RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2263
(232 letters)
>gnl|CDD|238492 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 = 64.5 bits (158), Expect = 6e-14
Identities = 29/78 (37%), Positives = 43/78 (55%), Gaps = 4/78 (5%)
Query: 21 LCKDIHGKIGLRVAAIHE---GVFVCLVQEGSPAALVGLRFGDQILQVNGKTVAGSNMHQ 77
L KD G +G + + G+FV V+ G PA GLR GD+IL+VNG +V G +
Sbjct: 6 LRKDPGGGLGFSLRGGKDSGGGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVEGLTHEE 65
Query: 78 VHALLRNCPVNNISIVVR 95
LL+N + +++ VR
Sbjct: 66 AVELLKNSG-DEVTLTVR 82
Score = 46.0 bits (110), Expect = 4e-07
Identities = 25/66 (37%), Positives = 33/66 (50%), Gaps = 7/66 (10%)
Query: 100 ERNVTLHKDSAGHVGFQFKRGQ-------IIRLVKESSASRNGLLTDHHILEVNGQNVVG 152
R VTL KD G +GF + G+ + R+ A R GL ILEVNG +V G
Sbjct: 1 VRTVTLRKDPGGGLGFSLRGGKDSGGGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVEG 60
Query: 153 LKNDSA 158
L ++ A
Sbjct: 61 LTHEEA 66
Score = 43.3 bits (103), Expect = 4e-06
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 150 VVGLKNDSAGHVGFQFKRGQ-------IIRLVKESSASRNGLLTDHHILEVNGQNVVGLK 202
V L+ D G +GF + G+ + R+ A R GL ILEVNG +V GL
Sbjct: 3 TVTLRKDPGGGLGFSLRGGKDSGGGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVEGLT 62
Query: 203 DKEIREIVEKAPCVINLTI 221
+E E+++ + + LT+
Sbjct: 63 HEEAVELLKNSGDEVTLTV 81
>gnl|CDD|238080 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 = 63.1 bits (154), Expect = 2e-13
Identities = 26/70 (37%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 27 GKIGLRVAAIHE-GVFVCLVQEGSPAALVGLRFGDQILQVNGKTVAGSNMHQVHALLRNC 85
G +G + E GV V V+ GSPA GL+ GD IL VNG V + V LL+
Sbjct: 1 GGLGFSIRGGTEGGVVVLSVEPGSPAERAGLQAGDVILAVNGTDVKNLTLEDVAELLKKE 60
Query: 86 PVNNISIVVR 95
+++ VR
Sbjct: 61 VGEKVTLTVR 70
Score = 34.2 bits (79), Expect = 0.006
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 177 SSASRNGLLTDHHILEVNGQNVVGLKDKEIREIVEKAP 214
S A R GL IL VNG +V L +++ E+++K
Sbjct: 24 SPAERAGLQAGDVILAVNGTDVKNLTLEDVAELLKKEV 61
Score = 28.8 bits (65), Expect = 0.56
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 129 SSASRNGLLTDHHILEVNGQNVVGLKNDSAGHVGFQFKRGQIIRLV 174
S A R GL IL VNG +V L + + + + G+ + L
Sbjct: 24 SPAERAGLQAGDVILAVNGTDVKNLTLEDVAEL-LKKEVGEKVTLT 68
>gnl|CDD|214570 smart00228, PDZ, Domain present in PSD-95, Dlg, and ZO-1/2. Also
called DHR (Dlg homologous region) or GLGF (relatively
well conserved tetrapeptide in these domains). Some
PDZs have been shown to bind C-terminal polypeptides;
others appear to bind internal (non-C-terminal)
polypeptides. Different PDZs possess different binding
specificities.
Length = 85
Score = 55.8 bits (135), Expect = 1e-10
Identities = 28/87 (32%), Positives = 39/87 (44%), Gaps = 5/87 (5%)
Query: 15 QMTKLFLCKDIHGKIGLRVAAI---HEGVFVCLVQEGSPAALVGLRFGDQILQVNGKTVA 71
+ + L K G +G + GV V V GSPAA GLR GD IL+VNG +V
Sbjct: 1 EPRLVELEKG-GGGLGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVE 59
Query: 72 GSNMHQVHALLRNCPVNNISIVVRDRP 98
G + LL+ +++ V
Sbjct: 60 GLTHLEAVDLLKKAG-GKVTLTVLRGG 85
Score = 43.9 bits (104), Expect = 3e-06
Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 8/75 (10%)
Query: 149 NVVGLKNDSAGHVGFQFKRGQIIRLVKESSASRNGLLTDHHILEVNGQNVVGLKDKEIRE 208
++VG K++ G V + +V S A++ GL ILEVNG +V GL E +
Sbjct: 17 SLVGGKDEGGGVV--------VSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVD 68
Query: 209 IVEKAPCVINLTIMP 223
+++KA + LT++
Sbjct: 69 LLKKAGGKVTLTVLR 83
Score = 40.1 bits (94), Expect = 7e-05
Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 100 ERNVTLHKDSAGHVGFQFKRGQ-------IIRLVKESSASRNGLLTDHHILEVNGQNVVG 152
R V L K G +GF G+ + +V S A++ GL ILEVNG +V G
Sbjct: 2 PRLVELEKGGGG-LGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEG 60
Query: 153 LKNDSA 158
L + A
Sbjct: 61 LTHLEA 66
>gnl|CDD|238488 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 = 54.5 bits (132), Expect = 3e-10
Identities = 27/80 (33%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 27 GKIGLRVAAIHEGVFVCLVQEGSPAALVGLRFGDQILQVNGKTVAGSNMHQVHALLRNCP 86
G IGL + G+ + V GSPAA G++ GD I+ ++G+ V G ++ V LLR
Sbjct: 2 GGIGLELKYDDGGLVITSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLLRGKA 61
Query: 87 VNNISIVV-RDRPFERNVTL 105
+ + + R R VTL
Sbjct: 62 GTKVRLTLKRGDGEPREVTL 81
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 50.0 bits (120), Expect = 3e-07
Identities = 33/144 (22%), Positives = 62/144 (43%), Gaps = 28/144 (19%)
Query: 29 IGLRVAAI-HEGVFVCLVQEGSPAALVGLRFGDQILQVNGKTVAGSNMHQVHALLRNCPV 87
IG+ + GV V +GSPAA G++ GD I++++GK+V G ++ + L+R P
Sbjct: 102 IGIELQMEDIGGVKVVSPIDGSPAAKAGIKPGDVIIKIDGKSVGGVSLDEAVKLIRGKPG 161
Query: 88 NNISIVVR----DRPFERNVT--------------LHKDSAGHVGFQFKRGQIIRLVKES 129
+++ + +PF +T + + G +G+ IR+
Sbjct: 162 TKVTLTILRAGGGKPFTVTLTREEIELEDVAAKEKVEEGGKGRIGY-------IRIPSFG 214
Query: 130 SASRNGLLTDHHILEVNGQNVVGL 153
+ L + + E+ Q GL
Sbjct: 215 EGTYEDL--EKALDELKKQGAKGL 236
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 46.1 bits (110), Expect = 4e-07
Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 6/77 (7%)
Query: 23 KDIHGKIGLRVA---AIHEGVFVCLVQEGSPAALVGLRFGDQILQVNGKTVAG-SNMHQV 78
K G +G + G+FV V G A GL+ GD+IL +NG+ + S+ V
Sbjct: 6 KSGRGGLGFSLVGGSDGDPGIFVSEVLPGGAAEAGGLQEGDRILSINGQDLENLSHDEAV 65
Query: 79 HALLRNCPVNNISIVVR 95
AL +++ +
Sbjct: 66 LALKG--SGGEVTLTIL 80
Score = 34.5 bits (80), Expect = 0.006
Identities = 13/57 (22%), Positives = 25/57 (43%)
Query: 166 KRGQIIRLVKESSASRNGLLTDHHILEVNGQNVVGLKDKEIREIVEKAPCVINLTIM 222
+ ++ +A GL IL +NGQ++ L E ++ + + LTI+
Sbjct: 24 PGIFVSEVLPGGAAEAGGLQEGDRILSINGQDLENLSHDEAVLALKGSGGEVTLTIL 80
Score = 33.4 bits (77), Expect = 0.014
Identities = 19/63 (30%), Positives = 28/63 (44%), Gaps = 7/63 (11%)
Query: 103 VTLHKDSAGHVGFQFKRGQ-------IIRLVKESSASRNGLLTDHHILEVNGQNVVGLKN 155
VTL K G +GF G + ++ +A GL IL +NGQ++ L +
Sbjct: 2 VTLEKSGRGGLGFSLVGGSDGDPGIFVSEVLPGGAAEAGGLQEGDRILSINGQDLENLSH 61
Query: 156 DSA 158
D A
Sbjct: 62 DEA 64
>gnl|CDD|238489 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 = 43.4 bits (103), Expect = 3e-06
Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 4/78 (5%)
Query: 29 IGLRVAAIHEGVFVCLVQEGSPAALVGLRFGDQILQVNGKTVAGSNMHQVHALLRNCPVN 88
+G + V GSPAA GL+ GD+IL +NG+ + + + ++ P
Sbjct: 3 LGFVPGGPPIEPVIGEVVPGSPAAKAGLKAGDRILAINGQKI--KSWEDLVDAVQENPGK 60
Query: 89 NISIVVR--DRPFERNVT 104
+++ V +T
Sbjct: 61 PLTLTVERNGETITLTLT 78
>gnl|CDD|233695 TIGR02037, degP_htrA_DO, periplasmic serine protease, Do/DeqQ
family. This family consists of a set proteins various
designated DegP, heat shock protein HtrA, and protease
DO. The ortholog in Pseudomonas aeruginosa is designated
MucD and is found in an operon that controls mucoid
phenotype. This family also includes the DegQ (HhoA)
paralog in E. coli which can rescue a DegP mutant, but
not the smaller DegS paralog, which cannot. Members of
this family are located in the periplasm and have
separable functions as both protease and chaperone.
