RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 039384
(104 letters)
>gnl|CDD|216392 pfam01255, Prenyltransf, Putative undecaprenyl diphosphate
synthase. Previously known as uncharacterized protein
family UPF0015, a single member of this family has been
identified as an undecaprenyl diphosphate synthase.
Length = 222
Score = 73.0 bits (180), Expect = 3e-17
Identities = 32/74 (43%), Positives = 43/74 (58%), Gaps = 7/74 (9%)
Query: 22 VQEYCEDKLDGSQALKEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLW 81
V+ D DG + E IDE+ I EK+++ + PDPD+ IR+SGE R SNFLLW
Sbjct: 132 VKRLARDVADGKLS-PEDIDEEVI------EKYLYTSDLPDPDLLIRTSGEKRLSNFLLW 184
Query: 82 QTSNCSLYSPAALW 95
Q++ LY LW
Sbjct: 185 QSAYAELYFTDTLW 198
>gnl|CDD|223099 COG0020, UppS, Undecaprenyl pyrophosphate synthase [Lipid
metabolism].
Length = 245
Score = 66.9 bits (164), Expect = 8e-15
Identities = 31/74 (41%), Positives = 42/74 (56%), Gaps = 7/74 (9%)
Query: 22 VQEYCEDKLDGSQALKEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLW 81
V++ ED G + E IDE+ I H++ + PDPD+ IR+SGE R SNFLLW
Sbjct: 154 VRKIAEDVAAGKLSP-EDIDEELI------SSHLYTSGLPDPDLLIRTSGEQRLSNFLLW 206
Query: 82 QTSNCSLYSPAALW 95
Q++ LY LW
Sbjct: 207 QSAYSELYFTDVLW 220
>gnl|CDD|184840 PRK14830, PRK14830, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 251
Score = 64.5 bits (158), Expect = 7e-14
Identities = 30/74 (40%), Positives = 38/74 (51%), Gaps = 7/74 (9%)
Query: 22 VQEYCEDKLDGSQALKEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLW 81
V+E +D LDG E I E+ I ++ PDPD+ IR+SGE R SNFLLW
Sbjct: 160 VKEIAKDVLDGKLNP-EDITEELISN------YLMTKGLPDPDLLIRTSGELRLSNFLLW 212
Query: 82 QTSNCSLYSPAALW 95
Q + Y LW
Sbjct: 213 QLAYSEFYFTDVLW 226
>gnl|CDD|237831 PRK14836, PRK14836, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 253
Score = 63.6 bits (155), Expect = 2e-13
Identities = 27/71 (38%), Positives = 39/71 (54%), Gaps = 7/71 (9%)
Query: 27 EDKLDGSQALKEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLWQTSNC 86
+ G A ++IDE + +H+ +A P+PD+ IR+SGE R SNFLLWQ +
Sbjct: 157 REVAAGKLAP-DEIDEAL------LAQHLALADLPEPDLFIRTSGELRISNFLLWQLAYT 209
Query: 87 SLYSPAALWLE 97
LY LW +
Sbjct: 210 ELYFTDTLWPD 220
>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 = 61.9 bits (151), Expect = 4e-13
Identities = 32/74 (43%), Positives = 42/74 (56%), Gaps = 7/74 (9%)
Query: 22 VQEYCEDKLDGSQALKEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLW 81
V+E E G + E IDE T+ KH++ +PDPD+ IR+SGE R SNFLLW
Sbjct: 138 VREIAEKVKAG-KLTPEDIDESTL------NKHLYTHDSPDPDLLIRTSGEQRLSNFLLW 190
Query: 82 QTSNCSLYSPAALW 95
Q++ LY LW
Sbjct: 191 QSAYSELYFSDVLW 204
>gnl|CDD|129165 TIGR00055, uppS, undecaprenyl diphosphate synthase. This enzyme
builds undecaprenyl diphosphate, a molecule that in
bacteria is used a carrier in synthesizing cell wall
components. Alternate name: undecaprenyl pyrophosphate
synthetase. Activity has been demonstrated
experimentally for members of this family from
Micrococcus luteus, E. coli, Haemophilus influenzae, and
Streptococcus pneumoniae [Cell envelope, Biosynthesis
and degradation of surface polysaccharides and
lipopolysaccharides].
