RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy683
(137 letters)
>gnl|CDD|221993 pfam13229, Beta_helix, Right handed beta helix region. This region
contains a parallel beta helix region that shares some
similarity with Pectate lyases.
Length = 157
Score = 67.5 bits (165), Expect = 3e-15
Identities = 29/105 (27%), Positives = 52/105 (49%), Gaps = 1/105 (0%)
Query: 21 AGIQIRTSSDPIVRHNKIHHGQHGGVYVHEKGVGLIEENEVYANTLAGVWITTGSAPVLR 80
+GI I SS+ + +N I + G+Y+ IE N + N G++I +GS +
Sbjct: 1 SGILINGSSNVTIENNTISNNGGNGIYIGGSSNITIENNTITNNGGYGIYI-SGSNNTIS 59
Query: 81 RNRIHSGKQVGVYFYDNGHGKLEDNDIFNHLYSGVQISNETTATL 125
N I + G+Y + + +E+N I N+ G+ +SN + T+
Sbjct: 60 NNTISNNGGGGIYLRGSSNNTIENNTIENNGGYGIYLSNSSNNTI 104
Score = 57.5 bits (139), Expect = 2e-11
Identities = 24/104 (23%), Positives = 46/104 (44%), Gaps = 2/104 (1%)
Query: 17 GNALAGIQIRTSSDPIVRHNKIHHGQHGGVYVHEKGVGLIEENEVYANTLAGVWITTGSA 76
N GI I + S+ + +N I + GG+Y+ IE N + N G++++ S
Sbjct: 43 NNGGYGIYI-SGSNNTISNNTISNNGGGGIYLRGSSNNTIENNTIENNGGYGIYLSNSSN 101
Query: 77 PVLRRNRIHSGKQVGVYFYDNGHG-KLEDNDIFNHLYSGVQISN 119
+ N I + G+ D+ + + +N I N+ G+ +
Sbjct: 102 NTIENNTISNNGGYGIVLEDSSNNVTITNNTISNNGGYGIYLIG 145
Score = 55.6 bits (134), Expect = 1e-10
Identities = 24/103 (23%), Positives = 46/103 (44%), Gaps = 1/103 (0%)
Query: 17 GNALAGIQIRTSSDPIVRHNKIHHGQHGGVYVHEKGVGLIEENEVYANTLAGVWITTGSA 76
N GI I SS+ + +N I + G+Y+ I N + N G+++ S
Sbjct: 20 NNGGNGIYIGGSSNITIENNTITNNGGYGIYISGSNNT-ISNNTISNNGGGGIYLRGSSN 78
Query: 77 PVLRRNRIHSGKQVGVYFYDNGHGKLEDNDIFNHLYSGVQISN 119
+ N I + G+Y ++ + +E+N I N+ G+ + +
Sbjct: 79 NTIENNTIENNGGYGIYLSNSSNNTIENNTISNNGGYGIVLED 121
Score = 48.6 bits (116), Expect = 4e-08
Identities = 23/93 (24%), Positives = 38/93 (40%), Gaps = 2/93 (2%)
Query: 17 GNALAGIQIRTSSDPIVRHNKIHHGQHGGVYVHEKGVGLIEENEVYANTLAGVWITTGSA 76
N GI +R SS+ + +N I + G+Y+ IE N + N G+ + S
Sbjct: 65 NNGGGGIYLRGSSNNTIENNTIENNGGYGIYLSNSSNNTIENNTISNNGGYGIVLEDSSN 124
Query: 77 PV-LRRNRIHSGKQVGVYFYDNGHG-KLEDNDI 107
V + N I + G+Y + +N I
Sbjct: 125 NVTITNNTISNNGGYGIYLIGGSSNNTITNNTI 157
Score = 27.1 bits (60), Expect = 2.4
Identities = 8/38 (21%), Positives = 19/38 (50%)
Query: 91 GVYFYDNGHGKLEDNDIFNHLYSGVQISNETTATLDAC 128
G+ + + +E+N I N+ +G+ I + T++
Sbjct: 2 GILINGSSNVTIENNTISNNGGNGIYIGGSSNITIENN 39
>gnl|CDD|218400 pfam05048, NosD, Periplasmic copper-binding protein (NosD). NosD
is a periplasmic protein which is thought to insert
copper into the exported reductase apoenzyme (NosZ).
This region forms a parallel beta helix domain.
