RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 023579
(280 letters)
>gnl|CDD|223248 COG0170, SEC59, Dolichol kinase [Lipid metabolism].
Length = 216
Score = 78.6 bits (194), Expect = 2e-17
Identities = 41/135 (30%), Positives = 67/135 (49%), Gaps = 12/135 (8%)
Query: 142 KELLRGPLYYVLMLILSALVFWRDSPVGVISLSMMCGGDGIADVIGRRFGSMKIFYNEKK 201
L G +Y++ +L++L+F V + + ++ GDG+A +IG+R+G K K
Sbjct: 91 GPGLGGIIYFIGGGLLASLLF--PIEVAIAGILVLALGDGLASIIGKRYGRHKRILGNGK 148
Query: 202 SWAGSISMFVFGFLVSTGMLYFYSILGYYQLDWIETLQRVALVSLVATVVESLPITEVVD 261
S GS++ F+ FLV + GY V V AT +E LP+ D
Sbjct: 149 SLEGSLAFFIASFLVL------LVLYGYLGAFVGAIGALVLEVGATATSLELLPL----D 198
Query: 262 DNISVPLASMVAAYL 276
DN+++PL + + AYL
Sbjct: 199 DNLTIPLFAALLAYL 213
>gnl|CDD|216329 pfam01148, CTP_transf_1, Cytidylyltransferase family. The members
of this family are integral membrane protein
cytidylyltransferases. The family includes phosphatidate
cytidylyltransferase EC:2.7.7.41 as well as Sec59 from
yeast. Sec59 is a dolichol kinase EC:2.7.1.108.
Length = 259
Score = 43.1 bits (102), Expect = 6e-05
Identities = 30/152 (19%), Positives = 50/152 (32%), Gaps = 21/152 (13%)
Query: 148 PLYYVLMLILSALVFWRDSPVGVISLSMMC--GGDGIADVIGRRFGSMKIF--YNEKKSW 203
PL+YV + + L+ + L ++ D A +G+ FG K+ + K+W
Sbjct: 109 PLFYVGLFLSLLLITNPFFGLLWALLLILVVWASDIGAYFVGKAFGKHKLAPKISPNKTW 168
Query: 204 AGSISMFVFGFLVST-GMLYFYSILGYYQLDWIETLQRVALVSLVATVVES--------- 253
G + FV LV L + L +LV +VES
Sbjct: 169 EGFLGGFVAAVLVGLLFSLLLGPYPSPLHALLLGLL--ASLVGQFGDLVESGFKRDFGIK 226
Query: 254 -----LPITEVVDDNISVPLASMVAAYLSFGY 280
+P + D + L + Y
Sbjct: 227 DSGKLIPGHGGILDRLDSLLFAAPIFYAFLYI 258
>gnl|CDD|223648 COG0575, CdsA, CDP-diglyceride synthetase [Lipid metabolism].
Length = 265
Score = 34.6 bits (80), Expect = 0.039
Identities = 30/116 (25%), Positives = 46/116 (39%), Gaps = 9/116 (7%)
Query: 141 PKELLRGPLYYVLMLILSALVFWRDSPVGVI-SLSMMCG---GDGIADVIGRRFGSMKIF 196
L G LY + L+ G+I L + G GD A +GRRFG K+
Sbjct: 104 SLFKLFGLLYVGVGLLALLPFRLGVLYSGLILLLLLFLGVWAGDIGAYFVGRRFGKHKLA 163
Query: 197 --YNEKKSWAGSISMFVFGFLVSTGMLYFYSILGYYQLDWIETLQRVALVSLVATV 250
+ KK+W G I + LV+ + +L L+ L L+ L + +
Sbjct: 164 PKISPKKTWEGFIGGALGAVLVA---VLVIFLLSSLILNIWTLLILGLLLVLTSQL 216
>gnl|CDD|189762 pfam00901, Orbi_VP5, Orbivirus outer capsid protein VP5.
cryoelectron microscopy indicates that VP5 is a trimer
implying that there are 360 copies of VP5 per virion.
Length = 507
Score = 30.8 bits (70), Expect = 0.82
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 11/73 (15%)
Query: 90 QRKLIQQNSTSTEARYFAALVPLVNCLRLVINGLSLVKDDGLIKSVTREGNPKELLRGPL 149
+R+L Q S + Y ++ ++ +L N +V D L +LRGPL
Sbjct: 441 KRRL--QRSRGSHPIYLGSMHYDISYAQLKRNAQRIVYDPEL---------QMHILRGPL 489
Query: 150 YYVLMLILSALVF 162
++ IL+AL
Sbjct: 490 HFQRRAILNALKH 502
>gnl|CDD|233788 TIGR02224, recomb_XerC, tyrosine recombinase XerC. The phage
integrase family describes a number of recombinases with
tyrosine active sites that transiently bind covalently
to DNA. Many are associated with mobile DNA elements,
including phage, transposons, and phase variation loci.
