RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3863
(285 letters)
>gnl|CDD|237676 PRK14329, PRK14329, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 467
Score = 191 bits (488), Expect = 6e-58
Identities = 75/148 (50%), Positives = 105/148 (70%), Gaps = 5/148 (3%)
Query: 54 KVYFEVFGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTCAIRENAEGKVWDRLR 113
K++ E +GCQMN D+E+V SIL+ +GY+ + EAD++LV TC+IR+NAE KV RL
Sbjct: 25 KLFIESYGCQMNFADSEIVASILQMAGYNTTENLEEADLVLVNTCSIRDNAEQKVRKRLE 84
Query: 114 FYRSMKQIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAGPDSYKDLPRLLALTY 173
+ ++K+ + K L +GVLGCMAERLK LLE+E+ +DLV GPD+Y DLP L+A
Sbjct: 85 KFNALKKKNPK-----LIVGVLGCMAERLKDKLLEEEKIVDLVVGPDAYLDLPNLIAEVE 139
Query: 174 SNQTAINVLLSLDETYADITPKAVSTDG 201
+ AINV+LS +ETYADI+P + +G
Sbjct: 140 EGRKAINVILSKEETYADISPVRLGGNG 167
Score = 111 bits (280), Expect = 6e-28
Identities = 44/65 (67%), Positives = 50/65 (76%)
Query: 3 VRLNEDSVSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEVFGC 62
VRL + VSAFVSIMRGCDNMCT+C+VPFTRGRERSR +SIL+EVR L K Y EV
Sbjct: 161 VRLGGNGVSAFVSIMRGCDNMCTFCVVPFTRGRERSRDPESILNEVRDLFAKGYKEVTLL 220
Query: 63 QMNVN 67
NV+
Sbjct: 221 GQNVD 225
>gnl|CDD|216191 pfam00919, UPF0004, Uncharacterized protein family UPF0004. This
family is the N terminal half of the Prosite family. The
C-terminal half has been shown to be related to MiaB
proteins. This domain is a nearly always found in
conjunction with pfam04055 and pfam01938 although its
function is uncertain.
Length = 98
Score = 130 bits (330), Expect = 1e-38
Identities = 47/105 (44%), Positives = 63/105 (60%), Gaps = 7/105 (6%)
Query: 54 KVYFEVFGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTCAIRENAEGKVWDRLR 113
KVY E GCQMN D+E++ +LK +GY V+ P EADVI+V TCA+RE AE K +R
Sbjct: 1 KVYIETLGCQMNQADSEIMAGLLKKAGYELVDDPEEADVIVVNTCAVREKAEQKSRQTIR 60
Query: 114 FYRSMKQIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAG 158
+ +K KI V GCMA+R + LL++ +DLV G
Sbjct: 61 RLKRLKNPDA-------KIVVTGCMAQRYPEELLKEIPEVDLVLG 98
>gnl|CDD|172808 PRK14332, PRK14332, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 449
Score = 123 bits (311), Expect = 1e-32
Identities = 63/148 (42%), Positives = 94/148 (63%), Gaps = 6/148 (4%)
Query: 52 SDKVYFEVFGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTCAIRENAEGKVWDR 111
KVY E +GCQMN D+ +V S+++ + YS N P +D+I + TCAIRENA K+++R
Sbjct: 10 LGKVYIETYGCQMNEYDSGIVSSLMRDAEYSTSNDPENSDIIFLNTCAIRENAHAKIYNR 69
Query: 112 LRFYRSMKQIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAGPDSYKDLPRLLAL 171
L +S+ + K++ L IGVLGCMA+ L L +E LDLV GPD+Y+ LP L+
Sbjct: 70 L---QSLGYLKKRNPN--LVIGVLGCMAQNLGDDLFHQELPLDLVVGPDNYRSLPELIQR 124
Query: 172 TYSNQTAINVL-LSLDETYADITPKAVS 198
+ + +I++ LS ETY +I P+ V+
Sbjct: 125 IRNGEKSISLTRLSKIETYDEIEPRVVN 152
Score = 75.8 bits (186), Expect = 2e-15
Identities = 52/161 (32%), Positives = 82/161 (50%), Gaps = 32/161 (19%)
Query: 8 DSVSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEVFGCQMNVN 67
+ + AFV+IMRGC+N CT+C+VP+TRGRERSR +SI+ E++ L +K +V NVN
Sbjct: 152 NGIQAFVTIMRGCNNFCTFCVVPYTRGRERSRDPKSIVREIQDLQEKGIRQVTLLGQNVN 211
Query: 68 -----DTE---VVWSILKSSGYSKVN----HPREADVILVMTCAIRENAEGKVWDRLRFY 115
T+ ++ +L + ++ HP++ L+ A +N
Sbjct: 212 SYKEQSTDFAGLIQMLLDETTIERIRFTSPHPKDFPDHLLSLMA--KNP----------- 258
Query: 116 RSMKQIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLV 156
R IH PL+ G + E +K+S KE+ LD+V
Sbjct: 259 RFCPNIH-----LPLQAGNTRVL-EEMKRS-YSKEEFLDVV 292
>gnl|CDD|232820 TIGR00089, TIGR00089, radical SAM methylthiotransferase, MiaB/RimO
family. This subfamily contains the tRNA-i(6)A37
modification enzyme, MiaB (TIGR01574). The phylogenetic
tree indicates 4 distinct clades, one of which
corresponds to MiaB. The other three clades are modelled
by hypothetical equivalogs (TIGR01125, TIGR01579 and
TIGR01578). Together, the four models hit every sequence
hit by the subfamily model without any overlap between
them. This subfamily is aparrently a part of a larger
superfamily of enzymes utilizing both a 4Fe4S cluster
and S-adenosyl methionine (SAM) to initiate radical
reactions. MiaB acts on a particular isoprenylated
Adenine base of certain tRNAs causing thiolation at an
aromatic carbon, and probably also transferring a methyl
grouyp from SAM to the thiol. The particular substrate
of the three other clades is unknown but may be very
closely related.