Members have a trypsin domain and two copies of a PDZ
domain. This protein protects bacteria from thermal and
other stresses and may be important for the survival of
bacterial pathogens.// The chaperone function is
dominant at low temperatures, whereas the proteolytic
activity is turned on at elevated temperatures [Protein
fate, Protein folding and stabilization, Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 428
Score = 44.5 bits (106), Expect = 2e-05
Identities = 48/183 (26%), Positives = 69/183 (37%), Gaps = 39/183 (21%)
Query: 38 EGVFVCLVQEGSPAALVGLRFGDQILQVNGKTVAGSNMHQVHALLRNCPVN---NISIVV 94
G V V GSPA GL+ GD I VNGK + S+ + + + I+
Sbjct: 257 RGALVAQVLPGSPAEKAGLKAGDVITSVNGKPI--SSFADLRRAIGTLKPGKKVTLGILR 314
Query: 95 RDRPFERNVTLHKDSAGHVGFQFKRGQIIRLVKESSASRNGL----LTDHHILEVNGQNV 150
+ + VTL G SS GL L+ E+
Sbjct: 315 KGKEKTITVTL--------------GASPEEQASSSNPFLGLTVANLSPEIRKELR---- 356
Query: 151 VGLKNDSAGHVGFQFKRGQIIRLVKESSASRNGLLTDHHILEVNGQNVVGLKDKEIREIV 210
LK D G V + ++V S A+R GL IL VN Q V + E+R+++
Sbjct: 357 --LKGDVKGVV--------VTKVVSGSPAARAGLQPGDVILSVNQQPVSSV--AELRKVL 404
Query: 211 EKA 213
+A
Sbjct: 405 ARA 407
Score = 39.9 bits (94), Expect = 6e-04
Identities = 20/41 (48%), Positives = 25/41 (60%)
Query: 31 LRVAAIHEGVFVCLVQEGSPAALVGLRFGDQILQVNGKTVA 71
LR+ +GV V V GSPAA GL+ GD IL VN + V+
Sbjct: 355 LRLKGDVKGVVVTKVVSGSPAARAGLQPGDVILSVNQQPVS 395
>gnl|CDD|238487 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 = 41.9 bits (99), Expect = 2e-05
Identities = 21/47 (44%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 38 EGVFVCLVQEGSPAALVGLRFGDQILQVNGKTVAGSNMHQVHALLRN 84
+GV V V GSPAA GL+ GD IL VNGK V ++ + L
Sbjct: 24 KGVLVASVDPGSPAAKAGLKPGDVILAVNGKPV--KSVADLRRALAE 68
Score = 26.4 bits (59), Expect = 4.3
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 170 IIRLVKESSASRNGLLTDHHILEVNGQNVVGLKDKEIREIVEKAP 214
+ + S A++ GL IL VNG+ V + D +R + +
Sbjct: 28 VASVDPGSPAAKAGLKPGDVILAVNGKPVKSVAD--LRRALAELK 70
>gnl|CDD|236802 PRK10942, PRK10942, serine endoprotease; Provisional.
Length = 473
Score = 44.0 bits (104), Expect = 3e-05
Identities = 45/186 (24%), Positives = 75/186 (40%), Gaps = 39/186 (20%)
Query: 39 GVFVCLVQEGSPAALVGLRFGDQILQVNGKTVAGSNMHQVHALLRNCPV-NNISI-VVRD 96
G FV V S AA G++ GD I +NGK + S+ + A + PV + +++ ++RD
Sbjct: 312 GAFVSQVLPNSSAAKAGIKAGDVITSLNGKPI--SSFAALRAQVGTMPVGSKLTLGLLRD 369
Query: 97 -RPFERNVTLHKDSAGHVGFQFKRGQIIRLVKESSASRNGLLTDHHILEVNGQNVVGLKN 155
+P NV L + S V S++ + + G V + N
Sbjct: 370 GKPVNVNVELQQSSQNQV---------------DSSNIFNGIEGAELSNKGGDKGVVVDN 414
Query: 156 DSAGHVGFQFKRGQIIRLVKESSASRNGLLTDHHILEVNGQNVVGLKDKEIREIVEKAPC 215
G + A++ GL I+ N Q V + E+R+I++ P
Sbjct: 415 VKPG-----------------TPAAQIGLKKGDVIIGANQQPVKNI--AELRKILDSKPS 455
Query: 216 VINLTI 221
V+ L I
Sbjct: 456 VLALNI 461
Score = 33.2 bits (76), Expect = 0.091
Identities = 15/34 (44%), Positives = 22/34 (64%)
Query: 38 EGVFVCLVQEGSPAALVGLRFGDQILQVNGKTVA 71
+GV V V+ G+PAA +GL+ GD I+ N + V
Sbjct: 408 KGVVVDNVKPGTPAAQIGLKKGDVIIGANQQPVK 441
>gnl|CDD|232883 TIGR00225, prc, C-terminal peptidase (prc). A C-terminal peptidase
with different substrates in different species including
processing of D1 protein of the photosystem II reaction
center in higher plants and cleavage of a peptide of 11
residues from the precursor form of penicillin-binding
protein in E.coli E.coli and H influenza have the most
distal branch of the tree and their proteins have an
N-terminal 200 amino acids that show no homology to
other proteins in the database [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Protein fate, Protein modification and repair].
