RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10329
(606 letters)
>gnl|CDD|216736 pfam01843, DIL, DIL domain. The DIL domain has no known function.
Length = 105
Score = 110 bits (277), Expect = 7e-29
Identities = 42/93 (45%), Positives = 61/93 (65%), Gaps = 2/93 (2%)
Query: 467 QVFKQLYYYIGASSLNNLLLRKELCHWTRGMQIRYNLSHLEQFTRDNKMADGEINEQLSP 526
Q+F QL+Y+I A N+LLLR++ C W+RG+QIRYNLS LE + R + + E L P
Sbjct: 1 QLFSQLFYFINAQLFNSLLLRRDFCSWSRGLQIRYNLSLLEDWCRSAGLEEA-AWEHLEP 59
Query: 527 LIQASQLLQARK-TQEDVNTVCEMCNKMSTNQL 558
L QA LLQ +K T ED+ +C++C ++ Q+
Sbjct: 60 LRQAVNLLQIKKSTIEDIEILCDLCPALNPAQI 92
>gnl|CDD|227355 COG5022, COG5022, Myosin heavy chain [Cytoskeleton].
Length = 1463
Score = 48.2 bits (115), Expect = 1e-05
Identities = 32/131 (24%), Positives = 64/131 (48%), Gaps = 3/131 (2%)
Query: 443 DLQALLMSFYKLLVLHGIDMEIINQVFKQLYYYIGASSLNNLLLRKELCHWTRGMQIRYN 502
L +LL S LL + ++ E++ L YI N L + W ++ YN
Sbjct: 1260 KLLSLLNSIDNLLSSYKLEEEVLPATINSLLQYINVGLFNALRTKASSLRWKSATEVNYN 1319
Query: 503 LSHLEQFTRDNKMADGEINEQLSPLIQASQLLQARK-TQEDVNTVCEMCNKMSTNQLESL 561
L+ + R+ +++D +E+L LIQA ++LQ K ++ + + C ++ ++++L
Sbjct: 1320 SEELDDWCREFEISDV--DEELEELIQAVKVLQLLKDDLNKLDELLDACYSLNPAEIQNL 1377
Query: 562 ENELNRARTEN 572
++ + A EN
Sbjct: 1378 KSRYDPADKEN 1388
Score = 28.9 bits (65), Expect = 9.9
Identities = 31/164 (18%), Positives = 54/164 (32%), Gaps = 35/164 (21%)
Query: 15 VVKKRYEDLDSTILWLTNLLRLLNLLKQYSGEKAFQTDNTEVQNAQCLANFDFREYRQVL 74
KKR+ L ++L + R+ +Q K D + + L
Sbjct: 856 KAKKRFSLLKKETIYLQSAQRVELAERQLQELKI---DVKSISS---------------L 897
Query: 75 SDTGVQLESEVDELKTRLMNDREKYLSEIQGLQDKNIKLSECLSKTYSTDVSHTQDSSST 134
++LESE+ ELK + +N++ L + + D
Sbjct: 898 KLVNLELESEIIELK-----------KSLSSDLIENLEFKTELIARL-KKLLNNIDLEEG 945
Query: 135 TSLESITPDHYLKIEVLKLVEENLKLKQALEVASASKDENEITR 178
S+E + E+ KL E KLK+ E ++ I
Sbjct: 946 PSIEYVKLP-----ELNKLHEVESKLKETSEEYEDLLKKSTILV 984
>gnl|CDD|153295 cd07611, BAR_Amphiphysin_I_II, The Bin/Amphiphysin/Rvs (BAR) domain
of Amphiphysin I and II. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions.
Amphiphysins function primarily in endocytosis and other
membrane remodeling events. They contain an N-terminal
BAR domain with an additional N-terminal amphipathic
helix (an N-BAR), a variable central domain, and a
C-terminal SH3 domain. Amphiphysin I proteins, enriched
in the brain and nervous system, contain domains that
bind clathrin, Adaptor Protein complex 2 (AP2), dynamin
and synaptojanin. They function in synaptic vesicle
endocytosis. Some amphiphysin II isoforms, also called
Bridging integrator 1 (Bin1), are localized in many
different tissues and may function in intracellular
vesicle trafficking. In skeletal muscle, Bin1 plays a
role in the organization and maintenance of the T-tubule
network. The N-BAR domain of amphiphysin forms a curved
dimer with a positively-charged concave face that can
drive membrane bending and curvature. Human
autoantibodies to amphiphysin-1 hinder GABAergic
signaling and contribute to the pathogenesis of
paraneoplastic stiff-person syndrome. Mutations in
amphiphysin-2 (BIN1) are associated with autosomal
recessive centronuclear myopathy.