This model represents XerC, one of two closely related
chromosomal proteins along with XerD (TIGR02225). XerC
and XerD are site-specific recombinases which help
resolve chromosome dimers to monomers for cell division
after DNA replication. In species with a large
chromosome and homologs of XerC on other replicons, the
chomosomal copy was preferred for building this model.
This model does not detect all XerC, as some apparent
XerC examples score in the gray zone between trusted
(450) and noise (410) cutoffs, along with some XerD
examples. XerC and XerD interact with cell division
protein FtsK [DNA metabolism, DNA replication,
recombination, and repair].
Length = 295
Score = 29.5 bits (67), Expect = 2.0
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 10/48 (20%)
Query: 27 PISPRVFRGSMSVWPARVSLD----PHTLRFRVSAAARVGHLLHDAGA 70
++PR + + A+ L PH LR S A HLL + GA
Sbjct: 213 RLTPRGVQYRLQQLRAKAGLPKHVHPHALRH--SFA---THLL-NNGA 254
>gnl|CDD|220620 pfam10183, ESSS, ESSS subunit of NADH:ubiquinone oxidoreductase
(complex I). This subunit is part of the mitochondrial
NADH:ubiquinone oxidoreductase (complex I). It carries
mitochondrial import sequences.
Length = 101
Score = 27.4 bits (61), Expect = 3.1
Identities = 14/63 (22%), Positives = 20/63 (31%)
Query: 162 FWRDSPVGVISLSMMCGGDGIADVIGRRFGSMKIFYNEKKSWAGSISMFVFGFLVSTGML 221
S G + G + GR F EK+ W F FGF ++ +L
Sbjct: 14 EGGGSSSGGAARRASAGHEEHERPNGRLFNKNPPPPGEKRKWEDWELPFYFGFFLTLVIL 73
Query: 222 YFY 224
Sbjct: 74 GVG 76
>gnl|CDD|222190 pfam13517, VCBS, Family description. This domain of about 100
residues is found in multiple (up to 35) copies in long
proteins from several species of Vibrio, Colwellia,
Bradyrhizobium, and Shewanella (hence the name VCBS) and
in smaller copy numbers in proteins from several other
bacteria. The large protein size and repeat copy
numbers, species distribution, and suggested activities
of several member proteins suggests a role for this
domain in adhesion (TIGR).
Length = 61
Score = 25.7 bits (57), Expect = 6.1
Identities = 7/35 (20%), Positives = 16/35 (45%)
Query: 179 GDGIADVIGRRFGSMKIFYNEKKSWAGSISMFVFG 213
GDG D++ G ++++ N ++ + G
Sbjct: 4 GDGRLDLVVASDGGVRLYLNNGDGTFTFVTSTLLG 38
>gnl|CDD|239649 cd03677, MM_CoA_mutase_beta, Coenzyme B12-dependent-methylmalonyl
coenzyme A (CoA) mutase (MCM) family, Beta subunit-like
subfamily; contains bacterial proteins similar to the
beta subunit of MCMs from Propionbacterium shermanni and
Streptomyces cinnamonensis, which are alpha/beta
heterodimers. For P. shermanni MCM, it is known that
only the alpha subunit binds coenzyme B12 and
substrates. The role of the beta subunit is unclear. MCM
catalyzes the isomerization of methylmalonyl-CoA to
succinyl-CoA. The reaction proceeds via radical
intermediates beginning with a substrate-induced
homolytic cleavage of the Co-C bond of coenzyme B12 to
produce cob(II)alamin and the deoxyadenosyl radical. MCM
plays an important role in the conversion of
propionyl-CoA to succinyl-CoA during the degradation of
propionate for the Krebs cycle. Methylobacterium
extorquens MCM participates in the glyoxylate
regeneration pathway. In M. extorquens, MCM forms a
complex with MeaB; MeaB may protect MCM from
irreversible inactivation. In some bacteria, MCM is
involved in the reverse metabolic reaction, the
rearrangement of succinyl-CoA to methylmalonyl-CoA.
Examples include P. shermanni MCM during propionic acid
fermentation and Streptomyces MCM in polyketide
biosynthesis.
Length = 424
Score = 27.6 bits (62), Expect = 8.6
Identities = 14/52 (26%), Positives = 17/52 (32%), Gaps = 8/52 (15%)
Query: 27 PISPRVFRGSMSVWPARVSLDP-HTLRFRVSAAARV----GHLLHDAGATAA 73
P+ GS L L R + R H+AGATAA
Sbjct: 150 PLGALARTGS---LFLEPDLARLAELAARSAPGLRAITVDAVPYHNAGATAA 198
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
0.325 0.138 0.408
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,356,279
Number of extensions: 1403371
Number of successful extensions: 2007
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1997
Number of HSP's successfully gapped: 63
Length of query: 280
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 184
Effective length of database: 6,679,618
Effective search space: 1229049712
Effective search space used: 1229049712
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.2 bits)