Length = 334
Score = 42.3 bits (100), Expect = 1e-04
Identities = 21/55 (38%), Positives = 35/55 (63%)
Query: 29 IGLRVAAIHEGVFVCLVQEGSPAALVGLRFGDQILQVNGKTVAGSNMHQVHALLR 83
IG++V + + EGSPA G++ GD+I+++NGK+VAG ++ AL+R
Sbjct: 53 IGIQVGMDDGEIVIVSPFEGSPAEKAGIKPGDKIIKINGKSVAGMSLDDAVALIR 107
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 38.4 bits (90), Expect = 3e-04
Identities = 27/83 (32%), Positives = 40/83 (48%), Gaps = 6/83 (7%)
Query: 27 GKIGLRVAAIH-EGVFVCLVQEGSPAALVGLRFGDQILQVNGKTVAGSNMHQVHALLRNC 85
G IG+RV GV V V+EGSPAA GL+ GD IL ++GK V ++ ++ N
Sbjct: 1 GDIGVRVVQNEGTGVTVVSVKEGSPAAKAGLKPGDIILSIDGKKVNSLT--ELIEVILNG 58
Query: 86 PVN---NISIVVRDRPFERNVTL 105
+++ + V L
Sbjct: 59 KPGDTVKLTVYRDGKKKTVEVKL 81
>gnl|CDD|177681 PLN00049, PLN00049, carboxyl-terminal processing protease;
Provisional.
Length = 389
Score = 38.9 bits (91), Expect = 0.001
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 47 EGSPAALVGLRFGDQILQVNGKTVAGSNMHQVHALLRNCPVNN-ISIVVRDRPFERNVTL 105
G PAA G+R GD IL ++G + G ++++ L+ P + + + +R P R VTL
Sbjct: 111 PGGPAARAGIRPGDVILAIDGTSTEGLSLYEAADRLQG-PEGSSVELTLRRGPETRLVTL 169
>gnl|CDD|182262 PRK10139, PRK10139, serine endoprotease; Provisional.
Length = 455
Score = 37.6 bits (87), Expect = 0.004
Identities = 44/190 (23%), Positives = 81/190 (42%), Gaps = 36/190 (18%)
Query: 36 IHEGVFVCLVQEGSPAALVGLRFGDQILQVNGKTVAGSNMHQVHALLRNC-PVNNISI-V 93
+ G FV V S +A G++ GD I +NGK + ++ ++ + + P + + +
Sbjct: 288 VQRGAFVSEVLPNSGSAKAGVKAGDIITSLNGKPL--NSFAELRSRIATTEPGTKVKLGL 345
Query: 94 VRD-RPFERNVTLHKDSAGHVGFQFKRGQIIRLVKESSASRNGLLTDHHILEVNGQNVVG 152
+R+ +P E VTL ++ ++I + + +G L D G
Sbjct: 346 LRNGKPLEVEVTLDTSTSSSAS-----AEMITPALQGATLSDGQLKD---------GTKG 391
Query: 153 LKNDSAGHVGFQFKRGQIIRLVKESSASRNGLLTDHHILEVNGQNVVGLKDKEIREIVEK 212
+K D +VK S A++ GL D I+ VN V + E+R+++
Sbjct: 392 IKIDE---------------VVKGSPAAQAGLQKDDVIIGVNRDRVNSI--AEMRKVLAA 434
Query: 213 APCVINLTIM 222
P +I L I+
Sbjct: 435 KPAIIALQIV 444
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 37.2 bits (86), Expect = 0.004
Identities = 23/70 (32%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 39 GVFVCLVQEGSPAALVGLRFGDQILQVNGKTVAGSNMHQVHALLRNCPVN---NISIVVR 95
G V V GSPAA G++ GD I VNGK VA + A + + + ++
Sbjct: 271 GAVVLGVLPGSPAAKAGIKAGDIITAVNGKPVASLSDLV--AAVASNRPGDEVALKLLRG 328
Query: 96 DRPFERNVTL 105
+ E VTL
Sbjct: 329 GKERELAVTL 338
>gnl|CDD|226483 COG3975, COG3975, Predicted protease with the C-terminal PDZ domain
[General function prediction only].
Length = 558
Score = 34.7 bits (80), Expect = 0.031
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 30 GLRVAAIHEGVFVCLVQEGSPAALVGLRFGDQILQVNGKT 69
GL+V + + V G PA GL GD+I+ +NG +
Sbjct: 454 GLKVKSEGGHEKITFVFPGGPAYKAGLSPGDKIVAINGIS 493
>gnl|CDD|238490 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 = 32.0 bits (73), Expect = 0.039
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 30 GLRVAAIHEGVFVCLVQEGSPAALVGLRFGDQILQVNG 67
GL + V V++ SPA GL GD+++ VNG
Sbjct: 4 GLTLDKEEGLGKVTFVRDDSPADKAGLVAGDELVAVNG 41
>gnl|CDD|223821 COG0750, COG0750, Predicted membrane-associated Zn-dependent
proteases 1 [Cell envelope biogenesis, outer membrane].
Length = 375
Score = 34.4 bits (79), Expect = 0.043
Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 45 VQEGSPAALVGLRFGDQILQVNGKTVAGSN-MHQVHALLRNCPVNNISIVV 94
V S AAL GLR GD+I+ V+G+ VA + + ++ N ++I+V
Sbjct: 136 VAPKSAAALAGLRPGDRIVAVDGEKVASWDDVRRLLVAAAGDVFNLLTILV 186
>gnl|CDD|238486 cd00986, PDZ_LON_protease, PDZ domain of ATP-dependent LON serine
proteases. Most PDZ domains bind C-terminal
polypeptides, though binding to internal
(non-C-terminal) polypeptides and even to lipids has
been demonstrated. In this bacterial subfamily of
protease-associated PDZ domains a C-terminal
beta-strand is thought to form the peptide-binding
groove base, a circular permutation with respect to PDZ
domains found in Eumetazoan signaling proteins.