Length = 429
Score = 116 bits (292), Expect = 7e-30
Identities = 47/116 (40%), Positives = 71/116 (61%), Gaps = 7/116 (6%)
Query: 54 KVYFEVFGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTCAIRENAEGKVWDRLR 113
KVY E +GCQMN D+E++ +LK +GY + P EADVI++ TCA+RE AE KV RL
Sbjct: 1 KVYIETYGCQMNEADSEIMAGLLKEAGYEVTDDPEEADVIIINTCAVREKAEQKVRSRLG 60
Query: 114 FYRSMKQIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAGPDSYKDLPRLL 169
+K+ + KI V GC+A+R + LL++ +D+V GP + + +P +
Sbjct: 61 ELAKLKKKNA-------KIVVAGCLAQREGEELLKRIPEVDIVLGPQNKERIPEAI 109
Score = 88.4 bits (220), Expect = 6e-20
Identities = 28/53 (52%), Positives = 34/53 (64%)
Query: 7 EDSVSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEV 59
AF+ I GCD CTYCIVP+ RGRERSRP + IL+EV+ L K E+
Sbjct: 136 FGKTRAFLKIQEGCDKFCTYCIVPYARGRERSRPPEDILEEVKELVSKGVKEI 188
>gnl|CDD|237679 PRK14340, PRK14340, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 445
Score = 113 bits (284), Expect = 1e-28
Identities = 48/143 (33%), Positives = 77/143 (53%), Gaps = 5/143 (3%)
Query: 52 SDKVYFEVFGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTCAIRENAEGKVWDR 111
K Y FGCQMN D+E++ ++L+ GY +AD++L+ TCA+RENA ++
Sbjct: 6 GRKFYIHTFGCQMNQADSEIITALLQDEGYVPAASEEDADIVLLNTCAVRENAVERIGHY 65
Query: 112 LRFYRSMKQIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAGPDSYKDLPRLLAL 171
L+ + K+ K L +GVLGC+ + ++ + +D +AGPD+Y+ LP L+A
Sbjct: 66 LQHLKGAKRRRKG-----LLVGVLGCVPQYEREEMFSMFPVIDFLAGPDTYRVLPGLIAD 120
Query: 172 TYSNQTAINVLLSLDETYADITP 194
+ + ETYA I P
Sbjct: 121 AREGARPAALDFNQSETYAGIEP 143
Score = 96.4 bits (240), Expect = 1e-22
Identities = 45/111 (40%), Positives = 66/111 (59%), Gaps = 14/111 (12%)
Query: 7 EDSVSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEVFGCQMNV 66
S+SAFV +MRGC+NMC +C+VPFTRGRERS P S+LDEVRAL++ Y E+ NV
Sbjct: 146 SGSISAFVPVMRGCNNMCAFCVVPFTRGRERSHPFASVLDEVRALAEAGYREITLLGQNV 205
Query: 67 ND----------TEVVWSILKSSGYSKV----NHPREADVILVMTCAIREN 103
N ++ ++ +++ ++ +HP++ LV T A R N
Sbjct: 206 NSYSDPEAGADFAGLLDAVSRAAPEMRIRFTTSHPKDISESLVRTIAARPN 256
>gnl|CDD|223694 COG0621, MiaB, 2-methylthioadenine synthetase [Translation,
ribosomal structure and biogenesis].
Length = 437
Score = 113 bits (284), Expect = 1e-28
Identities = 49/145 (33%), Positives = 81/145 (55%), Gaps = 12/145 (8%)
Query: 54 KVYFEVFGCQMNVNDTEVVWSILKSSGYSK-VNHPREADVILVMTCAIRENAEGKVWDRL 112
KVY E GCQMN+ D+E + +L+++GY + V P EADV+++ TCA+RE AE KV +
Sbjct: 4 KVYIETLGCQMNLYDSERMAGLLEAAGYEELVEDPEEADVVIINTCAVREKAEQKVRSAI 63
Query: 113 RFYRSMKQIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAGPDSYKDLPRLLALT 172
+ +K KI V GC+A+ ++ +LE+ +D+V GP + + LP +
Sbjct: 64 GELKKLKP--------DAKIIVTGCLAQAEEE-ILERAPEVDIVLGPQNKERLPEAIEKA 114
Query: 173 YSNQTAINVLLSL--DETYADITPK 195
+ V+LS +E + + P+
Sbjct: 115 LRGKKEFVVVLSFPEEEKFDKLPPR 139
Score = 86.5 bits (215), Expect = 3e-19
Identities = 26/53 (49%), Positives = 35/53 (66%)
Query: 7 EDSVSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEV 59
E V AFV I GC+ CT+CI+P+ RG+ERSRP + IL EV+ L + E+
Sbjct: 141 EGGVRAFVKIQEGCNKFCTFCIIPYARGKERSRPPEDILKEVKRLVAQGVKEI 193
>gnl|CDD|184628 PRK14331, PRK14331, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 437
Score = 107 bits (269), Expect = 1e-26
Identities = 51/134 (38%), Positives = 74/134 (55%), Gaps = 5/134 (3%)
Query: 54 KVYFEVFGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTCAIRENAEGKVWDRLR 113
K Y + FGCQMN ND+E + IL++ GY + EAD+ILV TC IRE + KV L
Sbjct: 2 KYYIKTFGCQMNFNDSEKIKGILQTLGYEPADDWEEADLILVNTCTIREKPDQKVLSHLG 61
Query: 114 FYRSMKQIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAGPDSYKDLPRLLALTY 173
Y+ +K+ + IGV GC+A+R +++K +D+V G + LP LL
Sbjct: 62 EYKKIKEKNPN-----ALIGVCGCLAQRAGYEIVQKAPFIDIVFGTFNIHHLPELLEQAK 116
Query: 174 SNQTAINVLLSLDE 187
+ AI +L +DE
Sbjct: 117 AGNKAIEILEEIDE 130
Score = 82.1 bits (203), Expect = 1e-17
Identities = 28/47 (59%), Positives = 37/47 (78%)
Query: 7 EDSVSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSD 53
++ A+V++MRGCD CTYC+VP TRG+ERSR + SILDEV+ L D
Sbjct: 143 DNKYCAYVTVMRGCDKKCTYCVVPKTRGKERSRRLGSILDEVQWLVD 189
>gnl|CDD|237673 PRK14325, PRK14325, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 444
Score = 106 bits (268), Expect = 3e-26
Identities = 44/117 (37%), Positives = 72/117 (61%), Gaps = 5/117 (4%)
Query: 54 KVYFEVFGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTCAIRENAEGKVWDRLR 113
K+Y + +GCQMN D+ + +L + GY + P EAD+IL+ TC+IRE A+ KV+ L
Sbjct: 5 KLYIKTYGCQMNEYDSSKMADLLGAEGYELTDDPEEADLILLNTCSIREKAQEKVFSELG 64
Query: 114 FYRSMKQIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAGPDSYKDLPRLLA 170
+R +K+ K L IGV GC+A++ + +L++ +D+V GP + LP ++A
Sbjct: 65 RWRKLKE--KNPD---LIIGVGGCVAQQEGEEILKRAPYVDIVFGPQTLHRLPEMIA 116
Score = 85.6 bits (213), Expect = 6e-19
Identities = 26/47 (55%), Positives = 35/47 (74%)
Query: 8 DSVSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDK 54
+ SAFVSIM GCD CT+C+VP+TRG E SRP+ +L EV L+++