Length = 226
Score = 60.9 bits (148), Expect = 1e-12
Identities = 26/75 (34%), Positives = 38/75 (50%), Gaps = 6/75 (8%)
Query: 26 CEDKLDGSQAL-----KEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLL 80
+ L + + K+ + I + + KH++ A P D+ IR+SGE R SNFLL
Sbjct: 130 RNEILHAVKQIAEKVKSGKLLPEDIDEET-LNKHLYTANLPPVDLLIRTSGEMRISNFLL 188
Query: 81 WQTSNCSLYSPAALW 95
WQ+S LY LW
Sbjct: 189 WQSSYAELYFTDILW 203
>gnl|CDD|237825 PRK14828, PRK14828, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 256
Score = 57.1 bits (138), Expect = 3e-11
Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 36 LKEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLWQTSNCSLYSPAALW 95
L E + D I H++ PDPD+ IR+SGE R S F+LWQ+++ Y W
Sbjct: 179 LAESVTVDAIST------HLYTGGQPDPDLVIRTSGEQRLSGFMLWQSAHSEYYFCETYW 232
>gnl|CDD|184841 PRK14831, PRK14831, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 249
Score = 56.5 bits (137), Expect = 6e-11
Identities = 24/58 (41%), Positives = 32/58 (55%), Gaps = 6/58 (10%)
Query: 38 EKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLWQTSNCSLYSPAALW 95
+IDE+ E ++ A DPD+ IR+SGE R SNFLLWQ + +Y LW
Sbjct: 173 SEIDENLF------ESELYTAGIKDPDLLIRTSGEMRISNFLLWQLAYAEIYVTDVLW 224
>gnl|CDD|237827 PRK14832, PRK14832, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 253
Score = 56.2 bits (135), Expect = 8e-11
Identities = 24/58 (41%), Positives = 34/58 (58%), Gaps = 6/58 (10%)
Query: 38 EKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLWQTSNCSLYSPAALW 95
+ ++E VE+H++ A P PD+ IR+SGE R SNFLLWQ + +Y LW
Sbjct: 171 DAVNEQL------VEQHLYTADTPPPDLLIRTSGEMRLSNFLLWQMAYTEMYFTDILW 222
>gnl|CDD|237830 PRK14835, PRK14835, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 275
Score = 54.5 bits (131), Expect = 4e-10
Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 3/82 (3%)
Query: 19 VPDVQEYCEDKLDGSQALKEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNF 78
V V+ + ++ +E E T + + H++ A PDPD IR+SGE R S F
Sbjct: 178 VDAVKSLLLEAAATGKSPEEVAAELTPE---HISAHLYTAGVPDPDFIIRTSGEIRLSGF 234
Query: 79 LLWQTSNCSLYSPAALWLEEKK 100
LLWQ++ Y W +K
Sbjct: 235 LLWQSAYSEYYFCDVYWPGFRK 256
>gnl|CDD|173302 PRK14841, PRK14841, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 233
Score = 53.8 bits (129), Expect = 5e-10
Identities = 28/71 (39%), Positives = 43/71 (60%), Gaps = 6/71 (8%)
Query: 31 DGSQALKEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLWQTSNCSLYS 90
D SQ K ++ E+T ++ ++++ PDPD+ IR+SGE R SNFLLWQ++ LY
Sbjct: 147 DVSQGKKIELTEETFRQ------YLYLPDVPDPDLIIRTSGEMRLSNFLLWQSAYSELYF 200
Query: 91 PAALWLEEKKK 101
LW + K+
Sbjct: 201 FKKLWPDFTKR 211
>gnl|CDD|237829 PRK14834, PRK14834, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 249
Score = 51.7 bits (124), Expect = 3e-09
Identities = 25/58 (43%), Positives = 30/58 (51%), Gaps = 6/58 (10%)
Query: 38 EKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLWQTSNCSLYSPAALW 95
ID +TI +D A PDPD+ IR+SGE R SNFLLWQ + L W
Sbjct: 167 ASIDAETISANLDT------ADIPDPDLIIRTSGEQRLSNFLLWQAAYSELLFVPIHW 218
>gnl|CDD|173303 PRK14842, PRK14842, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 241
Score = 50.8 bits (121), Expect = 7e-09
Identities = 22/61 (36%), Positives = 35/61 (57%)
Query: 37 KEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLWQTSNCSLYSPAALWL 96
+K+ + K + EK ++ + P D+ IR++GE R SNFLLWQ++ LY LW
