RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8980
(355 letters)
>gnl|CDD|217730 pfam03792, PBC, PBC domain. The PBC domain is a member of the TALE
(three-amino-acid loop extension) superclass of
homeodomain proteins.
Length = 192
Score = 335 bits (860), Expect = e-116
Identities = 149/197 (75%), Positives = 165/197 (83%), Gaps = 8/197 (4%)
Query: 30 PRKQDIGEILQQIMNITDQCLDEAQARKHTLNCHRMKPSLFSVLCEIKEKTVLSLRNTQE 89
R QDI ++LQQIM ITDQ LDEAQARKH LNCHRMKP+LFSVLCEIKEKT LS RN E
Sbjct: 4 QRSQDISDLLQQIMKITDQSLDEAQARKHALNCHRMKPALFSVLCEIKEKTALSTRNMPE 63
Query: 90 EEPPDPQLMRLDNMLIAEGVAGPEKGGGANAAASASAAASGGPGQPDNAIEHSDYRAKLA 149
++PPDPQL+RLDNML+AEGVAGP+K G AAA+ + PDN+IEHSDYRAKL+
Sbjct: 64 DDPPDPQLLRLDNMLLAEGVAGPDKSGLLAAAAAGTG--------PDNSIEHSDYRAKLS 115
Query: 150 QIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQIIHKKFSSIQMQL 209
QIRQIYH ELEKYEQAC EFT HVMNLLREQSRTRPI+ +EIERMV II +KF+ IQ QL
Sbjct: 116 QIRQIYHSELEKYEQACKEFTQHVMNLLREQSRTRPISQREIERMVNIISRKFNKIQFQL 175
Query: 210 KQSTCEAVMILRSRFLD 226
KQSTCEAVMILRSRFLD
Sbjct: 176 KQSTCEAVMILRSRFLD 192
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in
the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 76.1 bits (188), Expect = 7e-18
Identities = 26/61 (42%), Positives = 37/61 (60%), Gaps = 3/61 (4%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
RRKR F+ + E L + F NPYPS E +EELA++ +T QV WF N+R + K+
Sbjct: 1 RRKRTRFTPEQLEELEKEF---EKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57
Query: 288 N 288
+
Sbjct: 58 S 58
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 71.7 bits (177), Expect = 3e-16
Identities = 26/60 (43%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
RRKR F+ + E L + F N YPS E +EELA+K +T QV WF N+R ++K+
Sbjct: 1 RRKRTTFTPEQLEELEKEF---EKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 70.7 bits (174), Expect = 7e-16
Identities = 26/59 (44%), Positives = 37/59 (62%), Gaps = 3/59 (5%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286
RRKR +F+ + E L + F NPYPS E +EELA+K ++ QV WF N+R ++K
Sbjct: 2 RRKRTSFTPEQLEELEKEF---QKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57
>gnl|CDD|203350 pfam05920, Homeobox_KN, Homeobox KN domain. This is a homeobox
transcription factor KN domain conserved from fungi to
human and plants.
Length = 40
Score = 69.8 bits (172), Expect = 1e-15
Identities = 21/39 (53%), Positives = 25/39 (64%)
Query: 246 FYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIR 284
HL NPYPSEE K ELAR+ ++ Q+ NWF N R R
Sbjct: 2 LLEHLHNPYPSEEEKSELARQTGLSRKQIDNWFINARRR 40
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 48.6 bits (116), Expect = 5e-07
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 3/62 (4%)
Query: 226 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRY 285
+ KRR + + +L F NPYPS + +L+ N+ V WF NKR +
Sbjct: 50 PPKSKRRRTTDEQLMVLEREF---EINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKE 106
Query: 286 KK 287
KK
Sbjct: 107 KK 108
>gnl|CDD|227676 COG5386, COG5386, Cell surface protein [Cell envelope biogenesis,
outer membrane].