Sbjct: 145 EGPSAFVSIMEGCDKYCTFCVVPYTRGEEVSRPVDDVLAEVAQLAEQ 191
>gnl|CDD|184627 PRK14330, PRK14330, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 434
Score = 103 bits (258), Expect = 4e-25
Identities = 42/116 (36%), Positives = 65/116 (56%), Gaps = 8/116 (6%)
Query: 54 KVYFEVFGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTCAIRENAEGKVWDRLR 113
K Y + FGCQMN ND+E + +LK G+ ++P EADV+++ TCA+R +E K
Sbjct: 2 KFYIKTFGCQMNENDSETMAGLLKKEGFEPASNPEEADVVIINTCAVRRKSEEK------ 55
Query: 114 FYRSMKQIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAGPDSYKDLPRLL 169
Y + Q+ K R L IGV GC+AE+ ++ LL++ D V G + + +
Sbjct: 56 AYSELGQLLKLKRKKNLIIGVAGCVAEKEREKLLKRG--ADFVIGTRAVPKVTEAV 109
Score = 78.6 bits (194), Expect = 2e-16
Identities = 31/56 (55%), Positives = 42/56 (75%)
Query: 12 AFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEVFGCQMNVN 67
A+V+I+ GC+ CTYCIVP+TRGRE+SRPM+ IL+EV L+ + Y EV NV+
Sbjct: 142 AWVTIIYGCNRFCTYCIVPYTRGREKSRPMEDILEEVEKLAKQGYREVTFLGQNVD 197
>gnl|CDD|184624 PRK14327, PRK14327, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 509
Score = 98.2 bits (245), Expect = 4e-23
Identities = 58/157 (36%), Positives = 87/157 (55%), Gaps = 14/157 (8%)
Query: 33 RGRERSRPMQ--SILDEVRALSD--KVYFEVFGCQMNVNDTEVVWSILKSSGYSKVNHPR 88
RG+E + + I +E R + + K Y +GCQMN +DTEV+ I ++ GY +
Sbjct: 43 RGKEEVKYNRDFQIPEEFRGMGNGRKFYIRTYGCQMNEHDTEVMAGIFEALGYEPTDDTE 102
Query: 89 EADVILVMTCAIRENAEGKVWDRLRFYRSMKQIHKKHRTFP-LKIGVLGCMA--ERLKKS 145
+ADVIL+ TCAIRENAE KV+ + + +K R P L IGV GCM+ E +
Sbjct: 103 DADVILLNTCAIRENAENKVFGEIGHLKHLK------RENPDLLIGVCGCMSQEESVVNK 156
Query: 146 LLEKEQALDLVAGPDSYKDLPRLLALTY-SNQTAINV 181
+L+K Q +D++ G + LP +L Y S + + V
Sbjct: 157 ILKKYQHVDMIFGTHNIHRLPEILKEAYFSKEMVVEV 193
Score = 81.3 bits (201), Expect = 2e-17
Identities = 32/64 (50%), Positives = 45/64 (70%)
Query: 4 RLNEDSVSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEVFGCQ 63
++ E ++ A+V+IM GCD CTYCIVP+TRG+ERSR + I+ EVR L+ + Y E+
Sbjct: 206 KVREGNIKAWVNIMYGCDKFCTYCIVPYTRGKERSRRPEDIIQEVRHLARQGYKEITLLG 265
Query: 64 MNVN 67
NVN
Sbjct: 266 QNVN 269
>gnl|CDD|237675 PRK14328, PRK14328, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 439
Score = 97.4 bits (243), Expect = 6e-23
Identities = 41/118 (34%), Positives = 66/118 (55%), Gaps = 7/118 (5%)
Query: 54 KVYFEVFGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTCAIRENAEGKVWDRLR 113
K + E +GCQMN D+E + +LKS GY + + EAD+I+ TC +RENAE KV+ L
Sbjct: 3 KYFIETYGCQMNEEDSEKLAGMLKSMGYERTENREEADIIIFNTCCVRENAENKVFGNLG 62
Query: 114 FYRSMKQIHKKHRTFPLKIGVLGCMAER--LKKSLLEKEQALDLVAGPDSYKDLPRLL 169
+ +K+ + L IGV GCM ++ + + + +K +D++ G + P L
Sbjct: 63 ELKKLKE-----KNPNLIIGVCGCMMQQKGMAEKIKKKFPFVDIIFGTHNIHKFPEYL 115
Score = 87.0 bits (216), Expect = 2e-19
Identities = 32/61 (52%), Positives = 41/61 (67%)
Query: 7 EDSVSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEVFGCQMNV 66
+ V AFV+IM GC+N CTYCIVP+ RGRERSR + I+ E++ L + Y EV NV
Sbjct: 144 KSKVKAFVTIMYGCNNFCTYCIVPYVRGRERSRKPEDIIAEIKELVSEGYKEVTLLGQNV 203
Query: 67 N 67
N
Sbjct: 204 N 204
>gnl|CDD|233476 TIGR01574, miaB-methiolase, tRNA-N(6)-(isopentenyl)adenosine-37
thiotransferase enzyme MiaB. This model represents
homologs of the MiaB enzyme responsible for the
modification of the isopentenylated adenine-37 base of
most bacterial and eukaryotic tRNAs that read codons
beginning with uracil (all except tRNA(I,V) Ser).
Adenine-37 is next to the anticodon on the 3' side in
these tRNA's, and lack of modification at this site
leads to an increased spontaneous mutation frequency.
Isopentenylated A-37 is modified by methylthiolation at
position 2, either by MiaB alone or in concert with a
separate methylase yet to be discovered (MiaC?). MiaB
contains a 4Fe-4S cluster which is labile under
oxidizing conditions. Additionally, the sequence is
homologous (via PSI-BLAST searches) to the biotin
synthetase, BioB, which utilizes both an iron-sulfur
cluster and S-adenosym methionine (SAM) to generate a
radical which is responsible for initiating the
insertion of sulfur into the substrate. It is reasonable
to surmise that the methyl group of SAM becomes the
methyl group of the product, but this has not been
shown, and the possibility of a separate methylase
exists. This equivalog is a member of a subfamily
(TIGR00089) which contains several other hypothetical
equivalogs which are all probably enzymes with similar
function acting on different substrates. These enzymes
contain a TRAM domain (pfam01938) which is believed to
be responsible for binding to tRNAs. Hits to this model
span all major groups of bacteria and eukaryotes, but
not archaea, which are known to lack this particular
tRNA modification. The enzyme from Thermotoga maritima
has been cloned, expressed, spectroscopically
characterized and shown to complement the E. coli MiaB
enzyme [Protein synthesis, tRNA and rRNA base
modification].
