RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13812
(120 letters)
>gnl|CDD|215884 pfam00375, SDF, Sodium:dicarboxylate symporter family.
Length = 388
Score = 104 bits (261), Expect = 1e-27
Identities = 50/108 (46%), Positives = 67/108 (62%)
Query: 6 DTVGQLGLYFITVLLGLLIHGFILLPAMYTFFVREWPFRFTANMGQAIATAFGTASRLFI 65
T+G LG + +TV L L IH F++ P + F PF+F + A+ TAF TAS
Sbjct: 200 GTLGSLGKFVLTVYLALAIHLFVVYPLLLKFLTGLNPFKFLKKILPALLTAFSTASSAAT 259
Query: 66 GYNAMQCLEENNKIDPRISRFVMPIGATINMDGTALYEAVAAIFIAQV 113
++C E+N + I+ FV+P+GATINMDGTA+Y AVAAIFIAQ
Sbjct: 260 LPVTLECAEKNLGVSKSIASFVLPLGATINMDGTAIYLAVAAIFIAQA 307
>gnl|CDD|224220 COG1301, GltP, Na+/H+-dicarboxylate symporters [Energy production
and conversion].
Length = 415
Score = 93.1 bits (232), Expect = 1e-23
Identities = 37/108 (34%), Positives = 60/108 (55%)
Query: 6 DTVGQLGLYFITVLLGLLIHGFILLPAMYTFFVREWPFRFTANMGQAIATAFGTASRLFI 65
++ LG + V LGLL+ F++L + PF+F + +A+ AF T+S
Sbjct: 209 GSLLSLGKLVLAVYLGLLLFVFVVLGLLLKLLSGFSPFKFLRYISEALLLAFSTSSSEAT 268
Query: 66 GYNAMQCLEENNKIDPRISRFVMPIGATINMDGTALYEAVAAIFIAQV 113
M+ E++ + I FV+P+G T N+DGTA+Y+ +AA+FIAQ
Sbjct: 269 LPVTMEKAEKSLGVPKSIVSFVVPLGYTFNLDGTAIYQTLAALFIAQA 316
>gnl|CDD|183075 PRK11283, gltP, glutamate/aspartate:proton symporter; Provisional.
Length = 437
Score = 42.8 bits (101), Expect = 9e-06
Identities = 17/31 (54%), Positives = 26/31 (83%)
Query: 83 ISRFVMPIGATINMDGTALYEAVAAIFIAQV 113
I+ FV+P G + N+DG+ LY+++AAIFIAQ+
Sbjct: 300 ITSFVVPTGYSFNLDGSTLYQSIAAIFIAQL 330
>gnl|CDD|234968 PRK01663, PRK01663, C4-dicarboxylate transporter DctA; Reviewed.
Length = 428
Score = 35.3 bits (82), Expect = 0.003
Identities = 14/27 (51%), Positives = 21/27 (77%)
Query: 87 VMPIGATINMDGTALYEAVAAIFIAQV 113
V+P G + N+DGT++Y +AA+FIAQ
Sbjct: 293 VIPTGYSFNLDGTSIYLTMAAVFIAQA 319
>gnl|CDD|183850 PRK13027, PRK13027, C4-dicarboxylate transporter DctA; Reviewed.
Length = 421
Score = 32.7 bits (75), Expect = 0.030
Identities = 29/101 (28%), Positives = 48/101 (47%), Gaps = 16/101 (15%)
Query: 15 FITVLLGLL--IHGFILLPAMYTFFVREWPFRFTANMGQAIATAFGTASRLFIGYNAMQC 72
F+ V+LG + + GF + + ++RE + GTAS + M+
Sbjct: 233 FVVVVLGAVMRLAGFSVFKLIR--YLRE-----------ELLIVLGTASSDAVLPQVMRK 279
Query: 73 LEENNKIDPRISRFVMPIGATINMDGTALYEAVAAIFIAQV 113
LE + I V+P G + N+DG ++Y +AA+FIAQ
Sbjct: 280 LE-HMGIKDSTVGLVIPTGYSFNLDGFSIYLTLAAVFIAQA 319
>gnl|CDD|173158 PRK14695, PRK14695, serine/threonine transporter SstT; Provisional.