Length = 352
Score = 32.2 bits (73), Expect = 0.38
Identities = 16/87 (18%), Positives = 32/87 (36%), Gaps = 6/87 (6%)
Query: 254 YPSEEAKEELARKCNITVSQ-VSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSM 312
+ + + L K ++ + + N+ IR + + Q AA +
Sbjct: 143 FEVSDLSKPLTAKIHVVIPELGINYDHEYTIRLEFDTAIDQAAN---AATPNDDKNVAQP 199
Query: 313 GPSSQGTPTPMMSPAPPGG--PQDSMG 337
G ++ TPTP +P P P+ +
Sbjct: 200 GTTTPKTPTPQTTPNKPKVENPKTGLT 226
>gnl|CDD|239072 cd02257, Peptidase_C19, Peptidase C19 contains ubiquitinyl
hydrolases. They are intracellular peptidases that
remove ubiquitin molecules from polyubiquinated peptides
by cleavage of isopeptide bonds. They hydrolyse bonds
involving the carboxyl group of the C-terminal Gly
residue of ubiquitin The purpose of the
de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 255
Score = 32.1 bits (73), Expect = 0.38
Identities = 10/79 (12%), Positives = 30/79 (37%), Gaps = 6/79 (7%)
Query: 149 AQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQIIHKKFS-SIQM 207
+ ++ ++ ++ Q +EF +++ L E+ + + + +IH F ++
Sbjct: 13 SVLQALFSEQ-----QDAHEFLLFLLDKLHEELKKSSKRTSDSSSLKSLIHDLFGGKLES 67
Query: 208 QLKQSTCEAVMILRSRFLD 226
+ C + L
Sbjct: 68 TIVCLECGHESVSTEPELF 86
>gnl|CDD|238045 cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins.
Prokaryotic DNA binding proteins belonging to the
xenobiotic response element family of transcriptional
regulators.
Length = 58
Score = 28.7 bits (65), Expect = 0.59
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 261 EELARKCNITVSQVSNWFGNKR 282
EELA K ++ S +S KR
Sbjct: 16 EELAEKLGVSRSTISRIENGKR 37
>gnl|CDD|217888 pfam04091, Sec15, Exocyst complex subunit Sec15-like.
Length = 311
Score = 31.5 bits (72), Expect = 0.61
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 148 LAQIRQIYHQELEKYEQACNEFTTHVMNLLR-EQSRTRPIT 187
L QI QI LE +E+AC+E + L QS PI+
Sbjct: 92 LEQIVQIL-INLEYFEKACDELEKLLAQLRNIPQSIGGPIS 131
>gnl|CDD|197775 smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins.
Length = 56
Score = 28.6 bits (65), Expect = 0.63
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 261 EELARKCNITVSQVSNWFGNKRI 283
EELA K ++ S +S KR
Sbjct: 14 EELAEKLGVSRSTLSRIENGKRK 36
>gnl|CDD|182745 PRK10803, PRK10803, tol-pal system protein YbgF; Provisional.
Length = 263
Score = 30.9 bits (70), Expect = 0.80
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 9/70 (12%)
Query: 106 AEGVAGPEKGGGANAAASAS--AAASGGPGQPDNAIEHSDYRAKLAQIRQIYHQELEKYE 163
A+ +G + G A+A +A A +G P Q +A ++DY A +A + Q+ + +
Sbjct: 108 AQSTSGDQSGAAASATPAADAGTANAGAPVQSGDA--NTDYNAAIALV-----QDKSRQD 160
Query: 164 QACNEFTTHV 173
A F V
Sbjct: 161 DAIVAFQNFV 170
>gnl|CDD|226365 COG3846, TrbL, Type IV secretory pathway, TrbL components
[Intracellular trafficking and secretion].
Length = 452
Score = 31.3 bits (71), Expect = 0.90
Identities = 11/39 (28%), Positives = 16/39 (41%)
Query: 100 LDNMLIAEGVAGPEKGGGANAAASASAAASGGPGQPDNA 138
+ + P+ GG+ A SA A A+G P A
Sbjct: 381 TGVSVASGVGQAPKSAGGSAAGKSAVAKATGVQAAPGWA 419
>gnl|CDD|236573 PRK09567, nirA, ferredoxin-nitrite reductase; Reviewed.
