RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10850
(173 letters)
>gnl|CDD|216628 pfam01652, IF4E, Eukaryotic initiation factor 4E.
Length = 162
Score = 187 bits (477), Expect = 1e-61
Identities = 72/135 (53%), Positives = 90/135 (66%), Gaps = 3/135 (2%)
Query: 36 KLQYQYWFWYSRRTPGKVTSVQSYDDNLKLIQKFGSVEQFWEIYTHLVRPNEFQSFIDLH 95
LQ ++ WY RR PG + Y+DNLK I F +VE FW +Y ++ RP++ D H
Sbjct: 1 PLQNKWTLWYDRRPPGD--KSKDYEDNLKPIGTFDTVEDFWRLYNNIPRPSKLPLGSDYH 58
Query: 96 LFKVGVKPMWEDEANRNGGKWLIRLRKG-IASRCWENLILAMLGEQFMVGDEICGAVISV 154
LFK G+KPMWED AN+NGGKW IRL K R WE L+LA++GEQF DEICG V+SV
Sbjct: 59 LFKKGIKPMWEDPANKNGGKWTIRLPKSQNLDRFWEELLLALIGEQFDESDEICGVVLSV 118
Query: 155 RFQEDHISVWNKTSS 169
R +ED ISVW K +S
Sbjct: 119 RKKEDKISVWTKNAS 133
>gnl|CDD|227386 COG5053, CDC33, Translation initiation factor 4E (eIF-4E)
[Translation, ribosomal structure and biogenesis].
Length = 217
Score = 88.4 bits (219), Expect = 3e-22
Identities = 43/136 (31%), Positives = 69/136 (50%), Gaps = 7/136 (5%)
Query: 35 HKLQYQYWFWYSRRTPGKVTSVQSYDDNLKLIQKFGSVEQFWEIYTHLVRPNEFQSFIDL 94
H L + + W+ ++S+ D LK I F +VE+FW I ++ + D
Sbjct: 37 HPLAFHWTLWF---LKPPEDGLESWSDLLKSIITFETVEEFWYILHNISDASRLPRKSDY 93
Query: 95 HLFKVGVKPMWEDEANRNGGKWLIRLRKGIASRC---WENLILAMLGEQF-MVGDEICGA 150
++F+ G++P WEDEAN NGGKW +L+ R W +LA +GE G EI G
Sbjct: 94 NVFREGIRPEWEDEANMNGGKWSFQLKGKGCDRLDELWLRTLLAAIGETLDPTGSEIGGV 153
Query: 151 VISVRFQEDHISVWNK 166
V ++R +++W +
Sbjct: 154 VGNMRKGFYKLAIWTR 169
>gnl|CDD|240238 PTZ00040, PTZ00040, translation initiation factor E4; Provisional.
Length = 233
Score = 65.2 bits (159), Expect = 2e-13
Identities = 43/170 (25%), Positives = 71/170 (41%), Gaps = 28/170 (16%)
Query: 24 EDLPLTIPPHHHKLQYQYWFWYSRRTPGKVTSVQSYDDNLKLIQKFGSVEQFWEIYTHLV 83
+PL+ P L Y++ W + + Y D K + F SV++FW+++ ++
Sbjct: 30 TKIPLSTP---LPLSYKWVIW-EQVVKETIRKSNDYKDYTKPLASFDSVQKFWQLWFNIP 85
Query: 84 RPNEF--------------QSFID-LHLFKVGVKPMWEDEANRNGGKWLIRLRKGIASRC 128
+P+E + +D + +FK G++PMWED N GG + R S
Sbjct: 86 QPSELLTGKRMIRESSDGSEHVVDAVMIFKDGIQPMWEDPMNATGGHFEYRFWPTDVSPG 145
Query: 129 -----WENLILAMLGEQFMVGDEICGA----VISVRFQEDHISVWNKTSS 169
W NL+LA++G I G +S RF I +W
Sbjct: 146 QIDEYWNNLVLALIGSSLEHSSLINGIRLVDKLSGRFGVIRIEIWFTNLG 195
>gnl|CDD|219678 pfam07976, Phe_hydrox_dim, Phenol hydroxylase, C-terminal
dimerisation domain. Phenol hydroxylase acts a
homodimer, to hydroxylates phenol to catechol or similar
product. The enzyme is comprised of three domains. The
first two domains from the active site. The third
domain, this domain, is involved in forming the
dimerisation interface. The domain adopts a
thioredoxin-like fold.
Length = 169
Score = 29.5 bits (67), Expect = 0.55
Identities = 11/44 (25%), Positives = 17/44 (38%)
Query: 17 KRDDISLEDLPLTIPPHHHKLQYQYWFWYSRRTPGKVTSVQSYD 60
R ++ LEDLP + P K Y Y+ +Y+
Sbjct: 117 PRREVELEDLPELLRPFDGKYGLDYEKVYADDESYHEGHGDAYE 160
>gnl|CDD|239277 cd02979, PHOX_C, FAD-dependent Phenol hydoxylase (PHOX) family,
C-terminal TRX-fold domain; composed of proteins similar
to PHOX from the aerobic topsoil yeast Trichosporon
cutaneum. PHOX is a flavoprotein monooxygenase that
catalyzes the hydroxylation of phenol and simple phenol
derivatives in the ortho position with the consumption
of NADPH and oxygen. This is the first step in the
biodegradation and detoxification of phenolic compounds.