Length = 79
Score = 31.3 bits (71), Expect = 0.085
Identities = 16/34 (47%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 37 HEGVFVCLVQEGSPAALVGLRFGDQILQVNGKTV 70
+ GV+V V EG PAA L+ GD I+ V+GK
Sbjct: 7 YHGVYVTSVVEGMPAAGK-LKAGDHIIAVDGKPF 39
>gnl|CDD|238491 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 = 30.8 bits (70), Expect = 0.099
Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 31 LRVAAIHEGVFVCLVQEGSPAALVGLRFGDQILQVNGKTVAGSNMHQVHALLRN 84
L A+ GV + V GSPA L GD I +NG + + + L+
Sbjct: 4 LSAEAVA-GVVIVGVIVGSPAENAVLHTGDVIYSINGTPI--TTLEDFMEALKP 54
Score = 25.8 bits (57), Expect = 6.3
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 169 QIIRLVKESSASRNGLLTDHHILEVNGQNVVGLKDKEIREIVE--KAPCVINLTIMPSYV 226
I+ ++ S A L T I +NG + L+D E ++ K VI +T++PS
Sbjct: 13 VIVGVIVGSPAENAVLHTGDVIYSINGTPITTLED--FMEALKPTKPGEVITVTVLPSTT 70
Query: 227 YH 228
Sbjct: 71 KL 72
>gnl|CDD|182820 PRK10898, PRK10898, serine endoprotease; Provisional.
Length = 353
Score = 33.1 bits (76), Expect = 0.11
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 38 EGVFVCLVQEGSPAALVGLRFGDQILQVNGK--TVAGSNMHQV 78
+G+ V V PAA G++ D I+ VN K A M QV
Sbjct: 279 QGIVVNEVSPDGPAAKAGIQVNDLIISVNNKPAISALETMDQV 321
>gnl|CDD|182723 PRK10779, PRK10779, zinc metallopeptidase RseP; Provisional.
Length = 449
Score = 31.2 bits (71), Expect = 0.48
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 45 VQEGSPAALVGLRFGDQILQVNGKTVAGSNMHQVHALLRNCP 86
VQ S A+ GL+ GD+I++V+G+ + L+R+ P
Sbjct: 228 VQPNSAASKAGLQAGDRIVKVDGQPLTQ--WQTFVTLVRDNP 267
>gnl|CDD|234035 TIGR02860, spore_IV_B, stage IV sporulation protein B. SpoIVB, the
stage IV sporulation protein B of endospore-forming
bacteria such as Bacillus subtilis, is a serine
proteinase, expressed in the spore (rather than mother
cell) compartment, that participates in a proteolytic
activation cascade for Sigma-K. It appears to be
universal among endospore-forming bacteria and occurs
nowhere else [Cellular processes, Sporulation and
germination].
Length = 402
Score = 30.8 bits (70), Expect = 0.59
Identities = 23/95 (24%), Positives = 43/95 (45%), Gaps = 11/95 (11%)
Query: 49 SPAALVGLRFGDQILQVNGKTVAGSNMHQVHALLRNCPVNNISIVVR--DRPFERNVTLH 106
SP G++ GD+IL++NG+ + NM + L+ +++ + + E +
Sbjct: 124 SPGEEAGIQIGDRILKINGEKI--KNMDDLANLINKAGGEKLTLTIERGGKIIETVIKPV 181
Query: 107 KDSAGHVGFQFKRGQIIRLVKESSASRNGLLTDHH 141
KD +++ G IR SA+ G LT +
Sbjct: 182 KDKEEG---RYRIGLYIR----DSAAGIGTLTFYD 209
>gnl|CDD|131368 TIGR02315, ABC_phnC, phosphonate ABC transporter, ATP-binding
protein. Phosphonates are a class of
phosphorus-containing organic compound with a stable
direct C-P bond rather than a C-O-P linkage. A number of
bacterial species have operons, typically about 14 genes
in size, with genes for ATP-dependent transport of
phosphonates, degradation, and regulation of the
expression of the system. Members of this protein family
are the ATP-binding cassette component of tripartite ABC
transporters of phosphonates [Transport and binding
proteins, Anions].
Length = 243
Score = 30.3 bits (69), Expect = 0.62
Identities = 17/83 (20%), Positives = 34/83 (40%), Gaps = 21/83 (25%)
Query: 142 ILEVN------GQNVVGLKNDSAGHVGFQFKRGQIIRLVKESSASRNGLL---------T 186
+LEV LKN + G+ + ++ S A ++ LL +
Sbjct: 1 MLEVENLSKVYPNGKQALKN-----INLNINPGEFVAIIGPSGAGKSTLLRCINRLVEPS 55
Query: 187 DHHILEVNGQNVVGLKDKEIREI 209
IL + G ++ L+ K++R++
Sbjct: 56 SGSIL-LEGTDITKLRGKKLRKL 77
>gnl|CDD|234386 TIGR03900, prc_long_Delta, putative carboxyl-terminal-processing
protease, deltaproteobacterial. This model describes a
multidomain protein of about 1070 residues, restricted
to the order Myxococcales in the Deltaproteobacteria.
