RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9827
(627 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 = 82.6 bits (205), Expect = 2e-19
Identities = 35/82 (42%), Positives = 52/82 (63%), Gaps = 4/82 (4%)
Query: 51 PRFITFQKE--GSVGIRLTGGN--KVGIFVTAVQPGSPASLQGLQPGDKILKVNDMDMKG 106
R +T +K+ G +G L GG GIFV+ V+PG PA GL+ GD+IL+VN + ++G
Sbjct: 1 VRTVTLRKDPGGGLGFSLRGGKDSGGGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVEG 60
Query: 107 ITREEAVLFLLSLQDQIHLIVQ 128
+T EEAV L + D++ L V+
Sbjct: 61 LTHEEAVELLKNSGDEVTLTVR 82
Score = 51.4 bits (124), Expect = 2e-08
Identities = 24/86 (27%), Positives = 39/86 (45%), Gaps = 13/86 (15%)
Query: 201 RVQLSKSRKKDDFGIIL------GNKIFVKEVTHRLDNNASPGTH-QLAEGDVLLKINNH 253
V L K G L G IFV V P L GD +L++N
Sbjct: 3 TVTLRKD-PGGGLGFSLRGGKDSGGGIFVSRVEPG-----GPAERGGLRVGDRILEVNGV 56
Query: 254 PTDGMSVKEARKLIDSSKEKLSLTIR 279
+G++ +EA +L+ +S ++++LT+R
Sbjct: 57 SVEGLTHEEAVELLKNSGDEVTLTVR 82
Score = 46.0 bits (110), Expect = 1e-06
Identities = 18/39 (46%), Positives = 29/39 (74%)
Query: 148 IKVNDRIMSANGLSLENVEYGTAVQVLRDSGSTVTLKVR 186
++V DRI+ NG+S+E + + AV++L++SG VTL VR
Sbjct: 44 LRVGDRILEVNGVSVEGLTHEEAVELLKNSGDEVTLTVR 82
>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 = 77.4 bits (191), Expect = 1e-17
Identities = 32/81 (39%), Positives = 46/81 (56%), Gaps = 3/81 (3%)
Query: 51 PRFITFQKE-GSVGIRLTGG--NKVGIFVTAVQPGSPASLQGLQPGDKILKVNDMDMKGI 107
PR + +K G +G L GG G+ V++V PGSPA+ GL+ GD IL+VN ++G+
Sbjct: 2 PRLVELEKGGGGLGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGL 61
Query: 108 TREEAVLFLLSLQDQIHLIVQ 128
T EAV L ++ L V
Sbjct: 62 THLEAVDLLKKAGGKVTLTVL 82
Score = 45.8 bits (109), Expect = 2e-06
Identities = 24/90 (26%), Positives = 38/90 (42%), Gaps = 14/90 (15%)
Query: 198 QTLRVQLSKSRKKDDFGIIL------GNKIFVKEVTHRLDNNASPG-THQLAEGDVLLKI 250
+ V+L K G L G + V V SP L GDV+L++
Sbjct: 1 EPRLVELEKGGGG--LGFSLVGGKDEGGGVVVSSVVPG-----SPAAKAGLRVGDVILEV 53
Query: 251 NNHPTDGMSVKEARKLIDSSKEKLSLTIRR 280
N +G++ EA L+ + K++LT+ R
Sbjct: 54 NGTSVEGLTHLEAVDLLKKAGGKVTLTVLR 83
Score = 43.9 bits (104), Expect = 8e-06
Identities = 16/41 (39%), Positives = 25/41 (60%)
Query: 148 IKVNDRIMSANGLSLENVEYGTAVQVLRDSGSTVTLKVRRR 188
++V D I+ NG S+E + + AV +L+ +G VTL V R
Sbjct: 44 LRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLRG 84
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 71.1 bits (175), Expect = 2e-15
Identities = 28/74 (37%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 57 QKEGSVGIRLTGGN--KVGIFVTAVQPGSPASLQGLQPGDKILKVNDMDMKGITREEAVL 114
G +G L GG+ GIFV+ V PG A GLQ GD+IL +N D++ ++ +EAVL
Sbjct: 7 SGRGGLGFSLVGGSDGDPGIFVSEVLPGGAAEAGGLQEGDRILSINGQDLENLSHDEAVL 66
Query: 115 FLLSLQDQIHLIVQ 128
L ++ L +
Sbjct: 67 ALKGSGGEVTLTIL 80
Score = 44.9 bits (107), Expect = 3e-06
Identities = 17/39 (43%), Positives = 24/39 (61%)
Query: 148 IKVNDRIMSANGLSLENVEYGTAVQVLRDSGSTVTLKVR 186
++ DRI+S NG LEN+ + AV L+ SG VTL +
Sbjct: 42 LQEGDRILSINGQDLENLSHDEAVLALKGSGGEVTLTIL 80
Score = 38.4 bits (90), Expect = 7e-04
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 221 IFVKEVTHRLDNNASPGTHQLAEGDVLLKINNHPTDGMSVKEARKLIDSSKEKLSLTIR 279
IFV EV + L EGD +L IN + +S EA + S +++LTI
Sbjct: 26 IFVSEVLP----GGAAEAGGLQEGDRILSINGQDLENLSHDEAVLALKGSGGEVTLTIL 80
>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 = 63.9 bits (156), Expect = 6e-13
Identities = 25/54 (46%), Positives = 34/54 (62%)
Query: 60 GSVGIRLTGGNKVGIFVTAVQPGSPASLQGLQPGDKILKVNDMDMKGITREEAV 113
G +G + GG + G+ V +V+PGSPA GLQ GD IL VN D+K +T E+
Sbjct: 1 GGLGFSIRGGTEGGVVVLSVEPGSPAERAGLQAGDVILAVNGTDVKNLTLEDVA 54
Score = 36.5 bits (85), Expect = 0.002
Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 221 IFVKEVTHRLDNNASPGTHQLAEGDVLLKINNHPTDGMSVKEARKLI-DSSKEKLSLTIR 279
