RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15380
(1738 letters)
>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 = 213 bits (544), Expect = 5e-63
Identities = 77/219 (35%), Positives = 123/219 (56%), Gaps = 8/219 (3%)
Query: 1163 YFIPHHVVTKPDSPSSKMRIVYDASTKTSSGKSLNDILHAGSKMYNDLFCILLKFRLFPY 1222
+++PHH V KP ++K+R+V+DAS + + G SLND+L G + N LF +LL+FR
Sbjct: 2 WYLPHHAVIKPSKTTTKLRVVFDASARYN-GVSLNDMLLKGPDLLNSLFGVLLRFRQGKI 60
Query: 1223 ALNGDITKMFLQIKLLSDYWKFQKILWRFS-NKEKIDVYELRVVIFGTKASPYLAQRTVK 1281
A++ DI KMF Q+K+ + + LWR ++ K Y + VV FG ++P+LA R +K
Sbjct: 61 AVSADIEKMFHQVKVRPEDRDVLRFLWRKDGDEPKPIEYRMTVVPFGAASAPFLANRALK 120
Query: 1282 QLIDDESKNFPLACQYIGESLYMDDCVISFPSQKEAIEFFNQTVKLFASGGFRFTKWSSN 1341
Q +D A + I + Y+DD ++S + EA+ + + L GGF KW+SN
Sbjct: 121 QHAEDH--PHEAAAKIIKRNFYVDDILVSTDTLNEAVNVAKRLIALLKKGGFNLRKWASN 178
Query: 1342 SPEILEQIPIHDRLAEMVSWHTDDFSHKILGMLWNTSSD 1380
S E+L+ +P ++ D + K LG+ WN +D
Sbjct: 179 SQEVLDDLPEER----VLLDRDSDVTEKTLGLRWNPKTD 213
>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 = 142 bits (359), Expect = 8e-39
Identities = 61/145 (42%), Positives = 82/145 (56%), Gaps = 3/145 (2%)
Query: 1560 GLLAPVILWAKLLIRELCILKLDWDSIPPHHLVQLWQTFQAQLPLLESLAFPRHIGVYKD 1619
GLLAPV + AK+ ++E+ KL WD P L Q W F+ QL L+ + PR++
Sbjct: 18 GLLAPVTVRAKIFLQEIWRQKLGWDEEIPEELSQRWLAFRKQLSTLQQIRVPRYVPYSPA 77
Query: 1620 CKFQLIGFSDASEKGYGALIFSRVSLPNGSIVIQLICAKSRVSPLKVESIPRLELCAILL 1679
QL GF DASEK Y A ++ RV I + L+ AK+RV+PLK SIPRLELCA LL
Sbjct: 78 RNIQLHGFCDASEKAYAAAVYWRVE-EGEEIQVSLVAAKTRVAPLKTVSIPRLELCAALL 136
Query: 1680 MSSLLKVVIDSYTPRYPIDSIYCFT 1704
++ L + V + YC+T
Sbjct: 137 LTRLARAVKPEH--DVKPTDTYCWT 159
Score = 55.8 bits (135), Expect = 9e-09
Identities = 23/56 (41%), Positives = 33/56 (58%)
Query: 1404 GLLAPVILWAKLLIRELCILKLDWDSIPPPHLVQLWQTFQAQLPLLESLAFPRHIG 1459
GLLAPV + AK+ ++E+ KL WD P L Q W F+ QL L+ + PR++
Sbjct: 18 GLLAPVTVRAKIFLQEIWRQKLGWDEEIPEELSQRWLAFRKQLSTLQQIRVPRYVP 73
>gnl|CDD|202685 pfam03564, DUF1759, Protein of unknown function (DUF1759). This is
a family of proteins of unknown function. Most of the
members are gag-polyproteins.
