RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780773|ref|YP_003065186.1| zinc metallopeptidase
[Candidatus Liberibacter asiaticus str. psy62]
(349 letters)
>gnl|CDD|31093 COG0750, COG0750, Predicted membrane-associated Zn-dependent
proteases 1 [Cell envelope biogenesis, outer membrane].
Length = 375
Score = 165 bits (418), Expect = 2e-41
Identities = 116/370 (31%), Positives = 185/370 (50%), Gaps = 28/370 (7%)
Query: 7 FLLYTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLG 66
+ + ++L ++V +HE GH+ VAR C ++V FS+GFGP+L + G + +S IPLG
Sbjct: 5 IIAFIIALGVLVFVHELGHFWVARRCGVKVERFSIGFGPKLFSRKDKGGTEYVLSAIPLG 64
Query: 67 GYVSF----------SEDEKDMRSFFCAAPWKKILTVLAGPLANCVMAILFFTFFFYNTG 116
GYV E R+F + W++I V AGPL N ++AI+ F F+ G
Sbjct: 65 GYVKMLGEDAEEVVLKGPEPRPRAFNAKSVWQRIAIVFAGPLFNFILAIVLFVVLFFVIG 124
Query: 117 ---VMKPVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISL--V 171
V PVV V+P S AA+AG++ GD I+++DG V+++++V + +L +
Sbjct: 125 LVPVASPVVGEVAPKSAAALAGLRPGDRIVAVDGEKVASWDDVRRLLVAAAGDVFNLLTI 184
Query: 172 LYREHVGVLHLKVMPRLQDT----------VDRFGIKRQVPSVGISFSYDETKLHSR--- 218
L G H ++ + V ++G+S + +
Sbjct: 185 LVIRLDGEAHAVAAEIIKSLGLTPVVIPLKPGDKIVAVDVGAIGLSPNGEPDVGKVLVKY 244
Query: 219 TVLQSFSRGLDEISSITRGFLGVLSSAFGKDTRLNQISGPVGIARIAKNFFDHGFNAYIA 278
L++ +++ + + L +L D L +SGP+GIA+IA G +
Sbjct: 245 GPLEAVGLAVEKTGRLVKLTLKMLKKLITGDLSLKNLSGPIGIAKIAGAAASLGLINLLF 304
Query: 279 FLAMFSWAIGFMNLLPIPILDGGHLITFLLEMIRGKSLGVSVTRVITRMGLCIILFLFFL 338
FLA+ S +G +NLLPIP LDGGHL+ +LLE +RGK L V + R+GL ++L L L
Sbjct: 305 FLALLSINLGILNLLPIPPLDGGHLLFYLLEALRGKPLSERVEAALYRIGLALLLLLMLL 364
Query: 339 GIRNDIYGLM 348
ND+ L
Sbjct: 365 ATFNDLLRLF 374
>gnl|CDD|100084 cd06163, S2P-M50_PDZ_RseP-like, RseP-like Site-2 proteases (S2P),
zinc metalloproteases (MEROPS family M50A), cleave
transmembrane domains of substrate proteins, regulating
intramembrane proteolysis (RIP) of diverse signal
transduction mechanisms. In Escherichia coli, the S2P
homolog RseP is involved in the sigmaE pathway of
extracytoplasmic stress responses. Also included in this
group are such homologs as Bacillus subtilis YluC,
Mycobacterium tuberculosis Rv2869c S2P, and Bordetella
bronchiseptica HurP. Rv2869c S2P appears to have a role
in the regulation of prokaryotic lipid biosynthesis and
membrane composition and YluC of Bacillus has a role in
transducing membrane stress. This group includes
bacterial and eukaryotic S2P/M50s homologs with either
one or two PDZ domains present. PDZ domains are believed
to have a regulatory role. The RseP PDZ domain is
required for the inhibitory reaction that prevents
cleavage of its substrate, RseA..