Length = 238
Score = 40.8 bits (96), Expect = 5e-05
Identities = 24/104 (23%), Positives = 47/104 (45%), Gaps = 4/104 (3%)
Query: 22 GIQIRTSSDPIVRHNKIHHGQHGGVYVHEKGVGLIEENEVYANTLAGVWITTGSAPVLRR 81
GI + SS+ + +N I + ++ G+++ I N N G+ + S +R
Sbjct: 40 GIYLNNSSNNTITNNTISNNRY-GIHLMYSSNNTISNNTASNNG-YGIALMNSSNNTIRN 97
Query: 82 NRIHSGKQVGVYFYDNGHGKLEDNDIFNHLYSGVQISNETTATL 125
N I S G+ D+ + + +N I N+ G+ + N + T+
Sbjct: 98 NTI-SNNTYGILLSDSSNNTISNNTISNNGK-GIFLYNSSNNTI 139
Score = 33.5 bits (77), Expect = 0.017
Identities = 20/93 (21%), Positives = 37/93 (39%), Gaps = 3/93 (3%)
Query: 15 HCGNALAGIQIRTSSDPIVRHNKIHHGQHGGVYVHEKGVGLIEENEVYANTLAGVWITTG 74
N GI + SS+ + +N G+ + I N + NT G+ ++
Sbjct: 55 TISNNRYGIHLMYSSNNTISNNTAS-NNGYGIALMNSSNNTIRNNTISNNTY-GILLSDS 112
Query: 75 SAPVLRRNRIHSGKQVGVYFYDNGHGKLEDNDI 107
S + N I S G++ Y++ + + N I
Sbjct: 113 SNNTISNNTI-SNNGKGIFLYNSSNNTITGNRI 144
Score = 30.8 bits (70), Expect = 0.17
Identities = 12/74 (16%), Positives = 25/74 (33%), Gaps = 1/74 (1%)
Query: 36 NKIHHGQHGGVYVHEKGVGLIEENEVYANTLAGVWITTGSAPVLRRNRIHSGKQVGVYFY 95
N I G + N N G+++ S + N I + + G++
Sbjct: 8 NTIGIYNGRGGIYLSNSSNNVIINNTIINVRDGIYLNNSSNNTITNNTISNN-RYGIHLM 66
Query: 96 DNGHGKLEDNDIFN 109
+ + + +N N
Sbjct: 67 YSSNNTISNNTASN 80
>gnl|CDD|234521 TIGR04247, NosD_copper_fam, nitrous oxide reductase family
maturation protein NosD. Members of this family include
NosD, a repetitive periplasmic protein required for the
maturation of the copper-containing enzyme nitrous-oxide
reductase. NosD appears to be part of a complex with
NosF (an ABC transporter family ATP-binding protein) and
NosY (a six-helix transmembrane protein in the ABC-2
permease family). However, NosDFY-like complexes appear
to occur also in species whose copper requiring enzymes
are something other than nitrous-oxide reductase.
Length = 377
Score = 31.8 bits (73), Expect = 0.090
Identities = 21/94 (22%), Positives = 42/94 (44%), Gaps = 13/94 (13%)
Query: 21 AGIQIRTSSDPIVRHNKIHHGQHGGVYVHEKGVGLIEENEVYANT-----LAG----VWI 71
AGI++ + ++ +N++ G+Y+ E LIE N + G +W
Sbjct: 76 AGIKVEKADRAVIENNRLEDNLF-GIYLQEAHDSLIENNRITGKPDLRSNDRGNGIHLWN 134
Query: 72 TTGSAPVLRRNRIHSGKQVGVYFYDNGHGKLEDN 105
+ G+ V+ N + G+ G+Y + H + +N
Sbjct: 135 SPGN--VIEGNTVRGGRD-GIYIEFSHHNLIRNN 165
Score = 30.6 bits (70), Expect = 0.20
Identities = 23/96 (23%), Positives = 46/96 (47%), Gaps = 11/96 (11%)
Query: 18 NALAGIQIRTSSDPIVRHNKIH------HGQHG-GVYV-HEKGVGLIEENEVYANTLAGV 69
+ L GI ++ + D ++ +N+I G G+++ + G +IE N V G+
Sbjct: 95 DNLFGIYLQEAHDSLIENNRITGKPDLRSNDRGNGIHLWNSPGN-VIEGNTVR-GGRDGI 152
Query: 70 WITTGSAPVLRRNRIHSGKQVGVYFYDNGHGKLEDN 105
+I ++R N H+ + G++F + +EDN
Sbjct: 153 YIEFSHHNLIRNNTSHNLR-YGLHFMYSNDNLVEDN 187
>gnl|CDD|184793 PRK14696, tynA, tyramine oxidase; Provisional.
