RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 046012
(244 letters)
>gnl|CDD|223222 COG0144, Sun, tRNA and rRNA cytosine-C5-methylases [Translation,
ribosomal structure and biogenesis].
Length = 355
Score = 65.5 bits (160), Expect = 2e-12
Identities = 30/120 (25%), Positives = 52/120 (43%), Gaps = 7/120 (5%)
Query: 126 DAEKFLMLHKGAIQSALARLLVRNKVKSIEDLMALYQTPDVPKPRYVRVNTLKMDVDSAV 185
F H + L L ++ A+ P PR +RVNTLK DV+ +
Sbjct: 46 LRPAFRYSHPEWLVEKLPDALG------EDEAEAIAAALLRPPPRSLRVNTLKADVEELL 99
Query: 186 LELGKQ-FVVQKDDLVPDLLILPPGCDLHDHPLIVNGCVFLQGKASSMVAAALAPKPGWK 244
L + + +K ++ ++L + + P G +++Q +AS + A L PKPG +
Sbjct: 100 EALEEAGVLDEKPWVLDEVLRIEASGPIGRLPEFAEGLIYVQDEASQLPALVLDPKPGER 159
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 54.4 bits (132), Expect = 1e-08
Identities = 25/78 (32%), Positives = 46/78 (58%), Gaps = 2/78 (2%)
Query: 166 VPKPRYVRVNTLKMDVDSAVLELGKQ-FVVQKDDLVPDLLILPPGCDLHDHPLIVNGCVF 224
P +RVNTLK+ V+ + +L ++ + V++ L P+ L++ G ++ L +G +
Sbjct: 175 EPPKASIRVNTLKISVEELIEKLEEEGYEVEESLLSPEALVIEKG-NIAGTDLFKDGLIT 233
Query: 225 LQGKASSMVAAALAPKPG 242
+Q ++S +VA AL PK G
Sbjct: 234 IQDESSMLVAPALDPKGG 251
>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 = 39.8 bits (93), Expect = 9e-04
Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 1/77 (1%)
Query: 167 PKPRYVRVNTLKMDVDSAVLELGKQFV-VQKDDLVPDLLILPPGCDLHDHPLIVNGCVFL 225
P ++R+N K D + L + + DL PD + L +H P G V +
Sbjct: 163 RPPMWLRINRTKHSRDEWLALLAEAGMKGFPHDLAPDAVRLETPAAVHALPGFEEGWVTV 222
Query: 226 QGKASSMVAAALAPKPG 242
Q ++ VA LAP+
Sbjct: 223 QDASAQWVATWLAPQNE 239
>gnl|CDD|201649 pfam01189, Nol1_Nop2_Fmu, NOL1/NOP2/sun family.
Length = 277
Score = 30.0 bits (68), Expect = 1.1
Identities = 19/79 (24%), Positives = 28/79 (35%), Gaps = 2/79 (2%)
Query: 166 VPKPRYVRVNTLKMDVDSAVLELGKQFVVQK--DDLVPDLLILPPGCDLHDHPLIVNGCV 223
P +R N LK S + L V + L + + P NG V
Sbjct: 7 CSPPGTLRKNVLKTKRWSLLQALELAGVQLEPLGRYPHALPVGDLPYSIGSLPPFENGAV 66
Query: 224 FLQGKASSMVAAALAPKPG 242
+Q +S + A AL P+
Sbjct: 67 TVQDASSQLDAIALNPQED 85
>gnl|CDD|183769 PRK12819, flgG, flagellar basal body rod protein FlgG; Reviewed.
Length = 257
Score = 29.5 bits (66), Expect = 1.3
Identities = 14/56 (25%), Positives = 19/56 (33%), Gaps = 5/56 (8%)
Query: 1 MARTKTAATAPSGASAKTSRNGRLSNAERSAYFARRE-----AAKVLRLVLRGDAR 51
M P GA +G L +A AR + A + RLV R +
Sbjct: 135 MGENNERIRIPEGAKVAVQADGTLYDAVTQNNIARLQTKTVSAEQNDRLVQRENKS 190
>gnl|CDD|240419 PTZ00440, PTZ00440, reticulocyte binding protein 2-like protein;
Provisional.