Length = 593
Score = 31.1 bits (71), Expect = 1.0
Identities = 19/75 (25%), Positives = 28/75 (37%), Gaps = 8/75 (10%)
Query: 109 VAGPEKGGGANAAASASAAASGGPGQPDNAIEHSDYRAKLAQIRQIYHQELEKYEQACNE 168
A +G +A AA GP AI LA +++ QE K E+ N
Sbjct: 24 AARATRGAAGGQTPAAPAAEPTGPD----AIHIKAQDRFLAAGKKLCDQEKWKREE--NP 77
Query: 169 FTTHVMNLLREQSRT 183
F + L+ Q+
Sbjct: 78 FDAW--DRLKAQAAA 90
>gnl|CDD|132909 cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic RNA polymerase
II. The eukaryotic RPB3 subunit of RNA polymerase
(RNAP) II is involved in the assembly of RNAP subunits.
RNAP is a large multi-subunit complex responsible for
the synthesis of RNA. It is the principal enzyme of the
transcription process, and is a final target in many
regulatory pathways that control gene expression in all
living cells. At least three distinct RNAP complexes are
found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP
III. RNAP II is responsible for the synthesis of mRNA
precursor. The RPB3 subunit is similar to the bacterial
RNAP alpha subunit in that it contains two subdomains:
one subdomain is similar the eukaryotic
Rpb11/AC19/archaeal L subunit which is involved in
dimerization, and the other is an inserted beta sheet
subdomain. The RPB3 subunit heterodimerizes with the
RPB11 subunit, and together with RPB10 and RPB12,
anchors the two largest subunits, RPB1 and RPB2, and
stabilizes their association.
Length = 265
Score = 30.6 bits (70), Expect = 1.2
Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 16/89 (17%)
Query: 135 PDNAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSR----------TR 184
PDNA+ H+DY + +E K E AC E L ++ T
Sbjct: 182 PDNALRHTDY-----WYLEDEDKEWPKSENACIEEPPEKDALFDIDAKPDKFYFNVESTG 236
Query: 185 PITPKEI-ERMVQIIHKKFSSIQMQLKQS 212
+ P++I ++I+ KK + +Q+QL +
Sbjct: 237 ALPPEQIVLSGLEILKKKLADLQLQLSEE 265
>gnl|CDD|214822 smart00798, AICARFT_IMPCHas, AICARFT/IMPCHase bienzyme. This is a
family of bifunctional enzymes catalysing the last two
steps in de novo purine biosynthesis. The bifunctional
enzyme is found in both prokaryotes and eukaryotes. The
second last step is catalysed by
5-aminoimidazole-4-carboxamide ribonucleotide
formyltransferase (AICARFT), this enzyme catalyses the
formylation of AICAR with 10-formyl-tetrahydrofolate to
yield FAICAR and tetrahydrofolate. The last step is
catalysed by IMP (Inosine monophosphate) cyclohydrolase
(IMPCHase), cyclizing FAICAR
(5-formylaminoimidazole-4-carboxamide ribonucleotide) to
IMP.
Length = 311
Score = 30.2 bits (69), Expect = 1.6
Identities = 13/56 (23%), Positives = 26/56 (46%)
Query: 232 RNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
R ++ +E +N+ F + P EEA E L++K N+ + + + +K
Sbjct: 176 RPVDEETAEAINKIFLEVIIAPDFDEEALEILSKKKNLRLLECGPLPDPDGLEFKS 231
>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein. This
family includes archaebacterial L12, eukaryotic P0, P1
and P2.
Length = 88
Score = 28.0 bits (63), Expect = 2.0
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 105 IAEGVAGPEKGGGANAAASASAAASGGPG 133
I E +A A AAA+A+AAA+
Sbjct: 35 IKELIANGSAKLSAAAAAAAAAAAAAAAA 63
>gnl|CDD|221480 pfam12238, MSA-2c, Merozoite surface antigen 2c. This family of
proteins is found in eukaryotes. Proteins in this family
are typically between 263 and 318 amino acids in length.