+ V V + A L GDV+L +N +++++ +L+ EK++LT+R
Sbjct: 15 VVVLSVEP--GSPAERA--GLQAGDVILAVNGTDVKNLTLEDVAELLKKEVGEKVTLTVR 70
Score = 33.8 bits (78), Expect = 0.027
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 148 IKVNDRIMSANGLSLENVEYGTAVQVLRDS-GSTVTLKVR 186
++ D I++ NG ++N+ ++L+ G VTL VR
Sbjct: 31 LQAGDVILAVNGTDVKNLTLEDVAELLKKEVGEKVTLTVR 70
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 55.8 bits (135), Expect = 3e-08
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 3/80 (3%)
Query: 40 DLFSIFFVEPDPRFITFQKEGS---VGIRLTGGNKVGIFVTAVQPGSPASLQGLQPGDKI 96
D S + D G +GI L + G+ V + GSPA+ G++PGD I
Sbjct: 77 DPHSTYLDPEDAAEFRTDTSGEFGGIGIELQMEDIGGVKVVSPIDGSPAAKAGIKPGDVI 136
Query: 97 LKVNDMDMKGITREEAVLFL 116
+K++ + G++ +EAV +
Sbjct: 137 IKIDGKSVGGVSLDEAVKLI 156
Score = 33.8 bits (78), Expect = 0.25
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 147 HIKVNDRIMSANGLSLENVEYGTAVQVLR-DSGSTVTLKVRRRI 189
IK D I+ +G S+ V AV+++R G+ VTL + R
Sbjct: 129 GIKPGDVIIKIDGKSVGGVSLDEAVKLIRGKPGTKVTLTILRAG 172
Score = 33.5 bits (77), Expect = 0.38
Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 241 LAEGDVLLKINNHPTDGMSVKEARKLIDSSK-EKLSLTIRRE 281
+ GDV++KI+ G+S+ EA KLI K++LTI R
Sbjct: 130 IKPGDVIIKIDGKSVGGVSLDEAVKLIRGKPGTKVTLTILRA 171
>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 = 50.3 bits (121), Expect = 5e-08
Identities = 19/57 (33%), Positives = 35/57 (61%), Gaps = 1/57 (1%)
Query: 60 GSVGIRLTGGNKVGIFVTAVQPGSPASLQGLQPGDKILKVNDMDMKGITREEAVLFL 116
G +G+ L + G+ +T+V PGSPA+ G++ GD I+ ++ + G++ E+ V L
Sbjct: 2 GGIGLELKYDDG-GLVITSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLL 57
Score = 34.9 bits (81), Expect = 0.012
Identities = 14/57 (24%), Positives = 29/57 (50%), Gaps = 6/57 (10%)
Query: 148 IKVNDRIMSANGLSLENVEYGTAVQVLR-DSGSTVTLKVRRRIVLPASPEPQTLRVQ 203
IK D I++ +G ++ + V++LR +G+ V L ++R EP+ + +
Sbjct: 31 IKAGDIIVAIDGEPVDGLSLEDVVKLLRGKAGTKVRLTLKR-----GDGEPREVTLT 82
Score = 33.7 bits (78), Expect = 0.030
Identities = 14/44 (31%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 243 EGDVLLKINNHPTDGMSVKEARKLID-SSKEKLSLTIRREVPRP 285
GD+++ I+ P DG+S+++ KL+ + K+ LT++R P
Sbjct: 33 AGDIIVAIDGEPVDGLSLEDVVKLLRGKAGTKVRLTLKRGDGEP 76
>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 = 48.8 bits (117), Expect = 2e-07
Identities = 18/36 (50%), Positives = 24/36 (66%)
Query: 73 GIFVTAVQPGSPASLQGLQPGDKILKVNDMDMKGIT 108
G+ V +V PGSPA+ GL+PGD IL VN +K +
Sbjct: 25 GVLVASVDPGSPAAKAGLKPGDVILAVNGKPVKSVA 60
Score = 30.3 bits (69), Expect = 0.66
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 4/42 (9%)
Query: 241 LAEGDVLLKINNHPTDGMSVKEARKLIDSSK--EKLSLTIRR 280
L GDV+L +N P SV + R+ + K +K++LT+ R
Sbjct: 42 LKPGDVILAVNGKPVK--SVADLRRALAELKPGDKVTLTVLR 81
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 48.4 bits (116), Expect = 2e-07
Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 60 GSVGIRLTGGNKVGIFVTAVQPGSPASLQGLQPGDKILKVNDMDMKGITREEAVLFLLSL 119
G +G+R+ G+ V +V+ GSPA+ GL+PGD IL ++ + +T V+
Sbjct: 1 GDIGVRVVQNEGTGVTVVSVKEGSPAAKAGLKPGDIILSIDGKKVNSLTELIEVILNGKP 60
Query: 120 QDQIHLIVQNRRDEYEHV 137
D + L V R + + V
Sbjct: 61 GDTVKLTVY-RDGKKKTV 77
Score = 27.2 bits (61), Expect = 7.2
Identities = 12/42 (28%), Positives = 23/42 (54%), Gaps = 4/42 (9%)
Query: 241 LAEGDVLLKINNHPTDGMSVKEARKLIDSSK--EKLSLTIRR 280
L GD++L I+ + S+ E ++I + K + + LT+ R
Sbjct: 31 LKPGDIILSIDGKKVN--SLTELIEVILNGKPGDTVKLTVYR 70
>gnl|CDD|214504 smart00072, GuKc, Guanylate kinase homologues. Active enzymes
catalyze ATP-dependent phosphorylation of GMP to GDP.
Structure resembles that of adenylate kinase. So-called
membrane-associated guanylate kinase homologues (MAGUKs)
do not possess guanylate kinase activities; instead at
least some possess protein-binding functions.