Members contain a PDZ domain (pfam00595), an S41 family
peptidase domain (pfam03572), and an SH3 domain
(pfam06347). A core region of this family, including PDZ
and S41 regions, is described by TIGR00225, C-terminal
processing peptidase, which recognizes the Prc protease.
The species distribution of this family approximates
that of largely Deltaproteobacterial C-terminal putative
protein-sorting domain, TIGR03901, analogous to LPXTG
and PEP-CTERM, but the co-occurrence may reflect shared
restriction to the Myxococcales rather than a
substrate/target relationship.
Length = 973
Score = 30.9 bits (70), Expect = 0.67
Identities = 18/69 (26%), Positives = 34/69 (49%)
Query: 27 GKIGLRVAAIHEGVFVCLVQEGSPAALVGLRFGDQILQVNGKTVAGSNMHQVHALLRNCP 86
G +G+ + + V V G+PAA GL+ D I++++ ++ ++ LR P
Sbjct: 140 GGLGIVIGMRDRNLTVVRVIPGTPAARAGLQRNDVIVKIDDESTVNMTLNDAVGRLRGPP 199
Query: 87 VNNISIVVR 95
++I VR
Sbjct: 200 DTKVTIWVR 208
Score = 27.0 bits (60), Expect = 9.4
Identities = 8/37 (21%), Positives = 23/37 (62%)
Query: 122 IIRLVKESSASRNGLLTDHHILEVNGQNVVGLKNDSA 158
++R++ + A+R GL + I++++ ++ V + + A
Sbjct: 155 VVRVIPGTPAARAGLQRNDVIVKIDDESTVNMTLNDA 191
>gnl|CDD|232801 TIGR00054, TIGR00054, RIP metalloprotease RseP. Members of this
nearly universal bacterial protein family are regulated
intramembrane proteolysis (RIP) proteases. Older and
synonymous gene symbols include yaeL in E. coli, mmpA in
Caulobacter crescentus, etc. This family includes a
region that hits the PDZ domain, found in a number of
proteins targeted to the membrane by binding to a
peptide ligand. The N-terminal region of this family
contains a perfectly conserved motif HEXGH as found in a
number of metalloproteinases, where the Glu is the
active site and the His residues coordinate the metal
cation [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 419
Score = 29.8 bits (67), Expect = 1.4
Identities = 16/73 (21%), Positives = 29/73 (39%), Gaps = 4/73 (5%)
Query: 45 VQEGSPAALVGLRFGDQILQVNGKTVAGSNMHQVHALLRNCPVNNISIVVR--DRPFERN 102
V SPA GL+ GD I +NG+ + + + ++ P ++ I V +
Sbjct: 209 VTPNSPAEKAGLKEGDYIQSINGEKL--RSWTDFVSAVKENPGKSMDIKVERNGETLSIS 266
Query: 103 VTLHKDSAGHVGF 115
+T +G
Sbjct: 267 LTPEAKGKIGIGI 279
>gnl|CDD|197207 cd09108, PLDc_PMFPLD_like_1, Catalytic domain, repeat 1, of
phospholipase D from Streptomyces Sp. Strain PMF and
similar proteins. Catalytic domain, repeat 1, of
phospholipases D (PLD, EC 3.1.4.4) from Streptomyces Sp.
Strain PMF (PMFPLD) and similar proteins, which are
generally extracellular and bear N-terminal signal
sequences. PMFPLD hydrolyzes the terminal phosphodiester
bond of phospholipids with the formation of phosphatidic
acid and alcohols. Phosphatidic acid is an essential
compound involved in signal transduction. It also
catalyzes a transphosphatidylation of phospholipids to
acceptor alcohols, by which various phospholipids can be
synthesized. In contrast to eukaryotic PLDs, PMFPLD has
a compact structure, which consists of two catalytic
domains, but lacks the regulatory domains. Each
catalytic domain contains one copy of the HKD motif
(H-x-K-x(4)-D, where x represents any amino acid
residue) that characterizes the PLD superfamily. Two HKD
motifs from two domains form a single active site. Like
other PLD enzymes, PMFPLD may utilize a common two-step
ping-pong catalytic mechanism involving an
enzyme-substrate intermediate to cleave phosphodiester
bonds. The two histidine residues from the two HKD
motifs play key roles in the catalysis. Upon substrate
binding, a histidine residue from one HKD motif could
function as the nucleophile, attacking the
phosphodiester bond to create a covalent
phosphohistidine intermediate, while the other histidine
residue from the second HKD motif could serve as a
general acid, stabilizing the leaving group. A
calcium-dependent PLD from Streptomyce chromofuscus is
excluded from this family, since it displays very little
sequence homology with other Streptomyces PLDs.
Moreover, it does not contain the conserved HKD motif
and hydrolyzes the phospholipids via a different
mechanism.