There is a conserved SFT sequence motif. MSA-2 is a
plasma membrane glycoprotein which can be found in
Babesia bovis species.
Length = 201
Score = 29.4 bits (66), Expect = 2.2
Identities = 15/73 (20%), Positives = 20/73 (27%), Gaps = 1/73 (1%)
Query: 278 FGNKRIRYKKNIGKAQEEANLYAA-KKAAGASPYSMGPSSQGTPTPMMSPAPPGGPQDSM 336
F N + + + + N Y KA SSQGT T S +
Sbjct: 110 FCNDFLDSESPFMRIYKALNTYELVVKAPAEYYSPKHSSSQGTSTTRPSDGSATPNTSAP 169
Query: 337 GYSVNMNGDYSSP 349
N P
Sbjct: 170 PTPGNPAAQPEKP 182
>gnl|CDD|201759 pfam01381, HTH_3, Helix-turn-helix. This large family of DNA
binding helix-turn helix proteins includes Cro and CI.
Within the Neisseria gonorrhoeae phage associated
protein NGO0477, the full protein fold incorporates a
helix-turn-helix motif, but the function of this member
is unlikely to be that of a DNA-binding regulator, the
function of most other members, so is not necessarily
characteristic of the whole family.
Length = 55
Score = 26.7 bits (60), Expect = 2.7
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 260 KEELARKCNITVSQVSNWFGNKRI 283
+EELA K ++ S +S KR
Sbjct: 12 QEELAEKLGVSRSTISKIENGKRE 35
>gnl|CDD|180161 PRK05609, nusG, transcription antitermination protein NusG;
Validated.
Length = 181
Score = 29.0 bits (66), Expect = 2.8
Identities = 9/52 (17%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 170 TTHVMNLL-REQSRTRPITPKEIERMVQIIHKKFSSIQMQLKQSTCEAVMIL 220
T V + S+ P++ KE+E++++ + + + ++ E V ++
Sbjct: 85 TPGVTGFVGSTGSKPTPLSEKEVEKILKQLQEGVEKPKPKVDFEVGEMVRVI 136
>gnl|CDD|201451 pfam00804, Syntaxin, Syntaxin. Syntaxins are the prototype family
of SNARE proteins. They usually consist of three main
regions - a C-terminal transmembrane region, a central
SNARE domain which is characteristic of and conserved in
all syntaxins (pfam05739), and an N-terminal domain that
is featured in this entry. This domain varies between
syntaxin isoforms; in syntaxin 1A it is found as three
alpha-helices with a left-handed twist. It may fold back
on the SNARE domain to allow the molecule to adopt a
'closed' configuration that prevents formation of the
core fusion complex - it thus has an auto-inhibitory
role. The function of syntaxins is determined by their
localisation. They are involved in neuronal exocytosis,
ER-Golgi transport and Golgi-endosome transport, for
example. They also interact with other proteins as well
as those involved in SNARE complexes. These include
vesicle coat proteins, Rab GTPases, and tethering
factors.