PHOX contains three domains. The substrate and
FAD/NAD(P) binding sites are contained in the first two
domains, which adopt a complicated folding pattern. The
third or C-terminal domain contains a TRX fold and is
involved in dimerization. The functional unit of PHOX is
a dimer, although active tetramers of the recombinant
enzyme can be isolated when overproduced in bacteria.
Length = 167
Score = 28.8 bits (65), Expect = 0.90
Identities = 11/44 (25%), Positives = 17/44 (38%)
Query: 17 KRDDISLEDLPLTIPPHHHKLQYQYWFWYSRRTPGKVTSVQSYD 60
R +I L DLP + P K + Y Y+ +Y+
Sbjct: 85 PRREIELLDLPAVLRPFGEKKGWDYEKIYADDDSYHEGHGDAYE 128
>gnl|CDD|188618 cd09898, H3TH_53EXO, H3TH domain of the 5'-3' exonuclease of Taq
DNA polymerase I and homologs. H3TH
(helix-3-turn-helix) domains of the 5'-3' exonuclease
(53EXO) of mutli-domain DNA polymerase I and single
domain protein homologs are included in this family.
Taq DNA polymerase I contains a polymerase domain for
synthesizing a new DNA strand and a 53EXO domain for
cleaving RNA primers or damaged DNA strands. Taq's
53EXO recognizes and endonucleolytically cleaves a
structure-specific DNA substrate that has a bifurcated
downstream duplex and an upstream template-primer
duplex that overlaps the downstream duplex by 1 bp. The
53EXO cleaves the unpaired 5'-arm of the overlap flap
DNA substrate. 5'-3' exonucleases are members of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region/I
domain (not included here) and inserted within the PIN
domain is an atypical helix-hairpin-helix-2 (HhH2)-like
region. This atypical HhH2 region, the H3TH domain, has
an extended loop with at least three turns between the
first two helices, and only three of the four helices
appear to be conserved. Both the H3TH domain and the
helical arch/clamp region are involved in DNA binding.
Studies suggest that a glycine-rich loop in the H3TH
domain contacts the phosphate backbone of the template
strand in the downstream DNA duplex. The nucleases
within this family have a carboxylate rich active site
that is involved in binding essential divalent metal
ion cofactors (i. e., Mg2+ or Mn2+ or Zn2+) required
for nuclease activity. The first metal binding site is
composed entirely of Asp/Glu residues from the PIN
domain, whereas, the second metal binding site is
composed generally of two Asp residues from the PIN
domain and two Asp residues from the H3TH domain.
Together with the helical arch and network of amino
acids interacting with metal binding ions, the H3TH
region defines a positively charged active-site
DNA-binding groove in structure-specific 5' nucleases.
Length = 73
Score = 27.0 bits (61), Expect = 1.8
Identities = 8/20 (40%), Positives = 13/20 (65%), Gaps = 3/20 (15%)
Query: 63 LKLIQKFGSVEQFWEIYTHL 82
KL+Q++GS+E I +L
Sbjct: 30 AKLLQEYGSLE---NILANL 46
>gnl|CDD|236989 PRK11809, putA, trifunctional transcriptional regulator/proline
dehydrogenase/pyrroline-5-carboxylate dehydrogenase;
Reviewed.
Length = 1318
Score = 27.6 bits (62), Expect = 3.8
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 8/47 (17%)
Query: 113 GGKWLIRLRKGIASRCWENLILAMLGEQFMVGDEICGAVISVRFQED 159
G+ LIR KG+ ++ + ++GEQF+ G+ I A+ + R E+
Sbjct: 239 SGEPLIR--KGV------DMAMRLMGEQFVTGETIAEALANARKLEE 277
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 27.4 bits (62), Expect = 4.8
Identities = 8/20 (40%), Positives = 14/20 (70%), Gaps = 3/20 (15%)
Query: 63 LKLIQKFGSVEQFWEIYTHL 82
KL+Q++GS+E +Y +L
Sbjct: 201 AKLLQEYGSLE---GLYENL 217
>gnl|CDD|216458 pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-terminal SAM fold.
Length = 100
Score = 25.2 bits (56), Expect = 9.8
Identities = 8/20 (40%), Positives = 14/20 (70%), Gaps = 3/20 (15%)
Query: 63 LKLIQKFGSVEQFWEIYTHL 82
KL++++GS+E IY +L
Sbjct: 32 AKLLKEYGSLE---NIYENL 48
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
0.322 0.137 0.438
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,851,439
Number of extensions: 804714
Number of successful extensions: 629
Number of sequences better than 10.0: 1
Number of HSP's gapped: 624
Number of HSP's successfully gapped: 13
Length of query: 173
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 83
Effective length of database: 6,945,742
Effective search space: 576496586
Effective search space used: 576496586
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 (21.9 bits)
S2: 55 (24.9 bits)