Length = 182
Score = 130 bits (330), Expect = 5e-31
Identities = 44/115 (38%), Positives = 66/115 (57%), Gaps = 9/115 (7%)
Query: 7 FLLYTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLG 66
L + + L I++ +HE GH++VA+L ++V FS+GFGP+L + + +S IPLG
Sbjct: 1 ILAFILVLGILIFVHELGHFLVAKLFGVKVEEFSIGFGPKLFSFK-KGETEYSISAIPLG 59
Query: 67 GYVSF--------SEDEKDMRSFFCAAPWKKILTVLAGPLANCVMAILFFTFFFY 113
GYV ++ E D RSF W++IL V AGPLAN ++AI+ F
Sbjct: 60 GYVKMLGEDPEEEADPEDDPRSFNSKPVWQRILIVFAGPLANFLLAIVLFAVLLS 114
Score = 87.1 bits (217), Expect = 6e-18
Identities = 32/72 (44%), Positives = 44/72 (61%)
Query: 273 FNAYIAFLAMFSWAIGFMNLLPIPILDGGHLITFLLEMIRGKSLGVSVTRVITRMGLCII 332
F ++FLA+ S +G +NLLPIP LDGGHL+ L+E IRG+ L V +I +G ++
Sbjct: 109 FAVLLSFLALLSINLGILNLLPIPALDGGHLLFLLIEAIRGRPLSEKVEEIIQTIGFALL 168
Query: 333 LFLFFLGIRNDI 344
L L NDI
Sbjct: 169 LGLMLFVTFNDI 180
>gnl|CDD|100078 cd05709, S2P-M50, Site-2 protease (S2P) class of zinc
metalloproteases (MEROPS family M50) cleaves
transmembrane domains of substrate proteins, regulating
intramembrane proteolysis (RIP) of diverse signal
transduction mechanisms. Members of this family use
proteolytic activity within the membrane to transfer
information across membranes to integrate gene
expression with physiologic stresses occurring in
another cellular compartment. The domain core structure
appears to contain at least three transmembrane helices
with a catalytic zinc atom coordinated by three
conserved residues contained within the consensus
sequence HExxH, together with a conserved aspartate
residue. The S2P/M50 family of RIP proteases is widely
distributed; in eukaryotic cells, they regulate such
processes as sterol and lipid metabolism, and
endoplasmic reticulum (ER) stress responses. In
sterol-depleted mammalian cells, a two-step proteolytic
process releases the N-terminal domains of sterol
regulatory element-binding proteins (SREBPs) from
membranes of the ER. These domains translocate into the
nucleus, where they activate genes of cholesterol and
fatty acid biosynthesis. It is the second proteolytic
step that is carried out by the SREBP Site-2 protease
(S2P) which is present in this CD superfamily.
Prokaryotic S2P/M50 homologs have been shown to regulate
stress responses, sporulation, cell division, and cell
differentiation. In Escherichia coli, the S2P homolog
RseP is involved in the sigmaE pathway of
extracytoplasmic stress responses, and in Bacillus
subtilis, the S2P homolog SpoIVFB is involved in the
pro-sigmaK pathway of spore formation. Some of the
subfamilies within this hierarchy contain one or two PDZ
domain insertions, with putative regulatory roles, such
as the inhibition of substrate cleavage as seen by the
RseP PDZ domain..
Length = 180
Score = 86.9 bits (216), Expect = 7e-18
Identities = 38/121 (31%), Positives = 59/121 (48%), Gaps = 7/121 (5%)
Query: 8 LLYTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGG 67
L + ++L+I V +HE GH +VAR ++V FS GF + G + + LIPLGG
Sbjct: 1 LAFILALLISVTVHELGHALVARRLGVKVARFSGGF----TLNPLKHGDPYGIILIPLGG 56
Query: 68 YVSFSEDEKDMRSFFCAAPWKKILTVLAGPLANCVMAILFFTFFFYNTGVMKPVVSNVSP 127
Y + F W+++L LAGPLAN ++A+L G+ V +
Sbjct: 57 YAKPVGENPRA---FKKPRWQRLLVALAGPLANLLLALLLLLLLLLLGGLPPAPVGQAAS 113
Query: 128 A 128
+
Sbjct: 114 S 114
Score = 58.8 bits (143), Expect = 2e-09
Identities = 27/71 (38%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 272 GFNAYIAFLAMFSWAIGFMNLLPIPILDGGHLITFLLEMIRGKSLGVSVTRVITRMGLCI 331
G +AFLA+ + + NLLPIP LDGG ++ LLE IRG+ + G I
Sbjct: 115 GLANLLAFLALINLNLAVFNLLPIPPLDGGRILRALLEAIRGRVEE-----RLEAYGFAI 169
Query: 332 ILFLFFLGIRN 342
+L L L + N
Sbjct: 170 LLGLLLLLLLN 180
>gnl|CDD|111095 pfam02163, Peptidase_M50, Peptidase family M50.
