RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15173
(131 letters)
>gnl|CDD|129679 TIGR00591, phr2, photolyase PhrII. All proteins in this family for
which functions are known are DNA-photolyases used for
the direct repair of UV irradiation induced DNA damage.
Some repair 6-4 photoproducts while others repair
cyclobutane pyrimidine dimers. This family is based on
the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 454
Score = 91.0 bits (226), Expect = 1e-22
Identities = 31/60 (51%), Positives = 40/60 (66%)
Query: 72 QRAVLEVRRVLPKHSKAVDSFCEEAIVRRELADNFCYYNKNYDKVEGAFDWAKKTLNDHR 131
QRA V R ++V+ F EE +VRRELADNFC+YN YD + GA+ WA+ TL+DH
Sbjct: 271 QRAARAVERARGNAGESVEFFEEELVVRRELADNFCFYNPYYDSLCGAYWWARTTLDDHA 330
Score = 76.4 bits (188), Expect = 2e-17
Identities = 34/68 (50%), Positives = 42/68 (61%)
Query: 5 GLKEVHEDCKKLNIEFHFLIGGAHEILPQFVEKHKLGAVVIDFMPLREHMGWADTLKKDL 64
GL EV +C++L I FH L G E+LP FV+ H AVV DF PLR+ W + + K L
Sbjct: 79 GLDEVANECERLIIPFHLLDGPPKELLPYFVDLHAAAAVVTDFSPLRQPEQWDEAVGKLL 138
Query: 65 PKDVPLIQ 72
PKDVP Q
Sbjct: 139 PKDVPFQQ 146
>gnl|CDD|216167 pfam00875, DNA_photolyase, DNA photolyase. This domain binds a
light harvesting cofactor.
Length = 164
Score = 44.1 bits (105), Expect = 2e-06
Identities = 13/69 (18%), Positives = 25/69 (36%), Gaps = 1/69 (1%)
Query: 5 GLKEVHEDCKKLNIEFHFLIGGAHEILPQFVEKHKLGAVVIDFMPLREHMGWADTLKKDL 64
L ++ E KL I G E+LP+ ++ AV + +K+ L
Sbjct: 54 SLADLDESLAKLGIRLVVRRGDPAEVLPELAKELGASAVYWNRDYEPYERQRDAAVKEAL 113
Query: 65 PK-DVPLIQ 72
+ + +
Sbjct: 114 REAGIEVHS 122
>gnl|CDD|217559 pfam03441, FAD_binding_7, FAD binding domain of DNA photolyase.
Length = 276
Score = 39.2 bits (92), Expect = 2e-04
Identities = 11/65 (16%), Positives = 23/65 (35%), Gaps = 11/65 (16%)
Query: 71 IQRAVLEVRR-----VLPKHSKAVDSFCEEAIVRRELADNFCYYNKNYDKVEG-----AF 120
++ VR+ + ++F E ++ RE Y+N + ++
Sbjct: 47 PRQVYQAVRKAQGDSPEGGAKQGAEAFLSE-LIWREFYIQLLYHNPDLERENLNDAYDGL 105
Query: 121 DWAKK 125
WAK
Sbjct: 106 PWAKD 110
>gnl|CDD|223492 COG0415, PhrB, Deoxyribodipyrimidine photolyase [DNA replication,
recombination, and repair].
Length = 461
Score = 32.3 bits (74), Expect = 0.052
Identities = 9/61 (14%), Positives = 21/61 (34%), Gaps = 4/61 (6%)
Query: 71 IQRAVLEVRRVLPKHSKAVDSFCEEAIVRRELADNFCYYNKNYDKVEGAFDWAKKTLNDH 130
+ + + + E ++ RE + + +Y + +A+KTLN
Sbjct: 244 PREVYAALLAAESDAREGTAALINE-LIWRE---FYQHLLYHYPSLSRFEPFAEKTLNIP 299
Query: 131 R 131
Sbjct: 300 W 300
>gnl|CDD|212089 cd11520, SLC5sbd_SMCT2, Na(+)/monocarboxylate cotransporter SMCT2
and related proteins; solute-binding domain. SMCT2 is a
low-affinity transporter for short-chain fatty acids,
lactate, pyruvate, and nicotinate. Human SMCT2 (hSMCT2)
is encoded by the SLC5A12 gene. SMCT2 is expressed in
the kidney, small intestine, skeletal muscle, and
retina. In the kidney, it is expressed in the apical
membrane of the proximal convoluted tubule, along the
entire length of the tubule (in contrast to the
high-affinity monocarboxylate transporter SMCT1,
belonging to a different family, which is limited to the
S3 segment of the tubule). SMCT2 may initiate lactate
absorption in the early parts of the tubule. In the
retina, SMCT1 and SMCT2 may play a differential role in
monocarboxylate transport in a cell type-specific
manner, SMCT2 is expressed exclusively in Muller cells.