Sbjct: 155 AKKVTLEKPLKEKEFEKFLYTSPLPPVDLLIRTAGEQRLSNFLLWQSAYAELYFTDTLWP 214
Query: 97 E 97
+
Sbjct: 215 D 215
>gnl|CDD|173301 PRK14840, PRK14840, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 250
Score = 49.8 bits (119), Expect = 2e-08
Identities = 20/35 (57%), Positives = 23/35 (65%)
Query: 61 PDPDITIRSSGETRPSNFLLWQTSNCSLYSPAALW 95
PDPD+ IR+ GE R SNFLLWQ + LY LW
Sbjct: 192 PDPDLLIRTGGEMRVSNFLLWQIAYTELYVTDVLW 226
>gnl|CDD|184846 PRK14838, PRK14838, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 242
Score = 49.1 bits (117), Expect = 2e-08
Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 11/74 (14%)
Query: 22 VQEYCEDKLDGSQALKEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLW 81
+L+ E+I E++I + H+ PDPD+ IR+ GE R SN+LLW
Sbjct: 150 ATLVQNGELN-----PEEITEESISE------HLTTNFMPDPDLLIRTGGEIRLSNYLLW 198
Query: 82 QTSNCSLYSPAALW 95
Q + LY W
Sbjct: 199 QCAYSELYFCDTFW 212
>gnl|CDD|237826 PRK14829, PRK14829, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 243
Score = 48.2 bits (115), Expect = 5e-08
Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 17/76 (22%)
Query: 38 EKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLWQTSNCSL--------- 88
+++ E I H++ PD D+ +R+SGE R SNFLLWQ++ L
Sbjct: 167 DRVTEKMISD------HLYNPDMPDVDLFLRTSGEQRTSNFLLWQSAYAELDFVPKLFPD 220
Query: 89 YSPAALW--LEEKKKR 102
+ LW ++E R
Sbjct: 221 FGRDDLWAAIDEYAHR 236
>gnl|CDD|173288 PRK14827, PRK14827, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 296
Score = 45.3 bits (107), Expect = 8e-07
Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 6/58 (10%)
Query: 38 EKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLWQTSNCSLYSPAALW 95
E+I E TI + H+ PD D+ +R+SGE R SNF+LWQ + LW
Sbjct: 220 ERITESTIAR------HLQRPDIPDVDLFLRTSGEQRSSNFMLWQAAYAEYIFQDKLW 271
>gnl|CDD|237828 PRK14833, PRK14833, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 233
Score = 44.8 bits (106), Expect = 9e-07
Identities = 19/38 (50%), Positives = 24/38 (63%)
Query: 58 AVAPDPDITIRSSGETRPSNFLLWQTSNCSLYSPAALW 95
A P+ D+ IR+ GE R SNFLLWQ+S L+ LW
Sbjct: 170 ADLPEVDLLIRTGGEMRLSNFLLWQSSYAELFFTPILW 207
>gnl|CDD|182326 PRK10240, PRK10240, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 229
Score = 43.8 bits (103), Expect = 2e-06
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 28 DKLDGSQALKEKIDEDTIK-KLVDVE---KHMFMAVAPDPDITIRSSGETRPSNFLLWQT 83
D + G + L E++ + ++ +D E +H+ M D+ IR+ GE R SNFLLWQ
Sbjct: 126 DIVQGVRQLAEQVQQGNLQPDQIDEEMLNQHICMHELAPVDLVIRTGGEHRISNFLLWQI 185
Query: 84 SNCSLYSPAALW 95
+ LY LW
Sbjct: 186 AYAELYFTDVLW 197
>gnl|CDD|173298 PRK14837, PRK14837, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 230
Score = 42.9 bits (101), Expect = 4e-06
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 38 EKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLWQTSNCSLYSPAALWLE 97
E ++E+ K +D + PD D+ IR+ G+ R SNFLLW+ + C LW E
Sbjct: 155 ETLNENVFSKFLDNPE------LPDLDLLIRTGGDMRISNFLLWRIAYCEFIFSNVLWPE 208
>gnl|CDD|237832 PRK14839, PRK14839, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 239
Score = 40.9 bits (96), Expect = 2e-05
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 60 APDPDITIRSSGETRPSNFLLWQTSNCSLYSPAALW 95
D D+ IR+ GE R S+FLLW+++ L+ +W
Sbjct: 169 GGDVDLLIRTGGEKRLSDFLLWESAYAELHFTDRMW 204
>gnl|CDD|185571 PTZ00349, PTZ00349, dehydrodolichyl diphosphate synthetase;
Provisional.
