RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9998
(288 letters)
>gnl|CDD|146336 pfam03643, Vps26, Vacuolar protein sorting-associated protein 26.
Vacuolar protein sorting-associated protein (Vps) 26 is
one of around 50 proteins involved in protein
trafficking. In particular, Vps26 assembles into a
retromer complex with at least four other proteins Vps5,
Vps17, Vps29 and Vps35. This family also contains Down
syndrome critical region 3/A.
Length = 275
Score = 273 bits (700), Expect = 6e-92
Identities = 141/277 (50%), Positives = 174/277 (62%), Gaps = 65/277 (23%)
Query: 6 FGQSADIEIKLDGTDTRKLADIKSDDGKKERFYLYYDGESVTGQVNIVLKKHGSKLEHQG 65
FG DIEI LD +TRK ++K++DGKKE+ +YYDGESV+G+VNI LK G K+EHQG
Sbjct: 1 FGPPCDIEIVLDNEETRKTVEVKTEDGKKEKNPVYYDGESVSGKVNIRLKD-GKKVEHQG 59
Query: 66 IKIEFIGQIELYYDRGNHHEFVSLVKELARPGELIQNTTYKFEFLNVEKPYESYTGSNVF 125
IKIEF+GQIEL+YDRGN HEF +LV+ELA PGEL Q+ T+ FEF VEKPYESY
Sbjct: 60 IKIEFVGQIELFYDRGNPHEFTNLVRELAPPGELTQSKTFPFEFPLVEKPYESYI----- 114
Query: 126 TPRPNVFNENETIAKYEIMDGAPVRGESIPIRVFLAGYDLAPTMRDINKKFSVKYFLNLV 185
G VR ++YFL +
Sbjct: 115 --------------------GVNVR---------------------------LRYFLRVT 127
Query: 186 LMDEEDRRYFKQQVFTPNLIKELDIIVHTLSSYPEMNSPIKMEVGIEDCLHIEFEYNKCN 245
++ RR ++ KE D VH ++YPE N+ IKMEVGIEDCLHIEFEYNK +
Sbjct: 128 VV----RRL-------TDITKEKDFWVHNFTTYPETNNSIKMEVGIEDCLHIEFEYNK-S 175
Query: 246 TWNLKDVIVGKIYFLLVRIKIKHMEIAIIKRETTGTG 282
++LKDVIVGKIYFLLVRIKIKHME+ +I+RE+TGTG
Sbjct: 176 KYHLKDVIVGKIYFLLVRIKIKHMELQLIRRESTGTG 212
Score = 122 bits (309), Expect = 2e-33
Identities = 55/63 (87%), Positives = 60/63 (95%)
Query: 129 PNVFNENETIAKYEIMDGAPVRGESIPIRVFLAGYDLAPTMRDINKKFSVKYFLNLVLMD 188
PN F E+ETIAK+EIMDGAPVRGESIPIR+FLAGYDL PTMRD+NKKFSVKYFLNLVL+D
Sbjct: 213 PNTFTESETIAKFEIMDGAPVRGESIPIRLFLAGYDLTPTMRDVNKKFSVKYFLNLVLVD 272
Query: 189 EED 191
EED
Sbjct: 273 EED 275
>gnl|CDD|220123 pfam09138, Urm1, Urm1 (Ubiquitin related modifier). Urm1 is a
ubiquitin related protein that modifies proteins in the
yeast ubiquitin-like pathway urmylation. Structural
comparisons and phylogenetic analysis of the ubiquitin
superfamily has indicated that Urm1 has the most
conserved structural and sequence features of the common
ancestor of the entire superfamily.
Length = 96
Score = 28.0 bits (63), Expect = 1.8
Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 18/75 (24%)
Query: 66 IKIEFIGQIELYYDRGNHHEF-VSLVKELARPGELIQNTTYKFEFLNVEKPYESYTGSNV 124
I +EF+G +EL +D+ H+ + + G+LI Y N+
Sbjct: 2 ITVEFLGGLELLFDKQKKHKVTLPIDSGPVNMGDLID-----------------YIKKNL 44
Query: 125 FTPRPNVFNENETIA 139
RP VF E +T+
Sbjct: 45 IKERPEVFLEGDTVR 59
>gnl|CDD|238265 cd00475, CIS_IPPS, Cis (Z)-Isoprenyl Diphosphate Synthases
(cis-IPPS); homodimers which catalyze the successive
1'-4 condensation of the isopentenyl diphosphate (IPP)
molecule to trans,trans-farnesyl diphosphate (FPP) or to
cis,trans-FPP to form long-chain polyprenyl
diphosphates. A few can also catalyze the condensation
of IPP to trans-geranyl diphosphate to form the
short-chain cis,trans- FPP. In prokaryotes, the
cis-IPPS, undecaprenyl diphosphate synthase (UPP
synthase) catalyzes the formation of the carrier lipid
UPP in bacterial cell wall peptidooglycan biosynthesis.
Similarly, in eukaryotes, the cis-IPPS, dehydrodolichyl
diphosphate (dedol-PP) synthase catalyzes the formation
of the polyisoprenoid glycosyl carrier lipid dolichyl
monophosphate. cis-IPPS are mechanistically and
structurally distinct from trans-IPPS, lacking the DDXXD
motifs, yet requiring Mg2+ for activity.