Nicotine transport by hSMCT2 is inhibited by several
non-steroidal anti-inflammatory drugs. This subgroup
belongs to the solute carrier 5 (SLC5) transporter
family.
Length = 529
Score = 27.9 bits (62), Expect = 1.9
Identities = 9/32 (28%), Positives = 11/32 (34%)
Query: 25 GGAHEILPQFVEKHKLGAVVIDFMPLREHMGW 56
GG + +L D PLR H W
Sbjct: 206 GGFTNVWETAYNGSRLNIFDFDVDPLRRHTFW 237
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 27.3 bits (61), Expect = 2.5
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 7 KEVHEDCKKLNIEFHFLIGGAHEILPQFVEKHKLGAVVID 46
KE+ E I H ++G H ++ + VE +L V+ID
Sbjct: 328 KELLETIASGQI--HLVVG-THALIQEKVEFKRLALVIID 364
>gnl|CDD|217740 pfam03803, Scramblase, Scramblase. Scramblase is palmitoylated and
contains a potential protein kinase C phosphorylation
site. Scramblase exhibits Ca2+-activated phospholipid
scrambling activity in vitro. There are also possible
SH3 and WW binding motifs. Scramblase is involved in the
redistribution of phospholipids after cell activation or
injury.
Length = 223
Score = 26.2 bits (58), Expect = 4.8
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 40 LGAVVIDFMPL-REHMGWADTLKKDLPKDVPLIQRAVL 76
+G++ + L RE ADT P D+ + +AVL
Sbjct: 172 VGSISRKWGGLGREAFTDADTYVVRFPLDLDVKLKAVL 209
>gnl|CDD|235633 PRK05872, PRK05872, short chain dehydrogenase; Provisional.
Length = 296
Score = 26.1 bits (58), Expect = 5.5
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 13/56 (23%)
Query: 53 HMGWADT-LKKDLPKDVPLIQRAVLEVRRVLP-----KHS--KAVDSFCEEAIVRR 100
++ W DT L +D D+P + E+R LP S K +F + I RR
Sbjct: 185 YLSWIDTDLVRDADADLPAFR----ELRARLPWPLRRTTSVEKCAAAFV-DGIERR 235
>gnl|CDD|234825 PRK00726, murG, undecaprenyldiphospho-muramoylpentapeptide
beta-N- acetylglucosaminyltransferase; Provisional.
Length = 357
Score = 26.2 bits (59), Expect = 5.6
Identities = 16/72 (22%), Positives = 27/72 (37%), Gaps = 7/72 (9%)
Query: 14 KKLNIEFHFLIGGAHEILPQFVEKHKLGAVVIDFMPLREHMGWADTLKKDLPKDVPLIQR 73
KK E + +G A + + V K + I LR A K + +
Sbjct: 26 KKRGWEVLY-LGTARGMEARLVPKAGIEFHFIPSGGLRRKGSLA------NLKAPFKLLK 78
Query: 74 AVLEVRRVLPKH 85
VL+ R++L +
Sbjct: 79 GVLQARKILKRF 90
>gnl|CDD|119338 cd06570, GH20_chitobiase-like_1, A functionally uncharacterized
subgroup of the Glycosyl hydrolase family 20 (GH20)
catalytic domain found in proteins similar to the
chitobiase of Serratia marcescens, a
beta-N-1,4-acetylhexosaminidase that hydrolyzes the
beta-1,4-glycosidic linkages in oligomers derived from
chitin. Chitin is degraded by a two step process: i) a
chitinase hydrolyzes the chitin to oligosaccharides and
disaccharides such as di-N-acetyl-D-glucosamine and
chitobiose, ii) chitobiase then further degrades these
oligomers into monomers. This subgroup lacks the
C-terminal PKD (polycystic kidney disease I)-like domain
found in the chitobiases. The GH20 hexosaminidases are
thought to act via a catalytic mechanism in which the
catalytic nucleophile is not provided by solvent or the
enzyme, but by the substrate itself.