Length = 322
Score = 40.4 bits (94), Expect = 5e-05
Identities = 19/48 (39%), Positives = 32/48 (66%), Gaps = 1/48 (2%)
Query: 37 KEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLWQTS 84
K ++E+ I+ +V+ K + + P P+I IR+SGE R S+F+L+Q S
Sbjct: 231 KSFLNEEQIE-IVNYHKKLLTSDLPPPNILIRTSGEKRLSDFMLYQIS 277
>gnl|CDD|148689 pfam07230, Phage_T4_Gp20, Bacteriophage T4-like capsid assembly
protein (Gp20). This family consists of several
bacteriophage T4-like capsid assembly (or portal)
proteins. The exact mechanism by which the
double-stranded (ds) DNA bacteriophages incorporate the
portal protein at a unique vertex of the icosahedral
capsid is unknown. In phage T4, there is evidence that
this vertex, constituted by 12 subunits of gp20, acts as
an initiator for the assembly of the major capsid
protein and the scaffolding proteins into a prolate
icosahedron of precise dimensions. The regulation of
portal protein gene expression is an important regulator
of prohead assembly in bacteriophage T4.
Length = 500
Score = 26.5 bits (59), Expect = 2.8
Identities = 11/29 (37%), Positives = 19/29 (65%), Gaps = 2/29 (6%)
Query: 28 DKLDGSQALKEKIDE--DTIKKLVDVEKH 54
D D S+++K+KI E D + KL+D ++
Sbjct: 107 DNTDFSESIKKKIREEFDEVLKLLDFDRK 135
>gnl|CDD|206570 pfam14402, 7TM_transglut, 7 transmembrane helices usually fused
to an inactive transglutaminase. A family of seven
transmembrane helices fused to an inactive
transglutaminase domain. The transglutaminase domain is
predicted to be extracellularly located. Members of
this family are associated in gene neighborhoods with a
pepsin-like peptidase and an ATP-grasp of the
RimK-family. The ATP-grasp is predicted to modify the
7TM protein or a cofactor that interacts with it.
Length = 315
Score = 26.3 bits (59), Expect = 3.0
Identities = 9/20 (45%), Positives = 11/20 (55%), Gaps = 1/20 (5%)
Query: 70 SGE-TRPSNFLLWQTSNCSL 88
+GE P N LLW + SL
Sbjct: 51 TGEQGLPENLLLWWRGDESL 70
>gnl|CDD|238892 cd01911, proteasome_alpha, proteasome alpha subunit. The 20S
proteasome, multisubunit proteolytic complex, is the
central enzyme of nonlysosomal protein degradation in
both the cytosol and nucleus. It is composed of 28
subunits arranged as four homoheptameric rings that
stack on top of one another forming an elongated
alpha-beta-beta-alpha cylinder with a central cavity.
The proteasome alpha and beta subunits are members of
the N-terminal nucleophile (Ntn)-hydrolase superfamily.
Their N-terminal threonine residues are exposed as a
nucleophile in peptide bond hydrolysis. Mammals have 7
different alpha and 10 different beta proteasome
subunit genes while archaea have one of each.
Length = 209
Score = 25.9 bits (58), Expect = 4.1
Identities = 6/21 (28%), Positives = 14/21 (66%)
Query: 40 IDEDTIKKLVDVEKHMFMAVA 60
+D +++K+ ++ H+ AVA
Sbjct: 52 LDPSSVEKIFKIDDHIGCAVA 72
>gnl|CDD|178043 PLN02423, PLN02423, phosphomannomutase.
Length = 245
Score = 25.4 bits (56), Expect = 5.7
Identities = 15/44 (34%), Positives = 27/44 (61%), Gaps = 4/44 (9%)
Query: 25 YCEDKLDGSQALKEKIDEDTIKKLVDVEKHMFMAVAPDPDITIR 68
+ + KL G+Q+LK + ED +K+ ++ H ++A D DI I+
Sbjct: 77 HKDGKLIGTQSLKSFLGEDKLKEFINFTLH-YIA---DLDIPIK 116
>gnl|CDD|236732 PRK10662, PRK10662, beta-lactam binding protein AmpH;
Provisional.
Length = 378
Score = 25.0 bits (55), Expect = 9.0
Identities = 10/23 (43%), Positives = 11/23 (47%)
Query: 55 MFMAVAPDPDITIRSSGETRPSN 77
M + V RS GETRP N
Sbjct: 51 MALVVIDGNQRVFRSYGETRPGN 73
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
0.315 0.132 0.389
Gapped
Lambda K H
0.267 0.0829 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,389,962
Number of extensions: 452097
Number of successful extensions: 314
Number of sequences better than 10.0: 1
Number of HSP's gapped: 314
Number of HSP's successfully gapped: 36
Length of query: 104
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 35
Effective length of database: 7,877,176
Effective search space: 275701160
Effective search space used: 275701160
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: 42 (22.0 bits)
S2: 53 (24.0 bits)