RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9229
(258 letters)
>gnl|CDD|109891 pfam00853, Runt, Runt domain.
Length = 134
Score = 263 bits (675), Expect = 8e-91
Identities = 111/134 (82%), Positives = 125/134 (93%)
Query: 75 RTLGDFLSEHPGELVRTGSPQFVCTVLPPHWRSNKTLPVAFKVVALGDVMDGTIVTIRAG 134
R++ + L+EHPGELV+TGSP F+C+VLP HWRSNKTLPVAFKVVALG+V DGT+VTIRAG
Sbjct: 1 RSVVEVLAEHPGELVKTGSPNFLCSVLPSHWRSNKTLPVAFKVVALGEVPDGTMVTIRAG 60
Query: 135 NDENYCAELRNCTAVMKNQVAKFNDLRFVGRSGRGKSFTLTITISSSPPQVTTYSKAIKV 194
NDENYCAELRN TAVMKNQVAKFNDLRFVGRSGRGKSFTLTITI+++PPQV TY+KAIKV
Sbjct: 61 NDENYCAELRNATAVMKNQVAKFNDLRFVGRSGRGKSFTLTITIATNPPQVATYNKAIKV 120
Query: 195 TVDGPREPRSKTRK 208
TVDGPREPR K +K
Sbjct: 121 TVDGPREPRRKKQK 134
>gnl|CDD|224135 COG1214, COG1214, Inactive homolog of metal-dependent proteases,
putative molecular chaperone [Posttranslational
modification, protein turnover, chaperones].
Length = 220
Score = 30.5 bits (69), Expect = 0.66
Identities = 9/33 (27%), Positives = 13/33 (39%)
Query: 129 VTIRAGNDENYCAELRNCTAVMKNQVAKFNDLR 161
V I A E Y AE + + + V +L
Sbjct: 115 VAIDARRGEVYWAEYQRSGGLEEEAVLSAEELF 147
>gnl|CDD|220092 pfam09028, Mac-1, Mac 1. The bacterial protein Mac 1 adopts an
alpha/beta fold, with 14 beta strands and 9 alpha
helices. The N-terminal domain is made up predominantly
of alpha helices, whereas the C-terminal domain consists
predominantly of beta sheets. Mac 1 blocks
polymorphonuclear opsonophagocytosis, inhibits the
production of reactive oxygen species and contains IgG
endopeptidase activity.
Length = 333
Score = 30.4 bits (68), Expect = 0.92
Identities = 14/65 (21%), Positives = 23/65 (35%), Gaps = 2/65 (3%)
Query: 4 TGTTNTNS--PTEGNTGNLLNDTYSKMTSDILAERTLGDFLSEHPGELVRTEGNTGNLLN 61
G N S P + G L ND ++ TS + + +L+ + L
Sbjct: 188 DGQKNLGSIYPVPDSRGGLFNDVFAHDTSPKNLTNRIRCETKKEFEQLMNKTLDNKRALG 247
Query: 62 DTYSK 66
+SK
Sbjct: 248 LFWSK 252
>gnl|CDD|188461 TIGR03946, viomycin_VioC, arginine beta-hydroxylase,
Fe(II)/alpha-ketoglutarate-dependent. Members of this
protein family are L-arginine beta-hydroxylase, members
of a broader family of enzymes dependent on Fe(II),
alpha-ketoglutarate, and molecular oxygen. Enzymes in
the broader family but excluded by this model include
clavaminate synthase, taurine dioxygenase, and
prolyl-4-hydroxylase [Cellular processes, Biosynthesis
of natural products].
