RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9628
(112 letters)
>gnl|CDD|213394 cd12151, F1-ATPase_gamma, mitochondrial ATP synthase gamma subunit.
The F-ATPase is found in bacterial plasma membranes,
mitochondrial inner membranes and in chloroplast
thylakoid membranes. It has also been found in the
archaea Methanosarcina barkeri. It uses a proton
gradient to drive ATP synthesis and hydrolyzes ATP to
build the proton gradient. The extrinisic membrane
domain of F-ATPases is composed of alpha, beta, gamma,
delta, and epsilon (not present in bacteria) subunits
with a stoichiometry of 3:3:1:1:1. Alpha and beta
subunit form the globular catalytic moiety, a hexameric
ring of alternating subunits. Gamma, delta and epsilon
subunits form a stalk, connecting F1 to F0, the integral
membrane proton translocating domain.
Length = 282
Score = 61.4 bits (150), Expect = 1e-12
Identities = 26/93 (27%), Positives = 38/93 (40%), Gaps = 4/93 (4%)
Query: 16 IITIGDKSRAILQRLYGNNIILAANEVGRRPPTFLDASKVAQETSKY---NFTSGKIIYN 72
+I +G K R L+R G NI L +++G P F AS + + + IIYN
Sbjct: 112 LIVVGKKGRDYLKRR-GYNIALPFSDIGDDPTYFEAASIIEELILDFLNGEIDEVYIIYN 170
Query: 73 KFKSVVSYTTSDLPIFSLASVTAAPKLGVYDSL 105
KFKS +S + L + S
Sbjct: 171 KFKSAISQEPVVEQLLPLDKEEEEEESEGSRSD 203
>gnl|CDD|233292 TIGR01146, ATPsyn_F1gamma, ATP synthase, F1 gamma subunit. This
model describes the ATP synthase gamma subunit in
bacteria and its equivalents in organelles, namely,
mitochondria and chloroplast. F1/F0-ATP synthase is a
multisubunit, membrane associated enzyme found in
bacteria and organelles of higher eukaryotes, namely,
mitochondria and chloroplast. This enzyme is principally
involed in the synthesis of ATP from ADP and inorganic
phosphate by coupling the energy derived from the proton
electrochemical gradient across the biological membrane.
A brief description of this multisubunit enzyme complex:
F1 and F0 represent two major clusters of subunits. The
gamma subunit is the part of F1 cluster. Surrounding the
gamma subunit in a cylinder-like structure are three
alpha and three subunits in an alternating fashion. This
is the central catalytic unit whose different
conformations permit the binding of ADP and inorganic
phosphate and release of ATP [Energy metabolism,
ATP-proton motive force interconversion].
Length = 286
Score = 54.2 bits (131), Expect = 7e-10
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 15 QIITIGDKSRAILQRLYGNNIILAANEVGRRPPTFLDASKVAQET----SKYNFTSGKII 70
+++ IG K R+ +R G+NI+ + + PTF +AS +A + F I+
Sbjct: 113 KLVVIGRKGRSFFKR-RGDNIVASVTGLSD-QPTFEEASGIADKLLDAFDSGEFDEVYIV 170
Query: 71 YNKFKSVVSYTTSDLPIFSL 90
YNKF SV+S + + L
Sbjct: 171 YNKFVSVISQEPTVKQLLPL 190
>gnl|CDD|215808 pfam00231, ATP-synt, ATP synthase.
Length = 288
Score = 51.0 bits (123), Expect = 8e-09
Identities = 24/88 (27%), Positives = 42/88 (47%), Gaps = 8/88 (9%)
Query: 16 IITIGDKSRAILQRLYGNNIILAANEVGRRPPTFLDASKVAQETSKYNFTSGK-----II 70
+I IG K R +R G NII +G PTF +A+++A E + F +G+ ++
Sbjct: 115 LIVIGKKGRDFFKRR-GKNIIAEFTGLGD-KPTFEEAAEIADELIE-LFLNGEYDEVYLV 171
Query: 71 YNKFKSVVSYTTSDLPIFSLASVTAAPK 98
YNKF + +S + + + +
Sbjct: 172 YNKFVNALSQEPTVEQLLPIDIEEEEEE 199
>gnl|CDD|235535 PRK05621, PRK05621, F0F1 ATP synthase subunit gamma; Validated.