Length = 174
Score = 50.0 bits (120), Expect = 4e-07
Identities = 33/179 (18%), Positives = 63/179 (35%), Gaps = 12/179 (6%)
Query: 428 WDDVVFGDSISKFP-AYERVSLRHPGFIRPVVLFGPVADLARDKLLKDFPDKFSAPRKFN 486
+ + I + P A+ERV RP + G D ++F D +
Sbjct: 4 GKGTLLAELIQEIPDAFERVVSHTTRPPRPGEVNG--VDYHFVSK-EEFEDDIKSG---L 57
Query: 487 FILWATIKDTAMYQSSKEP---GMYQGKDSMYQGKDSMYQGKESMYQGKDSMYQGKDSMY 543
F+ W + Y +SKE +GK + + ++ S
Sbjct: 58 FLEWGEYEG-NYYGTSKETIRQVAEKGKHCLLDIDPQGVKQLRKAQLYPIVIFIAPPSSE 116
Query: 544 QGKDSMYQGKDIKKEVKIKLFEQSQKLEKVWSHVFTGTITLSGVDVWYRKTRELIEKQQ 602
+ + + Q E K +QK + + H+F I ++ Y + +E++E +Q
Sbjct: 117 ELERRLRQRGTETSERIQKRLAAAQKEAQEY-HLFDYVIVNDDLEDAYEELKEILEAEQ 174
>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 = 44.9 bits (107), Expect = 3e-06
Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 60 GSVGIRLTGGNKVGIFVTAVQPGSPASLQGLQPGDKILKVND 101
+G GG + + V PGSPA+ GL+ GD+IL +N
Sbjct: 1 AILGFVP-GGPPIEPVIGEVVPGSPAAKAGLKAGDRILAING 41
Score = 29.1 bits (66), Expect = 1.4
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 3/41 (7%)
Query: 241 LAEGDVLLKINNHPTDGMSVKEARKLIDSSKEK-LSLTIRR 280
L GD +L IN + + + K L+LT+ R
Sbjct: 30 LKAGDRILAINGQKIKSWE--DLVDAVQENPGKPLTLTVER 68
Score = 28.0 bits (63), Expect = 3.2
Identities = 13/41 (31%), Positives = 24/41 (58%), Gaps = 3/41 (7%)
Query: 148 IKVNDRIMSANGLSLENVEYGTAVQVLRDS-GSTVTLKVRR 187
+K DRI++ NG +++ E V ++++ G +TL V R
Sbjct: 30 LKAGDRILAINGQKIKSWE--DLVDAVQENPGKPLTLTVER 68
>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 = 48.8 bits (117), Expect = 5e-06
Identities = 46/221 (20%), Positives = 71/221 (32%), Gaps = 72/221 (32%)
Query: 73 GIFVTAVQPGSPASLQGLQPGDKILKVNDMDMKGITREEAVLFLLSLQDQIHLIVQNRRD 132
G V V PGSPA GL+ GD I VN + L+ I
Sbjct: 258 GALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFA---------DLRRAIGT------- 301
Query: 133 EYEHVVASQRGDSFHIKVNDRIMSANGLSLENVEYGTAVQVLRDSGSTVTLKVR------ 186
+K ++ + +LR G T+ V
Sbjct: 302 ---------------LKPGKKV---------------TLGILRK-GKEKTITVTLGASPE 330
Query: 187 -----RRIVLPASPEPQTLRVQLSKSRKKDDFGIILGNKIFVKEVTHRLDNNASPGTHQL 241
L + + ++ K D G+++ K V+ A L
Sbjct: 331 EQASSSNPFLGLTVANLSPEIRKELRLKGDVKGVVV-----TKVVSGSPAARA-----GL 380
Query: 242 AEGDVLLKINNHPTDGMSVKEARKLIDSSKEK--LSLTIRR 280
GDV+L +N P SV E RK++ +K+ ++L I R
Sbjct: 381 QPGDVILSVNQQPVS--SVAELRKVLARAKKGGRVALLILR 419
Score = 46.8 bits (112), Expect = 2e-05
Identities = 21/60 (35%), Positives = 29/60 (48%)
Query: 73 GIFVTAVQPGSPASLQGLQPGDKILKVNDMDMKGITREEAVLFLLSLQDQIHLIVQNRRD 132
G+ VT V GSPA+ GLQPGD IL VN + + VL ++ L++
Sbjct: 363 GVVVTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAELRKVLARAKKGGRVALLILRGGA 422
>gnl|CDD|212793 cd11859, SH3_ZO, Src homology 3 domain of the Tight junction
proteins, Zonula occludens (ZO) proteins. ZO proteins
are scaffolding proteins that associate with each other
and with other proteins of the tight junction, zonula
adherens, and gap junctions. They play roles in
regulating cytoskeletal dynamics at these cell
junctions. They are considered members of the MAGUK
(membrane-associated guanylate kinase) protein family,
which is characterized by the presence of a core of
three domains: PDZ, SH3, and guanylate kinase (GuK). The
GuK domain in MAGUK proteins is enzymatically inactive;
instead, the domain mediates protein-protein
interactions and associates intramolecularly with the
SH3 domain. Vertebrates contain three ZO proteins (ZO-1,
ZO-2, and ZO-3) with redundant and non-redundant roles.
They contain three PDZ domains, followed by SH3 and GuK
domains; in addition, ZO-1 and ZO-2 contains a
proline-rich (PR) actin binding domain at the C-terminus
while ZO-3 contains this PR domain between the second
and third PDZ domains. The C-terminal regions of the
three ZO proteins are unique. The SH3 domain of ZO-1 has
been shown to bind ZONAB, ZAK, afadin, and Galpha12. SH3
domains are protein interaction domains that bind to
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. They play
versatile and diverse roles in the cell including the
regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 62
Score = 42.7 bits (101), Expect = 1e-05
Identities = 13/20 (65%), Positives = 20/20 (100%)
Query: 367 LGRNNQEVQKGIIPNKARAE 386
+GRN+QE+++G+IPNK+RAE
Sbjct: 43 VGRNHQELERGVIPNKSRAE 62
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 46.0 bits (109), Expect = 4e-05
Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 2/67 (2%)
Query: 73 GIFVTAVQPGSPASLQGLQPGDKILKVNDMDMKGITREEAVLFLLSLQDQIHLIVQNRRD 132
G V V PGSPA+ G++ GD I VN + ++ A + D++ ++ R
Sbjct: 271 GAVVLGVLPGSPAAKAGIKAGDIITAVNGKPVASLSDLVAAVASNRPGDEV--ALKLLRG 328
Query: 133 EYEHVVA 139
E +A
Sbjct: 329 GKERELA 335
>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 = 41.6 bits (98), Expect = 8e-04
Identities = 19/52 (36%), Positives = 34/52 (65%), Gaps = 1/52 (1%)
Query: 62 VGIRLTGGNKVGIFVTAVQPGSPASLQGLQPGDKILKVNDMDMKGITREEAV 113
+GI++ G + I + + GSPA G++PGDKI+K+N + G++ ++AV
Sbjct: 53 IGIQV-GMDDGEIVIVSPFEGSPAEKAGIKPGDKIIKINGKSVAGMSLDDAV 103
Score = 34.3 bits (79), Expect = 0.15
Identities = 17/38 (44%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 244 GDVLLKINNHPTDGMSVKEARKLIDSSK-EKLSLTIRR 280
GD ++KIN GMS+ +A LI K K+SL I R
Sbjct: 83 GDKIIKINGKSVAGMSLDDAVALIRGKKGTKVSLEILR 120
>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 = 37.7 bits (88), Expect = 0.001
Identities = 11/36 (30%), Positives = 16/36 (44%)
Query: 73 GIFVTAVQPGSPASLQGLQPGDKILKVNDMDMKGIT 108
G+ + V GSPA L GD I +N + +
Sbjct: 11 GVVIVGVIVGSPAENAVLHTGDVIYSINGTPITTLE 46
>gnl|CDD|182723 PRK10779, PRK10779, zinc metallopeptidase RseP; Provisional.