Length = 210
Score = 28.9 bits (65), Expect = 2.0
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 62 ILQVNGK--TVAGSNMHQVHALLRNCPVNNISIVVR 95
+L V+G+ G N+ H L PV+++S+VVR
Sbjct: 160 LLVVDGEELLTGGYNLWDDHYLDGGNPVHDLSLVVR 195
>gnl|CDD|233696 TIGR02038, protease_degS, periplasmic serine pepetdase DegS. This
family consists of the periplasmic serine protease DegS
(HhoB), a shorter paralog of protease DO (HtrA, DegP)
and DegQ (HhoA). It is found in E. coli and several
other Proteobacteria of the gamma subdivision. It
contains a trypsin domain and a single copy of PDZ
domain (in contrast to DegP with two copies). A critical
role of this DegS is to sense stress in the periplasm
and partially degrade an inhibitor of sigma(E) [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Regulatory functions, Protein
interactions].
Length = 351
Score = 29.0 bits (65), Expect = 2.3
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 39 GVFVCLVQEGSPAALVGLRFGDQILQVNGKTVAGS-NMHQVHALLRNCPVNNISIVVRDR 97
G+ + V PAA G+ D IL+ +GK V G+ + A R ++++ + +
Sbjct: 279 GIVITGVDPNGPAARAGILVRDVILKYDGKDVIGAEELMDRIAETRPGSKVMVTVLRQGK 338
Query: 98 PFERNVTLHKDSA 110
E VT+ +
Sbjct: 339 QLELPVTIDEKPV 351
>gnl|CDD|100102 cd00387, Ribosomal_L7_L12, Ribosomal protein L7/L12. Ribosomal
protein L7/L12 refers to the large ribosomal subunit
proteins L7 and L12, which are identical except that L7
is acetylated at the N terminus. It is a component of
the L7/L12 stalk, which is located at the surface of the
ribosome. The stalk base consists of a portion of the
23S rRNA and ribosomal proteins L11 and L10. An extended
C-terminal helix of L10 provides the binding site for
L7/L12. L7/L12 consists of two domains joined by a
flexible hinge, with the helical N-terminal domain (NTD)
forming pairs of homodimers that bind to the extended
helix of L10. It is the only multimeric ribosomal
component, with either four or six copies per ribosome
that occur as two or three dimers bound to the L10
helix. L7/L12 is the only ribosomal protein that does
not interact directly with rRNA, but instead has
indirect interactions through L10. The globular
C-terminal domains of L7/L12 are highly mobile. They are
exposed to the cytoplasm and contain binding sites for
other molecules. Initiation factors, elongation factors,
and release factors are known to interact with the
L7/L12 stalk during their GTP-dependent cycles. The
binding site for the factors EF-Tu and EF-G comprises
L7/L12, L10, L11, the L11-binding region of 23S rRNA,
and the sarcin-ricin loop of 23S rRNA. Removal of L7/L12
has minimal effect on factor binding and it has been
proposed that L7/L12 induces the catalytically active
conformation of EF-Tu and EF-G, thereby stimulating the
GTPase activity of both factors. In eukaryotes, the
proteins that perform the equivalent function to L7/L12
are called P1 and P2, which do not share sequence
similarity with L7/L12. However, a bacterial L7/L12
homolog is found in some eukaryotes, in mitochondria and
chloroplasts. In archaea, the protein equivalent to
L7/L12 is called aL12 or L12p, but it is closer in
sequence to P1 and P2 than to L7/L12.
Length = 127
Score = 27.5 bits (62), Expect = 2.9
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 197 NVVGLKDKEIREIVEKAPCVI 217
+ GL KE +++VE AP V+
Sbjct: 82 EITGLGLKEAKDLVESAPKVL 102
>gnl|CDD|233152 TIGR00855, L12, ribosomal protein L7/L12. Ribosomal proteins L7
and L12 are synonymous except for post-translational
modification of the N-terminal amino acid. THis model
resembles pfam00542 but matches the full length of
prokaryotic and organellar proteins rather than just the
C-terminus [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 123
Score = 27.4 bits (61), Expect = 3.0
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 197 NVVGLKDKEIREIVEKAPCVI 217
+ GL KE +++VE AP V+
Sbjct: 77 EITGLGLKEAKDLVEGAPKVL 97
>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate
Hu-antigen R (HuR). This subgroup corresponds to the
RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1),
the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs
and enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 84
Score = 26.6 bits (58), Expect = 4.4
Identities = 12/19 (63%), Positives = 15/19 (78%)
Query: 51 AALVGLRFGDQILQVNGKT 69
A+L G R GD+ILQV+ KT
Sbjct: 61 ASLNGYRLGDKILQVSFKT 79
>gnl|CDD|226164 COG3638, COG3638, ABC-type phosphate/phosphonate transport system,
ATPase component [Inorganic ion transport and
metabolism].
Length = 258
Score = 27.2 bits (61), Expect = 6.3
Identities = 15/71 (21%), Positives = 31/71 (43%), Gaps = 17/71 (23%)
Query: 149 NVVGLKNDSAGHVGFQFKRGQIIRLVKESSASRNGLLTDHHI----------LEVNGQNV 198
LK+ V + +G+++ ++ S A ++ LL + + NG +
Sbjct: 16 GHQALKD-----VNLEINQGEMVAIIGPSGAGKSTLL--RSLNGLVDPTSGEILFNGVQI 68
Query: 199 VGLKDKEIREI 209
LK KE+R++
Sbjct: 69 TKLKGKELRKL 79
>gnl|CDD|179147 PRK00870, PRK00870, haloalkane dehalogenase; Provisional.