Length = 205
Score = 74.4 bits (183), Expect = 4e-14
Identities = 34/125 (27%), Positives = 57/125 (45%), Gaps = 7/125 (5%)
Query: 12 VSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGGYVSF 71
++L+I VV+HE GH +VAR ++V F++GFGP L + + G
Sbjct: 4 LALLISVVVHELGHALVARRFGVKVERFAIGFGPLLFLHLDGATEYTIRLMFGAFGAP-- 61
Query: 72 SEDEKDMRSFFCAAPWKKILTVLAGPLANCVMAILFFTFFFYNTGVMKPVVSNVSPASPA 131
R F + +++ LAGPLAN ++A+L G+ P V +
Sbjct: 62 -----INREFKKKSRKQRLKISLAGPLANFILALLLLALLLLLPGIPVPPVIGGVVVGSS 116
Query: 132 AIAGV 136
+++G
Sbjct: 117 SLSGP 121
Score = 64.0 bits (156), Expect = 5e-11
Identities = 39/107 (36%), Positives = 56/107 (52%), Gaps = 1/107 (0%)
Query: 237 GFLGVLSSAFGKDTRLNQISGPVGIARIAKNFFDHGFNAYIAFLAMFSWAIGFMNLLPIP 296
+ V G + +SGPV IA++ G A +AFLA+ + +G NLLPIP
Sbjct: 100 PGIPVPPVIGGVVVGSSSLSGPVAIAKVGSTSALSGLIALLAFLALLNLNLGLFNLLPIP 159
Query: 297 ILDGGHLITFLLEMIRGKSLGVSVTRVITRMGLCIILFLFFLGIRND 343
LDGGH++ LL +RG+ L I +GL ++L L L + ND
Sbjct: 160 PLDGGHILRALL-AVRGRPLNERAENYIYLVGLALLLLLILLLLFND 205
>gnl|CDD|29046 cd00989, PDZ_metalloprotease, PDZ domain of bacterial and plant
zinc metalloprotases, presumably membrane-associated or
integral membrane proteases, which may be involved in
signalling and regulatory mechanisms. May be responsible
for substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, and binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins..
Length = 79
Score = 61.4 bits (149), Expect = 3e-10
Identities = 25/79 (31%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 108 FTFFFYNTGVMKPVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHE 167
F ++PV+ V P SPAA AG+K GD I++++G + ++E++ V+ENP
Sbjct: 2 ILGFVPGGPPIEPVIGEVVPGSPAAKAGLKAGDRILAINGQKIKSWEDLVDAVQENPGKP 61
Query: 168 ISLVLYREHVGVLHLKVMP 186
++L + R + L + P
Sbjct: 62 LTLTVERNG-ETITLTLTP 79
>gnl|CDD|38132 KOG2921, KOG2921, KOG2921, Intramembrane metalloprotease
(sterol-regulatory element-binding protein (SREBP)
protease) [Posttranslational modification, protein
turnover, chaperones].
Length = 484
Score = 49.6 bits (118), Expect = 1e-06
Identities = 41/152 (26%), Positives = 63/152 (41%), Gaps = 25/152 (16%)
Query: 10 YTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGGYV 69
+ SL+I VV+HE GH + A ++V F + ++ I G +V
Sbjct: 126 FLTSLVITVVVHELGHALAAASEGVQVNGFGI-----------------FIAAIYPGAFV 168
Query: 70 SFSEDE-KDMRSF-----FCAAPWKKILTVLAGPLANCVMAILFFTFFFYNTGVMKPVVS 123
D + + SF FCA W + L LA ++ ++ F+ + GV V
Sbjct: 169 DLDNDHLQSLPSFRALRIFCAGIWHNFVFALLCVLALFLLPVILSPFYAHGEGVTVTEVP 228
Query: 124 NVSPASPAAIAGVKKGDCIISLDGITVSAFEE 155
+VSP G+ GD I SLDG V +
Sbjct: 229 SVSPLF--GPRGLSVGDVITSLDGCPVHKVSD 258
>gnl|CDD|29044 cd00987, PDZ_serine_protease, PDZ domain of tryspin-like serine
proteases, such as DegP/HtrA, which are oligomeric
proteins involved in heat-shock response, chaperone
function, and apoptosis. May be responsible for
substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins..
Length = 90
Score = 47.6 bits (113), Expect = 5e-06
Identities = 18/55 (32%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHE-ISLVLYR 174
+V++V P SPAA AG+K GD I++++G V + ++ + E + ++L + R
Sbjct: 27 LVASVDPGSPAAKAGLKPGDVILAVNGKPVKSVADLRRALAELKPGDKVTLTVLR 81
>gnl|CDD|29045 cd00988, PDZ_CTP_protease, PDZ domain of C-terminal processing-,
tail-specific-, and tricorn proteases, which function in
posttranslational protein processing, maturation, and
disassembly or degradation, in Bacteria, Archaea, and
plant chloroplasts. May be responsible for substrate
recognition and/or binding, as most PDZ domains bind
C-terminal polypeptides, and binding to internal
(non-C-terminal) polypeptides and even to lipids has
been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins..
Length = 85
Score = 47.5 bits (113), Expect = 6e-06
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 119 KPVVSNVSPASPAAIAGVKKGDCIISLDGITVSA--FEEVAPYVRENPLHEISLVLYREH 176
V+++V P SPAA AG+K GD I+++DG V E+V +R ++ L L R
Sbjct: 14 GLVITSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLLRGKAGTKVRLTLKRGD 73
Query: 177 VGVLHLKVMPR 187
+ +
Sbjct: 74 GEPREVTLTRL 84
>gnl|CDD|100082 cd06161, S2P-M50_SpoIVFB, SpoIVFB Site-2 protease (S2P), a zinc
metalloprotease (MEROPS family M50B), regulates
intramembrane proteolysis (RIP), and is involved in the
pro-sigmaK pathway of bacterial spore formation. SpoIVFB
(sporulation protein, stage IV cell wall formation, F
locus, promoter-distal B) is one of 4 proteins involved
in endospore formation; the others are SpoIVFA
(sporulation protein, stage IV cell wall formation, F
locus, promoter-proximal A), BofA (bypass-of-forespore
A), and SpoIVB (sporulation protein, stage IV cell wall
formation, B locus). SpoIVFB is negatively regulated by
SpoIVFA and BofA and activated by SpoIVB. It is thought
that SpoIVFB, SpoIVFA, and BofA are located in the
mother-cell membrane that surrounds the forespore and
that SpoIVB is secreted from the forespore into the
space between the two where it activates SpoIVFB..
