RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3060
(268 letters)
>gnl|CDD|109891 pfam00853, Runt, Runt domain.
Length = 134
Score = 195 bits (496), Expect = 2e-63
Identities = 76/94 (80%), Positives = 86/94 (91%)
Query: 23 RTLDSLLAEHPGELTRTGCPHVVCTVLPTHWRSNKTLPVAFKVVALGDVMDGTIVTIRAG 82
R++ +LAEHPGEL +TG P+ +C+VLP+HWRSNKTLPVAFKVVALG+V DGT+VTIRAG
Sbjct: 1 RSVVEVLAEHPGELVKTGSPNFLCSVLPSHWRSNKTLPVAFKVVALGEVPDGTMVTIRAG 60
Query: 83 NDENYCGELRNCTAVMKNQVAKFNDLRFVGRSGR 116
NDENYC ELRN TAVMKNQVAKFNDLRFVGRSGR
Sbjct: 61 NDENYCAELRNATAVMKNQVAKFNDLRFVGRSGR 94
>gnl|CDD|224135 COG1214, COG1214, Inactive homolog of metal-dependent proteases,
putative molecular chaperone [Posttranslational
modification, protein turnover, chaperones].
Length = 220
Score = 29.7 bits (67), Expect = 1.3
Identities = 8/33 (24%), Positives = 12/33 (36%)
Query: 77 VTIRAGNDENYCGELRNCTAVMKNQVAKFNDLR 109
V I A E Y E + + + V +L
Sbjct: 115 VAIDARRGEVYWAEYQRSGGLEEEAVLSAEELF 147
>gnl|CDD|215966 pfam00517, GP41, Retroviral envelope protein. This family includes
envelope protein from a variety of retroviruses. It
includes the GP41 subunit of the envelope protein
complex from human and simian immunodeficiency viruses
(HIV and SIV) which mediate membrane fusion during viral
entry. The family also includes bovine immunodeficiency
virus, feline immunodeficiency virus and Equine
infectious anaemia (EIAV). The family also includes the
Gp36 protein from mouse mammary tumour virus (MMTV) and
human endogenous retroviruses (HERVs).
Length = 204
Score = 29.3 bits (66), Expect = 1.5
Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 3/46 (6%)
Query: 125 WVGTLIWLIGIKNKH-QQYEIEISFLINQITASISELLRMYEKTLR 169
+ + IW N Q +E ++S L +I I E EK
Sbjct: 90 YNMSEIW--NHVNMTWQDWEDQVSLLEQKIYTIIEEAQNQQEKNKY 133
>gnl|CDD|234637 PRK00107, gidB, 16S rRNA methyltransferase GidB; Reviewed.
Length = 187
Score = 28.6 bits (65), Expect = 2.6
Identities = 9/48 (18%), Positives = 22/48 (45%), Gaps = 8/48 (16%)
Query: 156 SISELLRMYEKTLRLGHL---ILLVPIVPNHLSKIDIFTGGSLCGLVL 200
+I + ++E+ H+ + + P +P +D+ +G G+ L
Sbjct: 21 AIRDPEELWER-----HILDSLAIAPYLPGGERVLDVGSGAGFPGIPL 63
>gnl|CDD|219645 pfam07923, N1221, N1221-like protein. The sequences featured in
this family are similar to a hypothetical protein
product of ORF N1221 in the CPT1-SPC98 intergenic region
of the yeast genome. This encodes an acidic polypeptide
with several possible transmembrane regions.
Length = 293
Score = 28.8 bits (65), Expect = 2.9
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 2/27 (7%)
Query: 198 LVLLTHFSSGARWDSASAPSIPISNVV 224
LV LT + RWDSA S+PI ++
Sbjct: 193 LVFLTKYIERLRWDSA--LSMPIRKII 217
>gnl|CDD|198029 smart00961, RuBisCO_small, Ribulose bisphosphate carboxylase,
small chain. RuBisCO (ribulose-1,5-bisphosphate
carboxylase/oxygenase) is a bifunctional enzyme that
catalyses both the carboxylation and oxygenation of
ribulose-1,5-bisphosphate (RuBP), thus fixing carbon
dioxide as the first step of the Calvin cycle. RuBisCO
is the major protein in the stroma of chloroplasts, and
in higher plants exists as a complex of 8 large and 8
small subunits. The function of the small subunit is
unknown. While the large subunit is coded for by a
single gene, the small subunit is coded for by several
different genes, which are distributed in a tissue
specific manner. They are transcriptionally regulated
by light receptor phytochrome. which results in RuBisCO
being more abundant during the day when it is required.