Length = 146
Score = 69.7 bits (171), Expect = 1e-13
Identities = 40/121 (33%), Positives = 55/121 (45%), Gaps = 7/121 (5%)
Query: 441 FDGACIGNWPLFIEMYRINIHNRTDLTNAHKLQYLLSKLSGGALAVAAGIPPTEHNYQVI 500
F G I W F E++ IH++TDL K YL S L G A + +P T NY V
Sbjct: 1 FSGD-IKEWQAFWELFESLIHSKTDLPEIQKFNYLKSALEGEAATLVTHLPITAANYDVA 59
Query: 501 YDALLEKYDDKRNLATYYMDSLLNF---KTQSGS-LETFIDYFGANVAQVIYDALLEKYD 556
++AL E+YD+ R + ++ L+ S S L D AN + L E D
Sbjct: 60 WEALKERYDNPRVIIRSLLNKLMKLPSTNNDSVSQLRRLYD--EANEIIRQLEQLGENAD 117
Query: 557 D 557
D
Sbjct: 118 D 118
>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 = 41.9 bits (99), Expect = 8e-04
Identities = 27/125 (21%), Positives = 41/125 (32%), Gaps = 15/125 (12%)
Query: 1222 YALNGDITKMFLQI---KLLSDYWKFQK----ILWR----FSNKEKIDVYELRVVIFGTK 1270
+ L D+ K F I L F I WR N YE R + G+
Sbjct: 54 WFLKLDLKKAFDSIPHDPLDRPLTAFGLPQRFIRWRTFSVLVNGNPGGRYEWRGLPQGSV 113
Query: 1271 ASPYLAQRTVKQLIDDESKNFPLACQYIGESLYMDDCVISFPSQKEAIEFFNQTVKLFAS 1330
SP L + + + Y+ Y DD +I S +E E + ++
Sbjct: 114 LSPLLFNLFM-NELLRPLRKRFPGLTYL---RYADDILIFSKSPEELQEILEEVLEFLKE 169
Query: 1331 GGFRF 1335
G +
Sbjct: 170 LGLKL 174
>gnl|CDD|238823 cd01645, RT_Rtv, RT_Rtv: Reverse transcriptases (RTs) from
retroviruses (Rtvs). RTs catalyze the conversion of
single-stranded RNA into double-stranded viral DNA for
integration into host chromosomes. Proteins in this
subfamily contain long terminal repeats (LTRs) and are
multifunctional enzymes with RNA-directed DNA polymerase,
DNA directed DNA polymerase, and ribonuclease hybrid
(RNase H) activities. The viral RNA genome enters the
cytoplasm as part of a nucleoprotein complex, and the
process of reverse transcription generates in the
cytoplasm forming a linear DNA duplex via an intricate
series of steps. This duplex DNA is colinear with its RNA
template, but contains terminal duplications known as
LTRs that are not present in viral RNA. It has been
proposed that two specialized template switches, known as
strand-transfer reactions or "jumps", are required to
generate the LTRs.
Length = 213
Score = 39.2 bits (92), Expect = 0.009
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 4/75 (5%)
Query: 1260 YELRVVIFGTKASPYLAQRTVKQLIDDESKNFPLACQYIGESLYMDDCVISFPSQKEAIE 1319
Y+ +V+ G K SP + Q V Q ++ K +P Y YMDD +I+ + + E
Sbjct: 124 YQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYH----YMDDILIASDLEGQLRE 179
Query: 1320 FFNQTVKLFASGGFR 1334
+ + + G
Sbjct: 180 IYEELRQTLLRWGLT 194
>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein,
contains RING Zn-finger [Posttranslational modification,
protein turnover, chaperones / Intracellular trafficking
and secretion].
Length = 190
Score = 34.8 bits (80), Expect = 0.23
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 721 HDLCVNCLGTGHKANNCPSKSNCNIC 746
H +C NC GH++N+CP C C
Sbjct: 78 HSICYNCSWDGHRSNHCPKPKKCYNC 103
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 34.5 bits (79), Expect = 0.61
Identities = 14/27 (51%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 409 LAKPPPPAPTPAPAPISPISCGIKLQP 435
LA PPPP PTP PAP + L P
Sbjct: 2698 LADPPPPPPTPEPAP-HALVSATPLPP 2723
>gnl|CDD|227830 COG5543, COG5543, Uncharacterized conserved protein [Function
unknown].