Length = 208
Score = 45.6 bits (109), Expect = 2e-05
Identities = 31/119 (26%), Positives = 51/119 (42%), Gaps = 31/119 (26%)
Query: 7 FLLYTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLG 66
LL + L + V++HE GH +VAR IRV S ++L+P G
Sbjct: 30 GLLEALLLFLSVLLHELGHALVARRYGIRVRS---------------------ITLLPFG 68
Query: 67 GYVSFSEDEKDMRSFFCAAPWKKILTVLAGPLANCVMAILFFTFFFYNTGVMKPVVSNV 125
G E+ + P ++ + LAGPL + ++A LF + Y +S++
Sbjct: 69 GVAELEEEPET--------PKEEFVIALAGPLVSLLLAGLF--YLLYLLLPGGGPLSSL 117
Score = 31.4 bits (72), Expect = 0.34
Identities = 26/94 (27%), Positives = 40/94 (42%), Gaps = 11/94 (11%)
Query: 255 ISGPV------GIARIAKNFFDHGFNAY--IAFLAMFSWAIGFMNLLPIPILDGGHLITF 306
++GP+ G+ + G + FLA + +G NLLP LDGG ++
Sbjct: 88 LAGPLVSLLLAGLFYLLYLLLPGGGPLSSLLEFLAQVNLILGLFNLLPALPLDGGRVLRA 147
Query: 307 LLEMIRGKSLGVSVTRVITRMGLCIILFLFFLGI 340
LL G TR+ R+G + L LG+
Sbjct: 148 LLWRRTGYRRA---TRIAARIGQLFAILLVVLGL 178
>gnl|CDD|29042 cd00136, PDZ, PDZ domain, also called DHR (Dlg homologous region)
or GLGF (after a conserved sequence motif). Many PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. Heterodimerization through
PDZ-PDZ domain interactions adds to the domain's
versatility, and PDZ domain-mediated interactions may be
modulated dynamically through target phosphorylation.
Some PDZ domains play a role in scaffolding
supramolecular complexes. PDZ domains are found in
diverse signaling proteins in bacteria, archebacteria,
and eurkayotes. This CD contains two distinct structural
subgroups with either a N- or C-terminal beta-strand
forming the peptide-binding groove base. The circular
permutation placing the strand on the N-terminus appears
to be found in Eumetazoa only, while the C-terminal
variant is found in all three kingdoms of life, and
seems to co-occur with protease domains. PDZ domains
have been named after PSD95(post synaptic density
protein), DlgA (Drosophila disc large tumor suppressor),
and ZO1, a mammalian tight junction protein..
Length = 70
Score = 42.9 bits (101), Expect = 1e-04
Identities = 18/56 (32%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 120 PVVSNVSPASPAAIAGVKKGDCIISLDGITVSAF--EEVAPYVRENPLHEISLVLY 173
VV +V P SPA AG++ GD I++++G V E+VA +++ +++L +
Sbjct: 15 VVVLSVEPGSPAERAGLQAGDVILAVNGTDVKNLTLEDVAELLKKEVGEKVTLTVR 70
>gnl|CDD|38339 KOG3129, KOG3129, KOG3129, 26S proteasome regulatory complex,
subunit PSMD9 [Posttranslational modification, protein
turnover, chaperones].
Length = 231
Score = 43.1 bits (101), Expect = 1e-04
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 115 TGVMKP--VVSNVSPASPAAIAGVKKGDCII---SLDGITVSAFEEVAPYVRENPLHEIS 169
G M+P VV +V P SPA AG+ GD I+ ++ + +A V+ N +S
Sbjct: 134 LGPMRPFAVVDSVVPGSPADEAGLCVGDEILKFGNVHSGNFLPLQNIAAVVQSNEDQIVS 193
Query: 170 LVLYREHVGVLHLKVMPR 187
+ + RE + L + P+
Sbjct: 194 VTVIREG-QKVVLSLTPK 210
>gnl|CDD|100080 cd06159, S2P-M50_PDZ_Arch, Uncharacterized Archaeal homologs of
Site-2 protease (S2P), zinc metalloproteases (MEROPS
family M50) which cleave transmembrane domains of
substrate proteins, regulating intramembrane proteolysis
(RIP) of diverse signal transduction mechanisms. Members
of the S2P/M50 family of RIP proteases use proteolytic
activity within the membrane to transfer information
across membranes to integrate gene expression with
physiologic stresses occurring in another cellular
compartment. In eukaryotic cells they regulate such
processes as sterol and lipid metabolism, and
endoplasmic reticulum stress responses. In prokaryotes
they regulate such processes as sporulation, cell
division, stress response, and cell differentiation.