Length = 284
Score = 41.6 bits (99), Expect = 2e-05
Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 8/70 (11%)
Query: 15 QIITIGDKSRAILQRLYGNNIILAANEVGRRPPTFLDASKVAQETSKYNFTSGK-----I 69
++I IG K +R N ++ +G +P TF +A +A++ + +G+ I
Sbjct: 113 KLIVIGRKGVDFFKRRGIN-VVAEYTGLGDQP-TFEEAIGIAKKLLDA-YDNGEFDELYI 169
Query: 70 IYNKFKSVVS 79
+YNKF + +S
Sbjct: 170 VYNKFVNTLS 179
>gnl|CDD|223302 COG0224, AtpG, F0F1-type ATP synthase, gamma subunit [Energy
production and conversion].
Length = 287
Score = 37.6 bits (88), Expect = 5e-04
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 8/70 (11%)
Query: 16 IITIGDKSRAILQRLYGNNIILAANEVGRRPPTFLDASKVAQETSKYNFTSGK-----II 70
+I IG K ++ G NI+ + +G P +F +A ++A + F G+ ++
Sbjct: 112 LILIGKKGIDFFKKR-GYNILESFTGLGDNP-SFEEAIQIADKILDA-FLEGEIDELYLV 168
Query: 71 YNKFKSVVSY 80
YNKFK+ +S
Sbjct: 169 YNKFKNALSQ 178
>gnl|CDD|176917 cd08908, START_STARD12-like, C-terminal lipid-binding START domain
of mammalian STARD12 and related proteins, which also
have an N-terminal Rho GTPase-activating protein
(RhoGAP) domain. This subgroup includes the
steroidogenic acute regulatory protein (StAR)-related
lipid transfer (START) domains of STARD12 (also known as
DLC-1, Arhgap7, and p122-RhoGAP) and related proteins.
It belongs to the START domain family, and in turn to
the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC)
domain superfamily of proteins that bind hydrophobic
ligands. SRPBCC domains have a deep hydrophobic
ligand-binding pocket. Proteins belonging to this
subgroup also have an N-terminal SAM (sterile alpha
motif) domain and a RhoGAP domain, and have a
SAM-RhoGAP-START domain organization. The precise
function of the START domain in this subgroup is
unclear.
Length = 204
Score = 27.7 bits (61), Expect = 1.2
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 68 KIIYNKFKSVVSYTTSDLPIFSLASVTAAPKLGVYDSLWKRCVE 111
K + KFK VSY+TS+ S V+ P L LW+ +E
Sbjct: 20 KEVKEKFKGWVSYSTSEQAELSYKKVSEGPPL----RLWRTTIE 59
>gnl|CDD|116100 pfam07479, NAD_Gly3P_dh_C, NAD-dependent glycerol-3-phosphate
dehydrogenase C-terminus. NAD-dependent
glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the
interconversion of dihydroxyacetone phosphate and
L-glycerol-3-phosphate. This family represents the
C-terminal substrate-binding domain.
Length = 145
Score = 26.0 bits (58), Expect = 3.5
Identities = 9/40 (22%), Positives = 16/40 (40%)
Query: 17 ITIGDKSRAILQRLYGNNIILAANEVGRRPPTFLDASKVA 56
+ GD ++A L +I +G P TF + +
Sbjct: 26 LGFGDNTKAALITRGLMEMIKFGAALGGGPETFFGLAGLG 65
>gnl|CDD|217703 pfam03737, Methyltransf_6, Demethylmenaquinone methyltransferase.
Members of this family are demethylmenaquinone
methyltransferases that convert dimethylmenaquinone
(DMK) to menaquinone (MK) in the final step of
menaquinone biosynthesis. This region is also found at
the C-terminus of the DlpA protein.
Length = 154
Score = 25.7 bits (57), Expect = 4.3
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 58 ETSKYNFTSGKIIYNKFKSVVSYTTSDLPIFSLASV-TAAPKLGVYD 103
+K N G ++Y + V + DLPIF+L + AA K G+ +
Sbjct: 81 TLAKKNGWEGVVVYGCVRDVDALRELDLPIFALGTTPCAAVKTGIGE 127
>gnl|CDD|188015 TIGR00008, infA, translation initiation factor IF-1. This family
consists of translation initiation factor IF-1 as found
in bacteria and chloroplasts. This protein, about 70
residues in length, consists largely of an S1 RNA
binding domain (pfam00575) [Protein synthesis,
Translation factors].