Length = 319
Score = 29.6 bits (66), Expect = 0.32
Identities = 25/107 (23%), Positives = 49/107 (45%), Gaps = 8/107 (7%)
Query: 1 MKSLSD----TVGQLGLYFITVLLGLLIHGFILLPAMYTFFVREWPFRFTANMGQ--AIA 54
K++SD ++ G+ + ++ +L ++ P + FF+R P+ N + +
Sbjct: 113 FKTISDKGVGSLANYGILLVLLVTTMLFVAPVVNPLIAFFFMRRNPYPLVWNCLRVSGVT 172
Query: 55 TAFGTASRLFIGYNAMQCLEENNKIDPRISRFVMPIGATINMDGTAL 101
F +S I N C + ++P +P+G+TINM G A+
Sbjct: 173 AFFTRSSATNIPVNMKLC--HDLGLNPDTYSVSIPLGSTINMAGVAI 217
>gnl|CDD|220299 pfam09586, YfhO, Bacterial membrane protein YfhO. This protein is
a conserved membrane protein. The yfhO gene is
transcribed in Difco sporulation medium and the
transcription is affected by the YvrGHb two-component
system. Some members of this family have been annotated
as glycosyl transferases of the PMT family.
Length = 835
Score = 28.7 bits (65), Expect = 0.78
Identities = 8/28 (28%), Positives = 12/28 (42%)
Query: 10 QLGLYFITVLLGLLIHGFILLPAMYTFF 37
Q + I+ LL I +LLP +
Sbjct: 212 QFLRFIISSLLSGGISAVVLLPTVLGLL 239
>gnl|CDD|176887 cd08878, RHO_alpha_C_DMO-like, C-terminal catalytic domain of the
oxygenase alpha subunit of dicamba O-demethylase and
related aromatic ring hydroxylating dioxygenases.
C-terminal catalytic domain of the oxygenase alpha
subunit of Stenotrophomonas maltophilia dicamba
O-demethylase (DMO) and related Rieske-type non-heme
iron aromatic ring-hydroxylating oxygenases (RHOs, also
known as aromatic ring hydroxylating dioxygenases). RHOs
utilize non-heme Fe(II) to catalyze the addition of
hydroxyl groups to the aromatic ring, an initial step in
the oxidative degradation of aromatic compounds. RHOs
are composed of either two or three protein components,
and are comprised of an electron transport chain (ETC)
and an oxygenase. The ETC transfers reducing equivalents
from the electron donor to the oxygenase component,
which in turn transfers electrons to the oxygen
molecules. The oxygenase components are oligomers,
either (alpha)n or (alpha)n(beta)n. The alpha subunits
are the catalytic components and have an N-terminal
domain, which binds a Rieske-like 2Fe-2S cluster, and
the C-terminal catalytic domain which binds the non-heme
Fe(II). The Fe(II) is co-ordinated by conserved His and
Asp residues. Oxygenases belonging to this subgroup
include the alpha subunits of carbazole
1,9a-dioxygenase, phthalate dioxygenase, vanillate
O-demethylase, Pseudomonas putida 2-oxoquinoline
8-monooxygenase, and Comamonas testosteroni T-2
p-toluenesulfonate dioxygenase. It also includes the
C-terminal domain of the lignin biphenyl-specific
O-demethylase (LigX) of the 5,5'-dehydrodivanillic acid
O- demethylation system of Sphingomonas paucimobilis
SYK-6. This subfamily belongs 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.
Length = 196
Score = 27.8 bits (62), Expect = 1.4
Identities = 9/63 (14%), Positives = 18/63 (28%)
Query: 58 GTASRLFIGYNAMQCLEENNKIDPRISRFVMPIGATINMDGTALYEAVAAIFIAQVRFVI 117
T R + E R+ F++P I+ + + ++
Sbjct: 55 VTYRRWREDEDPPPFGFEGPVDRWRVIEFLLPNVLLIDPGVAPAGTREQGVRMRVTHWIT 114
Query: 118 PIT 120
PI
Sbjct: 115 PID 117
>gnl|CDD|223097 COG0018, ArgS, Arginyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 577
Score = 27.2 bits (61), Expect = 2.5
Identities = 18/87 (20%), Positives = 28/87 (32%), Gaps = 8/87 (9%)
Query: 13 LYFITVLLGLLIHGFILLPAMYTFFVREWPFRFTANMGQAIATAFGTASRLF--IGYNAM 70
L + LLG +LL + + G + T L G A
Sbjct: 352 LKAVLELLGYGPDKEVLLHQGVGLVRGGEGVKMSTRAGNVV-----TLDDLLDEAGERAP 406
Query: 71 QCLEENNKIDPRISRFVMPIGATINMD 97
+ +EE + + I+ V I A D
Sbjct: 407 EEMEEKEEKNEEIAEVV-GIDAVRYAD 432
>gnl|CDD|225956 COG3422, COG3422, Uncharacterized conserved protein [Function
unknown].