This group appears to be limited to Archaeal S2P/M50s
homologs with additional putative N-terminal
transmembrane spanning regions, relative to the core
protein, and either one or two PDZ domains present..
Length = 263
Score = 42.3 bits (100), Expect = 2e-04
Identities = 28/106 (26%), Positives = 46/106 (43%), Gaps = 23/106 (21%)
Query: 12 VSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGGYVSF 71
++L++ VV+HE H ++AR+ I+V S + +IP G +V
Sbjct: 115 IALVVGVVVHELSHGILARVEGIKVKSGGLLL-----------------LIIPPGAFVEP 157
Query: 72 SEDEKDMRSFFCAAPWKKILTVLAGPLANCVMAILFFT-FFFYNTG 116
E+E A ++ AG AN V+A++ F FF Y
Sbjct: 158 DEEE-----LNKADRRIRLRIFAAGVTANFVVALIAFALFFLYWIF 198
Score = 33.8 bits (78), Expect = 0.069
Identities = 23/77 (29%), Positives = 33/77 (42%), Gaps = 14/77 (18%)
Query: 275 AYIAF-LAMFSW------AIGFMNLLPIPILDGGHLITFLLEMIRGKSLGVS-------V 320
A IAF L W +G N LP LDGGH+ LLE + + +
Sbjct: 185 ALIAFALFFLYWIFWINFLLGLFNCLPAIPLDGGHVFRDLLEALLRRFPSEKAERVVNAI 244
Query: 321 TRVITRMGLCIILFLFF 337
T ++ + L +LF+ F
Sbjct: 245 TYYLSSLVLLSLLFMIF 261
>gnl|CDD|31136 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 41.5 bits (97), Expect = 3e-04
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 119 KPVVSNVSPASPAAIAGVKKGDCIISLDGITVS--AFEEVAPYVRENPLHEISLVLYRE 175
V + SPAA AG+K GD II +DG +V + +E +R P +++L + R
Sbjct: 113 GVKVVSPIDGSPAAKAGIKPGDVIIKIDGKSVGGVSLDEAVKLIRGKPGTKVTLTILRA 171
>gnl|CDD|30614 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 39.8 bits (92), Expect = 0.001
Identities = 24/57 (42%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 120 PVVSNVSPASPAAIAGVKKGDCIISLDGITV-SAFEEVAPYVRENPLHEISLVLYRE 175
VV V P SPAA AG+K GD I +++G V S + VA P E++L L R
Sbjct: 272 AVVLGVLPGSPAAKAGIKAGDIITAVNGKPVASLSDLVAAVASNRPGDEVALKLLRG 328
>gnl|CDD|144258 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 38.4 bits (90), Expect = 0.003
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 11/65 (16%)
Query: 121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISLVLYREHVGVL 180
VS V P A G++ GD I+S++G + E L L + G +
Sbjct: 27 FVSEVLPGGAAEAGGLQVGDRILSINGQDLENMSHD----------EAVLAL-KGSGGEV 75
Query: 181 HLKVM 185
L ++
Sbjct: 76 TLTIL 80
>gnl|CDD|100081 cd06160, S2P-M50_like_2, Uncharacterized homologs of Site-2
protease (S2P), zinc metalloproteases (MEROPS family
M50) which cleave transmembrane domains of substrate
proteins, regulating intramembrane proteolysis (RIP) of
diverse signal transduction mechanisms. Members of the
S2P/M50 family of RIP proteases use proteolytic
activity within the membrane to transfer information
across membranes to integrate gene expression with
physiologic stresses occurring in another cellular
compartment. In eukaryotic cells they regulate such
processes as sterol and lipid metabolism, and
endoplasmic reticulum stress responses. In prokaryotes
they regulate such processes as sporulation, cell
division, stress response, and cell differentiation.
This group includes bacterial, eukaryotic, and Archaeal
S2P/M50s homologs with additional putative N- and
C-terminal transmembrane spanning regions, relative to
the core protein, and no PDZ domains..
Length = 183
Score = 36.8 bits (86), Expect = 0.009
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 3 WLDCFLLYTVSLIIIVVIHEFGHYMVARLCNIRV 36
L L + ++L+ I+ IHE GHY+ AR ++
Sbjct: 29 LLLQGLPFALALLAILGIHEMGHYLAARRHGVKA 62
Score = 30.3 bits (69), Expect = 0.79
Identities = 15/65 (23%), Positives = 27/65 (41%), Gaps = 4/65 (6%)
Query: 276 YIAFLAMFSWAIGFMNLLPIPILDGGHLITFLLEMIRGKSLGVSVTRVITRMGLCIILFL 335
+A + +NLLP+ LDGGH++ L G+ + + + + L+L
Sbjct: 114 GLAVAGWVGLLVTALNLLPVGQLDGGHIVRALF----GRRVAALIGIGLLVALGLLALYL 169
Query: 336 FFLGI 340
F
Sbjct: 170 SFSIW 174
>gnl|CDD|38761 KOG3553, KOG3553, KOG3553, Tax interaction protein TIP1 [Cell
wall/membrane/envelope biogenesis].