Length = 438
Score = 95.7 bits (238), Expect = 2e-22
Identities = 42/117 (35%), Positives = 67/117 (57%), Gaps = 6/117 (5%)
Query: 54 KVYFEVFGCQMNVNDTEVVWSIL-KSSGYSKVNHPREADVILVMTCAIRENAEGKVWDRL 112
K++ + +GCQMNV D+E + ++L GY+ +EADV+L+ TC++RE AE KV+ L
Sbjct: 1 KLFIQTYGCQMNVRDSEHMAALLTAKEGYALTEDAKEADVLLINTCSVREKAEHKVFGEL 60
Query: 113 RFYRSMKQIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAGPDSYKDLPRLL 169
++ + KK L IGV GCMA L + ++ +D V G + LP+ +
Sbjct: 61 GGFKKL----KKKNPD-LIIGVCGCMASHLGNEIFQRAPYVDFVFGTRNIHRLPQAI 112
Score = 85.2 bits (211), Expect = 1e-18
Identities = 31/62 (50%), Positives = 40/62 (64%)
Query: 6 NEDSVSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEVFGCQMN 65
NE +F++IM GC+ CTYCIVP+TRG E SRP IL EV+ L++K E+ N
Sbjct: 141 NEGIYKSFINIMIGCNKFCTYCIVPYTRGDEISRPFDDILQEVQKLAEKGVREITLLGQN 200
Query: 66 VN 67
VN
Sbjct: 201 VN 202
>gnl|CDD|237677 PRK14333, PRK14333, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 448
Score = 89.0 bits (221), Expect = 4e-20
Identities = 45/111 (40%), Positives = 62/111 (55%), Gaps = 5/111 (4%)
Query: 60 FGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTCAIRENAEGKVWDRLRFYRSMK 119
FGCQMN D+E + IL+ GY +AD++L TC IR+NAE KV+ L +
Sbjct: 14 FGCQMNKADSERMAGILEDMGYQWAEDELQADLVLYNTCTIRDNAEQKVYSYLG-----R 68
Query: 120 QIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAGPDSYKDLPRLLA 170
Q +KH+ L + V GC+A++ +SLL + LDLV GP L LL
Sbjct: 69 QAKRKHKNPDLTLVVAGCVAQQEGESLLRRVPELDLVMGPQHANRLEDLLE 119
Score = 56.6 bits (137), Expect = 3e-09
Identities = 21/53 (39%), Positives = 38/53 (71%)
Query: 7 EDSVSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEV 59
+ S++A+V+++ GC+ CTYC+VP RG+E+SR ++I E+ L+ + Y E+
Sbjct: 145 DSSITAWVNVIYGCNERCTYCVVPSVRGKEQSRTPEAIRAEIEELAAQGYKEI 197
>gnl|CDD|237678 PRK14335, PRK14335, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 455
Score = 88.0 bits (218), Expect = 1e-19
Identities = 39/143 (27%), Positives = 70/143 (48%), Gaps = 8/143 (5%)
Query: 56 YFEVFGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTCAIRENAEGKVWDRLRFY 115
+FE +GCQMNV ++ + +L + G++K DV+++ TC++R AE +V+ RL +
Sbjct: 4 FFETYGCQMNVAESASMEQLLLARGWTKAVDAETCDVLIINTCSVRITAETRVFGRLGLF 63
Query: 116 RSMKQIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAGPDSYKDLPRLLALTYSN 175
S+ KK R F + ++GCMAERL + ++ +D V G ++ L + +
Sbjct: 64 SSL----KKKRAFFII--LMGCMAERLHDEIQKEFPRIDYVVGTFAHARLESIFQEIEAK 117
Query: 176 QTAINVLLSLDETYADITPKAVS 198
+ + VS
Sbjct: 118 LKQDD--YRFEFISERYREHPVS 138
Score = 72.2 bits (177), Expect = 2e-14
Identities = 30/63 (47%), Positives = 41/63 (65%)
Query: 5 LNEDSVSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEVFGCQM 64
+E S +F+ IM GC+N C+YCIVP+ RGRE SR + +IL E+ LS+K E+
Sbjct: 147 YSEGSFQSFIPIMNGCNNFCSYCIVPYVRGREISRDLDAILQEIDVLSEKGVREITLLGQ 206
Query: 65 NVN 67
NVN
Sbjct: 207 NVN 209
>gnl|CDD|237674 PRK14326, PRK14326, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 502
Score = 87.4 bits (217), Expect = 2e-19
Identities = 43/150 (28%), Positives = 85/150 (56%), Gaps = 9/150 (6%)
Query: 41 MQSILDEVRALSDKVYFEV--FGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTC 98
+ A + Y +V +GCQMNV+D+E + +L+++GY + ++ADV++ TC
Sbjct: 1 GEGAAPPAAARGARTY-QVRTYGCQMNVHDSERLAGLLEAAGYVRAAEGQDADVVVFNTC 59
Query: 99 AIRENAEGKVWDRLRFYRSMKQIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAG 158
A+RENA+ +++ L +K+ + ++I V GC+A++ + ++L++ +D+V G
Sbjct: 60 AVRENADNRLYGNLGHLAPVKRANPG-----MQIAVGGCLAQKDRDTILKRAPWVDVVFG 114
Query: 159 PDSYKDLPRLLALTYSNQTA-INVLLSLDE 187
+ LP LL N+ A + + SL++
Sbjct: 115 THNIGSLPTLLERARHNKEAQVEIAESLEQ 144
Score = 67.8 bits (166), Expect = 7e-13
Identities = 41/107 (38%), Positives = 54/107 (50%), Gaps = 17/107 (15%)
Query: 7 EDSVSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEVFGCQMNV 66
E + +A+VSI GC+N CT+CIVP RG+E+ R IL EV+AL D+ EV NV
Sbjct: 154 ESAYAAWVSISVGCNNTCTFCIVPSLRGKEKDRRPGDILAEVQALVDEGVLEVTLLGQNV 213
Query: 67 N-------DTEVVWSILKS----SGYSKVN----HPRE--ADVILVM 96
N D +L++ G +V HP E DVI M
Sbjct: 214 NAYGVSFGDRGAFSKLLRACGEIDGLERVRFTSPHPAEFTDDVIEAM 260
>gnl|CDD|172813 PRK14337, PRK14337, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 446
Score = 84.4 bits (209), Expect = 2e-18
Identities = 33/58 (56%), Positives = 42/58 (72%)
Query: 10 VSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEVFGCQMNVN 67
SAFV+IM+GCDN C YCIVP+TRGR++SR ++LDE RAL D+ E+ NVN
Sbjct: 148 ASAFVNIMQGCDNFCAYCIVPYTRGRQKSRSSAAVLDECRALVDRGAREITLLGQNVN 205
Score = 65.9 bits (161), Expect = 4e-12
Identities = 39/130 (30%), Positives = 60/130 (46%), Gaps = 6/130 (4%)
Query: 60 FGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTCAIRENAEGKVWDRLRFYRSMK 119
FGCQMNVND++ + L + G+++ EA V +V TC++R+ E KV+ L R
Sbjct: 11 FGCQMNVNDSDWLARALVARGFTEAPE-EEARVFIVNTCSVRDKPEQKVYSLLGRIRHAT 69
Query: 120 QIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAGPDSYKDLPRLLALTYSNQTAI 179
+ K F + V GC+A+++ + + LV G D P+ L
Sbjct: 70 K--KNPDVF---VAVGGCVAQQIGSGFFSRFPQVRLVFGTDGIAMAPQALERLAEEPDLR 124
Query: 180 NVLLSLDETY 189
LL E Y
Sbjct: 125 LSLLDFSEHY 134
>gnl|CDD|233480 TIGR01579, MiaB-like-C, MiaB-like tRNA modifying enzyme. This
clade of sequences is closely related to MiaB, a
modifier of isopentenylated adenosine-37 of certain
eukaryotic and bacterial tRNAs (see TIGR01574). Sequence
alignments suggest that this equivalog performs the same
chemical transformation as MiaB, perhaps on a different
(or differently modified) tRNA base substrate. This
clade is a member of a subfamily (TIGR00089) and spans
low GC Gram positive bacteria, alpha and epsilon
proteobacteria, Campylobacter, Porphyromonas, Aquifex,
Thermotoga, Chlamydia, Treponema and Fusobacterium
[Protein synthesis, tRNA and rRNA base modification].
