RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7867
(484 letters)
>gnl|CDD|109297 pfam00233, PDEase_I, 3'5'-cyclic nucleotide phosphodiesterase.
Length = 237
Score = 349 bits (898), Expect = e-119
Identities = 148/289 (51%), Positives = 180/289 (62%), Gaps = 52/289 (17%)
Query: 123 FHNSTHAADVTQSTNVLLNSPALEDVFTPLEIMAALFAATIHDVDHPGLTNQFLINSSSE 182
+HN HAADVTQ+T++LL + ALE T LEI+A LFAA IHDVDH G N F INS SE
Sbjct: 1 YHNWRHAADVTQTTHLLLLTLALERYLTDLEILALLFAAAIHDVDHRGTNNSFQINSKSE 60
Query: 183 LALMYNDESVLENHHLAVAFKLLQNEGCDILCNLNKKQKQTLRKMVIDMVLSTDIRSQNL 242
LA++YNDESVLENHHLA AFKLLQ+E C+I NL+KK QTLR +VI+M+L+TD
Sbjct: 61 LAILYNDESVLENHHLAQAFKLLQDEECNIFQNLSKKDFQTLRDLVIEMILATD------ 114
Query: 243 AVAFKLLQNEGCDILCNLNKKQKQTLRKMVIDMVLSTDMSKHMSLLADLKTMVETKKVAG 302
MS H L DLKTMVE KK
Sbjct: 115 --------------------------------------MSLHFQKLKDLKTMVEQKKRL- 135
Query: 303 SGVLLLDNYTDRIQVLENLVHCADLSNPTKPLPLYRKWVDLLMEEFFQQGDKERELNLDI 362
+ +I +L L+H ADLSNPTKP L+R+W +L+MEEFF QGD EREL L
Sbjct: 136 -------DLDHKILLLSLLMHAADLSNPTKPWKLHRRWAELIMEEFFDQGDLERELGLPP 188
Query: 363 SPMCDRLSATIEKSQVGFIDYIVHPLWETWADLVHPDAQEILDMLEENR 411
SPMCDR SA + KSQVGFID+IV P+++ AD+V D Q +LD +E+NR
Sbjct: 189 SPMCDRTSAYVPKSQVGFIDFIVEPIFKLLADVVEKDIQPLLDTIEDNR 237
>gnl|CDD|214679 smart00471, HDc, Metal dependent phosphohydrolases with conserved
'HD' motif. Includes eukaryotic cyclic nucleotide
phosphodiesterases (PDEc). This profile/HMM does not
detect HD homologues in bacterial glycine aminoacyl-tRNA
synthetases (beta subunit).
Length = 124
Score = 48.1 bits (114), Expect = 6e-07
Identities = 28/99 (28%), Positives = 41/99 (41%), Gaps = 17/99 (17%)
Query: 121 NPFHNSTHAADVTQSTNVLLNSPALEDVFTPLEIMAALFAATIHDVDHPGLTNQFLINSS 180
+ +H H+ V Q L L D+ L AA +HD+ PG + FL+ +
Sbjct: 1 SDYHVFEHSLRVAQLAAALAEELGLLDIE------LLLLAALLHDIGKPGTPDSFLVKT- 53
Query: 181 SELALMYNDESVLENHHLAVAFKLLQNEGCDILCNLNKK 219
SVLE+HH A LL+ E IL + +
Sbjct: 54 ----------SVLEDHHFIGAEILLEEEEPRILEEILRT 82
>gnl|CDD|238032 cd00077, HDc, Metal dependent phosphohydrolases with conserved 'HD'
motif.