Length = 69
Score = 25.0 bits (55), Expect = 4.5
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 54 KVAQETSKYNFTSGKIIYNK 73
+V E S Y+ T G+I Y
Sbjct: 50 RVKVELSPYDLTRGRITYRL 69
>gnl|CDD|214332 CHL00010, infA, translation initiation factor 1.
Length = 78
Score = 25.0 bits (55), Expect = 5.6
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 54 KVAQETSKYNFTSGKIIY 71
+V E S Y+ T G+IIY
Sbjct: 52 RVKVELSPYDLTKGRIIY 69
>gnl|CDD|241338 cd13184, FERM_C_4_1_family, Protein 4.1 family FERM domain C-lobe.
The protein 4.1 family includes four well-defined
members: erythroid protein 4.1 (4.1R), the bestknown and
characterized member, 4.1G (general), 4.1N (neuronal),
and 4.1 B (brain). The less well understood 4.1O/FRMD3
is not a true member of this family and is not included
in this hierarchy. Besides three highly conserved
domains, FERM, SAB (spectrin and actin binding domain)
and CTD (C-terminal domain), the proteins from this
family contain several unique domains: U1, U2 and U3.
FERM domains like other members of the FERM domain
superfamily have a cloverleaf architecture with three
distinct lobes (FERM_N, FERM_M, FERM_C/N, alpha-, and
C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3). The C-lobe/F3
within the FERM domain is part of the PH domain family.
The brain is a particularly rich source of protein 4.1
isoforms. The various 4.1R, 4.1G, 4.1N, and 4.1B mRNAs
are all expressed in distinct patterns within the brain.
It is likely that 4.1 proteins play important functional
roles in the brain including motor coordination and
spatial learning, postmitotic differentiation, and
synaptic architecture and function. In addition they are
found in nonerythroid, nonneuronal cells where they may
play a general structural role in nuclear architecture
and/or may interact with splicing factors. The FERM C
domain is the third structural domain within the FERM
domain. The FERM domain is found in the
cytoskeletal-associated proteins such as ezrin, moesin,
radixin, 4.1R, and merlin. These proteins provide a link
between the membrane and cytoskeleton and are involved
in signal transduction pathways. The FERM domain is also
found in protein tyrosine phosphatases (PTPs) , the
tyrosine kinases FAK and JAK, in addition to other
proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 113
Score = 25.3 bits (56), Expect = 5.7
Identities = 10/24 (41%), Positives = 12/24 (50%), Gaps = 6/24 (25%)
Query: 88 FSLASVTAAPKLGVYDSLWKRCVE 111
F L + AA +L WK CVE
Sbjct: 90 FKLPNHRAAKRL------WKVCVE 107
>gnl|CDD|187543 cd05232, UDP_G4E_4_SDR_e, UDP-glucose 4 epimerase, subgroup 4,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
bacterial proteins, and includes the Staphylococcus
aureus capsular polysaccharide Cap5N, which may have a
role in the synthesis of UDP-N-acetyl-d-fucosamine. This
subgroup has the characteristic active site tetrad and
NAD-binding motif of the extended SDRs. Extended SDRs
are distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they 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 numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. 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.
Length = 303
Score = 25.4 bits (56), Expect = 7.2
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 10 PSMTNQIITIGDKSRAILQRLYGN---NIILAANEVGRRPPTFLDAS 53
P+ + RA++QRL+G+ + NE+G RPP L+
Sbjct: 253 PAGLLRFAAKLLGKRAVIQRLFGSLQYDPEKTQNELGWRPPISLEEG 299
>gnl|CDD|234752 PRK00413, thrS, threonyl-tRNA synthetase; Reviewed.
Length = 638
Score = 25.0 bits (56), Expect = 9.3
Identities = 7/13 (53%), Positives = 9/13 (69%)
Query: 20 GDKSRAILQRLYG 32
GD +LQR+YG
Sbjct: 207 GDSKNKMLQRIYG 219
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
0.314 0.128 0.358
Gapped
Lambda K H
0.267 0.0698 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,269,197
Number of extensions: 422406
Number of successful extensions: 372
Number of sequences better than 10.0: 1
Number of HSP's gapped: 365
Number of HSP's successfully gapped: 23
Length of query: 112
Length of database: 10,937,602
Length adjustment: 76
Effective length of query: 36
Effective length of database: 7,566,698
Effective search space: 272401128
Effective search space used: 272401128
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: 53 (24.3 bits)