Length = 124
Score = 36.6 bits (84), Expect = 0.010
Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 122 VSNVSPASPAAIAGVKKGDCIISLDG--ITVSAFEEVAPYVRENPL 165
V+ VS SPA IAG++ D I+ ++G T+ ++ + + +
Sbjct: 63 VTRVSEGSPAEIAGLRIHDKILQVNGWDFTMVTHDQAVKRITKEEV 108
>gnl|CDD|29048 cd00991, PDZ_archaeal_metalloprotease, PDZ domain of archaeal zinc
metalloprotases, presumably membrane-associated or
integral membrane proteases, which may be involved in
signalling and regulatory mechanisms. May be responsible
for substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, and binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins..
Length = 79
Score = 36.4 bits (84), Expect = 0.013
Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVREN-PLHEISLVLYREH 176
V+ V SPA A + GD I S++G ++ E+ ++ P I++ +
Sbjct: 13 VIVGVIVGSPAENAVLHTGDVIYSINGTPITTLEDFMEALKPTKPGEVITVTVLPST 69
>gnl|CDD|29049 cd00992, PDZ_signaling, PDZ domain found in a variety of Eumetazoan
signaling molecules, often in tandem arrangements. May
be responsible for specific protein-protein
interactions, as most PDZ domains bind C-terminal
polypeptides, and binding to internal (non-C-terminal)
polypeptides and even to lipids has been demonstrated.
In this subfamily of PDZ domains an N-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in proteases..
Length = 82
Score = 35.6 bits (82), Expect = 0.020
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 118 MKPVVSNVSPASPAAIAGVKKGDCIISLDGITVSA--FEEVAPYVRENPLHEISLVL 172
VS V P PA G++ GD I+ ++G++V EE ++ + E++L +
Sbjct: 26 GGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVEGLTHEEAVELLKNSG-DEVTLTV 81
>gnl|CDD|100085 cd06164, S2P-M50_SpoIVFB_CBS, SpoIVFB Site-2 protease (S2P), a zinc
metalloprotease (MEROPS family M50B), regulates
intramembrane proteolysis (RIP), and is involved in the
pro-sigmaK pathway of bacterial spore formation. In this
subgroup, SpoIVFB (sporulation protein, stage IV cell
wall formation, F locus, promoter-distal B) contains two
tandem repeats of the cystathionine beta-synthase (CBS
pair) domain. SpoIVFB is one of 4 proteins involved in
endospore formation; the others are SpoIVFA (sporulation
protein, stage IV cell wall formation, F locus,
promoter-proximal A), BofA (bypass-of-forespore A), and
SpoIVB (sporulation protein, stage IV cell wall
formation, B locus). SpoIVFB is negatively regulated by
SpoIVFA and BofA and activated by SpoIVB. It is thought
that SpoIVFB, SpoIVFA, and BofA are located in the
mother-cell membrane that surrounds the forespore and
that SpoIVB is secreted from the forespore into the
space between the two where it activates SpoIVFB. It has
been proposed that the CBS domain may play a regulatory
role, although its exact function is unknown..
Length = 227
Score = 35.2 bits (82), Expect = 0.028
Identities = 25/101 (24%), Positives = 39/101 (38%), Gaps = 29/101 (28%)
Query: 8 LLYTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGG 67
L + L V++HE GH +VAR +G + IT L GG
Sbjct: 46 LAAALLLFASVLLHELGHSLVAR-----------RYGIPVRSIT----------LFLFGG 84
Query: 68 YVSFSEDEKDMRSFFCAAPWKKILTVLAGPLANCVMAILFF 108
+ P ++ + +AGPL + V+A+LF
Sbjct: 85 VARLERE--------PETPGQEFVIAIAGPLVSLVLALLFL 117
>gnl|CDD|32177 COG1994, SpoIVFB, Zn-dependent proteases [General function
prediction only].
Length = 230
Score = 35.0 bits (80), Expect = 0.033
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 5/67 (7%)
Query: 274 NAYIAFLAMFSWAIGFMNLLPIPILDGGHLITFLLEMIRGKSLGVSVTRVITRMGLCIIL 333
A++A LA+ + + NLLPIP LDGG ++ LL G ++ I L +L
Sbjct: 137 FAFLAALALVNLVLALFNLLPIPPLDGGRVLRALLPRRYGAAI-----AAIELAALLGLL 191
Query: 334 FLFFLGI 340
L GI
Sbjct: 192 VLILAGI 198
>gnl|CDD|33755 COG3975, COG3975, Predicted protease with the C-terminal PDZ domain
[General function prediction only].
