Score = 29.5 bits (67), Expect = 6.4
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 46 DFEQYYKAQKICPENEWDSMLETL----KKDLPTAFRIT 80
D E Y K + + W+ +LETL K T RIT
Sbjct: 191 DEETYKKINRPVIPDAWERILETLELLPSKKTRTVIRIT 229
>gnl|CDD|214416 MTH00066, ND5, NADH dehydrogenase subunit 5; Provisional.
Length = 598
Score = 29.5 bits (67), Expect = 7.5
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 3/28 (10%)
Query: 497 KIIYFTS---PMVKNIIQSNENNLKIIN 521
+IIYF+S P + NENN IIN
Sbjct: 422 RIIYFSSMKFPRSLPLSPINENNPLIIN 449
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 29.2 bits (66), Expect = 8.5
Identities = 16/86 (18%), Positives = 29/86 (33%), Gaps = 6/86 (6%)
Query: 11 NKSFAQKRREKEQKKANPKTDTRHENYAEIVRENKDFEQYYKAQKICPENEWDSMLETLK 70
+K E E+ K + + + + +K E +L+ LK
Sbjct: 115 EAEIEKKEEELEKAKNKFLDKAWKKLAKKYDSNLSEALKGLNYKKNFKEK----LLKELK 170
Query: 71 KDLPTAFRITNCSPEEAKALLSIVES 96
+ A + S EE KA + + S
Sbjct: 171 SVILNA--SSLLSLEELKAKIKTLFS 194
>gnl|CDD|180842 PRK07107, PRK07107, inosine 5-monophosphate dehydrogenase;
Validated.
Length = 502
Score = 28.9 bits (65), Expect = 8.8
Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 14/92 (15%)
Query: 488 LTRCLVGKKKIIYFTSPMVKNIIQS-NENNLKIINTGVKSFARCDNKVMGCAFRFCQEGL 546
L + G++ I P+V I+QS +++N+ I + AR G +F F + +
Sbjct: 37 LVKFKKGEESAITLNIPLVSAIMQSVSDDNMAI------ALAREG----GLSFIFGSQSI 86
Query: 547 SSMKAFIGEKRKVRVNREELITILNNSTPEQP 578
S A + R+V+ + + +N TP+
Sbjct: 87 ESEAAMV---RRVKNYKAGFVVSDSNLTPDNT 115
>gnl|CDD|232887 TIGR00232, tktlase_bact, transketolase, bacterial and yeast. This
model is designed to capture orthologs of bacterial
transketolases. The group includes two from the yeast
Saccharomyces cerevisiae but excludes dihydroxyactetone
synthases (formaldehyde transketolases) from various
yeasts and the even more distant mammalian
transketolases. Among the family of thiamine
diphosphate-dependent enzymes that includes
transketolases, dihydroxyacetone synthases, pyruvate
dehydrogenase E1-beta subunits, and
deoxyxylulose-5-phosphate synthases, mammalian and
bacterial transketolases seem not to be orthologous
[Energy metabolism, Pentose phosphate pathway].
Length = 653
Score = 28.9 bits (65), Expect = 9.5
Identities = 12/59 (20%), Positives = 24/59 (40%), Gaps = 2/59 (3%)
Query: 20 EKEQKKANPKTDTRHENYAEIVRENKD-FEQYYKAQKICPENEWDSMLETLKKDLPTAF 77
+++ K + + E+ +E D F++ K + E EW+ + KK P
Sbjct: 263 DEDVKLTKKNLGWNYNPF-EVPQEVYDHFQKTVKERGAKAEQEWNELFAAYKKKYPELA 320
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 0.404
Gapped
Lambda K H
0.267 0.0669 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 32,733,430
Number of extensions: 3179080
Number of successful extensions: 2943
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2918
Number of HSP's successfully gapped: 40
Length of query: 646
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 543
Effective length of database: 6,369,140
Effective search space: 3458443020
Effective search space used: 3458443020
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: 62 (27.8 bits)