Length = 211
Score = 34.9 bits (80), Expect = 0.066
Identities = 14/35 (40%), Positives = 22/35 (62%)
Query: 90 TRLMNDREKYLSEIQGLQDKNIKLSECLSKTYSTD 124
TRL + YL+ I+G+Q+ + KL+E L + Y D
Sbjct: 29 TRLQRELRAYLAAIKGMQEASKKLTESLHEVYEPD 63
>gnl|CDD|185769 cd09246, BRO1_Alix_like_1, Protein-interacting, N-terminal,
Bro1-like domain of an Uncharacterized family of the
BRO1_Alix_like superfamily. This domain family is
comprised of uncharacterized proteins. It belongs to the
BRO1_Alix_like superfamily which includes the Bro1-like
domains of mammalian Alix (apoptosis-linked gene-2
interacting protein X), His-Domain type N23 protein
tyrosine phosphatase (HD-PTP, also known as PTPN23),
RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and
Rim20 (also known as PalA) from Saccharomyces
cerevisiae, Ustilago maydis Rim23 (also known as PalC),
and related domains. Alix, HD-PTP, Brox, Bro1, Rim20 and
Rim23 interact with the ESCRT (Endosomal Sorting
Complexes Required for Transport) system. Alix
participates in membrane remodeling processes during the
budding of enveloped viruses, vesicle budding inside
late endosomal multivesicular bodies (MVBs), and the
abscission reactions of mammalian cell division. It also
functions in apoptosis. HD-PTP and Bro1 function in
endosomal trafficking, with HD-PTP having additional
functions in cell migration. Rim20 and Rim23 play roles
in the response to the external pH via the Rim101
pathway. Bro1-like domains are boomerang-shaped, and
part of the domain is a tetratricopeptide repeat
(TPR)-like structure. Bro1-like domains bind components
of the ESCRT-III complex: CHMP4 (in the case of Alix,
Brox and HD-PTP) and Snf7 (in the case of yeast Bro1 and
Rim20). The Bro1-like domains of Alix, HD-PTP, Brox, and
Rhophilin can bind human immunodeficiency virus type 1
(HIV-1) nucleocapsid. In addition to this Bro1-like
domain, Alix, Bro1, Rim20, HD_PTP, and proteins
belonging to this uncharacterized family, also have a
V-shaped (V) domain. The Alix V-domain is a dimerization
domain, and contains a binding site for the retroviral
late assembly (L) domain YPXnL motif, which is partially
conserved in the BRO1_Alix_like superfamily. Many
members of this superfamily also have a proline-rich
region (PRR), a protein interaction domain.
Length = 353
Score = 31.6 bits (72), Expect = 1.2
Identities = 28/137 (20%), Positives = 50/137 (36%), Gaps = 14/137 (10%)
Query: 451 FYKLLVLHGIDMEIINQVFKQ--LYY-----YIGASSLNNLLLRKELCHWTRGMQIRYNL 503
FY+ V G + +++ KQ YY + + L + W +Q++
Sbjct: 189 FYEKAVADGKSPAVCSKLAKQARSYYEEALEALDSPPLKGHFDKS----WVAHVQLKAAY 244
Query: 504 SHLEQFTRDNKM--ADGEINEQLSPLIQASQLLQARKTQEDVNTVCEMCNKMSTNQLESL 561
E R K +I E+++ L AS L + Q E+ +S + + +
Sbjct: 245 FRAEALYRAAKDLHEKEDIGEEIARLRAASDALAEARKQAKGVNGDELIEAVSELE-QVI 303
Query: 562 ENELNRARTENADLRHV 578
L RA EN +
Sbjct: 304 NELLERAEKENDCVYLD 320
>gnl|CDD|201379 pfam00661, Matrix, Viral matrix protein. Found in Morbillivirus
and paramyxovirus, pneumovirus.