Length = 721
Score = 29.8 bits (67), Expect = 0.44
Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 49 HEKGVGL-IEENEVYANTLAGVWITTGSAPVLR 80
H+ G+G ++NE NT A VW+TTG+ V R
Sbjct: 654 HDTGLGQYSKDNESLDNTDAVVWMTTGTTHVAR 686
>gnl|CDD|199848 cd03866, M14_CPM, Peptidase M14 carboxypeptidase subfamily
N/E-like; Carboxypeptidase M subgroup. Peptidase M14
Carboxypeptidase (CP) M (CPM) belongs to the N/E
subfamily of the M14 family of metallocarboxypeptidases
(MCPs).The M14 family are zinc-binding CPs which
hydrolyze single, C-terminal amino acids from
polypeptide chains, and have a recognition site for the
free C-terminal carboxyl group, which is a key
determinant of specificity. CPM is an extracellular
glycoprotein, bound to cell membranes via a
glycosyl-phosphatidylinositol on the C-terminus of the
protein. It specifically removes C-terminal basic
residues such as lysine and arginine from peptides and
proteins. The highest levels of CPM have been found in
human lung and placenta, but significant amounts are
present in kidney, blood vessels, intestine, brain, and
peripheral nerves. CPM has also been found in soluble
form in various body fluids, including amniotic fluid,
seminal plasma and urine. Due to its wide distribution
in a variety of tissues, it is believed that it plays an
important role in the control of peptide hormones and
growth factor activity on the cell surface and in the
membrane-localized degradation of extracellular
proteins, for example it hydrolyses the C-terminal
arginine of epidermal growth factor (EGF) resulting in
des-Arg-EGF which binds to the EGF receptor (EGFR) with
an equal or greater affinity than native EGF. CPM is a
required processing enzyme that generates specific
agonists for the B1 receptor.
Length = 292
Score = 27.2 bits (60), Expect = 2.7
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 11/51 (21%)
Query: 70 WITTGSAPVLRRNRIHSGKQVGVYFYDNGHGKLE---------DNDIFNHL 111
W+ + + VL N +H G V Y YDNG+G E D+D+F +L
Sbjct: 159 WLKSETF-VLSAN-LHGGALVASYPYDNGNGGSEQQGYRSVTPDDDVFVYL 207
>gnl|CDD|163517 TIGR03805, beta_helix_1, parallel beta-helix repeat-containing
protein. Members of this protein family contain a
tandem pair of beta-helix repeats (see TIGR03804). Each
repeat is expected to consist of three beta strands that
form a single turn as they form a right-handed helix of
stacked beta-structure. Member proteinsa occur regularly
in two-gene pairs along with another uncharacterized
protein family; both protein families exhibit either
lipoprotein or regular signal peptides, suggesting
transit through the plasma membrane, and the two may be
fused. The function of the pair is unknown [Unknown
function, General].
Length = 314
Score = 26.9 bits (60), Expect = 4.0
Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 9/73 (12%)
Query: 22 GIQIRTSSDPIVRH--------NKIHHGQHGGVYVHEKGVGLIEENEVYANTLAGVWITT 73
G++++ S I+R K +G +G V V L+E++ V + AG+++
Sbjct: 79 GVKVKGSDGIIIRRLRVEWTGGPKSSNGAYGIYPVESTNV-LVEDSYVRGASDAGIYVGQ 137
Query: 74 GSAPVLRRNRIHS 86
V+R N
Sbjct: 138 SQNIVVRNNVAEE 150
>gnl|CDD|184335 PRK13802, PRK13802, bifunctional indole-3-glycerol phosphate
synthase/tryptophan synthase subunit beta; Provisional.
Length = 695
Score = 26.9 bits (59), Expect = 4.5
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 21 AGIQIRTS-SDPIVRHNKIHHGQHGGVYVHEKGVGLIEENE-VYANTLA 67
AG +++ S + P+ H + GQ GG YV E + ++E E VY A
Sbjct: 259 AGARVKASETTPLSEHQGPYWGQFGGRYVPEALITALDELERVYTQAKA 307
>gnl|CDD|215485 PLN02895, PLN02895, phosphoacetylglucosamine mutase.
Length = 562
Score = 26.5 bits (59), Expect = 5.1
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 90 VGVYFYDNGHG 100
+GVYF NGHG
Sbjct: 384 IGVYFEANGHG 394
>gnl|CDD|224851 COG1940, NagC, Transcriptional regulator/sugar kinase
[Transcription / Carbohydrate transport and metabolism].
Length = 314
Score = 26.3 bits (58), Expect = 5.4
Identities = 10/50 (20%), Positives = 19/50 (38%), Gaps = 2/50 (4%)
Query: 32 IVRHNKIHHGQHGGVYVHEKGVGLIEENEVYANTLAGVWITTGSAPVLRR 81
I+ + K+ G +G E G +++ + G T S + R
Sbjct: 148 IIVNGKLLRGANG--NAGEIGHMVVDPDGECGCGRRGCLETYASGRAILR 195
>gnl|CDD|214788 smart00722, CASH, Domain present in carbohydrate binding proteins
and sugar hydrolses.
