RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13892
(628 letters)
>gnl|CDD|147520 pfam05380, Peptidase_A17, Pao retrotransposon peptidase.
Corresponds to Merops family A17. These proteins are
homologous to aspartic proteinases encoded by
retroposons and retroviruses.
Length = 159
Score = 124 bits (312), Expect = 5e-33
Identities = 56/162 (34%), Positives = 87/162 (53%), Gaps = 6/162 (3%)
Query: 174 KRLLLSVLASFFDILGLWTPIIMSLKLLVQSAWIQKKEWDDELDSKDKEKFLEIVDSMNF 233
KR +LS +AS FD LGL P+ + K+ +Q W QK WD+E+ + +++L ++
Sbjct: 3 KREVLSQVASIFDPLGLLAPVTVRAKIFLQEIWRQKLGWDEEIPEELSQRWLAFRKQLST 62
Query: 234 VSNIPVARYFDVPNNHDDQSVRYELHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKS 293
+ I V RY +++ +LH F DA +YA+ VY R V +I+ ++V AK+
Sbjct: 63 LQQIRVPRYV---PYSPARNI--QLHGFCDASEKAYAAAVYWR-VEEGEEIQVSLVAAKT 116
Query: 294 RVAPTNKPTLPRLELLGALIAYRSLKFVKNSLHINIDKCYLW 335
RVAP ++PRLEL AL+ R + VK + Y W
Sbjct: 117 RVAPLKTVSIPRLELCAALLLTRLARAVKPEHDVKPTDTYCW 158
>gnl|CDD|238822 cd01644, RT_pepA17, RT_pepA17: Reverse transcriptase (RTs) in
retrotransposons. This subfamily represents the RT
domain of a multifunctional enzyme. C-terminal to the RT
domain is a domain homologous to aspartic proteinases
(corresponding to Merops family A17) encoded by
retrotransposons and retroviruses. RT catalyzes DNA
replication from an RNA template and is responsible for
the replication of retroelements.
Length = 213
Score = 125 bits (315), Expect = 9e-33
Identities = 50/157 (31%), Positives = 72/157 (45%), Gaps = 8/157 (5%)
Query: 5 ALIGDIEKAFLNVGLNEGERDYTRILWVKDVAKPLDSDNVVVLRHTRLPFGVVSSPFLLS 64
A+ DIEK F V + +RD R LW KD D + R T +PFG S+PFL +
Sbjct: 61 AVSADIEKMFHQVKVRPEDRDVLRFLWRKD----GDEPKPIEYRMTVVPFGAASAPFLAN 116
Query: 65 CVIRTHLDKYSGDY-IDQLKNNIYMDNILCGVNNEEEIENFVGTARKVFSDASLNLREWA 123
++ H + + + +K N Y+D+IL + E N + NLR+WA
Sbjct: 117 RALKQHAEDHPHEAAAKIIKRNFYVDDILVSTDTLNEAVNVAKRLIALLKKGGFNLRKWA 176
Query: 124 SNYPSVL--IGTLSPELVNTSRVQN-TLGMLWDTQED 157
SN VL + L S V TLG+ W+ + D
Sbjct: 177 SNSQEVLDDLPEERVLLDRDSDVTEKTLGLRWNPKTD 213
>gnl|CDD|215698 pfam00078, RVT_1, Reverse transcriptase (RNA-dependent DNA
polymerase). A reverse transcriptase gene is usually
indicative of a mobile element such as a retrotransposon
or retrovirus. Reverse transcriptases occur in a variety
of mobile elements, including retrotransposons,
retroviruses, group II introns, bacterial msDNAs,
hepadnaviruses, and caulimoviruses.
Length = 194
Score = 43.1 bits (102), Expect = 1e-04
Identities = 25/125 (20%), Positives = 48/125 (38%), Gaps = 9/125 (7%)
Query: 2 YRCALIGDIEKAFLNVGLNEGERDYT------RILWVKDVAKPLDSDNVVVLRHTRLPFG 55
+ L D++KAF ++ + +R T R + + + ++ + LP G
Sbjct: 52 SKWFLKLDLKKAFDSIPHDPLDRPLTAFGLPQRFIRWRTFSVLVNGNPGGRYEWRGLPQG 111
Query: 56 VVSSPFLLSCVIRTH-LDKYSGDYIDQLKNNIYMDNILCGVNNEEEIENFVGTARKVFSD 114
V SP L + + L + L Y D+IL + EE++ + + +
Sbjct: 112 SVLSPLL--FNLFMNELLRPLRKRFPGLTYLRYADDILIFSKSPEELQEILEEVLEFLKE 169
Query: 115 ASLNL 119
L L
Sbjct: 170 LGLKL 174
>gnl|CDD|238825 cd01647, RT_LTR, RT_LTR: Reverse transcriptases (RTs) from
retrotransposons and retroviruses which have long
terminal repeats (LTRs) in their DNA copies but not in
their RNA template. RT catalyzes DNA replication from an
RNA template, and is responsible for the replication of
retroelements. An RT gene is usually indicative of a
mobile element such as a retrotransposon or retrovirus.