Length = 449
Score = 39.7 bits (93), Expect = 0.004
Identities = 19/40 (47%), Positives = 26/40 (65%), Gaps = 1/40 (2%)
Query: 61 SVGIRLTGGNKVGIFVTAVQPGSPASLQGLQPGDKILKVN 100
S+GIR G ++ + VQP S AS GLQ GD+I+KV+
Sbjct: 211 SLGIRPRGP-QIEPVLAEVQPNSAASKAGLQAGDRIVKVD 249
>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 = 39.0 bits (91), Expect = 0.006
Identities = 23/125 (18%), Positives = 46/125 (36%), Gaps = 25/125 (20%)
Query: 35 QPGSPDLFS---------IFFVEPDPRFITFQKEGSVGIRLTGGNKVGIFVTAVQPGSPA 85
PG D+ + + + TF+ + + G K+ ++ V P SPA
Sbjct: 159 IPGFKDVRQQIADIAGEPMVEILAERENWTFEVMKEL---IPRGPKIEPVLSDVTPNSPA 215
Query: 86 SLQGLQPGDKILKVNDMDMKGITREEAVLFLLSLQDQIHLIVQNRRDEYEHVVASQRGDS 145
GL+ GD I +N ++ S D + + +N + + + G++
Sbjct: 216 EKAGLKEGDYIQSINGEKLR------------SWTDFVSAVKENPGKSMD-IKVERNGET 262
Query: 146 FHIKV 150
I +
Sbjct: 263 LSISL 267
>gnl|CDD|212959 cd12026, SH3_ZO-1, Src homology 3 domain of the Tight junction
protein, Zonula occludens protein 1. ZO-1 is a
scaffolding protein that associates with other ZO
proteins and other proteins of the tight junction,
zonula adherens, and gap junctions. ZO proteins play
roles in regulating cytoskeletal dynamics at these cell
junctions. ZO-1 plays an essential role in embryonic
development. It regulates the assembly and dynamics of
the cortical cytoskeleton at cell-cell junctions. It is
considered a member of the MAGUK (membrane-associated
guanylate kinase) protein family, which is characterized
by the presence of a core of three domains: PDZ, SH3,
and guanylate kinase (GuK). The GuK domain in MAGUK
proteins is enzymatically inactive; instead, the domain
mediates protein-protein interactions and associates
intramolecularly with the SH3 domain. The C-terminal
region of ZO-1 is the largest of the three ZO proteins
and contains an actin-binding region and domains of
unknown function designated alpha and ZU5. The SH3
domain of ZO-1 has been shown to bind ZONAB, ZAK,
afadin, and Galpha12. SH3 domains are protein
interaction domains that bind to proline-rich ligands
with moderate affinity and selectivity, preferentially
to PxxP motifs. They play versatile and diverse roles in
the cell including the regulation of enzymes, changing
the subcellular localization of signaling pathway
components, and mediating the formation of multiprotein
complex assemblies.
Length = 65
Score = 35.4 bits (81), Expect = 0.007
Identities = 13/20 (65%), Positives = 19/20 (95%)
Query: 367 LGRNNQEVQKGIIPNKARAE 386
+G+N++EV++GIIPNK RAE
Sbjct: 46 IGKNHKEVERGIIPNKNRAE 65
>gnl|CDD|182820 PRK10898, PRK10898, serine endoprotease; Provisional.
Length = 353
Score = 38.4 bits (90), Expect = 0.008
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 73 GIFVTAVQPGSPASLQGLQPGDKILKVND 101
GI V V P PA+ G+Q D I+ VN+
Sbjct: 280 GIVVNEVSPDGPAAKAGIQVNDLIISVNN 308
>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 = 34.7 bits (80), Expect = 0.014
Identities = 19/77 (24%), Positives = 30/77 (38%), Gaps = 18/77 (23%)
Query: 54 ITFQKEGSVGIRLTGGNKVGIFVTAVQPGSPASLQGLQPGDKILKVN-------DMDMKG 106
+T KE +G VT V+ SPA GL GD+++ VN +K
Sbjct: 5 LTLDKEEGLGK-----------VTFVRDDSPADKAGLVAGDELVAVNGWRVDALQDRLKE 53
Query: 107 ITREEAVLFLLSLQDQI 123
+ V + D++
Sbjct: 54 YQAGDPVELTVFRDDRL 70
>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 = 37.9 bits (88), Expect = 0.015
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 73 GIFVTAVQPGSPASLQGLQPGDKILKVNDMDMKGITREE 111
GI +T V P PA+ G+ D ILK + D I EE
Sbjct: 279 GIVITGVDPNGPAARAGILVRDVILKYDGKD--VIGAEE 315
>gnl|CDD|177681 PLN00049, PLN00049, carboxyl-terminal processing protease;
Provisional.
Length = 389
Score = 37.4 bits (87), Expect = 0.017
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 11/77 (14%)
Query: 46 FVEPDPRFITFQKEGS-----VGIRLT-----GGNKVGIFVTAVQPGSPASLQGLQPGDK 95
F+EP+ +F + + VG+ + G G+ V A PG PA+ G++PGD
Sbjct: 67 FLEPE-KFKSLRSGTKGAVTGVGLEVGYPTGSDGPPAGLVVVAPAPGGPAARAGIRPGDV 125
Query: 96 ILKVNDMDMKGITREEA 112
IL ++ +G++ EA
Sbjct: 126 ILAIDGTSTEGLSLYEA 142
Score = 31.6 bits (72), Expect = 1.2
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 244 GDVLLKINNHPTDGMSVKE-ARKLIDSSKEKLSLTIRRE 281
GDV+L I+ T+G+S+ E A +L + LT+RR
Sbjct: 123 GDVILAIDGTSTEGLSLYEAADRLQGPEGSSVELTLRRG 161
>gnl|CDD|226483 COG3975, COG3975, Predicted protease with the C-terminal PDZ domain
[General function prediction only].