Length = 221
Score = 28.8 bits (65), Expect = 2.9
Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 10/64 (15%)
Query: 53 VLKKHGSKLEHQGIKIEFIGQIELYYDRGNHHEFVSLVKELARPGELIQNTTYKFEFLNV 112
VL++ +LE G++I IG + L + SL KE+ + E +N T F LNV
Sbjct: 75 VLRRILKELEKLGVRIRIIGDLSLLPE--------SLQKEIKKAEEATKNNT-GF-TLNV 124
Query: 113 EKPY 116
Y
Sbjct: 125 AFNY 128
>gnl|CDD|192722 pfam11210, DUF2996, Protein of unknown function (DUF2996). This
family of proteins has no known function.
Length = 118
Score = 27.6 bits (62), Expect = 3.3
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 33 KKERFYLYYDGESVTGQVNIVLKKHGSK 60
K RF+L + E +T L + GS+
Sbjct: 56 KGRRFWLCFPEEDITSPKTFSLAESGSE 83
>gnl|CDD|225825 COG3287, COG3287, Uncharacterized conserved protein [Function
unknown].
Length = 379
Score = 28.5 bits (64), Expect = 4.9
Identities = 19/72 (26%), Positives = 29/72 (40%), Gaps = 12/72 (16%)
Query: 1 MSFFGF----GQSADIEIKLDGTDTRKLADIK------SDDGKKERFYLYYDGESVTGQV 50
G S E+ LDG L I +DD + ER Y++ +GE
Sbjct: 128 RPVLALTFIDGLSTSEEVLLDGAVLAALETIPIFGGSAADDLEFERTYVFDEGEVHEDAA 187
Query: 51 NIVLKKHGSKLE 62
I+L G++L+
Sbjct: 188 VILL--FGTQLK 197
>gnl|CDD|237503 PRK13780, PRK13780, phosphocarrier protein HPr; Provisional.
Length = 88
Score = 26.6 bits (59), Expect = 5.5
Identities = 11/20 (55%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 1 MSFFGFGQSADIEIKLDGTD 20
MS G GQ ADI I +G D
Sbjct: 51 MSL-GVGQGADITISAEGAD 69
>gnl|CDD|213701 TIGR02336, TIGR02336, 1,3-beta-galactosyl-N-acetylhexosamine
phosphorylase. Members of this family are found in
phylogenetically diverse bacteria, including Clostridium
perfringens (in the Firmicutes), Bifidobacterium longum
and Propionibacterium acnes (in the Actinobacteria), and
Vibrio vulnificus (in the Proteobacteria), most of which
occur as mammalian pathogens or commensals. The nominal
activity, 1,3-beta-galactosyl-N-acetylhexosamine
phosphorylase (EC 2.4.1.211), varies somewhat from
instance to instance in relative rates for closely
related substrates [Energy metabolism, Biosynthesis and
degradation of polysaccharides].
Length = 719
Score = 28.3 bits (63), Expect = 6.3
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 17 DGTDTRKLADIKSDDGKKERFYLYY 41
DGT TR +ADI + RF Y+
Sbjct: 338 DGTTTRMIADIPGVKYTEGRFLPYF 362
>gnl|CDD|176519 cd08577, PI-PLCc_GDPD_SF_unchar3, Uncharacterized hypothetical
proteins similar to the catalytic domains of
Phosphoinositide-specific phospholipaseand
Glycerophosphodiester phosphodiesterases. This
subfamily corresponds to a group of uncharacterized
hypothetical proteins similar to the catalytic domains
of Phosphoinositide-specific phospholipase C (PI-PLC),
and glycerophosphodiester phosphodiesterases (GP-GDE),
and also sphingomyelinases D (SMases D) and similar
proteins. They hydrolyze the 3'-5' phosphodiester bonds
in different substrates, utilizing a similar mechanism
of general base and acid catalysis involving two
conserved histidine residues.
Length = 228
Score = 27.6 bits (62), Expect = 7.3
Identities = 12/43 (27%), Positives = 17/43 (39%), Gaps = 12/43 (27%)
Query: 24 LADIKSDDGK------------KERFYLYYDGESVTGQVNIVL 54
L DIK+D + YL Y + V G V +V+
Sbjct: 82 LIDIKTDGESTYPALEEVLKPYIDIGYLSYYDKLVPGPVTVVI 124
>gnl|CDD|235776 PRK06300, PRK06300, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 299
Score = 27.5 bits (61), Expect = 7.5
Identities = 13/44 (29%), Positives = 26/44 (59%), Gaps = 8/44 (18%)
Query: 190 EDRRYFKQQVFTPNLIKE--------LDIIVHTLSSYPEMNSPI 225
E++RY +T + + E +DI+VH+L++ PE++ P+
Sbjct: 94 ENKRYKDLSGYTISEVAEQVKKDFGHIDILVHSLANSPEISKPL 137
>gnl|CDD|218869 pfam06043, Reo_P9, Reovirus P9-like family.
Length = 333
Score = 27.5 bits (61), Expect = 9.1
Identities = 19/83 (22%), Positives = 30/83 (36%), Gaps = 17/83 (20%)
Query: 129 PNVFNENETIAKYEIMDGAPVRGESIPIRVFLAGYDLAPTMRDINKKFSVKYFLNLVLMD 188
PN ++ I KY P+ + + GY+ R NK+F+ Y+ L D
Sbjct: 196 PNSYDRQLNIEKYR------------PLLISIIGYEWLFGTRVKNKEFNHLYYQ-LATFD 242
Query: 189 EED----RRYFKQQVFTPNLIKE 207
R + PN I +
Sbjct: 243 NYPFDLLRFQLPSLISVPNSILQ 265
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
0.321 0.141 0.408
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,205,799
Number of extensions: 1506064
Number of successful extensions: 1140
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1137
Number of HSP's successfully gapped: 24
Length of query: 288
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 192
Effective length of database: 6,679,618
Effective search space: 1282486656
Effective search space used: 1282486656
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 (26.1 bits)