Length = 145
Score = 45.4 bits (107), Expect = 9e-06
Identities = 24/113 (21%), Positives = 42/113 (37%), Gaps = 26/113 (23%)
Query: 124 HNSTHAADVTQSTNVLLNSPALEDVFTPLEIMAALFAATIHDVDHPGLTNQFLINSSSEL 183
H H+ V Q L A E + +I AA +HD+ PG +
Sbjct: 2 HRFEHSLRVAQLARRL----AEELGLSEEDIELLRLAALLHDIGKPGTPDAI-------- 49
Query: 184 ALMYNDESVLENHHLAVAFKLLQNEGCDILCNLNKKQKQTLRKMVIDMVLSTD 236
+ES LE H V ++ L + + + K++ +++L+ D
Sbjct: 50 ---TEEESELEKDHAIVGAEI-----------LRELLLEEVIKLIDELILAVD 88
>gnl|CDD|224346 COG1429, CobN, Cobalamin biosynthesis protein CobN and related
Mg-chelatases [Coenzyme metabolism].
Length = 1388
Score = 34.3 bits (79), Expect = 0.19
Identities = 15/39 (38%), Positives = 18/39 (46%)
Query: 387 PLWETWADLVHPDAQEILDMLEENRDWYQNYIVHPLWET 425
P+ + HPDA EI + L E DWY N P T
Sbjct: 166 PVRPPKEGIYHPDAGEIFENLREYLDWYINGFYDPGAPT 204
Score = 30.1 bits (68), Expect = 3.9
Identities = 14/39 (35%), Positives = 18/39 (46%)
Query: 421 PLWETWADLVHPDAQEILDMLEENRDWYQSMIPPSPPPT 459
P+ + HPDA EI + L E DWY + PT
Sbjct: 166 PVRPPKEGIYHPDAGEIFENLREYLDWYINGFYDPGAPT 204
>gnl|CDD|182059 PRK09752, PRK09752, adhesin; Provisional.
Length = 1250
Score = 31.6 bits (71), Expect = 1.2
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 3/24 (12%)
Query: 440 MLEENRDWY---QSMIPPSPPPTD 460
++E+N DWY Q + PPSPP D
Sbjct: 904 LVEDNNDWYLRSQEVTPPSPPDPD 927
>gnl|CDD|132825 cd07292, PX_SNX6, The phosphoinositide binding Phox Homology domain
of Sorting Nexin 6. The PX domain is a phosphoinositide
(PI) binding module present in many proteins with
diverse functions. Sorting nexins (SNXs) make up the
largest group among PX domain containing proteins. They
are involved in regulating membrane traffic and protein
sorting in the endosomal system. The PX domain of SNXs
binds PIs and targets the protein to PI-enriched
membranes. SNXs differ from each other in PI-binding
specificity and affinity, and the presence of other
protein-protein interaction domains, which help
determine subcellular localization and specific function
in the endocytic pathway. SNX6 forms a stable complex
with SNX1 and may be a component of the retromer
complex, a membrane coat multimeric complex required for
endosomal retrieval of lysosomal hydrolase receptors to
the Golgi, acting as a mammalian equivalent of yeast
Vsp17p. It interacts with the receptor serine/threonine
kinases from the transforming growth factor-beta family.
It also plays roles in enhancing the degradation of EGFR
and in regulating the activity of Na,K-ATPase through
its interaction with Translationally Controlled Tumor
Protein (TCTP). SNX6 harbors a Bin/Amphiphysin/Rvs (BAR)
domain, which detects membrane curvature, C-terminal to
the PX domain, similar to other sorting nexins including
SNX1-2. The PX-BAR structural unit helps determine the
specific membrane-targeting of some SNXs.
Length = 141
Score = 30.1 bits (67), Expect = 1.3
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 439 DMLEENRDWYQSMIPPSPPPTDLGDATKQEQGQEEEDEG 477
D EN D+ +IPP+PP D DA++++ + E EG
Sbjct: 49 DSFVENEDYAGYIIPPAPPRPDF-DASREKLQKLGEGEG 86
>gnl|CDD|153115 cd01057, AAMH_A, Aromatic and Alkene Monooxygenase Hydroxylase,
subunit A, ferritin-like diiron-binding domain.