Length = 558
Score = 37.4 bits (87), Expect = 0.020
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 58 KEGSVGIRLTGGNKVGIFVTAVQPGSPASLQGLQPGDKILKVN 100
+ +G+++ +T V PG PA GL PGDKI+ +N
Sbjct: 449 EAYYLGLKVKSEGG-HEKITFVFPGGPAYKAGLSPGDKIVAIN 490
>gnl|CDD|212961 cd12028, SH3_ZO-3, Src homology 3 domain of the Tight junction
protein, Zonula occludens protein 3. ZO-3 is a
scaffolding protein that associates with other ZO
proteins and other proteins of the tight junction,
zonula adherens, and gap junctions. ZO proteins play
roles in regulating cytoskeletal dynamics at these cell
junctions. ZO-3 is critical for epidermal barrier
function. It regulates cyclin D1-dependent cell
proliferation. It is considered a member of the MAGUK
(membrane-associated guanylate kinase) protein family,
which is characterized by the presence of a core of
three domains: PDZ, SH3, and guanylate kinase (GuK). The
GuK domain in MAGUK proteins is enzymatically inactive;
instead, the domain mediates protein-protein
interactions and associates intramolecularly with the
SH3 domain. The C-terminal region of ZO-3 is the
smallest of the three ZO proteins. The SH3 domain of the
related protein ZO-1 has been shown to bind ZONAB, ZAK,
afadin, and Galpha12. SH3 domains are protein
interaction domains that bind to proline-rich ligands
with moderate affinity and selectivity, preferentially
to PxxP motifs. They play versatile and diverse roles in
the cell including the regulation of enzymes, changing
the subcellular localization of signaling pathway
components, and mediating the formation of multiprotein
complex assemblies.
Length = 65
Score = 33.3 bits (76), Expect = 0.032
Identities = 12/20 (60%), Positives = 19/20 (95%)
Query: 367 LGRNNQEVQKGIIPNKARAE 386
+GR+ +E++KGIIPN++RAE
Sbjct: 46 MGRDLREMEKGIIPNQSRAE 65
>gnl|CDD|236802 PRK10942, PRK10942, serine endoprotease; Provisional.
Length = 473
Score = 36.3 bits (84), Expect = 0.044
Identities = 18/41 (43%), Positives = 26/41 (63%), Gaps = 1/41 (2%)
Query: 67 TGGNKVGIFVTAVQPGSPASLQGLQPGDKILKVNDMDMKGI 107
GG+K G+ V V+PG+PA+ GL+ GD I+ N +K I
Sbjct: 404 KGGDK-GVVVDNVKPGTPAAQIGLKKGDVIIGANQQPVKNI 443
Score = 32.4 bits (74), Expect = 0.71
Identities = 44/146 (30%), Positives = 64/146 (43%), Gaps = 24/146 (16%)
Query: 148 IKVNDRIMSANGLSLENVEYGTAVQVLRDSGSTVTLKVRRRIVLPASPEPQTLRVQLSKS 207
IK D I S NG + + A GS +TL + R +P + V+L +S
Sbjct: 329 IKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLR------DGKPVNVNVELQQS 382
Query: 208 RK-KDDFGII--------LGNKIFVKEVTHRLDNNASPGTHQ----LAEGDVLLKINNHP 254
+ + D I L NK K V +DN PGT L +GDV++ N P
Sbjct: 383 SQNQVDSSNIFNGIEGAELSNKGGDKGV--VVDN-VKPGTPAAQIGLKKGDVIIGANQQP 439
Query: 255 TDGMSVKEARKLIDSSKEKLSLTIRR 280
++ E RK++DS L+L I+R
Sbjct: 440 VK--NIAELRKILDSKPSVLALNIQR 463
Score = 29.7 bits (67), Expect = 5.5
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 73 GIFVTAVQPGSPASLQGLQPGDKILKVN 100
G FV+ V P S A+ G++ GD I +N
Sbjct: 312 GAFVSQVLPNSSAAKAGIKAGDVITSLN 339
>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 = 0.18
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 75 FVTAVQPGSPASLQGLQPGDKILKVNDMDMKGIT--REEAVLFLLSLQDQIHLIVQNRRD 132
V V P S A+L GL+PGD+I+ V+ + R V + + + ++V R D
Sbjct: 132 VVGEVAPKSAAALAGLRPGDRIVAVDGEKVASWDDVRRLLVAAAGDVFNLLTILVI-RLD 190
Query: 133 EYEHVVASQR 142
H VA++
Sbjct: 191 GEAHAVAAEI 200
>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 = 33.9 bits (78), Expect = 0.27
Identities = 19/48 (39%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 235 SPG-THQLAEGDVLLKINNHPTDGMSVKEARKLI-DSSKEKLSLTIRR 280
SPG + GD +LKIN M + LI + EKL+LTI R
Sbjct: 124 SPGEEAGIQIGDRILKINGEKIKNMD--DLANLINKAGGEKLTLTIER 169
Score = 29.6 bits (67), Expect = 5.4
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 83 SPASLQGLQPGDKILKVNDMDMKG 106
SP G+Q GD+ILK+N +K
Sbjct: 124 SPGEEAGIQIGDRILKINGEKIKN 147
>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 = 33.6 bits (77), Expect = 0.36
Identities = 16/40 (40%), Positives = 24/40 (60%)
Query: 74 IFVTAVQPGSPASLQGLQPGDKILKVNDMDMKGITREEAV 113
+ V V PG+PA+ GLQ D I+K++D +T +AV
Sbjct: 153 LTVVRVIPGTPAARAGLQRNDVIVKIDDESTVNMTLNDAV 192
>gnl|CDD|212960 cd12027, SH3_ZO-2, Src homology 3 domain of the Tight junction
protein, Zonula occludens protein 2. ZO-2 is a
scaffolding protein that associates with other ZO
proteins and other proteins of the tight junction,
zonula adherens, and gap junctions. ZO proteins play
roles in regulating cytoskeletal dynamics at these cell
junctions. ZO-2 plays an essential role in embryonic
development. It is critical for the blood-testis barrier
integrity and male fertility. It also regulates the
expression of cyclin D1 and cell proliferation. It is
considered a member of the MAGUK (membrane-associated
guanylate kinase) protein family, which is characterized
by the presence of a core of three domains: PDZ, SH3,
and guanylate kinase (GuK). The GuK domain in MAGUK
proteins is enzymatically inactive; instead, the domain
mediates protein-protein interactions and associates
intramolecularly with the SH3 domain. The C-terminal
region of ZO-2 contains an actin-binding region and a
domain of unknown function designated beta. The SH3
domain of the related protein ZO-1 has been shown to
bind ZONAB, ZAK, afadin, and Galpha12. SH3 domains are
protein interaction domains that bind to proline-rich
ligands with moderate affinity and selectivity,
preferentially to PxxP motifs. They play versatile and
diverse roles in the cell including the regulation of
enzymes, changing the subcellular localization of
signaling pathway components, and mediating the
formation of multiprotein complex assemblies.