Length = 311
Score = 26.2 bits (58), Expect = 6.4
Identities = 10/19 (52%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 54 MGWADTLKKDLPKDVPLIQ 72
+GW + L DLPK+V +IQ
Sbjct: 204 IGWDEVLHPDLPKNV-VIQ 221
>gnl|CDD|224032 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains
DnaJ-type Zn finger domain [DNA replication,
recombination, and repair].
Length = 715
Score = 26.2 bits (58), Expect = 6.6
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 60 LKKDLPKDVPLIQRAVLEVRRVLPKHSKAVDSFC-----EEAIV 98
LK D+ I+RAVLE R ++ +H D +C E+AI+
Sbjct: 325 LKPDMVDVAKEIRRAVLEGRPIIIRHHADADGYCAGVALEKAIL 368
>gnl|CDD|216969 pfam02310, B12-binding, B12 binding domain. This domain binds to
B12 (adenosylcobamide), it is found in several enzymes,
such as glutamate mutase, methionine synthase, and
methylmalonyl-CoA mutase. It contains a conserved
DxHxxGx(41)SxVx(26)GG motif, which is important for B12
binding.
Length = 121
Score = 25.4 bits (56), Expect = 7.8
Identities = 9/42 (21%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 5 GLKEVHEDCKKLNIEFHFLIGGAH-EILPQFVEKHKLGAVVI 45
KE+ E K++ ++GG H P+ + + G +
Sbjct: 67 AAKELIELLKRIRPRVKVVVGGPHPTADPEEILRAAPGIDDV 108
>gnl|CDD|237634 PRK14179, PRK14179, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 284
Score = 25.5 bits (56), Expect = 8.8
Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 3/23 (13%)
Query: 24 IGGAHEILPQFVEKHKLGAVVID 46
IG H + +FV K GAVVID
Sbjct: 209 IGRGHFVTKEFV---KEGAVVID 228
>gnl|CDD|163144 TIGR03123, one_C_unchar_1, probable H4MPT-linked C1 transfer
pathway protein. This protein family was identified, by
the method of partial phylogenetic profiling, as related
to the use of tetrahydromethanopterin (H4MPT) as a C-1
carrier. Characteristic markers of the H4MPT-linked C1
transfer pathway include formylmethanofuran
dehydrogenase subunits, methenyltetrahydromethanopterin
cyclohydrolase, etc. Tetrahydromethanopterin, a
tetrahydrofolate analog, occurs in methanogenic archaea,
bacterial methanotrophs, planctomycetes, and a few other
lineages [Central intermediary metabolism, One-carbon
metabolism].
Length = 318
Score = 25.4 bits (56), Expect = 9.9
Identities = 22/108 (20%), Positives = 37/108 (34%), Gaps = 25/108 (23%)
Query: 24 IGGAHEILPQFVEKHKLGAVVIDFMPLREHMGWADTLKKDLPKDVPLIQRAVLEVRRVLP 83
IGGA+ + E ++ V + PL W K + + E+
Sbjct: 5 IGGANTKAAELDEDGRIKEVHQLYCPL-----W---------KGNDKLAETLKEI----- 45
Query: 84 KHSKAVDSFCEEAIVRR-ELADNFCYYNKNYDKVEGAFDWAKKTLNDH 130
S+ + S A+ ELAD C+ +K + VE +
Sbjct: 46 --SQDLSSADNVAVTMTGELAD--CFEDKA-EGVEFILAAVESAFGSP 88
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
0.323 0.140 0.432
Gapped
Lambda K H
0.267 0.0716 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,936,797
Number of extensions: 637992
Number of successful extensions: 587
Number of sequences better than 10.0: 1
Number of HSP's gapped: 587
Number of HSP's successfully gapped: 26
Length of query: 131
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 45
Effective length of database: 7,123,158
Effective search space: 320542110
Effective search space used: 320542110
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.2 bits)