Aromatic and Alkene Monooxygenase Hydroxylases, subunit
A (AAMH_A). Subunit A of the soluble hydroxylase of
multicomponent, aromatic and alkene monooxygenases are
members of a superfamily of ferritin-like iron-storage
proteins. AAMH exists as a hexamer (an
alpha2-beta2-gamma2 homodimer) with each alpha-subunit
housing one nonheme diiron center embedded in a
four-helix bundle. The N-terminal domain of the alpha-
and noncatalytic beta-subunits possess nearly identical
folds, however, the beta-subunit lacks critical diiron
ligands and a C-terminal domain found in the
alpha-subunit. Methane monooxygenase is a multicomponent
enzyme found in methanotrophic bacteria that catalyzes
the hydroxylation of methane and higher alkenes (as
large as octane). Phenol monooxygenase, found in a
diverse group of bacteria, catalyses the hydroxylation
of phenol, chloro- and methyl-phenol and naphthol. Both
enzyme systems consist of three components: the
hydroxylase, a coupling protein and a reductase. In the
MMO hydroxylase, dioxygen and substrate interact with
the diiron center in a hydrophobic cavity at the active
site. The reductase component and protein coupling
factor provide electrons from NADH for reducing the
oxidized binuclear iron-oxo cluster to its reduced form.
Reaction with dioxygen produces a peroxy-bridged complex
and dehydration leads to the formation of complex Q,
which is thought to be the oxygenating species that
carries out the insertion of an oxygen atom into a C-H
bond of the substrate. The toluene monooxygenase
systems, toluene 2-, 3-, and 4-monooxygenase, are
similar to MMO but with an additional component, a
Rieske-type ferredoxin. The alkene monooxygenase from
Xanthobacter strain Py2 is closely related to aromatic
monooxygenases and catalyzes aromatic monohydroxylation
of benzene, toluene, and phenol. Alkane
omega-hydroxylase (AlkB) and xylene monooxygenase are
members of a distinct class of integral membrane diiron
proteins and are not included in this CD.
Length = 465
Score = 30.7 bits (70), Expect = 1.9
Identities = 14/61 (22%), Positives = 18/61 (29%), Gaps = 10/61 (16%)
Query: 381 IDYIVHPLWETWADLV-----HPDAQEILDM--LEENR-DWYQNYIVHPLWETWADLVHP 432
D+ H L + PDA +M EE WY+ Y WE
Sbjct: 311 KDWYHHQLALGFYAWWPTNFWRPDAPTPEEMEWFEEKYPGWYKYY--GKFWEEIRKNAAE 368
Query: 433 D 433
Sbjct: 369 G 369
>gnl|CDD|220923 pfam10980, DUF2787, Protein of unknown function (DUF2787). This
bacterial family of proteins has no known function.
Length = 128
Score = 28.3 bits (64), Expect = 3.9
Identities = 12/42 (28%), Positives = 16/42 (38%), Gaps = 6/42 (14%)
Query: 410 NRDWYQNYIVHPLWETWADLVHPDAQEILDMLEENRDWYQSM 451
N YQ W L HP+ +E+ + E N Y M
Sbjct: 83 NGWVYQPDS------GWLPLAHPEVKELYQLWESNFLAYLDM 118
>gnl|CDD|233692 TIGR02031, BchD-ChlD, magnesium chelatase ATPase subunit D. This
model represents one of two ATPase subunits of the
trimeric magnesium chelatase responsible for insertion
of magnesium ion into protoporphyrin IX. This is an
essential step in the biosynthesis of both chlorophyll
and bacteriochlorophyll. This subunit is found in green
plants, photosynthetic algae, cyanobacteria and other
photosynthetic bacteria. Unlike subunit I (TIGR02030),
this subunit is not found in archaea [Biosynthesis of
cofactors, prosthetic groups, and carriers, Chlorophyll
and bacteriochlorphyll].
Length = 589
Score = 29.8 bits (67), Expect = 3.9
Identities = 9/31 (29%), Positives = 13/31 (41%)
Query: 453 PPSPPPTDLGDATKQEQGQEEEDEGREGSDL 483
PP PP + E Q + D+G E +
Sbjct: 276 PPPPPEPPEPEEEPDEPDQTDPDDGEETDQI 306
>gnl|CDD|225680 COG3138, AstA, Arginine/ornithine N-succinyltransferase beta
subunit [Amino acid transport and metabolism].