Length = 558
Score = 34.6 bits (79), Expect = 0.047
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 121 VVSNVSPASPAAIAGVKKGDCIISLDGITVS 151
++ V P PA AG+ GD I++++GI+
Sbjct: 465 KITFVFPGGPAYKAGLSPGDKIVAINGISDQ 495
>gnl|CDD|29047 cd00990, PDZ_glycyl_aminopeptidase, PDZ domain associated with
archaeal and bacterial M61 glycyl-aminopeptidases. May
be responsible for substrate recognition and/or binding,
as most PDZ domains bind C-terminal polypeptides, and
binding to internal (non-C-terminal) polypeptides and
even to lipids has been demonstrated. In this subfamily
of protease-associated PDZ domains a C-terminal
beta-strand is presumed to form the peptide-binding
groove base, a circular permutation with respect to PDZ
domains found in Eumetazoan signaling proteins..
Length = 80
Score = 34.1 bits (78), Expect = 0.059
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAF-EEVAPYVRENPLHEISLVLYRE 175
V+ V SPA AG+ GD +++++G V A + + Y +P + L ++R+
Sbjct: 15 KVTFVRDDSPADKAGLVAGDELVAVNGWRVDALQDRLKEYQAGDP---VELTVFRD 67
>gnl|CDD|100079 cd06158, S2P-M50_like_1, Uncharacterized homologs of Site-2
protease (S2P), zinc metalloproteases (MEROPS family
M50) which cleave transmembrane domains of substrate
proteins, regulating intramembrane proteolysis (RIP) of
diverse signal transduction mechanisms. Members of the
S2P/M50 family of RIP proteases use proteolytic activity
within the membrane to transfer information across
membranes to integrate gene expression with physiologic
stresses occurring in another cellular compartment. In
eukaryotic cells they regulate such processes as sterol
and lipid metabolism, and endoplasmic reticulum stress
responses. In prokaryotes they regulate such processes
as sporulation, cell division, stress response, and cell
differentiation. This group includes bacterial,
eukaryotic, and Archaeal S2P/M50s homologs with a
minimal core protein and no PDZ domains..
Length = 181
Score = 32.9 bits (76), Expect = 0.12
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 5/68 (7%)
Query: 273 FNAYIAFLAMFSWAIGFMNLLPIPILDGGHLITFLLEMIRGKSLGVSVTRVITRMGLCII 332
+A+ + + + NLLPIP LDG ++ LL ++ + G I+
Sbjct: 117 LFLMLAYGVLINLVLAVFNLLPIPPLDGSKILAALLPRRLAEAY-----ARLEPYGFLIL 171
Query: 333 LFLFFLGI 340
L L F GI
Sbjct: 172 LALLFTGI 179
>gnl|CDD|37352 KOG2141, KOG2141, KOG2141, Protein involved in high osmolarity
signaling pathway [Signal transduction mechanisms].
Length = 822
Score = 31.9 bits (72), Expect = 0.28
Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 14/83 (16%)
Query: 270 DHGFNAYIAFLAM------------FSWAI--GFMNLLPIPILDGGHLITFLLEMIRGKS 315
+ +N + A LA+ F +A+ F L + + +L L +I
Sbjct: 665 EKTYNPFYALLALKFCEFNKNLKKTFQFALWDRFKELEQLSLFRISNLAKLLASLISNAV 724
Query: 316 LGVSVTRVITRMGLCIILFLFFL 338
L ++V + + M L F
Sbjct: 725 LSLTVLKHVDFMELNARRTTFLK 747
>gnl|CDD|38740 KOG3532, KOG3532, KOG3532, Predicted protein kinase [General
function prediction only].
Length = 1051
Score = 30.1 bits (67), Expect = 0.99
Identities = 10/76 (13%), Positives = 28/76 (36%), Gaps = 5/76 (6%)
Query: 86 PWKKILTVLAGPLANCVMAILFFTFFFYNTGVMKPVVSNVSPASPAAIAGVKKGDCIISL 145
+L + + + ++F V V S A A K GD ++++
Sbjct: 371 HVVNVLDTFSRYDVSSPIGLVF-----DKNTNRAVKVCTVEDNSLADKAAFKPGDVLVAI 425
Query: 146 DGITVSAFEEVAPYVR 161
+ + + + + +++
Sbjct: 426 NNVPIRSERQATRFLQ 441
>gnl|CDD|38758 KOG3550, KOG3550, KOG3550, Receptor targeting protein Lin-7
[Extracellular structures].