Length = 414
Score = 73.6 bits (181), Expect = 8e-15
Identities = 25/53 (47%), Positives = 35/53 (66%)
Query: 7 EDSVSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEV 59
E AF+ + GC+ C+YCI+PF RGR RS PM++IL +V+ L K Y E+
Sbjct: 135 EGHTRAFIKVQDGCNFFCSYCIIPFARGRSRSVPMEAILKQVKILVAKGYKEI 187
Score = 57.8 bits (140), Expect = 1e-09
Identities = 29/109 (26%), Positives = 48/109 (44%), Gaps = 12/109 (11%)
Query: 57 FEVFGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTCAIRENAEGKVWDRLRFYR 116
E GC++N ++E + + L GY V +ADV ++ TC + A+ K
Sbjct: 1 IETLGCRVNQYESESLKNQLIQKGYEVVPDEDKADVYIINTCTVTAKADSK--------- 51
Query: 117 SMKQIHKKHRTFP-LKIGVLGCMAERLKKSLLEKEQALDLVAGPDSYKD 164
+ + I + R P KI V GC A+ K L + + + + KD
Sbjct: 52 ARRAIRRARRQNPTAKIIVTGCYAQSNPKELADLKD--VDLVLGNKEKD 98
>gnl|CDD|184630 PRK14334, PRK14334, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 440
Score = 73.3 bits (180), Expect = 9e-15
Identities = 38/116 (32%), Positives = 66/116 (56%), Gaps = 6/116 (5%)
Query: 54 KVYFEVFGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTCAIRENAEGKVWDRLR 113
K + +GCQMN DT +V S L S G V+ EAD +LV TCA+R GK +++R
Sbjct: 2 KAHIITYGCQMNEYDTHLVESELVSLGAEIVDSVDEADFVLVNTCAVR----GKPVEKVR 57
Query: 114 FYRSMKQIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAGPDSYKDLPRLL 169
+ ++ K+ PL +G++GC+A+ + + ++ +D++ GP + D+ + L
Sbjct: 58 --SLLGELRKEKAQRPLVVGMMGCLAQLEEGQQMARKFGVDVLLGPGALTDIGKAL 111
Score = 67.9 bits (166), Expect = 6e-13
Identities = 29/59 (49%), Positives = 35/59 (59%)
Query: 9 SVSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEVFGCQMNVN 67
+SA ++IMRGC++ CTYCIVP TRG E SR IL E+ L EV NVN
Sbjct: 137 KLSAHLTIMRGCNHHCTYCIVPTTRGPEVSRHPDLILRELELLKAAGVQEVTLLGQNVN 195
>gnl|CDD|184632 PRK14336, PRK14336, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 418
Score = 72.6 bits (178), Expect = 2e-14
Identities = 36/111 (32%), Positives = 59/111 (53%), Gaps = 5/111 (4%)
Query: 54 KVYFEVFGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTCAIRENAEGKVWDRLR 113
Y GCQMN ++E + + + GYS + +A+++LV +C +RE+AE KV +RL
Sbjct: 3 GYYLWTIGCQMNQAESERLGRLFELWGYSLADKAEDAELVLVNSCVVREHAENKVINRLH 62
Query: 114 FYRSMKQIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAGPDSYKD 164
R +K + K LKI + GC+ + + +K +D + GP S D
Sbjct: 63 LLRKLKNKNPK-----LKIALTGCLVGQDISLIRKKFPFVDYIFGPGSMPD 108
Score = 68.0 bits (166), Expect = 5e-13
Identities = 30/58 (51%), Positives = 38/58 (65%)
Query: 10 VSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEVFGCQMNVN 67
VSA V+IM+GCDN CTYC+VP+ RGRE+SR + I EV L + EV NV+
Sbjct: 124 VSANVTIMQGCDNFCTYCVVPYRRGREKSRSIAEIGCEVAELVRRGSREVVLLGQNVD 181
>gnl|CDD|184633 PRK14338, PRK14338, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 459
Score = 70.6 bits (173), Expect = 8e-14
Identities = 31/112 (27%), Positives = 58/112 (51%), Gaps = 9/112 (8%)
Query: 61 GCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTCAIRENAEGKVWDRLRFYRSMKQ 120
GCQMNV+D+E + + L+ GYS P +AD I++ +C++R +AE ++ +L + +K+
Sbjct: 29 GCQMNVSDSERLEAALQGVGYSPAERPEDADFIVLNSCSVRASAEERILGKLGELQRLKR 88
Query: 121 IHKKHRTFPLKIGVLGCMAERLKKSLLEKEQAL-DLVAGPDSYKDLPRLLAL 171
+I + GCM +S+ + + D P + ++AL
Sbjct: 89 QRPD-----TRIVLWGCMVGPNNQSIFAERLPMVDHFVSP---SAVDEVVAL 132
Score = 67.9 bits (166), Expect = 7e-13
Identities = 22/50 (44%), Positives = 35/50 (70%)
Query: 10 VSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEV 59
V+ V I+ GC+ C+YC++P RGRERSRP+ I++EVR ++ + E+
Sbjct: 155 VTVHVPIIYGCNMSCSYCVIPLRRGRERSRPLAEIVEEVRRIAARGAKEI 204
>gnl|CDD|184634 PRK14339, PRK14339, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 420
Score = 68.5 bits (168), Expect = 4e-13
Identities = 27/56 (48%), Positives = 32/56 (57%)
Query: 12 AFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEVFGCQMNVN 67
+ V+I GCD CTYCIVP TRG+E S PM IL E + E+F NVN
Sbjct: 129 SLVNISIGCDKKCTYCIVPHTRGKEISIPMDLILKEAEKAVNNGAKEIFLLGQNVN 184
Score = 53.5 bits (129), Expect = 4e-08
Identities = 29/96 (30%), Positives = 49/96 (51%), Gaps = 8/96 (8%)
Query: 64 MNVNDTEVVWSIL-KSSGYSKVNHPREADVILVMTCAIRENAEGKVWDRLRFYRSMKQIH 122
MNV D+E + + L + Y +EAD+IL+ TC++RE K++ + +
Sbjct: 1 MNVRDSEHMIAELSQKEDYKLTQDIKEADLILINTCSVREKPVHKLFSEIGQF------- 53
Query: 123 KKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAG 158
K + KIGV GC A L + ++++ +D V G
Sbjct: 54 NKIKKEGAKIGVCGCTASHLGEEIIKRAPYVDFVLG 89
>gnl|CDD|214792 smart00729, Elp3, Elongator protein 3, MiaB family, Radical SAM.