Length = 59
Score = 24.7 bits (54), Expect = 4.6
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 40 EWPFRFTANMGQAIATAFGTASR 62
E+ FR A G+ I T+ G S+
Sbjct: 14 EYRFRLKAANGEIILTSEGYKSK 36
>gnl|CDD|240132 cd04862, PaeLigD_Pol_like, PaeLigD_Pol_like: Polymerase (Pol)
domain of bacterial LigD proteins similar to Pseudomonas
aeruginosa (Pae) LigD. The LigD Pol domain belongs to
the archaeal/eukaryal primase (AEP) superfamily. In
prokaryotes, LigD along with Ku is required for
non-homologous end joining (NHEJ)-mediated repair of DNA
double-strand breaks (DSB). NHEJ-mediated DNA DSB repair
is error-prone. PaeLigD is monomeric, containing an
N-terminal phosphoesterase module, a central polymerase
(Pol) domain, and a C-terminal ATP-dependent ligase
domain. It has been suggested that LigD Pol contributes
to NHEJ-mediated DNA DSB repair in vivo, by filling in
short 5'-overhangs with ribonucleotides; the filled in
termini would then be sealed by the associated LigD
ligase domain, resulting in short stretches of RNA
incorporated into the genomic DNA. The PaeLigD Pol
domain in vitro, in a manganese-dependent fashion,
catalyzes templated extensions of 5'-overhang duplex
DNA, and nontemplated single-nucleotide additions to
blunt-end duplex DNA; it preferentially adds single
ribonucleotides at blunt DNA ends. PaeLigD Pol adds a
correctly paired rNTP to the DNA primer termini more
rapidly than it does a correctly paired dNTP; it has
higher infidelity as an RNA polymerase than it does as a
DNA polymerase, which is in keeping with the mutagenic
property of NHEJ-mediated DNA DSB repair.
Length = 227
Score = 26.0 bits (58), Expect = 4.9
Identities = 11/31 (35%), Positives = 14/31 (45%), Gaps = 5/31 (16%)
Query: 37 FVREWPFRFTANMGQAIATAFGTASRLFIGY 67
R P RF A MG+A ++FI Y
Sbjct: 170 LARTNPDRFVATMGKAKRVG-----KIFIDY 195
>gnl|CDD|232787 TIGR00023, TIGR00023, acyl-phosphate glycerol 3-phosphate
acyltransferase. This model represents the full length
of acylphosphate:glycerol 3-phosphate acyltransferase,
and integral membrane protein about 200 amino acids in
length, called PlsY in Streptococcus pneumoniae, YneS in
Bacillus subtilis, and YgiH in E. coli. It is found in a
single copy in a large number of bacteria, including the
Mycoplasmas but not Mycobacteria or spirochetes, for
example. Its partner is PlsX (see TIGR00182), and the
pair can replace PlsB for synthesizing
1-acylglycerol-3-phosphate [Fatty acid and phospholipid
metabolism, Biosynthesis].
Length = 196
Score = 26.2 bits (58), Expect = 5.0
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 3/47 (6%)
Query: 15 FITVLLGLLIHGFILLPAMYTFFV---REWPFRFTANMGQAIATAFG 58
+ V L L+ F LP + +P F G+ +AT+ G
Sbjct: 67 MLAVALSFLLGLFDFLPGLVAIAAVLGHIFPIFFKFKGGKGVATSGG 113
>gnl|CDD|226159 COG3633, SstT, Na+/serine symporter [Amino acid transport and
metabolism].