Length = 333
Score = 30.2 bits (68), Expect = 1.0
Identities = 23/73 (31%), Positives = 30/73 (41%), Gaps = 17/73 (23%)
Query: 75 RTLGDF-LSEHPGELVRTGSP--QFVCTVLPPHWRSNKT----LPVAFKVV----ALGDV 123
R L F L + LV G+ Q P HWR +T LP+ F ++ LGDV
Sbjct: 47 RFLDRFRLDDPSHALVIRGNDVDQDRLGPTPEHWRDAQTPGSRLPLEFLLMLYAALLGDV 106
Query: 124 M------DGTIVT 130
DG +V
Sbjct: 107 FGWATQQDGRVVH 119
>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 = 29.5 bits (67), Expect = 2.0
Identities = 20/92 (21%), Positives = 28/92 (30%), Gaps = 15/92 (16%)
Query: 173 TLTITISSSPPQV------------TTYSKAIKVTVDGPREPRSKTRKSFTLTITISSSP 220
T+TIT Q+ TT KAIK + + + + TI
Sbjct: 717 TITITFQLPKGQLSLDDLQLYGLNYTTLKKAIKKLKEQQLKVTKYSDNKLSGTINTKKKD 776
Query: 221 PQVTT---YSKAIKVTVDGPREPRSKTILMMT 249
+ T Y K VDG + K
Sbjct: 777 GLLYTTIPYDKGWTAKVDGKKVKIKKVNGGFI 808
Score = 27.6 bits (62), Expect = 8.3
Identities = 23/134 (17%), Positives = 41/134 (30%), Gaps = 14/134 (10%)
Query: 104 HWRSNKTLPVAFKVVALGDVMDGTIVTIR-AGNDENYCAELRNCTAV------MKNQVAK 156
+ + +V+ LG + G +TI L + +K + K
Sbjct: 693 YTLNRTFNYYRTQVINLGYRVKGQTITITFQLPKGQL--SLDDLQLYGLNYTTLKKAIKK 750
Query: 157 FNDLRFVGRSGRGKSFTLTITISSSPPQVTT---YSKAIKVTVDGPREPRSKTRKSFTLT 213
+ + + TI + T Y K VDG + K F +
Sbjct: 751 LKEQQLKVTKYSDNKLSGTINTKKKDGLLYTTIPYDKGWTAKVDGKKVKIKKVNGGF-IG 809
Query: 214 ITISSSPPQVT-TY 226
+ + Q+T TY
Sbjct: 810 VPLPKGKHQITLTY 823
>gnl|CDD|214653 smart00410, IG_like, Immunoglobulin like. IG domains that cannot
be classified into one of IGv1, IGc1, IGc2, IG.
Length = 85
Score = 26.7 bits (59), Expect = 3.8
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 169 GKSFTLTITISSSP-PQVTTYSKAIKVTVDGPREPRSKTRKSFTLTIT 215
G+S TL+ S SP P+VT Y + K+ + R S++ + TLTI+
Sbjct: 9 GESVTLSCEASGSPPPEVTWYKQGGKLLAESGRFSVSRSGSTSTLTIS 56
>gnl|CDD|214652 smart00409, IG, Immunoglobulin.
Length = 85
Score = 26.7 bits (59), Expect = 3.8
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 169 GKSFTLTITISSSP-PQVTTYSKAIKVTVDGPREPRSKTRKSFTLTIT 215
G+S TL+ S SP P+VT Y + K+ + R S++ + TLTI+
Sbjct: 9 GESVTLSCEASGSPPPEVTWYKQGGKLLAESGRFSVSRSGSTSTLTIS 56
>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 = 28.2 bits (64), Expect = 4.6
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 117 VVALGDVMDGTIVTIRAGNDEN 138
+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 = 27.7 bits (63), Expect = 6.4
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 117 VVALGDVMDGTIVTIRAGNDEN 138
+VA D+MDG + IR D
Sbjct: 160 IVAPSDMMDGRVGAIREALDAA 181
>gnl|CDD|224799 COG1887, TagB, Putative glycosyl/glycerophosphate transferases
involved in teichoic acid biosynthesis
TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer
membrane].
Length = 388
Score = 27.4 bits (61), Expect = 8.4
Identities = 9/38 (23%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 38 LGDFLSEHPGELVRTEGNTGNLLNDTYSKMTSDILAER 75
D+ E PGE+V T+ + + Y + + L +
Sbjct: 325 YLDYKFEAPGEVVETQEELIDAI-KPYDEDGNYDLEKL 361
>gnl|CDD|215945 pfam00490, ALAD, Delta-aminolevulinic acid dehydratase.
Length = 322
Score = 27.0 bits (61), Expect = 9.3
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 117 VVALGDVMDGTIVTIRAGNDEN 138
+VA D+MDG + IR DE
Sbjct: 161 IVAPSDMMDGRVGAIREALDEA 182
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 0.130 0.373
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: 12,590,582
Number of extensions: 1155791
Number of successful extensions: 925
Number of sequences better than 10.0: 1
Number of HSP's gapped: 921
Number of HSP's successfully gapped: 27
Length of query: 258
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 163
Effective length of database: 6,723,972
Effective search space: 1096007436
Effective search space used: 1096007436
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 58 (25.8 bits)