Length = 153
Score = 25.9 bits (56), Expect = 5.6
Identities = 16/87 (18%), Positives = 29/87 (33%), Gaps = 5/87 (5%)
Query: 12 MMVHCGNALAGIQIRTSSDPIVRHNKIHHGQHGGVYVHEKGVGLIEENEVYANTLA---G 68
+ + +I+ G G+ V GL N + N +A G
Sbjct: 69 SGDPVIQNDGTGKNLIIDNVTFNGTEINSG--AGIVVTAGSEGLFIGNRIIGNYVATGDG 126
Query: 69 VWITTGSAPVLRRNRIHSGKQVGVYFY 95
+++ S L NRI+ + G+
Sbjct: 127 NYLSDSSGGDLIGNRIYDNNRDGIAVV 153
>gnl|CDD|100088 cd03086, PGM3, PGM3 (phosphoglucomutase 3), also known as PAGM
(phosphoacetylglucosamine mutase) and AGM1
(N-acetylglucosamine-phosphate mutase), is an essential
enzyme found in eukaryotes that reversibly catalyzes the
conversion of GlcNAc-6-phosphate into GlcNAc-1-phosphate
as part of the UDP-N-acetylglucosamine (UDP-GlcNAc)
biosynthetic pathway. UDP-GlcNAc is an essential
metabolite that serves as the biosynthetic precursor of
many glycoproteins and mucopolysaccharides. AGM1 is a
member of the alpha-D-phosphohexomutase superfamily,
which catalyzes the intramolecular phosphoryl transfer
of sugar substrates. The alpha-D-phosphohexomutases have
four domains with a centrally located active site formed
by four loops, one from each domain. All four domains
are included in this alignment model.
Length = 513
Score = 26.0 bits (58), Expect = 6.9
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 90 VGVYFYDNGHG 100
+GVYF NGHG
Sbjct: 352 IGVYFEANGHG 362
>gnl|CDD|234360 TIGR03804, para_beta_helix, parallel beta-helix repeat (two
copies). This model represents a tandem pair of an
approximately 22-amino acid (each) repeat homologous to
the beta-strand repeats that stack in a right-handed
parallel beta-helix in the periplasmic C-5 mannuronan
epimerase, AlgA, of Pseudomonas aeruginosa. A homology
domain consisting of a longer tandem array of these
repeats is described in the SMART database as CASH
(SM00722), and is found in many carbohydrate-binding
proteins and sugar hydrolases. A single repeat is
represented by SM00710. This TIGRFAMs model represents a
flavor of the parallel beta-helix-forming repeat based
on prokaryotic sequences only in its seed alignment,
although it also finds many eukaryotic sequences.
Length = 44
Score = 24.0 bits (53), Expect = 7.8
Identities = 9/42 (21%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 68 GVWITTGSAPVLRRNRIHSGKQVGVYFYDNGHGKLEDNDIFN 109
G+++ + S L N + G+Y D+ + L +N +
Sbjct: 1 GIYLESSSNNTLENNTASNNSY-GIYLTDSSNNTLSNNTASS 41
>gnl|CDD|238521 cd01088, MetAP2, Methionine Aminopeptidase 2. E.C. 3.4.11.18. Also
known as methionyl aminopeptidase and peptidase M.
Catalyzes release of N-terminal amino acids,
preferentially methionine, from peptides and arylamides.
Length = 291
Score = 25.7 bits (57), Expect = 9.2
Identities = 14/59 (23%), Positives = 22/59 (37%), Gaps = 14/59 (23%)
Query: 43 HGGVYV---HEKGVGLIEENEVYA-NTLAGVWITTGSAPVLRRNRIHSGKQVGVYFYDN 97
H G + +EE +VYA A TTG + +H G + +Y +
Sbjct: 159 HAGKSIPNVKGGEGTRLEEGDVYAIEPFA----TTG------KGYVHDGPECSIYMLNR 207
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
0.319 0.136 0.412
Gapped
Lambda K H
0.267 0.0487 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,959,990
Number of extensions: 613795
Number of successful extensions: 431
Number of sequences better than 10.0: 1
Number of HSP's gapped: 414
Number of HSP's successfully gapped: 32
Length of query: 137
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 50
Effective length of database: 7,078,804
Effective search space: 353940200
Effective search space used: 353940200
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 (21.8 bits)
S2: 54 (25.2 bits)