Length = 207
Score = 29.6 bits (66), Expect = 1.4
Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 18/84 (21%)
Query: 125 VSPASPAAIA----GVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISLVLYREHVGVL 180
+S P +A G+K+GD ++S++G++V E HE ++ L + VG +
Sbjct: 119 ISRIIPGGVADRHGGLKRGDQLLSVNGVSV-----------EGEHHEKAVELLKAAVGSV 167
Query: 181 HLKV--MPRLQDTVD-RFGIKRQV 201
L V P++ + ++ RF +R
Sbjct: 168 KLVVRYTPKVLEEMEARFEKQRSA 191
>gnl|CDD|30714 COG0365, Acs, Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases
[Lipid metabolism].
Length = 528
Score = 28.7 bits (64), Expect = 2.4
Identities = 20/110 (18%), Positives = 38/110 (34%), Gaps = 20/110 (18%)
Query: 81 FFCAAP--WKKILT-VLAGPLANCVMAILFFTFFFYNTGVMKPVVS----NVSPASPAAI 133
F+ ++ W L + PLA+ +L+ FY+ + + + SP +
Sbjct: 216 FWNSSDPGWIYGLWYSVFSPLASGATTVLYDGRPFYSPERLWEALEKYKVTIFGTSPTFL 275
Query: 134 AGVKKGDCIISLDG----ITVSAFEEVAPYVRENPLHEISLVLYREHVGV 179
+ K D + SA E PL+ + + +GV
Sbjct: 276 RRLMKLGLGEPYDLSSLRVLGSAGE---------PLNPEAFEWFYSALGV 316
>gnl|CDD|38750 KOG3542, KOG3542, KOG3542, cAMP-regulated guanine nucleotide
exchange factor [Signal transduction mechanisms].
Length = 1283
Score = 28.6 bits (63), Expect = 2.8
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 122 VSNVSPASPAAIAGVKKGDCIISLDG 147
V+ V P S AA G+K+GD I+ ++G
Sbjct: 566 VAEVFPGSKAAREGLKRGDQILEVNG 591
>gnl|CDD|100083 cd06162, S2P-M50_PDZ_SREBP, Sterol regulatory element-binding
protein (SREBP) Site-2 protease (S2P), a zinc
metalloprotease (MEROPS family M50A), regulates
intramembrane proteolysis (RIP) of SREBP and is part of
a signal transduction mechanism involved in sterol and
lipid metabolism. In sterol-depleted mammalian cells, a
two-step proteolytic process releases the N-terminal
domains of SREBPs from membranes of the endoplasmic
reticulum (ER). These domains translocate into the
nucleus, where they activate genes of cholesterol and
fatty acid biosynthesis. The first cleavage occurs at
Site-1 within the ER lumen to generate an intermediate
that is subsequently released from the membrane by
cleavage at Site-2, which lies within the first
transmembrane domain. It is the second proteolytic step
that is carried out by the SREBP Site-2 protease (S2P)
which is present in this CD family. This group appears
to be limited to eumetazoan proteins and contains one
PDZ domain..
Length = 277
Score = 27.8 bits (62), Expect = 4.5
Identities = 25/102 (24%), Positives = 40/102 (39%), Gaps = 22/102 (21%)
Query: 10 YTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGGYV 69
Y +L+I V+HE GH + A +RV GFG +I G YV
Sbjct: 130 YFTALLISGVVHEMGHGVAAVREQVRV----NGFG-------------IFFFIIYPGAYV 172
Query: 70 SFSEDEKDMRSFFCAAPWKKILTVLAGPLANCVMAILFFTFF 111
D ++ S P +++ AG N V+ ++ +
Sbjct: 173 DLFTDHLNLIS-----PVQQLRIFCAGVWHNFVLGLVGYLLL 209
>gnl|CDD|33283 COG3480, SdrC, Predicted secreted protein containing a PDZ domain
[Signal transduction mechanisms].
Length = 342
Score = 27.6 bits (61), Expect = 5.1
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 122 VSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISLVLYREHVG 178
V +V SP ++ GD II++DG ++ +E+ YV + + Y H
Sbjct: 134 VLSVIDNSPF-KGKLEAGDTIIAVDGEPFTSSDELIDYVSSKKPGDEVTIDYERHNE 189
>gnl|CDD|35586 KOG0365, KOG0365, KOG0365, Beta subunit of farnesyltransferase
[Posttranslational modification, protein turnover,
chaperones].
Length = 423
Score = 27.3 bits (60), Expect = 6.5
Identities = 12/37 (32%), Positives = 17/37 (45%)
Query: 64 PLGGYVSFSEDEKDMRSFFCAAPWKKILTVLAGPLAN 100
P GG+ E E D+RS +CA +L + L
Sbjct: 186 PDGGFRMHVEGEVDVRSAYCALSVASLLNIPMDELFE 222
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.330 0.145 0.443
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,426,161
Number of extensions: 247836
Number of successful extensions: 916
Number of sequences better than 10.0: 1
Number of HSP's gapped: 901
Number of HSP's successfully gapped: 56
Length of query: 349
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 254
Effective length of database: 4,210,882
Effective search space: 1069564028
Effective search space used: 1069564028
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 58 (26.0 bits)