RTs are present in a variety of mobile elements,
including retrotransposons, retroviruses, group II
introns, bacterial msDNAs, hepadnaviruses, and
Caulimoviruses.
Length = 177
Score = 31.8 bits (73), Expect = 0.63
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 5/53 (9%)
Query: 48 RHTRLPFGVVSSPFLLSCVIRTHLDKYSGDYIDQLKNNIYMDNILCGVNNEEE 100
+TR+PFG+ ++P ++ L GD+++ +Y+D+IL EEE
Sbjct: 92 EYTRMPFGLKNAPATFQRLMNKILGDLLGDFVE-----VYLDDILVYSKTEEE 139
>gnl|CDD|163503 TIGR03791, TTQ_mauG, tryptophan tryptophylquinone biosynthesis
enzyme MauG. Members of this protein family are the
tryptophan tryptophylquinone biosynthesis (TTQ) enzyme
MauG, as found in Methylobacterium extorquens and
related species. This protein is required to complete
the maturation of the TTQ cofactor in the methylamine
dehydrogenase light (beta) chain.
Length = 291
Score = 29.6 bits (66), Expect = 4.2
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 201 LVQSAWIQKKEWDDELDSKDKEKFLEIV--DSMNFVSNIPVARYFDVP 246
++ AW WD DS + + L I D MNF ++ + R V
Sbjct: 58 VLNLAWGTAFMWDGRADSLEAQAILPITAADEMNFEMDLLLERLKAVA 105
>gnl|CDD|181518 PRK08643, PRK08643, acetoin reductase; Validated.
Length = 256
Score = 29.7 bits (67), Expect = 4.2
Identities = 13/61 (21%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 95 VNNEEEIENFVGTARKVFSDASLNLREWASNYPSVLIGTLSPELVNTSRVQNTLGMLWDT 154
V++ +++ V F D ++ + A P+ I T++ E + N G++W
Sbjct: 60 VSDRDQVFAAVRQVVDTFGDLNVVVNN-AGVAPTTPIETITEEQFDKVYNINVGGVIWGI 118
Query: 155 Q 155
Q
Sbjct: 119 Q 119
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 29.5 bits (67), Expect = 5.6
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 467 TCYVKKFINLCRKRSEFKGPISLEEFSGSKTEWLKYAQEKY 507
+CY +K INL K+S K + E FS + Y+ EK
Sbjct: 116 SCYKQKLINLYYKQSNLKEILKEENFSNFNLNY--YSDEKD 154
>gnl|CDD|215926 pfam00450, Peptidase_S10, Serine carboxypeptidase.
Length = 415
Score = 29.5 bits (67), Expect = 6.0
Identities = 7/62 (11%), Positives = 20/62 (32%), Gaps = 1/62 (1%)
Query: 308 LLGALIAYRSLKFVKNSLHINIDKCYLWIDNQCVIHWLTGNKVLPTFVNNRVKEIKASVF 367
+ Y + V+ +LH N W + G+ + + + + ++
Sbjct: 273 DESYVEKYLNRPDVRKALHANKGSVGEWSRCNDEVFNWYGDDISKSMLPI-LPKLLEGGL 331
Query: 368 PI 369
+
Sbjct: 332 RV 333
>gnl|CDD|219043 pfam06469, DUF1088, Domain of Unknown Function (DUF1088). This
family is found in the neurobeachins. The function of
this region is not known.
Length = 169
Score = 28.3 bits (63), Expect = 8.3
Identities = 16/52 (30%), Positives = 22/52 (42%), Gaps = 11/52 (21%)
Query: 568 IVTDVHRACFHNGASQTLATLRLDYWITQGRSAVKQILKSCVNCKRFRQGPY 619
I+TD H A + +SQ RLDYW R +RF + P+
Sbjct: 81 ILTDKHGAWGDSSSSQPHEFWRLDYWEDDLRRR-----------RRFVRNPF 121
>gnl|CDD|225795 COG3256, NorB, Nitric oxide reductase large subunit [Inorganic ion
transport and metabolism].
Length = 717
Score = 29.0 bits (65), Expect = 9.6
Identities = 13/72 (18%), Positives = 26/72 (36%), Gaps = 7/72 (9%)
Query: 285 RTNIVFAKSRVAPTNKPTLPRLELLGALIAYRSLKFVKNSLHINIDKCYLWIDNQCVIH- 343
R N+ K + T + L L G + + + ++ +D+ + W V+H
Sbjct: 400 RANVTATKLKGRKTTLIAILLLSLTGIGLFFLFGLYNPEWTNLAVDEYWRWW----VVHL 455
Query: 344 WLTGNKVLPTFV 355
W+ G
Sbjct: 456 WVEG--FWEVIA 465
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
0.321 0.138 0.426
Gapped
Lambda K H
0.267 0.0739 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,990,959
Number of extensions: 3110936
Number of successful extensions: 2304
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2295
Number of HSP's successfully gapped: 17
Length of query: 628
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 525
Effective length of database: 6,369,140
Effective search space: 3343798500
Effective search space used: 3343798500
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: 62 (27.6 bits)