This superfamily contains MoaA, NifB, PqqE,
coproporphyrinogen III oxidase, biotin synthase and
MiaB families, and includes a representative in the
eukaryotic elongator subunit, Elp-3. Some members of
the family are methyltransferases.
Length = 216
Score = 64.7 bits (158), Expect = 2e-12
Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 10 VSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDKVYFEVF-------GC 62
A I RGC CT+C P RG+ RSR +++++ E+ L++K E G
Sbjct: 1 PLALYIITRGCPRRCTFCSFPSLRGKLRSRYLEALVREIELLAEKGEKEGLVGTVFIGGG 60
Query: 63 QMNVNDTEVVWSILK 77
+ E + +L+
Sbjct: 61 TPTLLSPEQLEELLE 75
>gnl|CDD|233479 TIGR01578, MiaB-like-B, MiaB-like tRNA modifying enzyme,
archaeal-type. This clade of sequences is closely
related to MiaB, a modifier of isopentenylated
adenosine-37 of certain eukaryotic and bacterial tRNAs
(see TIGR01574). Sequence alignments suggest that this
equivalog performs the same chemical transformation as
MiaB, perhaps on a different (or differently modified)
tRNA base substrate. This clade is a member of a
subfamily (TIGR00089) and spans the archaea and
eukaryotes. The only archaeal miaB-like genes are in
this clade, while eukaryotes have sequences described by
This model as well as ones falling within the scope of
the MiaB equivalog model [Protein synthesis, tRNA and
rRNA base modification].
Length = 420
Score = 60.2 bits (146), Expect = 2e-10
Identities = 32/115 (27%), Positives = 57/115 (49%), Gaps = 14/115 (12%)
Query: 54 KVYFEVFGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTCAIRENAEGKVWDRLR 113
KVY E +GC +N D+E++ + L + G+ VN+ EAD+ ++ TC ++ E + R+
Sbjct: 1 KVYVETYGCTLNNGDSEIMKNSLAAYGHELVNNAEEADLAILNTCTVKNKTEDTMLYRI- 59
Query: 114 FYRSMKQIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAGPDSYKDLPRL 168
S+ + K + V GCM + K+S+ + VA + + RL
Sbjct: 60 --ESLMRNGK-------HVVVAGCMPQAQKESVYDN----GSVASVLGVQAIDRL 101
Score = 45.2 bits (107), Expect = 2e-05
Identities = 14/50 (28%), Positives = 26/50 (52%)
Query: 2 DVRLNEDSVSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRAL 51
+ ++ + + I +GC C+YCI RG+ S P + I+++ R L
Sbjct: 125 LPKPRKNPLIEIIPINQGCLGNCSYCITKHARGKLASYPPEKIVEKARQL 174
>gnl|CDD|233279 TIGR01125, TIGR01125, ribosomal protein S12 methylthiotransferase
RimO. Members of this protein are the
methylthiotransferase RimO, which modifies a conserved
Asp residue in ribosomal protein S12. This clade of
radical SAM family proteins is closely related to the
tRNA modification bifunctional enzyme MiaB (see
TIGR01574), and it catalyzes the same two types of
reactions: a radical-mechanism sulfur insertion, and a
methylation of the inserted sulfur. This clade spans
alpha and gamma proteobacteria, cyano bacteria,
Deinococcus, Porphyromonas, Aquifex, Helicobacter,
Campylobacter, Thermotoga, Chlamydia, Streptococcus
coelicolor and Clostridium, but does not include most
other gram positive bacteria, archaea or eukaryotes
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 430
Score = 59.0 bits (143), Expect = 6e-10
Identities = 30/113 (26%), Positives = 54/113 (47%), Gaps = 12/113 (10%)
Query: 54 KVYFEVFGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTCAIRENAEGKVWDRL- 112
K+ F GC N+ D+EV+ IL+ +GY + +AD ++V TC E+A + D +
Sbjct: 1 KIGFISLGCPKNLVDSEVMLGILREAGYEVTPNYEDADYVIVNTCGFIEDARQESIDTIG 60
Query: 113 RFYRSMKQIHKKHRTFPLKIGVLGCMAERLKKSLLEKEQALDLVAGPDSYKDL 165
+ K K+ V GC+ +R K+ L E+ + + G +++
Sbjct: 61 ELADAGK-----------KVIVTGCLVQRYKEELKEEIPEVHAITGSGDVENI 102
Score = 57.4 bits (139), Expect = 2e-09
Identities = 18/43 (41%), Positives = 28/43 (65%)
Query: 12 AFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDK 54
A++ + GC+ C +CI+P RG+ RSRP++ IL E L D+
Sbjct: 137 AYLKVAEGCNRRCAFCIIPSIRGKLRSRPIEEILKEAERLVDQ 179
>gnl|CDD|237838 PRK14862, rimO, ribosomal protein S12 methylthiotransferase;
Provisional.