Length = 103
Score = 27.7 bits (62), Expect = 3.5
Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 4/65 (6%)
Query: 148 LAQIRQIYHQELEKYEQACNEFTT-HVMNLLREQSRTRPITPKEIERMVQIIHKKFSSIQ 206
++ +I +E++K Q E H L S +E+E + Q I + +I+
Sbjct: 6 FDEVEEI-REEIQKIRQNLEELQKLHKRILTAPDSDKE--LREELEELTQEIKQLARAIK 62
Query: 207 MQLKQ 211
+LK
Sbjct: 63 KKLKS 67
>gnl|CDD|132755 cd07070, NR_LBD_SF-1, The ligand binding domain of nuclear
receptor steroidogenic factor 1, a member of nuclear
receptor superfamily. The ligand binding domain of
nuclear receptor steroidogenic factor 1 (SF-1): SF-1, a
member of the nuclear hormone receptor superfamily, is
an essential regulator of endocrine development and
function and is considered a master regulator of
reproduction. Most nuclear receptors function as
homodimer or heterodimers, however SF-1 binds to its
target genes as a monomer, recognizing the variations
of the DNA sequence motif, T/CCA AGGTCA. SF-1 functions
cooperatively with other transcription factors to
modulate gene expression. Phospholipids have been
determined as potential ligands of SF-1. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, SF-1 has a
central well conserved DNA binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 237
Score = 28.4 bits (63), Expect = 4.9
Identities = 12/41 (29%), Positives = 20/41 (48%), Gaps = 7/41 (17%)
Query: 51 DEAQARKHTLNC-------HRMKPSLFSVLCEIKEKTVLSL 84
DE Q R L C +P+ F +LC + ++T +S+
Sbjct: 14 DEDQVRARILGCLQEPQKSRPDQPAPFGLLCRMADQTFISI 54
>gnl|CDD|217775 pfam03874, RNA_pol_Rpb4, RNA polymerase Rpb4. This family includes
the Rpb4 protein. This family also includes C17 (aka
CGRP-RCP) is an essential subunit of RNA polymerase III.
C17 forms a subcomplex with C25 which is likely to be
the counterpart of subcomplex Rpb4/7 in Pol II.
Length = 110
Score = 27.5 bits (62), Expect = 4.9
Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 3/59 (5%)
Query: 212 STCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNP--YPSEEAKEELARKCN 268
+ E + IL+ + RR+ R + + IL + +L+ + E+ EL +
Sbjct: 3 TNSEVLEILKKELEERRRESRYVEENLNTILRK-TLEYLNKFSRLKNPESARELVEELK 60
>gnl|CDD|173644 cd05079, PTKc_Jak1_rpt2, Catalytic (repeat 2) domain of the Protein
Tyrosine Kinase, Janus kinase 1. Protein Tyrosine
Kinase (PTK) family; Janus kinase 1 (Jak1); catalytic
(c) domain (repeat 2). The PTKc family is part of a
larger superfamily that includes the catalytic domains
of other kinases such as protein serine/threonine
kinases, RIO kinases, and phosphoinositide 3-kinase
(PI3K). PTKs catalyze the transfer of the
gamma-phosphoryl group from ATP to tyrosine (tyr)
residues in protein substrates. Jak1 is a member of the
Janus kinase (Jak) subfamily of proteins, which are
cytoplasmic (or nonreceptor) tyr kinases containing an
N-terminal FERM domain, followed by a Src homology 2
(SH2) domain, a pseudokinase domain, and a C-terminal
tyr kinase domain. Jaks are crucial for cytokine
receptor signaling. They are activated by
autophosphorylation upon cytokine-induced receptor
aggregation, and subsequently trigger downstream
signaling events such as the phosphorylation of signal
transducers and activators of transcription (STATs).
Jak1 is widely expressed in many tissues. Many cytokines
are dependent on Jak1 for signaling, including those
that use the shared receptor subunits common gamma chain
(IL-2, IL-4, IL-7, IL-9, IL-15, IL-21) and gp130 (IL-6,
IL-11, oncostatin M, G-CSF, and IFNs, among others). The
many varied interactions of Jak1 and its ubiquitous
expression suggest many biological roles. Jak1 is
important in neurological development, as well as in
lymphoid development and function. It also plays a role
in the pathophysiology of cardiac hypertrophy and heart
failure. A mutation in the ATP-binding site of Jak1 was
identified in a human uterine leiomyosarcoma cell line,
resulting in defective cytokine induction and antigen
presentation, thus allowing the tumor to evade the
immune system.
Length = 284
Score = 28.4 bits (63), Expect = 5.3
Identities = 12/47 (25%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 134 QPDNAIEHS-DYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLRE 179
+P++ H D + ++ +R +YH+ + KY+ C E + + L+ E
Sbjct: 42 KPESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIME 88
>gnl|CDD|217365 pfam03097, BRO1, BRO1-like domain. This domain is found in a
number proteins including Rhophilin and BRO1. It is
known to have a role in endosomal targeting. ESCRT-III
subunit Snf7 binds to a conserved hydrophobic patch in
the BRO1 domain that is required for protein complex
formation and for the protein-sorting function of BRO1.