Length = 1400
Score = 34.6 bits (79), Expect = 0.61
Identities = 22/83 (26%), Positives = 33/83 (39%), Gaps = 7/83 (8%)
Query: 502 DALLEKYDDKRNLATYYMDSLLNFKTQSGSLETFIDYFGANVAQVIYDALLEKYDDKRNL 561
D L+ Y D R L+T LL ++ S S F+D AN +V ++
Sbjct: 480 DLLVSNYADIRKLST---KILLGLESMSESRGLFLDTLDANALKVKIESHQSHDVHGDAG 536
Query: 562 ATYYMDSLLNFKIQSGSLETFID 584
AT Y I+S +F+
Sbjct: 537 ATVYC----VEFIKSCQSRSFVG 555
>gnl|CDD|219834 pfam08424, NRDE-2, NRDE-2, necessary for RNA interference. This is
a family of eukaryotic proteins. Eukaryotic cells
express a wide variety of endogenous small regulatory
RNAs that regulate heterochromatin formation,
developmental timing, defence against parasitic nucleic
acids, and genome rearrangement. Many small regulatory
RNAs are thought to function in nuclei, and in plants
and fungi small interfering (si)RNAs associate with
nascent transcripts and direct chromatin and/or DNA
modifications. This family protein, NRDE-2, is required
for small interfering (si)RNA-mediated silencing in
nuclei. NRDE-2 associates with the Argonaute protein
NRDE-3 within nuclei and is recruited by NRDE-3/siRNA
complexes to nascent transcripts that have been targeted
by RNA interference, RNAi, the process whereby
double-stranded RNA (dsRNA) directs the
sequence-specific degradation of mRNA.
Length = 324
Score = 33.9 bits (78), Expect = 0.68
Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 5/57 (8%)
Query: 189 EFLDI----FSRFSSYPKLLNVMVYVLRFAKILTSKGFISAQDLNLTESVVIKIIQN 241
++LD FS FS Y K+ LR K + S Q + E V++ +
Sbjct: 106 KYLDFRQGDFSTFS-YSKVRKTYEKCLRALKAALNGTITSHQAVPELEEVMLYLFLR 161
>gnl|CDD|197667 smart00343, ZnF_C2HC, zinc finger.
Length = 17
Score = 29.3 bits (67), Expect = 0.77
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 724 CVNCLGTGHKANNCPS 739
C NC GH A +CPS
Sbjct: 2 CYNCGKEGHIARDCPS 17
>gnl|CDD|218147 pfam04556, DpnII, DpnII restriction endonuclease. Members of this
family are type II restriction enzymes (EC:3.1.21.4).
They recognise the double-stranded unmethylated sequence
GATC and cleave before G-1.
http://rebase.neb.com/rebase/enz/DpnII.html.
Length = 284
Score = 33.4 bits (77), Expect = 0.90
Identities = 31/140 (22%), Positives = 61/140 (43%), Gaps = 23/140 (16%)
Query: 144 NEFLDIFSVESWPIRSYSEFKNHEDIPEQKTVSSV--------VLVGVENLNNEFLDIFS 195
+FL+ S R+ F + E + K V + L+G ++++NEF ++F
Sbjct: 4 EDFLETLSET---NRTLDYFVDWEKV--FKNVKKIEIELNILNYLIGKDDIDNEFRELFK 58
Query: 196 RFSSYPKLLNVMVYVL--RFAKILTSKGFISAQDLNLTESVVIKIIQNHHFKDIIDKDLN 253
+ YP++L V+ +L R K + LNL K + + +D +
Sbjct: 59 K---YPEVLKVLPILLAIRDKKKDKLLANGNLDFLNLDFKK--KNYDDENIEDYYE---F 110
Query: 254 LAESVVIKIIQNHHFKDIID 273
L ++ ++ + QN K ++D
Sbjct: 111 LEKTGLLDLFQNKLIKSLVD 130
>gnl|CDD|133136 cd00303, retropepsin_like, Retropepsins; pepsin-like aspartate
proteases. The family includes pepsin-like aspartate
proteases from retroviruses, retrotransposons and
retroelements, as well as eukaryotic
dna-damage-inducible proteins (DDIs), and bacterial
aspartate peptidases. While fungal and mammalian pepsins
are bilobal proteins with structurally related N and
C-terminals, retropepsins are half as long as their
fungal and mammalian counterparts. The monomers are
structurally related to one lobe of the pepsin molecule
and retropepsins function as homodimers. The active site
aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it
does in pepsin. Retroviral aspartyl protease is
synthesized as part of the POL polyprotein that contains
an aspartyl protease, a reverse transcriptase, RNase H,
and an integrase. The POL polyprotein undergoes specific
enzymatic cleavage to yield the mature proteins. In
aspartate peptidases, Asp residues are ligands of an
activated water molecule in all examples where catalytic
residues have been identified. This group of aspartate
peptidases is classified by MEROPS as the peptidase
family A2 (retropepsin family, clan AA), subfamily A2A.