Length = 348
Score = 30.8 bits (70), Expect = 2.0
Identities = 14/53 (26%), Positives = 24/53 (45%)
Query: 230 MFEFEKSDINIIMKRLITDKFLEGISVVFNACNVIRKKERTYLGMFEFEKSDI 282
E + ++K L+ D +G SV + N+ +KK + E+ KS I
Sbjct: 204 TLRIECKPDSPLVKSLLDDDGGKGASVWVHLGNITKKKNKKKSYSVEYCKSKI 256
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein. Members of this
protein family have a signal peptide, a strongly
conserved SH3 domain, a variable region, and then a
C-terminal hydrophobic transmembrane alpha helix region.
Length = 198
Score = 29.6 bits (67), Expect = 3.6
Identities = 28/110 (25%), Positives = 44/110 (40%), Gaps = 15/110 (13%)
Query: 80 QLESEVDELKTRLMNDREKY---LSEIQGLQDKNIKLSECLSKTYSTDVSHTQDSSSTTS 136
+L+ E+ EL+ L +E+ E Q L+ + L L + Q S++
Sbjct: 70 ELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQLSANAIE 129
Query: 137 LESITPDHYLKIEVLKLVEENLKLKQALEVASASKD---ENEITRMIVEG 183
L+ E +L EE +LKQ E A + ENE R + G
Sbjct: 130 LDE---------ENRELREELAELKQENEALEAENERLQENEQRRWFLYG 170
>gnl|CDD|233884 TIGR02478, 6PF1K_euk, 6-phosphofructokinase, eukaryotic type.
Members of this family are eukaryotic (with one
exception) ATP-dependent 6-phosphofructokinases (EC
2.7.1.11) in which two tandem copies of the
phosphofructokinase are found. Members are found, often
including several isozymes, in animals and fungi and in
the bacterium Propionibacterium acnes KPA171202 (a human
skin commensal).
Length = 746
Score = 30.0 bits (68), Expect = 4.7
Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 10/47 (21%)
Query: 79 VQLESEVDELKTRLMNDREKYLSEIQGLQDKNIKLSECLSKTYSTDV 125
L+ +++ LK R L I +E SK Y+TD
Sbjct: 592 KDLQEDIEHLKETFAEGRAGKL----------ILRNEKASKVYTTDF 628
>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of
this protein are LonB, a paralog of the ATP-dependent
protease La (LonA, TIGR00763). LonB proteins are found
strictly, and almost universally, in endospore-forming
bacteria. This protease was shown, in Bacillus subtilis,
to be expressed specifically in the forespore, during
sporulation, under control of sigma(F). The lonB gene,
despite location immediately upstream of lonA, was shown
to be monocistronic. LonB appears able to act on
sigma(H) for post-translation control, but lonB mutation
did not produce an obvious sporulation defect under the
conditions tested. Note that additional paralogs of LonA
and LonB occur in the Clostridium lineage and this model
selects only one per species as the protein that
corresponds to LonB in B. subtilis [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Cellular processes, Sporulation and germination].
Length = 531
Score = 29.7 bits (67), Expect = 5.0
Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 12/78 (15%)
Query: 164 LEV-ASASKDENEITRMIVEGSSSPPSLDEESMLGHHDSLIMSNSKLNVSVSNSCNVIRK 222
LEV A+A + EN + V G ++EE + G S+ S SV N V+
Sbjct: 365 LEVEATAERAENLPGSINVTGI-----IEEEEIGGSGKSVR-RKSSARGSVENVLAVL-- 416
Query: 223 KERTYLGMFEFEKSDINI 240
R+ G+ + DI+I
Sbjct: 417 --RSVFGI-NPQNYDIHI 431
>gnl|CDD|226175 COG3649, COG3649, CRISPR system related protein [Defense
mechanisms].