Length = 374
Score = 28.4 bits (64), Expect = 6.5
Identities = 9/40 (22%), Positives = 15/40 (37%), Gaps = 5/40 (12%)
Query: 151 IRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKE 190
I Y ++ +E E LR+ + P +P E
Sbjct: 22 ILSTYGEDPSLFEDDLAELNK-----LRQDAVNVPGSPDE 56
>gnl|CDD|237537 PRK13875, PRK13875, conjugal transfer protein TrbL; Provisional.
Length = 440
Score = 28.3 bits (64), Expect = 7.4
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 106 AEGVAGPEKGGGANAAASASAAASGGPGQPDNA 138
G GGGA AA+A+AA + G P A
Sbjct: 372 RAGARST--GGGAGGAAAAAAAGAAAAGPPAWA 402
>gnl|CDD|206779 cd11386, MCP_signal, Methyl-accepting chemotaxis protein (MCP),
signaling domain. Methyl-accepting chemotaxis proteins
(MCPs or chemotaxis receptors) are an integral part of
the transmembrane protein complex that controls
bacterial chemotaxis, together with the histidine
kinase CheA, the receptor-coupling protein CheW,
receptor-modification enzymes, and localized
phosphatases. MCPs contain a four helix trans membrane
region, an N-terminal periplasmic ligand binding
domain, and a C-terminal HAMP domain followed by a
cytoplasmic signaling domain. This C-terminal signaling
domain dimerizes into a four-helix bundle and interacts
with CheA through the adaptor protein CheW.
Length = 200
Score = 27.6 bits (62), Expect = 7.7
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 27 DLEPRKQDIGEILQQIMNITDQ 48
+LE +IGEI++ I +I +Q
Sbjct: 58 ELEESSAEIGEIVEVIDDIAEQ 79
>gnl|CDD|218411 pfam05067, Mn_catalase, Manganese containing catalase. Catalases
are important antioxidant metalloenzymes that catalyze
disproportionation of hydrogen peroxide, forming
dioxygen and water. Two families of catalases are known,
one having a heme cofactor, and this family that is a
structurally distinct family containing non-heme
manganese.
Length = 283
Score = 28.0 bits (62), Expect = 8.1
Identities = 30/113 (26%), Positives = 45/113 (39%), Gaps = 17/113 (15%)
Query: 223 RFLDAR-RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNK 281
FL AR +N +A EIL E + P+P + K+E+ARK S+ G++
Sbjct: 173 SFLLARETVHQNQFYKALEILEEVETIVVPVPFPRKLEKQEVARKL-FNFSR-----GDE 226
Query: 282 RIRYKKNIGKAQEEANLYAAKKAAGASPYSMGPSSQGTPTPMMSPAPPGGPQD 334
+ G+A + + K GA G P P + PAP
Sbjct: 227 STIGRWAKGEAPDGGGAFEYVKEPGA----------GAPIPDLRPAPMISHNT 269
>gnl|CDD|240343 PTZ00280, PTZ00280, Actin-related protein 3; Provisional.
Length = 414
Score = 28.2 bits (63), Expect = 8.3
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 165 ACNEFTTHVMNLLREQSRTRPITPKEIERMVQIIHKKFSSI 205
A + T + +LRE R PI ++I + Q I +K+ +
Sbjct: 193 AGRDITNFIQQMLRE--RGEPIPAEDILLLAQRIKEKYCYV 231
>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase. This model describes reverse gyrase,
found in both archaeal and bacterial thermophiles. This
enzyme, a fusion of a type I topoisomerase domain and a
helicase domain, introduces positive supercoiling to
increase the melting temperature of DNA double strands.