Length = 63
Score = 29.9 bits (67), Expect = 0.57
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 369 RNNQEVQKGIIPNKARAE 386
R E++KG+IPNK+RAE
Sbjct: 46 RIGNELEKGLIPNKSRAE 63
>gnl|CDD|197876 smart00792, Agouti, Agouti protein. The agouti protein regulates
pigmentation in the mouse hair follicle producing a
black hair with a subapical yellow band. A highly
homologous protein agouti signal protein (ASIP) is
present in humans and is expressed at highest levels in
adipose tissue where it may play a role in energy
homeostasis and possibly human pigmentation.
Length = 124
Score = 31.0 bits (70), Expect = 0.76
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 229 RLDNNASPGTHQLAEGDVLLKINNHPTDGMSVKEARKLIDSSKEKLSLT-IRREVPRP 285
+N+S +Q V + N +S +EA K + KEK +LT + R PR
Sbjct: 30 GARSNSSL--NQADFPSVSIVGLNKKPKKISAEEAEKKLLQKKEKKALTNVLRPEPRS 85
>gnl|CDD|132322 TIGR03279, cyano_FeS_chp, putative FeS-containing
Cyanobacterial-specific oxidoreductase. Members of this
protein family are predicted FeS-containing
oxidoreductases of unknown function, apparently
restricted to and universal across the Cyanobacteria.
The high trusted cutoff score for this model, 700 bits,
excludes homologs from other lineages. This exclusion
seems justified because a significant number of sequence
positions are simultaneously unique to and invariant
across the Cyanobacteria, suggesting a specialized,
conserved function, perhaps related to photosynthesis. A
distantly related protein family, TIGR03278, in
universal in and restricted to archaeal methanogens, and
may be linked to methanogenesis.
Length = 433
Score = 30.9 bits (70), Expect = 2.2
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 76 VTAVQPGSPASLQGLQPGDKILKVN 100
++AV PGS A G +PGD ++ +N
Sbjct: 2 ISAVLPGSIAEELGFEPGDALVSIN 26
>gnl|CDD|201353 pfam00625, Guanylate_kin, Guanylate kinase.
Length = 183
Score = 29.6 bits (67), Expect = 2.9
Identities = 19/70 (27%), Positives = 29/70 (41%), Gaps = 16/70 (22%)
Query: 455 RPVVLFGP---VADLARDKLLKDFPDKFSAPRKFNFILWATIKDTAMYQSSKEPGMYQGK 511
RP+VL GP + LL ++P+KF + + T + PG GK
Sbjct: 3 RPIVLSGPSGVGKSHIKKALLDEYPEKFG------YSVSHTTRP-------PRPGEVDGK 49
Query: 512 DSMYQGKDSM 521
D + K+ M
Sbjct: 50 DYHFVSKEEM 59
>gnl|CDD|223949 COG1018, Hmp, Flavodoxin reductases (ferredoxin-NADPH reductases)
family 1 [Energy production and conversion].
Length = 266
Score = 29.9 bits (68), Expect = 3.2
Identities = 18/86 (20%), Positives = 32/86 (37%), Gaps = 19/86 (22%)
Query: 31 VTAVQPGSPDLFSIFFVEPDPRFITFQKEGSVGIRLT-GGNKV--------------GIF 75
VT+V+P + D+FS PD + F+ + + L GG +
Sbjct: 10 VTSVEPETDDVFSFTLEPPDGLRLDFEPGQYITVGLPNGGEPLLRAYSLSSAPDEDSLYR 69
Query: 76 VTA-VQPGSPAS---LQGLQPGDKIL 97
++ + G S L+ GD +
Sbjct: 70 ISVKREDGGGGSNWLHDHLKVGDTLE 95
>gnl|CDD|178580 PLN03003, PLN03003, Probable polygalacturonase At3g15720.
Length = 456
Score = 30.4 bits (68), Expect = 3.2
Identities = 25/98 (25%), Positives = 47/98 (47%), Gaps = 6/98 (6%)
Query: 153 RIMSANGLSLENVEYGTAVQVLRDSGSTVTLKVRRRIVLPASPEPQTLRVQLSKSRKKDD 212
R+++ NG++L+NVE + + G + K R+ + S + + SKS D
Sbjct: 279 RMITFNGITLDNVENPIIIDQFYNGGDSDNAKDRKSSAVEVSKVVFSNFIGTSKSEYGVD 338
Query: 213 FGI---ILGNKIFVKEVTHRLDNNASPGTHQLAEGDVL 247
F + +IF++++ AS G+ Q+A+G L
Sbjct: 339 FRCSERVPCTEIFLRDMKIE---TASSGSGQVAQGQCL 373
>gnl|CDD|203029 pfam04495, GRASP55_65, GRASP55/65 PDZ-like domain. GRASP55 (Golgi
re-assembly stacking protein of 55 kDa) and GRASP65 (a
65 kDa) protein are highly homologous. GRASP55 is a
component of the Golgi stacking machinery. GRASP65, an
N-ethylmaleimide- sensitive membrane protein required
for the stacking of Golgi cisternae in a cell-free
system. This region appears to be related to the PDZ
domain.