Length = 283
Score = 29.2 bits (65), Expect = 6.5
Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 3/77 (3%)
Query: 12 VKRVVKKRYEDLDSTILWLTN---LLRLLNLLKQYSGEKAFQTDNTEVQNAQCLANFDFR 68
+KR ++ R D+ I T + +L ++ E + + E++N C D R
Sbjct: 46 IKRKIRNRLADMYDEIFVQTGERVVDDFRSLEDRFVKELGAKDVDKEIENDACQKWIDVR 105
Query: 69 EYRQVLSDTGVQLESEV 85
+ QV + + S V
Sbjct: 106 LFGQVFPQSKKGMSSGV 122
>gnl|CDD|237616 PRK14127, PRK14127, cell division protein GpsB; Provisional.
Length = 109
Score = 27.7 bits (62), Expect = 6.5
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 8/60 (13%)
Query: 84 EVDELKTRLMNDREKYLSEIQGLQDKNIKLS---ECLSKT-----YSTDVSHTQDSSSTT 135
EVD+ ++ D E + EI+ LQ +N +L + L+K S+ V+ TQ SSS T
Sbjct: 27 EVDKFLDDVIKDYEAFQKEIEELQQENARLKAQVDELTKQVSVGASSSSVATTQPSSSAT 86
>gnl|CDD|213277 cd05909, AAS_C, C-terminal domain of the acyl-acyl carrier protein
synthetase (also called 2-acylglycerophosphoethanolamine
acyltransferase, Aas). Acyl-acyl carrier protein
synthase (Aas) is a membrane protein responsible for a
minor pathway of incorporating exogenous fatty acids
into membrane phospholipids. Its in vitro activity is
characterized by the ligation of free fatty acids
between 8 and 18 carbons in length to the acyl carrier
protein sulfydryl group (ACP-SH) in the presence of ATP
and Mg2+. However, its in vivo function is as a
2-acylglycerophosphoethanolamine (2-acyl-GPE)
acyltransferase. The reaction occurs in two steps: the
acyl chain is first esterified to acyl carrier protein
(ACP) via a thioester bond, followed by a second step
where the acyl chain is transferred to a
2-acyllysophospholipid, thus completing the
transacylation reaction. This model represents the
C-terminal domain of the enzyme, which belongs to the
class I adenylate-forming enzyme family, including
acyl-CoA synthetases.
Length = 489
Score = 29.1 bits (66), Expect = 7.4
Identities = 9/27 (33%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 403 EEKINSIVIPA-ILEFESIPVMSSGKP 428
E + ++ +P IL + IP++ SGK
Sbjct: 454 EAGLPNLAVPRKILHVDEIPLLGSGKT 480
>gnl|CDD|187590 cd05329, TR_SDR_c, tropinone reductase-I and II (TR-1, and
TR-II)-like, classical (c) SDRs. This subgroup includes
TR-I and TR-II; these proteins are members of the SDR
family. TRs catalyze the NADPH-dependent reductions of
the 3-carbonyl group of tropinone, to a beta-hydroxyl
group. TR-I and TR-II produce different stereoisomers
from tropinone, TR-I produces tropine
(3alpha-hydroxytropane), and TR-II, produces
pseudotropine (sigma-tropine, 3beta-hydroxytropane).
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 251
Score = 28.6 bits (64), Expect = 9.6
Identities = 25/106 (23%), Positives = 43/106 (40%), Gaps = 27/106 (25%)
Query: 151 LKLVEENLKLKQALEVASASKDENEITR---------MIVEGSSSPPSLDEESMLGHHDS 201
+VEE L EV + ++++ E+ VEGS S E
Sbjct: 20 YAIVEELAGL--GAEVYTCARNQKELDECLTEWREKGFKVEGSVCDVSSRSE-----RQE 72
Query: 202 LI-----MSNSKLNVSVSNSCNVIRKKERTYLGMFEFEKSDINIIM 242
L+ KLN+ V+N+ IRK+ + ++ + D ++IM
Sbjct: 73 LMDTVASHFGGKLNILVNNAGTNIRKEAK------DYTEEDYSLIM 112
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
0.318 0.133 0.368
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 29,783,733
Number of extensions: 2906230
Number of successful extensions: 2791
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2781
Number of HSP's successfully gapped: 54
Length of query: 606
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 503
Effective length of database: 6,369,140
Effective search space: 3203677420
Effective search space used: 3203677420
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 (21.7 bits)
S2: 62 (27.5 bits)