Length = 2722
Score = 28.6 bits (64), Expect = 3.3
Identities = 29/130 (22%), Positives = 59/130 (45%), Gaps = 19/130 (14%)
Query: 82 KHLSIIKQVLDSASILNSKWKRQEELVYILTYDILFG---QEISLVGDAEKFL-----ML 133
KH + K L+ S+L+S ++E+++ L ++ LFG ++I + D+E F+ ++
Sbjct: 351 KHYASFKFSLEMLSMLDSLLIKKEKILNNL-FNKLFGDLKEKIETLLDSEYFISKYTNII 409
Query: 134 HKGAIQSALARLLVRNKVKSIEDLMALYQTPDVPKPRYVRVNTLKMDVDSAVLELGKQFV 193
A +++ + I D ALY + + +K D + EL K+ +
Sbjct: 410 SLSEHTLKAAEDVLKENSQKIADY-ALYSN--------LEIIEIKKKYDEKINEL-KKSI 459
Query: 194 VQKDDLVPDL 203
Q L+ +
Sbjct: 460 NQLKTLISIM 469
>gnl|CDD|132263 TIGR03219, salicylate_mono, salicylate 1-monooxygenase. Members of
this protein family are salicylate 1-monooxygenase, also
called salicylate hydroxylase. This enzyme converts
salicylate to catechol, which is a common intermediate
in the degradation of a number of aromatic compounds
(phenol, toluene, benzoate, etc.). The gene for this
protein may occur in catechol degradation genes, such as
those of the meta-cleavage pathway.
Length = 414
Score = 27.9 bits (62), Expect = 4.7
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 11/63 (17%)
Query: 121 ISLVGDAEKFLMLHKGA-----IQSA--LARLL--VRNKVKSIEDLMALYQTPDVPKPRY 171
++L+GDA ++ H+GA ++ A LARLL + + L+ Y DV +PR
Sbjct: 302 VALIGDAAHAMLPHQGAGAGQGLEDAYFLARLLGDTELEAGDLPALLEAYD--DVRRPRA 359
Query: 172 VRV 174
RV
Sbjct: 360 CRV 362
>gnl|CDD|189017 cd09610, M3B_PepF_5, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 472
Score = 27.6 bits (62), Expect = 6.9
Identities = 15/65 (23%), Positives = 24/65 (36%), Gaps = 7/65 (10%)
Query: 43 RLVLRGDARRRAVGSIKSLVYSPSVKNKKATFALVCQTLKHLSIIKQVLDSASILNS--K 100
L D + + I +L+ SP + +K + + LK S I N+ K
Sbjct: 72 SLRFEFDGEKLTLEEILALLRSPDREVRKKAAKALTKGLKKNSRT-----LTLIYNTVVK 126
Query: 101 WKRQE 105
K E
Sbjct: 127 DKDIE 131
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 27.6 bits (62), Expect = 8.3
Identities = 23/126 (18%), Positives = 44/126 (34%), Gaps = 17/126 (13%)
Query: 56 GSIKSLVYSPSVKNKKATFALVCQTLKHLSIIKQVLDSASILNSKWKRQEELVYILTYDI 115
G K+L+ + + K LV L+ + + L + ++ + ++
Sbjct: 19 GGAKALLIAALAEEKPNPVLLVTADLQEADRLAEDLRFFP--------DQPVLLLPDWET 70
Query: 116 LFGQEISLVGDAEKFLMLHKGAIQSALARLLVRNKVKSIEDLMALYQTPDVPKPRYVRVN 175
L S D + AL RL K + + AL +P P ++ N
Sbjct: 71 LPYDRFSPSQDI-------VSSRLEALRRLAQGKKGIVVVPVNAL--LQKLPPPDFLEEN 121
Query: 176 TLKMDV 181
+L + V
Sbjct: 122 SLTLKV 127
>gnl|CDD|188481 TIGR03966, actino_HemFlav, heme/flavin dehydrogenase, mycofactocin
system. Members of this protein family possess an
N-terminal heme-binding domain and C-terminal
flavodehydrogenase domain, and share homology to yeast
flavocytochrome b2, to E. coli L-lactate dehydrogenase
[cytochrome], to (S)-mandelate dehydrogenase, etc. This
enzyme appears only in the context of the mycofactocin
system. Interestingly, it is absent from the four
species detected so far with mycofactocin but without an
F420 biosynthesis system.
Length = 385
Score = 27.0 bits (60), Expect = 9.9
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 3/33 (9%)
Query: 177 LKMDVDSAVLELGKQFVVQKDDLVPDLLILPPG 209
L+ +DSA+L LGK V +L + L++P G
Sbjct: 353 LRQGIDSALLGLGKASV---HELSREDLVIPEG 382
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
0.320 0.133 0.377
Gapped
Lambda K H
0.267 0.0779 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,144,642
Number of extensions: 1158274
Number of successful extensions: 1031
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1029
Number of HSP's successfully gapped: 21
Length of query: 244
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 150
Effective length of database: 6,768,326
Effective search space: 1015248900
Effective search space used: 1015248900
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 (21.8 bits)
S2: 58 (26.0 bits)