Length = 336
Score = 29.7 bits (67), Expect = 4.0
Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 13/62 (20%)
Query: 367 DRLSATIEKSQVGFIDYIV--HPLW------ETWADL--VHPDAQEILDMLEENRDWYQN 416
D L T Q FI ++ HP++ E A + VHPD +LE+ Y+
Sbjct: 192 DYLCGT---GQKAFIAELMPKHPIYVHLLSEEAQAVIGQVHPDTAPARAVLEKEGFRYRG 248
Query: 417 YI 418
Y+
Sbjct: 249 YV 250
>gnl|CDD|188336 TIGR03535, DapD_actino,
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
N-succinyltransferase. This enzyme is part of the
diaminopimelate pathway of lysine biosynthesis. This
model represents a clade of the enzyme specific to
Actinobacteria. Alternate name: tetrahydrodipicolinate
N-succinyltransferase.
Length = 319
Score = 29.3 bits (66), Expect = 4.5
Identities = 17/53 (32%), Positives = 20/53 (37%), Gaps = 2/53 (3%)
Query: 42 KKDRGGPPGRTVPMSHISGVKRPLTHTNSFTG--EKLPKHGVETASEEELGNN 92
GGP G V +SG L NS +G E L + G E L N
Sbjct: 267 PVAAGGPDGEVVKARELSGASNLLFRRNSVSGAVEALARKGQGIELNEALHAN 319
>gnl|CDD|179571 PRK03369, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 488
Score = 29.3 bits (66), Expect = 4.5
Identities = 9/26 (34%), Positives = 18/26 (69%)
Query: 426 WADLVHPDAQEILDMLEENRDWYQSM 451
WA + P+A +L++ E++ DW+ +M
Sbjct: 178 WAPSLRPEAGAVLNIAEDHLDWHGTM 203
>gnl|CDD|219804 pfam08346, AntA, AntA/AntB antirepressor. In E. coli the two
proteins AntA and AntB have 62% amino acid identities
near their N termini. AntA appears to be encoded by a
truncated and divergent copy of AntB. The two proteins
are homologous to putative antirepressors found in
numerous bacteriophages, such as the hypothetical
antirepressor protein encoded by the gene LO142 of the
bacteriophage 933W.
Length = 70
Score = 26.4 bits (59), Expect = 6.9
Identities = 8/39 (20%), Positives = 16/39 (41%)
Query: 251 NEGCDILCNLNKKQKQTLRKMVIDMVLSTDMSKHMSLLA 289
E D + K + D L+ DM+K ++++
Sbjct: 30 VENQDFIVVSQKVSNGKGGRPRKDYALTLDMAKELAMME 68
>gnl|CDD|227055 COG4711, COG4711, Predicted membrane protein [Function unknown].
Length = 217
Score = 28.2 bits (63), Expect = 8.6
Identities = 16/66 (24%), Positives = 21/66 (31%), Gaps = 1/66 (1%)
Query: 241 NLAVAFKLLQNEGCDILCNLNKKQKQTLRKMVIDMVLSTDMSKHMSLLADLKTMVETK-K 299
L V F L G N + TL M I + S M + D ++ E K
Sbjct: 8 MLPVLFLLNYYIGFRKRKNWREAVIDTLEAMAIGFICSAAMLWLFGEMTDKLSLKEIVIK 67
Query: 300 VAGSGV 305
V
Sbjct: 68 EVFESV 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 0.0564 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,657,594
Number of extensions: 2404397
Number of successful extensions: 2399
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2390
Number of HSP's successfully gapped: 25
Length of query: 484
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 383
Effective length of database: 6,457,848
Effective search space: 2473355784
Effective search space used: 2473355784
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: 41 (21.6 bits)
S2: 61 (27.6 bits)