Length = 96
Score = 27.5 bits (62), Expect = 3.0
Identities = 15/23 (65%), Positives = 18/23 (78%), Gaps = 2/23 (8%)
Query: 16 SAEVLAERTLDSLLAEHPGELTR 38
+AEVLAE L++ LAEHPGE R
Sbjct: 56 AAEVLAE--LEACLAEHPGEYVR 76
>gnl|CDD|181159 PRK07890, PRK07890, short chain dehydrogenase; Provisional.
Length = 258
Score = 28.0 bits (63), Expect = 5.3
Identities = 23/89 (25%), Positives = 33/89 (37%), Gaps = 16/89 (17%)
Query: 19 VLAERTLDSLLAEHPGELTRTG---------------CPHVVCTVLPTHWRSNKTLPVAF 63
VLA RT L E E+ G C ++V L R + + AF
Sbjct: 33 VLAART-AERLDEVAAEIDDLGRRALAVPTDITDEDQCANLVALALERFGRVDALVNNAF 91
Query: 64 KVVALGDVMDGTIVTIRAGNDENYCGELR 92
+V ++ + D RA + N G LR
Sbjct: 92 RVPSMKPLADADFAHWRAVIELNVLGTLR 120
>gnl|CDD|238226 cd00384, ALAD_PBGS, Porphobilinogen synthase (PBGS), which is also
called delta-aminolevulinic acid dehydratase (ALAD),
catalyzes the condensation of two 5-aminolevulinic acid
(ALA) molecules to form the pyrrole porphobilinogen
(PBG), which is the second step in the biosynthesis of
tetrapyrroles, such as heme, vitamin B12 and
chlorophyll. This reaction involves the formation of a
Schiff base link between the substrate and the enzyme.
PBGSs are metalloenzymes, some of which have a second,
allosteric metal binding site, beside the metal ion
binding site in their active site. Although PBGS is a
family of homologous enzymes, its metal ion utilization
at catalytic site varies between zinc and magnesium
and/or potassium. PBGS can be classified into two groups
based on differences in their active site metal binding
site. They either contain a cysteine-rich zinc binding
site (consensus DXCXCX(Y/F)X3G(H/Q)CG) or an
aspartate-rich magnesium binding site (consensus
DXALDX(Y/F)X3G(H/Q)DG). The cysteine-rich zinc binding
site appears more common. Most members represented by
this model also have a second allosteric magnesium
binding site (consensus RX~164DX~65EXXXD, missing in a
eukaryotic subfamily with cysteine-rich zinc binding
site).
Length = 314
Score = 27.8 bits (63), Expect = 6.1
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 65 VVALGDVMDGTIVTIRAGNDEN 86
+VA D+MDG + IR DE
Sbjct: 153 IVAPSDMMDGRVAAIREALDEA 174
>gnl|CDD|214968 smart01004, ALAD, Delta-aminolevulinic acid dehydratase. This
entry represents porphobilinogen (PBG) synthase (PBGS,
or 5-aminoaevulinic acid dehydratase, or ALAD, ), which
functions during the second stage of tetrapyrrole
biosynthesis. This enzyme catalyses a Knorr-type
condensation reaction between two molecules of ALA to
generate porphobilinogen, the pyrrolic building block
used in later steps. The structure of the enzyme is
based on a TIM barrel topology made up of eight
identical subunits, where each subunit binds to a metal
ion that is essential for activity, usually zinc (in
yeast, mammals and certain bacteria) or magnesium (in
plants and other bacteria). A lysine has been implicated
in the catalytic mechanism. The lack of PBGS enzyme
causes a rare porphyric disorder known as ALAD
porphyria, which appears to involve conformational
changes in the enzyme.
Length = 321
Score = 27.3 bits (62), Expect = 8.6
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 65 VVALGDVMDGTIVTIRAGNDEN 86
+VA D+MDG + IR D
Sbjct: 160 IVAPSDMMDGRVGAIREALDAA 181
>gnl|CDD|222936 PHA02855, PHA02855, anti-apoptotic membrane protein; Provisional.
Length = 180
Score = 27.1 bits (60), Expect = 8.8
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 128 TLIWLIGIKNKHQQYEIEISFLINQITASISE 159
+LI +I K ++ I +S LIN+I ISE
Sbjct: 99 SLISMIAEKKGYKNNNIVMSDLINEIANKISE 130
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
0.320 0.136 0.411
Gapped
Lambda K H
0.267 0.0905 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,522,529
Number of extensions: 1258322
Number of successful extensions: 1018
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1017
Number of HSP's successfully gapped: 18
Length of query: 268
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 173
Effective length of database: 6,723,972
Effective search space: 1163247156
Effective search space used: 1163247156
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (25.8 bits)