Length = 92
Score = 30.8 bits (70), Expect = 1.1
Identities = 19/81 (23%), Positives = 32/81 (39%), Gaps = 6/81 (7%)
Query: 881 LDVYGKPHEMRFLLDCASMSNILSLSACKQLGLKTLFVATDLK---GVGSISSPVQGQVT 937
L +R L+D + N +S S K+LGL + T LK GS + +
Sbjct: 1 LKGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILP 60
Query: 938 MRFGSRFDKRYNYTIKALVVN 958
+ G +T+ V++
Sbjct: 61 VTIG---IGGKTFTVDFYVLD 78
>gnl|CDD|198379 cd00495, Ribosomal_L25_TL5_CTC, Ribosomal L25/TL5/CTC N-terminal 5S
rRNA binding domain. L25 is a single-domain protein,
homologous to the N-terminal domain of TL5 and CTC. CTC
is a known stress protein, and proteins of this family
are believed to have two functions, acting as both
ribosomal and stress proteins. In Escherichia coli,
cells deleted for L25 were found to be viable; however,
these cells grew slowly and had impaired protein
synthesis capability. In Bacillus subtilis, CTC is
induced under stress conditions and located in the
ribosome; it has been proposed that CTC may be necessary
for accurate translation under stress conditions.
Ribosomal_L25_TL5_CTC is mostly found in bacteria, with
a few exceptions such as plants or stramenopiles. Due to
its limited taxonomic diversity and the viability of
cells deleted for L25, this protein is not believed to
be necessary for ribosomal assembly. Eukaryotes contain
a protein called L25, which is not homologous to
bacterial L25, but rather to bacterial L23.
Length = 90
Score = 30.5 bits (70), Expect = 1.4
Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 228 LNLTESVVIKIIQNHHFKDIIDKDLNLA---ESVVIKIIQNHHFKDII 272
+++ + K+++ +I+ L + E+V+IK +Q H KD I
Sbjct: 38 ISVDAKELEKLLRKEGENTVIE--LEIDGKKENVLIKDVQRHPVKDEI 83
Score = 29.0 bits (66), Expect = 5.6
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 205 NVMVYVLR--FAKILTSKGFISAQDLNL---TESVVIKIIQNHHFKDII 248
+ + V K+L +G + +L + E+V+IK +Q H KD I
Sbjct: 35 PIPISVDAKELEKLLRKEGENTVIELEIDGKKENVLIKDVQRHPVKDEI 83
>gnl|CDD|236764 PRK10808, PRK10808, outer membrane protein A; Reviewed.
Length = 351
Score = 32.7 bits (75), Expect = 1.7
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 404 YKDGELAKPPPPAPTPAPAPI 424
Y+ G+ P AP PAPAP+
Sbjct: 194 YRFGQEEAAPVVAPAPAPAPV 214
>gnl|CDD|216648 pfam01690, PLRV_ORF5, Potato leaf roll virus readthrough protein.
This family consists mainly of the potato leaf roll
virus readthrough protein. This is generated via a
readthrough of open reading frame 3 a coat protein
allowing transcription of open reading frame 5 to give
an extended coat protein with a large c-terminal
addition or read through domain. The readthrough protein
is thought to play a role in the circulative aphid
transmission of potato leaf roll virus. Also in the
family is open reading frame 6 from beet western yellows
virus and potato leaf roll virus both luteovirus and an
unknown protein from cucurbit aphid-borne yellows virus
a closterovirus.
Length = 460
Score = 32.8 bits (75), Expect = 2.0
Identities = 10/12 (83%), Positives = 10/12 (83%)
Query: 412 PPPPAPTPAPAP 423
PPPPAPTP P P
Sbjct: 15 PPPPAPTPEPTP 26
>gnl|CDD|233037 TIGR00592, pol2, DNA polymerase (pol2). All proteins in this
superfamily for which functions are known are DNA
polymerases.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 = 1172
Score = 32.7 bits (74), Expect = 2.6
Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 12/63 (19%)
Query: 60 IQQNMKVDSLYHVSGTENPADGLSRGLLPNQFIDYKIYFSGPSWLT---EDVESWPIRSY 116
+ ++K + +HV G+ + G L + KI GP WL D +P RS+
Sbjct: 432 LPSDLKGQTFWHVFGS-------NTGNLERFLLLRKIK--GPCWLAVKGPDELEYPRRSW 482
Query: 117 SEF 119
++
Sbjct: 483 CKY 485
>gnl|CDD|233572 TIGR01779, TonB-B12, TonB-dependent vitamin B12 receptor. This
model represents the TonB-dependent outer membrane
receptor found in gamma proteobacteria responsible for
translocating the cobalt-containing vitamin B12
(cobalamin) [Transport and binding proteins, Other,
Transport and binding proteins, Porins].