Length = 136
Score = 29.1 bits (66), Expect = 3.3
Identities = 23/63 (36%), Positives = 29/63 (46%), Gaps = 10/63 (15%)
Query: 79 VQPGSPASLQGLQP-GDKILKVNDMDMKGITREEAVLFLL---SLQDQIHLIVQNRRDEY 134
V P SPA+L GLQP D I+ + G+ R E LF L + L V N E
Sbjct: 48 VHPNSPAALAGLQPYSDYIIGTDS----GLLRGEDDLFELVESHEGRPLKLYVYNS--ET 101
Query: 135 EHV 137
+ V
Sbjct: 102 DVV 104
>gnl|CDD|182262 PRK10139, PRK10139, serine endoprotease; Provisional.
Length = 455
Score = 30.3 bits (68), Expect = 3.8
Identities = 20/50 (40%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 65 RLTGGNKVGIFVTAVQPGSPASLQGLQPGDKILKVNDMDMKGITREEAVL 114
+L G K GI + V GSPA+ GLQ D I+ VN + I VL
Sbjct: 384 QLKDGTK-GIKIDEVVKGSPAAQAGLQKDDVIIGVNRDRVNSIAEMRKVL 432
>gnl|CDD|182027 PRK09681, PRK09681, putative type II secretion protein GspC;
Provisional.
Length = 276
Score = 29.7 bits (66), Expect = 4.6
Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 3/79 (3%)
Query: 64 IRLTGGNKVGIFVTAVQPGSPASL---QGLQPGDKILKVNDMDMKGITREEAVLFLLSLQ 120
I+LT K GI AV+PG+ SL G + GD + +N D A++ L
Sbjct: 196 IQLTPVRKEGIVGYAVKPGADRSLFDASGFKEGDIAIALNQQDFTDPRAMIALMRQLPSM 255
Query: 121 DQIHLIVQNRRDEYEHVVA 139
D I L V + ++ +A
Sbjct: 256 DSIQLTVLRKGARHDISIA 274
>gnl|CDD|198282 cd10419, SH2_Src_Fyn_isoform_b_like, Src homology 2 (SH2) domain
found in Fyn isoform b like proteins. Fyn is a member
of the Src non-receptor type tyrosine kinase family of
proteins. This cd contains the SH2 domain found in Fyn
isoform b type proteins. Fyn is involved in the control
of cell growth and is required in the following
pathways: T and B cell receptor signaling,
integrin-mediated signaling, growth factor and cytokine
receptor signaling, platelet activation, ion channel
function, cell adhesion, axon guidance, fertilization,
entry into mitosis, and differentiation of natural
killer cells, oligodendrocytes and keratinocytes. The
protein associates with the p85 subunit of
phosphatidylinositol 3-kinase and interacts with the
Fyn-binding protein. Alternatively spliced transcript
variants encoding distinct isoforms exist. Fyn is
primarily localized to the cytoplasmic leaflet of the
plasma membrane. Tyrosine phosphorylation of target
proteins by Fyn serves to either regulate target protein
activity, and/or to generate a binding site on the
target protein that recruits other signaling molecules.
FYN has been shown to interact with a number of proteins
including: BCAR1, Cbl, Janus kinase, nephrin, Sky,
tyrosine kinase, Wiskott-Aldrich syndrome protein, and
Zap-70. Fyn has a unique N-terminal domain, an SH3
domain, an SH2 domain, a kinase domain and a regulatory
tail, as do the other members of the family. In general
SH2 domains are involved in signal transduction. They
typically bind pTyr-containing ligands via two surface
pockets, a pTyr and hydrophobic binding pocket, allowing
proteins with SH2 domains to localize to tyrosine
phosphorylated sites.
Length = 101
Score = 28.1 bits (62), Expect = 5.2
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 394 NATKKELSASESRGSFFKRRRNSHRRSKSLSKDHWDDVVFGDSISKF 440
+A ++ LS RG+F R + + + SLS WDD+ GD + +
Sbjct: 14 DAERQLLSFGNPRGTFLIRESETTKGAYSLSIRDWDDMK-GDHVKHY 59
>gnl|CDD|220460 pfam09894, DUF2121, Uncharacterized protein conserved in archaea
(DUF2121). This domain, found in various hypothetical
archaeal proteins, has no known function.
Length = 194
Score = 28.8 bits (65), Expect = 6.6
Identities = 15/72 (20%), Positives = 27/72 (37%), Gaps = 20/72 (27%)
Query: 204 LSKSRKKDDFGIILGNKIFVKEVTHRLDNNASPGTHQLAEGDVLLKINNHPTDGMSVKEA 263
SKS I+ GNK + KE+ + + + MS+K+
Sbjct: 111 TSKSVGGGSGIIVFGNK-YTKEIAEKE-------------------LKKNWKKKMSLKDI 150
Query: 264 RKLIDSSKEKLS 275
R + + E++S
Sbjct: 151 RDIFEKIMEEVS 162
>gnl|CDD|198231 cd10368, SH2_Src_Fyn, Src homology 2 (SH2) domain found in Fyn.
Fyn is a member of the Src non-receptor type tyrosine
kinase family of proteins. Fyn is involved in the
control of cell growth and is required in the following
pathways: T and B cell receptor signaling,
integrin-mediated signaling, growth factor and cytokine
receptor signaling, platelet activation, ion channel
function, cell adhesion, axon guidance, fertilization,
entry into mitosis, and differentiation of natural
killer cells, oligodendrocytes and keratinocytes. The
protein associates with the p85 subunit of
phosphatidylinositol 3-kinase and interacts with the
Fyn-binding protein. Alternatively spliced transcript
variants encoding distinct isoforms exist. Fyn is
primarily localized to the cytoplasmic leaflet of the
plasma membrane. Tyrosine phosphorylation of target
proteins by Fyn serves to either regulate target protein
activity, and/or to generate a binding site on the
target protein that recruits other signaling molecules.
FYN has been shown to interact with a number of proteins
including: BCAR1, Cbl, Janus kinase, nephrin, Sky,
tyrosine kinase, Wiskott-Aldrich syndrome protein, and
Zap-70. Fyn has a unique N-terminal domain, an SH3
domain, an SH2 domain, a kinase domain and a regulatory
tail, as do the other members of the family. In general
SH2 domains are involved in signal transduction. They
typically bind pTyr-containing ligands via two surface
pockets, a pTyr and hydrophobic binding pocket, allowing
proteins with SH2 domains to localize to tyrosine
phosphorylated sites.