Length = 440
Score = 51.0 bits (123), Expect = 2e-07
Identities = 17/40 (42%), Positives = 25/40 (62%)
Query: 12 AFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRAL 51
A++ I GC++ CT+CI+P RG SRP+ +L E L
Sbjct: 141 AYLKISEGCNHRCTFCIIPSMRGDLVSRPIGDVLREAERL 180
Score = 30.6 bits (70), Expect = 0.87
Identities = 20/69 (28%), Positives = 30/69 (43%), Gaps = 14/69 (20%)
Query: 54 KVYFEVFGCQMNVNDTEVVWSILKSSGYSKVNHPREADVILVMTC------------AIR 101
K+ F GC + D+E + + L++ GY AD+++V TC AI
Sbjct: 9 KIGFVSLGCPKALVDSERILTQLRAEGYEISPSYDGADLVIVNTCGFIDSAVQESLEAIG 68
Query: 102 E--NAEGKV 108
E GKV
Sbjct: 69 EALAENGKV 77
>gnl|CDD|234441 TIGR04014, B12_SAM_MJ_0865, B12-binding domain/radical SAM domain
protein, MJ_0865 family. Members of this family have
both a B12 binding homology domain (pfam02310) and a
radical SAM domain (pfam04055), and occur only once per
genome. This protein occurs so far only in methanogenic
archaea. Some species with members of this family have a
related protein with similar domain architecture (see
TIGR04013) [Unknown function, Enzymes of unknown
specificity].
Length = 434
Score = 45.5 bits (108), Expect = 2e-05
Identities = 19/43 (44%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 11 SAFVSIMRGCDNMCTYCIVPFTRGRE-RSRPMQSILDEVRALS 52
+ ++ RGC CT+C VP GR RSRP++ I++EVR L
Sbjct: 160 NVYIETHRGCPGNCTFCQVPRFFGRRIRSRPLEDIVEEVRELK 202
>gnl|CDD|217866 pfam04055, Radical_SAM, Radical SAM superfamily. Radical SAM
proteins catalyze diverse reactions, including unusual
methylations, isomerisation, sulphur insertion, ring
formation, anaerobic oxidation and protein radical
formation.
Length = 165
Score = 42.9 bits (101), Expect = 4e-05
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 14 VSIMRGCDNMCTYCIVPFT--RGRERSRPMQSILDEVRALSDKVYFEVF 60
+ + RGC+ CTYC P RG+ R + IL+E + L+ V
Sbjct: 1 IIVTRGCNLRCTYCAFPSIRARGKGRELSPEEILEEAKELARLGVEVVI 49
>gnl|CDD|234928 PRK01254, PRK01254, hypothetical protein; Provisional.
Length = 707
Score = 41.2 bits (97), Expect = 4e-04
Identities = 19/43 (44%), Positives = 29/43 (67%), Gaps = 1/43 (2%)
Query: 14 VSIMRGCDNMCTYCIVPFTRGR-ERSRPMQSILDEVRALSDKV 55
V+IMRGC C++C + GR +SR +SI++E+ A+ DKV
Sbjct: 376 VNIMRGCFGGCSFCSITEHEGRIIQSRSEESIINEIEAIRDKV 418
>gnl|CDD|223963 COG1032, COG1032, Fe-S oxidoreductase [Energy production and
conversion].
Length = 490
Score = 41.1 bits (96), Expect = 5e-04
Identities = 10/49 (20%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 6 NEDSVSAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDK 54
++ + V RGC C +C + + R R + +++E++ L ++
Sbjct: 194 AGENRAFSVETSRGCPRGCRFCSIT-KHFKYRRRRPERVVEEIKELIEE 241
>gnl|CDD|213908 TIGR04295, B12_rSAM_oligo, B12-binding domain/radical SAM domain
protein, rhizo-twelve system. A variety of bacteria,
including multiple species of Bradyrhizobium,
Mesorhizobium, and Methylobacterium, have a typically
twelve-gene cassette (hence the designation
rhizo-twelve) for the biosynthesis of some unknown
oligosaccaride. This family is a B12-binding
domain/radical SAM domain protein found in roughly have
of these cassettes, but nowhere else.
Length = 422
Score = 38.2 bits (89), Expect = 0.003
Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 6/56 (10%)
Query: 11 SAFVSIMRGCDNMCTYCIVPFTRGRERSRPMQSILDEVRALSDK----VYF--EVF 60
A V RGC CT+C R + R RP+ +IL+E+ AL + VYF E+F
Sbjct: 200 GAEVETSRGCPYHCTFCAKDNFRNKYRKRPLATILEEIDALIAQGVRYVYFIDEIF 255
>gnl|CDD|234390 TIGR03904, SAM_YgiQ, uncharacterized radical SAM protein YgiQ.
Members of this family are fairly widespread
uncharacterized radical SAM family proteins, many of
which are designated YgiQ [Unknown function, Enzymes of
unknown specificity].
Length = 559
Score = 37.8 bits (89), Expect = 0.005
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 14 VSIMRGCDNMCTYCIVPFTRGRE-RSRPMQSILDEVRALSDK 54
++ RGC C++C + F +GR +SR +SIL E + L+
Sbjct: 298 ITSHRGCFGGCSFCAITFHQGRIIQSRSEESILREAKRLTKM 339
>gnl|CDD|132511 TIGR03471, HpnJ, hopanoid biosynthesis associated radical SAM
protein HpnJ. The sequences represented by this model
are members of the radical SAM superfamily of enzymes
(pfam04055). These enzymes utilize an iron-sulfur redox
cluster and S-adenosylmethionine to carry out diverse
radical mediated reactions. The member of this clade
from Acidithiobacillus ferrooxidans ATCC 23270
(AFE_0975) is found in the same locus as squalene-hopene
cyclase (SHC, TIGR01507) and other genes associated with
the biosynthesis of hopanoid natural products.
Similarly, in Ralstonia eutropha JMP134 (Reut_B4901)
this gene is adjacent to HpnAB, IspH and HpnH
(TIGR03470), although SHC itself is elsewhere in the
genome. Notably, this gene (here named HpnJ) and three
others form a conserved set (HpnIJKL) which occur in a
subset of all genomes containing the SHC enzyme. This
relationship was discerned using the method of partial
phylogenetic profiling. This group includes Zymomonas
mobilis, the organism where the initial hopanoid
biosynthesis locus was described consisting of the genes
HpnA-E and SHC (HpnF). Continuing past SHC are found a
phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and
another radical SAM enzyme (ZMO0874), HpnH. Although
discontinuous in Z. mobilis, we continue the gene symbol
sequence with HpnIJKL. One of the well-described
hopanoid intermediates is bacteriohopanetetrol. In the
conversion from hopene several reactions must occur in
the side chain for which a radical mechanism might be
reasonable. These include the four (presumably
anaerobic) hydroxylations and a methyl shift.