Length = 302
Score = 27.2 bits (61), Expect = 6.4
Identities = 18/40 (45%), Positives = 20/40 (50%), Gaps = 5/40 (12%)
Query: 22 CKDIHGKIGLRVAAIHEGVFVCLVQEGSPAALVGLRFGDQ 61
C+D G IGLR+AA H F LV A GL GD
Sbjct: 121 CQDWGGLIGLRLAAEHPDRFARLV-----VANTGLPTGDG 155
>gnl|CDD|220306 pfam09599, IpaC_SipC, Salmonella-Shigella invasin protein C
(IpaC_SipC). This entry represents a family of proteins
associated with bacterial type III secretion systems,
which are injection machines for virulence factors into
host cell cytoplasm. Characterized members of this
protein family are known to be secreted and are
described as invasins, including IpaC from Shigella
flexneri and SipC from Salmonella typhimurium. Members
may be referred to as invasins, pathogenicity island
effectors, and cell invasion proteins.
Length = 337
Score = 27.2 bits (60), Expect = 7.5
Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 7/81 (8%)
Query: 112 HVGFQFKRGQIIRLVKESSASRNGLLTDHH--ILEVNGQNVVGLKNDSAGHVGFQFKRGQ 169
G + G + K++ N L + L++NGQN L D HV + G
Sbjct: 153 AKGLSKQSGAL----KKNLKPSNKLSAEAAQLKLQLNGQNAPKLVADELKHVKIKRTTGD 208
Query: 170 IIRLVKESS-ASRNGLLTDHH 189
++++++ + N L+ H
Sbjct: 209 ATKMLQKNKITASNKALSAEH 229
>gnl|CDD|180487 PRK06247, PRK06247, pyruvate kinase; Provisional.
Length = 476
Score = 27.2 bits (61), Expect = 8.2
Identities = 11/24 (45%), Positives = 12/24 (50%)
Query: 27 GKIGLRVAAIHEGVFVCLVQEGSP 50
GK+ L V A VC V EG P
Sbjct: 129 GKVRLVVEACDGDDVVCRVVEGGP 152
>gnl|CDD|130386 TIGR01319, glmL_fam, conserved hypothetical protein. This small
family includes, so far, an uncharacterized protein from
E. coli O157:H7 and GlmL from Clostridium tetanomorphum
and Clostridium cochlearium. GlmL is located between the
genes for the two subunits, epsilon (GlmE) and sigma
(GlmS), of the coenzyme-B12-dependent glutamate mutase
(methylaspartate mutase), the first enzyme in a pathway
of glutamate fermentation. Members shows significant
sequence similarity to the hydantoinase branch of the
hydantoinase/oxoprolinase family (pfam01968).
Length = 463
Score = 27.3 bits (60), Expect = 8.3
Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 7/61 (11%)
Query: 6 PSLEDMKYHQMTKLFLCKDIHGKIGLRVAAIHEGVFVCLVQEGSPAALVGLRFGDQILQV 65
S D H + + F + + G +G+RV+AI + E S + F D +
Sbjct: 271 LSKPDTTLHGLEEPFAKRTVEGDLGMRVSAI-------SLGEASAKEKLNKNFADNPADL 323
Query: 66 N 66
+
Sbjct: 324 D 324
>gnl|CDD|224042 COG1117, PstB, ABC-type phosphate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 253
Score = 26.7 bits (60), Expect = 9.0
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 195 GQNVVGLKDKEIREIVEKA 213
G + G+KDKE+ EIVE +
Sbjct: 111 GLRLHGIKDKELDEIVESS 129
>gnl|CDD|239997 cd04625, CBS_pair_12, The CBS domain, named after human CBS, is a
small domain originally identified in cystathionine
beta-synthase and is subsequently found in a wide range
of different proteins. CBS domains usually occur in
tandem repeats. They associate to form a so-called
Bateman domain or a CBS pair based on crystallographic
studies in bacteria. The CBS pair was used as a basis
for this cd hierarchy since the human CBS proteins can
adopt the typical core structure and form an
intramolecular CBS pair. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains and this has been used to help
in its classification here. It has been proposed that
the CBS domain may play a regulatory role, although its
exact function is unknown. Mutations of conserved
residues within this domain are associated with a
variety of human hereditary diseases, including
congenital myotonia, idiopathic generalized epilepsy,
hypercalciuric nephrolithiasis, and classic Bartter
syndrome (CLC chloride channel family members),
Wolff-Parkinson-White syndrome (gamma 2 subunit of
AMP-activated protein kinase), retinitis pigmentosa (IMP
dehydrogenase-1), and homocystinuria (cystathionine
beta-synthase).
Length = 112
Score = 25.8 bits (57), Expect = 9.7
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 183 GLLTDHHILEVNGQNVVGLKDKEIREIVEKAPCVIN 218
GLLT +L+ Q+ G+ D +R I+ P V +
Sbjct: 37 GLLTFREVLQAMAQHGAGVLDTTVRAIMNPEPIVAS 72
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 0.138 0.403
Gapped
Lambda K H
0.267 0.0695 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,474,800
Number of extensions: 1070170
Number of successful extensions: 1030
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1024
Number of HSP's successfully gapped: 68
Length of query: 232
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 138
Effective length of database: 6,768,326
Effective search space: 934028988
Effective search space used: 934028988
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: 57 (25.8 bits)