Length = 614
Score = 32.1 bits (73), Expect = 3.4
Identities = 13/45 (28%), Positives = 18/45 (40%)
Query: 582 FIDYFGANVAALKALDLPNLSEFFLFYLGNSKLDESTRKQFELSL 626
FI+ + A PNL++ + GN L T K EL
Sbjct: 397 FIEELRFTASYGTAFKAPNLNQLYYPSYGNPNLQPETSKSAELGF 441
>gnl|CDD|227109 COG4768, COG4768, Uncharacterized protein containing a divergent
version of the methyl-accepting chemotaxis-like domain
[General function prediction only].
Length = 139
Score = 30.5 bits (69), Expect = 3.8
Identities = 20/89 (22%), Positives = 29/89 (32%), Gaps = 11/89 (12%)
Query: 866 TTQTTVLLGTVKILVLDVYGKPHEMRFLLD-CASMSNILSLSACKQLGLKTLFVATDL-- 922
T +T LL L DV GK + + D + + L +AT
Sbjct: 51 THETEELLHKTNTLAEDVQGKVATLDPVFDAVKDLG-----QSVSDLNQSVRHLATRATN 105
Query: 923 ---KGVGSISSPVQGQVTMRFGSRFDKRY 948
K I+ V V +F + KR
Sbjct: 106 AVEKNEKKIAQAVVSNVASKFFKKKKKRA 134
>gnl|CDD|233722 TIGR02093, P_ylase, glycogen/starch/alpha-glucan phosphorylases.
This family consists of phosphorylases. Members use
phosphate to break alpha 1,4 linkages between pairs of
glucose residues at the end of long glucose polymers,
releasing alpha-D-glucose 1-phosphate. The nomenclature
convention is to preface the name according to the
natural substrate, as in glycogen phosphorylase, starch
phosphorylase, maltodextrin phosphorylase, etc. Name
differences among these substrates reflect differences in
patterns of branching with alpha 1,6 linkages. Members
include allosterically regulated and unregulated forms. A
related family, TIGR02094, contains examples known to act
well on particularly small alpha 1,4 glucans, as may be
found after import from exogenous sources [Energy
metabolism, Biosynthesis and degradation of
polysaccharides].
Length = 794
Score = 31.9 bits (73), Expect = 4.4
Identities = 12/26 (46%), Positives = 18/26 (69%), Gaps = 3/26 (11%)
Query: 1263 RVVIFGTKASP--YLAQRTVKQLIDD 1286
R VIFG KA+P ++A+ +K LI+
Sbjct: 567 RTVIFGGKAAPGYHMAKLIIK-LINS 591
>gnl|CDD|215533 PLN02983, PLN02983, biotin carboxyl carrier protein of acetyl-CoA
carboxylase.
Length = 274
Score = 31.0 bits (70), Expect = 4.6
Identities = 8/15 (53%), Positives = 9/15 (60%)
Query: 412 PPPPAPTPAPAPISP 426
P PA +P P P SP
Sbjct: 173 PSAPASSPPPTPASP 187
>gnl|CDD|216471 pfam01386, Ribosomal_L25p, Ribosomal L25p family. Ribosomal
protein L25 is an RNA binding protein, that binds 5S
rRNA. This family includes Ctc from B. subtilis, which
is induced by stress.
Length = 87
Score = 29.0 bits (66), Expect = 4.8
Identities = 13/48 (27%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 228 LNLTESVVIKIIQNHHFKDIIDKDLNLA---ESVVIKIIQNHHFKDII 272
+++ E + K+++ +I+ L + E+V+IK +Q H KD I
Sbjct: 37 ISVDEKELEKLLREAGENTVIE--LKIDGKKENVLIKDVQRHPVKDKI 82
>gnl|CDD|215868 pfam00343, Phosphorylase, Carbohydrate phosphorylase. The members of
this family catalyze the formation of glucose 1-phosphate
from one of the following polyglucoses; glycogen, starch,
glucan or maltodextrin.