Length = 407
Score = 25.8 bits (57), Expect = 6.2
Identities = 28/105 (26%), Positives = 47/105 (44%), Gaps = 8/105 (7%)
Query: 3 SLSDT-VGQLGLY--FITVLLG-LLIHGFILLPAMYTFFVREWPFR--FTANMGQAIATA 56
+L++T G L Y + VL+G +L ++ P + + +R P+ T +
Sbjct: 201 TLAETGFGALWGYAQLLAVLVGCMLFVALVVNPLIVYWKIRRNPYPLVLTCLRESGVTAF 260
Query: 57 FGTASRLFIGYNAMQCLEENNKIDPRISRFVMPIGATINMDGTAL 101
F +S I N C + +D +P+GATINM G A+
Sbjct: 261 FTRSSAANIPVNMALC--KKLGLDEDTYSVSIPLGATINMAGAAI 303
>gnl|CDD|176554 cd08613, GDPD_GDE4_like_1, Glycerophosphodiester phosphodiesterase
domain of uncharacterized bacterial homologs of
mammalian glycerophosphodiester phosphodiesterase GDE4.
This subfamily corresponds to the glycerophosphodiester
phosphodiesterase domain (GDPD) present in
uncharacterized bacterial homologs of mammalian GDE4, a
transmembrane protein whose cellular function has not
been elucidated yet.
Length = 309
Score = 25.8 bits (57), Expect = 6.5
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 25 HGFILLPAMYTFFVREWPFRFTANMGQAIATAFGTASRLFIGY 67
+ +L+P Y ++ WP RF A M A GT L Y
Sbjct: 236 NTTLLIPLNYAPWLWGWPNRFLARM-----EAAGTRVILVGPY 273
>gnl|CDD|226143 COG3616, COG3616, Predicted amino acid aldolase or racemase [Amino
acid transport and metabolism].
Length = 368
Score = 25.8 bits (57), Expect = 6.5
Identities = 12/45 (26%), Positives = 17/45 (37%), Gaps = 5/45 (11%)
Query: 45 FTANMGQAIATAFGTASRLFIGYN-----AMQCLEENNKIDPRIS 84
A +G+A A + + Y A+ L E PRIS
Sbjct: 71 TCATLGEAEVFADAGIDDILLAYPLPGRAALAALAELLADPPRIS 115
>gnl|CDD|178342 PLN02741, PLN02741, riboflavin synthase.
Length = 194
Score = 25.4 bits (56), Expect = 7.5
Identities = 11/33 (33%), Positives = 20/33 (60%), Gaps = 6/33 (18%)
Query: 74 EENN-----KIDPRISRFVMPIGATINMDGTAL 101
E ++ K DP + ++++P G I +DGT+L
Sbjct: 115 EGDSLWVKVKADPELLKYIVPKG-FIAVDGTSL 146
>gnl|CDD|224736 COG1823, COG1823, Predicted Na+/dicarboxylate symporter [General
function prediction only].
Length = 458
Score = 25.4 bits (56), Expect = 9.3
Identities = 20/102 (19%), Positives = 41/102 (40%), Gaps = 7/102 (6%)
Query: 11 LGLYFITVLLGLLIHGFILLPAMYTFFVREWPFRFTANMGQAIATAFGTASRLFIGYNAM 70
+ +I + + ++HG +L P ++ + + AF + S +
Sbjct: 264 IVASYIAIFIMFVVHGILL------ALNGVNPIKYFKKVWPVLTFAFTSRSSAATIPLNI 317
Query: 71 QCLEENNKIDPRISRFVMPIGATINMDGTA-LYEAVAAIFIA 111
+ + I+ F GATI +G A +Y A+ A+ +A
Sbjct: 318 ETQTRKLGVPEGIANFAASFGATIGQNGCAGIYPAMLAVMVA 359
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
0.331 0.144 0.431
Gapped
Lambda K H
0.267 0.0801 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,314,834
Number of extensions: 565611
Number of successful extensions: 922
Number of sequences better than 10.0: 1
Number of HSP's gapped: 915
Number of HSP's successfully gapped: 75
Length of query: 120
Length of database: 10,937,602
Length adjustment: 83
Effective length of query: 37
Effective length of database: 7,256,220
Effective search space: 268480140
Effective search space used: 268480140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 53 (24.1 bits)