Length = 472
Score = 35.5 bits (82), Expect = 0.030
Identities = 16/41 (39%), Positives = 28/41 (68%), Gaps = 4/41 (9%)
Query: 13 FVSIM--RGCDNMCTYCIVPFTRG--RERSRPMQSILDEVR 49
++S+ RGC + CT+C+ P T G R R+R +S+++EV+
Sbjct: 197 YISLYTGRGCPSKCTFCLWPQTVGGHRYRTRSAESVIEEVK 237
>gnl|CDD|223962 COG1031, COG1031, Uncharacterized Fe-S oxidoreductase [Energy
production and conversion].
Length = 560
Score = 34.3 bits (79), Expect = 0.066
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 5/38 (13%)
Query: 18 RGC----DNMCTYCIVPFTRGRERSRPMQSILDEVRAL 51
RGC C++C P RGR RP + +++EV+AL
Sbjct: 191 RGCPRRVSGGCSFCTEPV-RGRPEFRPPEDVVEEVKAL 227
>gnl|CDD|234440 TIGR04013, B12_SAM_MJ_1487, B12-binding domain/radical SAM domain
protein, MJ_1487 family. Members of this family have
both a B12 binding homology domain (pfam02310) and a
radical SAM domain (pfam04055), and occur only once per
genome. Some species with members of this family have a
related protein with similar domain architecture. This
protein is occurs largely in archaeal methanogens but
also in a few bacteria, including Thermotoga maritima
and Myxococcus xanthus [Unknown function, Enzymes of
unknown specificity].
Length = 382
Score = 33.8 bits (78), Expect = 0.083
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 16 IMRGCDNMCTYCIVPFTRGRE-RSRPMQSILDEVRALSDK 54
I RGC C YC P GR R R ++SI+ + + D+
Sbjct: 156 ITRGCPFGCAYCQTPRIFGRRMRHRSIESIVRYAKRMVDR 195
>gnl|CDD|239272 cd02974, AhpF_NTD_N, Alkyl hydroperoxide reductase F subunit
(AhpF) N-terminal domain (NTD) family, N-terminal
TRX-fold subdomain; AhpF is a homodimeric flavoenzyme
which catalyzes the NADH-dependent reduction of the
peroxiredoxin AhpC, which in turn catalyzes the
reduction of hydrogen peroxide and organic
hydroperoxides. AhpF contains an NTD forming two
contiguous TRX-fold subdomain similar to Pyrococcus
furiosus protein disulfide oxidoreductase (PfPDO). It
also contains a catalytic core similar to TRX reductase
containing FAD and NADH binding domains with an active
site disulfide. The proposed mechanism of action of
AhpF is similar to a TRX/TRX reductase system. The flow
of reducing equivalents goes from NADH -> catalytic
core of AhpF -> NTD of AhpF -> AhpC -> peroxide
substrates. The N-terminal TRX-fold subdomain of AhpF
NTD is redox inactive, but is proposed to contain an
important residue that aids in the catalytic function
of the redox-active CXXC motif contained in the
C-terminal TRX-fold subdomain.
Length = 94
Score = 30.2 bits (69), Expect = 0.32
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 28 IVPFTRGRERSRPMQSILDEVRALSDKVYFEVFG 61
+V E+S + +L+E+ +LSDK+ E
Sbjct: 23 LVASLDDSEKSAELLELLEEIASLSDKITLEEDN 56
>gnl|CDD|234874 PRK00955, PRK00955, hypothetical protein; Provisional.
Length = 620
Score = 32.2 bits (74), Expect = 0.34
Identities = 15/39 (38%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 14 VSIMRGCDNMCTYCIVPFTRGRE-RSRPMQSILDEVRAL 51
++ RGC C++C + F +GR +SR +SIL E + L
Sbjct: 296 ITSHRGCFGGCSFCAITFHQGRFIQSRSQESILREAKEL 334
>gnl|CDD|99938 cd05506, Bromo_plant1, Bromodomain, uncharacterized subfamily
specific to plants. Might function as a global
transcription factor. Bromodomains are 110 amino acid
long domains, that are found in many chromatin
associated proteins. Bromodomains can interact
specifically with acetylated lysine.
Length = 99
Score = 29.6 bits (67), Expect = 0.50
Identities = 21/62 (33%), Positives = 26/62 (41%), Gaps = 8/62 (12%)
Query: 47 EVRALSDKVYFEVFGCQMNVNDTEVVWSILKSSGYSKVNHPRE--ADVILVMTCAIRENA 104
+V AL YF++ M D V L+ YS P E ADV L A+R N
Sbjct: 26 DVVALGLPDYFDIIKKPM---DLGTVKKKLEKGEYSS---PEEFAADVRLTFANAMRYNP 79
Query: 105 EG 106
G
Sbjct: 80 PG 81
>gnl|CDD|225799 COG3260, COG3260, Ni,Fe-hydrogenase III small subunit [Energy
production and conversion].
Length = 148
Score = 30.0 bits (68), Expect = 0.67
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 84 VNHPREADVILVMTCAIRENAE 105
VN PR AD++LV R+ E
Sbjct: 44 VNSPRHADILLVTGAVTRQMRE 65
>gnl|CDD|237942 PRK15317, PRK15317, alkyl hydroperoxide reductase subunit F;
Provisional.
Length = 517
Score = 28.2 bits (64), Expect = 5.9
Identities = 9/23 (39%), Positives = 17/23 (73%)
Query: 36 ERSRPMQSILDEVRALSDKVYFE 58
E+S ++ +L+E+ +LSDK+ E
Sbjct: 31 EKSAELKELLEEIASLSDKITVE 53
>gnl|CDD|236813 PRK10993, PRK10993, outer membrane protease; Reviewed.
Length = 314
Score = 28.1 bits (63), Expect = 6.2
Identities = 18/72 (25%), Positives = 24/72 (33%), Gaps = 15/72 (20%)
Query: 186 DETYA-DIT-------PKAVSTDGRRSIYVDGRWSIYVDGRWRR----KLGQQMVD---G 230
DE Y ++T S YV +YV+G + R K Q+ D G
Sbjct: 229 DEHYLRNLTFRDKFKNSPYYSASINAGYYVTPNAKLYVEGAYNRYFEGKGDTQIYDHATG 288
Query: 231 RSMSMDDGGGAS 242
S D G
Sbjct: 289 TSSYFKDAAGIE 300
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
0.322 0.136 0.409
Gapped
Lambda K H
0.267 0.0684 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,343,102
Number of extensions: 1343934
Number of successful extensions: 1191
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1159
Number of HSP's successfully gapped: 73
Length of query: 285
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 189
Effective length of database: 6,679,618
Effective search space: 1262447802
Effective search space used: 1262447802
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: 58 (26.2 bits)