Length = 712
Score = 31.2 bits (71), Expect = 5.5
Identities = 15/26 (57%), Positives = 20/26 (76%), Gaps = 3/26 (11%)
Query: 1263 RVVIFGTKASP--YLAQRTVKQLIDD 1286
RVVIFG KA+P Y+A+R +K LI+
Sbjct: 484 RVVIFGGKAAPGYYMAKRIIK-LINS 508
>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 = 30.3 bits (69), Expect = 5.5
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 8/50 (16%)
Query: 1260 YELRVVIFGTKASPYLAQRTVKQLIDDESKNFPLACQYIGESLYMDDCVI 1309
YE + FG K +P QR + +++ D +F Y+DD ++
Sbjct: 91 YEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEV--------YLDDILV 132
>gnl|CDD|233989 TIGR02739, TraF, type-F conjugative transfer system pilin assembly
protein TraF. This protein is part of a large group of
proteins involved in conjugative transfer of plasmid
DNA, specifically the F-type system. This protein has
been predicted to contain a thioredoxin fold and has
been shown to be localized to the periplasm. Unlike the
related protein TrbB (TIGR02738), TraF does not contain
a conserved pair of cysteines and has been shown not to
function as a thiol disulfide isomerase by
complementation of an Ecoli DsbA defect. The protein is
believed to be involved in pilin assembly. Even more
closely related than TrbB is a clade of genes
(TIGR02740) which do contain the CXXC motif, but it is
unclear whether these genes are involved in type-F
conjugation systems per se.
Length = 256
Score = 30.8 bits (70), Expect = 5.7
Identities = 15/61 (24%), Positives = 22/61 (36%), Gaps = 8/61 (13%)
Query: 372 KKYRLAISSPISGFSSSSFPVNRVEEMVGYIKYKDGELAK------PPPPAPTPAPAPIS 425
L + S P+N E G+ Y + + K P P P+ P P+S
Sbjct: 1 NFRLLPLLVSGLLVSLHPDPLNEKPE--GWQWYNEPKEEKEEKKPKPVPLQPSQEPPPLS 58
Query: 426 P 426
P
Sbjct: 59 P 59
>gnl|CDD|233312 TIGR01209, TIGR01209, RNA ligase, Pab1020 family. Members of this
family are found, so far, in a single copy per genome and
largely in thermophiles, of which only Aquifex aeolicus
is bacterial rather than archaeal. PSI-BLAST converges
after a single iteration to the whole of this family and
reveals no convincing similarity to any other protein.
The member protein Pab1020 has been characterized as an
RNA ligase with circularization activity [Transcription,
RNA processing].
Length = 374
Score = 31.2 bits (71), Expect = 5.8
Identities = 27/130 (20%), Positives = 50/130 (38%), Gaps = 29/130 (22%)
Query: 1255 EKIDVYELRVVIFGTKA---------SPYLAQRTVKQLID----DESKNFPLACQYIG-E 1300
EK++ Y +R+V +G P+ +R + LID D++ + L + G E
Sbjct: 85 EKMNGYNVRIVKYGGNVYALTRGGFICPFTTER-LPDLIDLEFFDDNPDLVLCGEMAGPE 143
Query: 1301 SLYMDDCVISFPSQKEAIEFFNQTVKLFASGGF-----RFT---KWSSNSPEILEQIPI- 1351
+ Y +P KE + FF ++ + R K+ EIL
Sbjct: 144 NPYT---PEYYPEVKEDLGFFLFDIREGKTNRSLPVEERLELAEKYGLPHVEILGVYTAD 200
Query: 1352 --HDRLAEMV 1359
+ + E++
Sbjct: 201 EAVEEIYEII 210
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 0.137 0.414
Gapped
Lambda K H
0.267 0.0869 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 87,625,009
Number of extensions: 8712876
Number of successful extensions: 7387
Number of sequences better than 10.0: 1
Number of HSP's gapped: 7373
Number of HSP's successfully gapped: 37
Length of query: 1738
Length of database: 10,937,602
Length adjustment: 110
Effective length of query: 1628
Effective length of database: 6,058,662
Effective search space: 9863501736
Effective search space used: 9863501736
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: 66 (28.9 bits)