Generally, these gyrases are encoded as a single
polypeptide. An exception was found in Methanopyrus
kandleri, where enzyme is split within the topoisomerase
domain, yielding a heterodimer of gene products
designated RgyB and RgyA [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1171
Score = 28.3 bits (63), Expect = 8.5
Identities = 13/77 (16%), Positives = 26/77 (33%), Gaps = 23/77 (29%)
Query: 183 TRPITPKEIERMVQ------------------IIHKKFSSIQMQ-----LKQSTCEAVMI 219
TRP+ +++R++ +I ++F + QM+ K+ T +A
Sbjct: 966 TRPLDVDDLQRLILEGVIELEGLTREHLRLYDLIFRRFMASQMRPAKVDTKEITLKADGK 1025
Query: 220 LRSRFLDARRKRRNFSK 236
R F
Sbjct: 1026 EAEEEGIVEIVERGFEL 1042
>gnl|CDD|176475 cd08638, DNA_pol_A_theta, DNA polymerase theta is a low-fidelity
family A enzyme implicated in translesion synthesis and
in somatic hypermutation. DNA polymerase theta is a
low-fidelity family A enzyme implicated in translesion
synthesis (TLS) and in somatic hypermutation (SHM).
DNA-dependent DNA polymerases can be classified in six
main groups based upon phylogenetic relationships with
E. coli polymerase I (classA), E. coli polymerase II
(class B), E.coli polymerase III (class C),
euryarchaaeota polymerase II (class D), human polymerase
beta (class x), E. coli UmuC/DinB and eukaryotic RAP
30/Xeroderma pigmentosum variant (class Y). Family A
polymerase functions primarily to fill DNA gaps that
arise during DNA repair, recombination and replication.
Pol theta is an exception among family A polymerases and
generates processive single base substitutions. Family A
polymerase are found primarily in organisms related to
prokaryotes and include prokaryotic DNA polymerase I
(pol I) ,mitochondrial polymerase delta, and several
bacteriphage polymerases including those from
odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is
have two functional domains located on the same
polypeptide; a 5'-3' polymerase and 5'-3' exonuclease.
Pol I uses its 5' nuclease activity to remove the
ribonucleotide portion of newly synthesized Okazaki
fragments and DNA polymerase activity to fill in the
resulting gap. Polymerase theta mostly has
amino-terminal helicase domain, a carboxy-terminal
polymerase domain and an intervening space region.
Length = 373
Score = 28.0 bits (63), Expect = 8.9
Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 7/77 (9%)
Query: 185 PITPKEIERMVQIIHKKFSSIQMQLKQSTCEAVMI-------LRSRFLDARRKRRNFSKQ 237
P+E+ER ++ K ++ + +ST + V+ L L+ R+ + +
Sbjct: 3 GFDPEELERQRALLQAKLKELEEEAYRSTSKEVLEQLKRLHPLPKLILEYRKLSKLLTTY 62
Query: 238 ASEILNEYFYSHLSNPY 254
+L S Y
Sbjct: 63 VEPLLLLCKLSSSLQMY 79
>gnl|CDD|221459 pfam12200, DUF3597, Domain of unknown function (DUF3597). This
family of proteins is found in bacteria, eukaryotes and
viruses. Proteins in this family are typically between
126 and 281 amino acids in length. The function of this
domain is unknown. The structure of this domain has been
found to contain five helices with a long flexible loop
between helices one and two.
Length = 124
Score = 26.9 bits (60), Expect = 9.8
Identities = 13/51 (25%), Positives = 18/51 (35%)
Query: 110 AGPEKGGGANAAASASAAASGGPGQPDNAIEHSDYRAKLAQIRQIYHQELE 160
A A A + +AAA+ P A D A L + Q+L
Sbjct: 14 AAAAPAPAAAPATAPAAAAAAAPAATPPAAASVDVAAVLDALAAKKGQKLN 64
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
0.313 0.129 0.371
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,132,650
Number of extensions: 1734738
Number of successful extensions: 2002
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1980
Number of HSP's successfully gapped: 63
Length of query: 355
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 257
Effective length of database: 6,590,910
Effective search space: 1693863870
Effective search space used: 1693863870
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 (21.9 bits)
S2: 60 (26.9 bits)