Length = 101
Score = 27.7 bits (61), Expect = 6.7
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 394 NATKKELSASESRGSFFKRRRNSHRRSKSLSKDHWDDVVFGDSISKF 440
+A ++ LS RG+F R + + + SLS WDD+ GD + +
Sbjct: 14 DAERQLLSFGNPRGTFLIRESETTKGAYSLSIRDWDDMK-GDHVKHY 59
>gnl|CDD|222404 pfam13829, DUF4191, Domain of unknown function (DUF4191).
Length = 223
Score = 29.0 bits (66), Expect = 6.7
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 357 VSPINNSMDSLGRNNQEVQKGIIPNKAR 384
V ++ + +LG + KG P AR
Sbjct: 189 VDAVSKRLKALGSPRLPIPKGPDPKGAR 216
>gnl|CDD|181018 PRK07530, PRK07530, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 292
Score = 29.2 bits (66), Expect = 6.8
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 6/45 (13%)
Query: 345 LLDVSLSQLDRPVSPINNSMDSLGRNNQEVQKGIIPNKARAEELA 389
L DVS +L+ ++ IN ++ ++V KG I +ARA LA
Sbjct: 32 LNDVSADRLEAGLATINGNLA------RQVAKGKISEEARAAALA 70
>gnl|CDD|130171 TIGR01101, V_ATP_synt_F, vacuolar ATP synthase F subunit. This
model describes the vacuolar ATP synthase F subunit (14
kDa subunit) in eukaryotes. In some archaeal species
this protein subunit is referred as G subunit [Transport
and binding proteins, Cations and iron carrying
compounds].
Length = 115
Score = 27.9 bits (62), Expect = 6.9
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 209 KKDDFGIILGNKIFVKEVTHRLDNNASP 236
K+DD IIL N+ + + H +D +
Sbjct: 57 KRDDIAIILINQHIAEMIRHAVDAHTRS 84
>gnl|CDD|179543 PRK03137, PRK03137, 1-pyrroline-5-carboxylate dehydrogenase;
Provisional.
Length = 514
Score = 29.1 bits (66), Expect = 7.0
Identities = 20/52 (38%), Positives = 24/52 (46%), Gaps = 15/52 (28%)
Query: 36 PGSPDLFSIFFVE-PDPRFITFQKEGSVGIRLTGGNKVG--IFVTA--VQPG 82
PGS + V+ P RFITF TG +VG I+ A VQPG
Sbjct: 235 PGSGSEVGDYLVDHPKTRFITF----------TGSREVGLRIYERAAKVQPG 276
>gnl|CDD|133136 cd00303, retropepsin_like, Retropepsins; pepsin-like aspartate
proteases. The family includes pepsin-like aspartate
proteases from retroviruses, retrotransposons and
retroelements, as well as eukaryotic
dna-damage-inducible proteins (DDIs), and bacterial
aspartate peptidases. While fungal and mammalian pepsins
are bilobal proteins with structurally related N and
C-terminals, retropepsins are half as long as their
fungal and mammalian counterparts. The monomers are
structurally related to one lobe of the pepsin molecule
and retropepsins function as homodimers. The active site
aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it
does in pepsin. Retroviral aspartyl protease is
synthesized as part of the POL polyprotein that contains
an aspartyl protease, a reverse transcriptase, RNase H,
and an integrase. The POL polyprotein undergoes specific
enzymatic cleavage to yield the mature proteins. In
aspartate peptidases, Asp residues are ligands of an
activated water molecule in all examples where catalytic
residues have been identified. This group of aspartate
peptidases is classified by MEROPS as the peptidase
family A2 (retropepsin family, clan AA), subfamily A2A.
Length = 92
Score = 27.3 bits (61), Expect = 7.7
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 167 YGTAVQVLRDSGSTVTL---KVRRRIVLPASPEPQTLRVQL 204
G V+ L DSG++V + +++ LP P L+V+
Sbjct: 6 NGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKG 46
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 29.1 bits (65), Expect = 7.7
Identities = 16/55 (29%), Positives = 26/55 (47%)
Query: 179 STVTLKVRRRIVLPASPEPQTLRVQLSKSRKKDDFGIILGNKIFVKEVTHRLDNN 233
+ +VR+RI PA E QTL + L + + + K FV+ V L+ +
Sbjct: 226 TITAARVRQRIYFPADEEKQTLLLGLLSRSEGARTMVFVNTKAFVERVARTLERH 280
>gnl|CDD|220211 pfam09375, Peptidase_M75, Imelysin. The imelysin peptidase was
first identified in Pseudomonas aeruginosa. The active
site residues have not been identified. However, His201
and Glu204 are completely conserved in the family and
occur in an HXXE motif that is also found in family M14.
Length = 282
Score = 28.9 bits (65), Expect = 8.2
Identities = 12/41 (29%), Positives = 17/41 (41%), Gaps = 9/41 (21%)
Query: 440 FPAYERVSLRHPGFIRPVVLFGPVADLARDKLLKDFPDKFS 480
A++RV FGPV DL R+ + +PD
Sbjct: 42 RLAWQRVE---------PFRFGPVDDLNREGQINFWPDDEG 73
>gnl|CDD|110829 pfam01864, DUF46, Putative integral membrane protein DUF46. This
archaebacterial protein has no known function. It
contains several predicted transmembrane regions,
suggesting it is an integral membrane protein.
Length = 175
Score = 28.2 bits (63), Expect = 8.8
Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 4/40 (10%)
Query: 407 GSFFKRRRNSHRRSKSLSKDHWDDVV----FGDSISKFPA 442
GSF KRR N R S + D D ++ F + PA
Sbjct: 105 GSFIKRRLNIERGSPAPILDQLDFLIGALLFAYPVKLIPA 144
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
0.315 0.133 0.380
Gapped
Lambda K H
0.267 0.0603 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,698,696
Number of extensions: 3104984
Number of successful extensions: 2631
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2629
Number of HSP's successfully gapped: 88
Length of query: 627
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 524
Effective length of database: 6,369,140
Effective search space: 3337429360
Effective search space used: 3337429360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 62 (27.9 bits)