RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9487
(101 letters)
>gnl|CDD|223717 COG0644, FixC, Dehydrogenases (flavoproteins) [Energy production
and conversion].
Length = 396
Score = 66.3 bits (162), Expect = 3e-14
Identities = 29/97 (29%), Positives = 41/97 (42%), Gaps = 16/97 (16%)
Query: 1 MAFGMPMNNHGNYVVRLGHVVKWLGEQAEAMGVEIYPGIPASEVLYHGDGSVKGIATGDV 60
+ + Y+V KWL E+AE G E+YPG + V+ DG V G+ GD
Sbjct: 78 EKVAIEVPVGEGYIVDRAKFDKWLAERAEEAGAELYPGTRVTGVIREDDGVVVGVRAGD- 136
Query: 61 GIAKDGSPKDTFARGMELHAKVTIFAEGCHGHLTKSL 97
E+ AKV I A+G + L + L
Sbjct: 137 ---------------DEVRAKVVIDADGVNSALARKL 158
>gnl|CDD|182273 PRK10157, PRK10157, putative oxidoreductase FixC; Provisional.
Length = 428
Score = 34.9 bits (80), Expect = 0.004
Identities = 26/90 (28%), Positives = 37/90 (41%), Gaps = 19/90 (21%)
Query: 9 NHGNYVVRLGHVVKWLGEQAEAMGVEIYPGIPASEVLYHGDGSVKGI-ATGDVGIAKDGS 67
+ +Y V WL EQAE G ++ GI ++ DG V G+ A GDV
Sbjct: 99 SQRSYSVLRSKFDAWLMEQAEEAGAQLITGIRVDNLVQR-DGKVVGVEADGDV------- 150
Query: 68 PKDTFARGMELHAKVTIFAEGCHGHLTKSL 97
+ AK I A+G + L + L
Sbjct: 151 ----------IEAKTVILADGVNSILAEKL 170
>gnl|CDD|176156 cd08467, PBP2_SyrM, The C-terminal substrate binding of LysR-type
symbiotic regulator SyrM, which activates expression of
nodulation gene NodD3, contains the type 2 periplasmic
binding fold. Rhizobium is a nitrogen fixing bacteria
present in the roots of leguminous plants, which fixes
atmospheric nitrogen to the soil. Most Rhizobium
species possess multiple nodulation (nod) genes for the
development of nodules. For example, Rhizobium meliloti
possesses three copies of nodD genes. NodD1 and NodD2
activate nod operons when Rhizobium is exposed to
inducers synthesized by the host plant, while NodD3
acts independent of plant inducers and requires the
symbiotic regulator SyrM for nod gene expression. SyrM
activates the expression of the regulatory nodulation
gene nodD3. In turn, NodD3 activates expression of
syrM. In addition, SyrM is involved in
exopolysaccharide synthesis. This substrate-binding
domain shows significant homology to the type 2
periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis.
Length = 200
Score = 33.2 bits (76), Expect = 0.010
Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 9/61 (14%)
Query: 3 FGMPMNNHGNYVVRLGHVVKWLGEQAEAMGVEIYPGIPASEVLYHGDGSVKGIATGDVGI 62
F + M ++ + L + L E+A PG+ D + +G+ G + +
Sbjct: 2 FTLAMPDYAEVAL-LPRLAPRLRERA--------PGLDLRLCPIGDDLAERGLEQGTIDL 52
Query: 63 A 63
A
Sbjct: 53 A 53
>gnl|CDD|178245 PLN02639, PLN02639, oxidoreductase, 2OG-Fe(II) oxygenase family
protein.
Length = 337
Score = 32.1 bits (73), Expect = 0.032
Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 9/57 (15%)
Query: 19 HVVKWLGEQAEAMGVEIYPGIPASEVLY----HGDGSVKGIATGDVGIA-----KDG 66
++ LGEQ + M V YP P E+ Y H D + I D +A KDG
Sbjct: 180 YIKNVLGEQGQHMAVNYYPPCPEPELTYGLPAHTDPNALTILLQDQQVAGLQVLKDG 236
>gnl|CDD|182194 PRK10015, PRK10015, oxidoreductase; Provisional.
Length = 429
Score = 31.9 bits (72), Expect = 0.035
Identities = 27/88 (30%), Positives = 38/88 (43%), Gaps = 17/88 (19%)
Query: 10 HGNYVVRLGHVVKWLGEQAEAMGVEIYPGIPASEVLYHGDGSVKGIATGDVGIAKDGSPK 69
H +Y V + WL EQAE G + PG+ ++ G+ V G+ GD
Sbjct: 100 HASYTVLRNRLDPWLMEQAEQAGAQFIPGVRVDALVREGN-KVTGVQAGD---------- 148
Query: 70 DTFARGMELHAKVTIFAEGCHGHLTKSL 97
D L A V I A+G + L +SL
Sbjct: 149 DI------LEANVVILADGVNSMLGRSL 170
>gnl|CDD|182262 PRK10139, PRK10139, serine endoprotease; Provisional.
Length = 455
Score = 30.7 bits (69), Expect = 0.098
Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 5/56 (8%)
Query: 28 AEAMGVEIYPGIPASEVLYHGDGSVK-GIATGDVGIAKDGSPKDTFARGMELHAKV 82
A+A +++ G SEVL GS K G+ GD+ + +G P ++FA EL +++
Sbjct: 281 AKAFNLDVQRGAFVSEVL-PNSGSAKAGVKAGDIITSLNGKPLNSFA---ELRSRI 332
>gnl|CDD|216400 pfam01266, DAO, FAD dependent oxidoreductase. This family includes
various FAD dependent oxidoreductases:
Glycerol-3-phosphate dehydrogenase EC:1.1.99.5,
Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine
oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1.
Length = 234
Score = 29.2 bits (66), Expect = 0.24
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 20 VVKWLGEQAEAMGVEIYPGIPASEVLYHGDG 50
+++ L AEA+GVEI G + + G G
Sbjct: 149 LLRALARAAEALGVEILEGTEVTGLEREGGG 179
>gnl|CDD|235977 PRK07233, PRK07233, hypothetical protein; Provisional.
Length = 434
Score = 28.7 bits (65), Expect = 0.42
Identities = 15/43 (34%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 24 LGEQAEAMGVEIYPGIPASEVLYHGDGSVKGIATGDVGIAKDG 66
L E EA G EI G P + V+ G G V G+ D
Sbjct: 204 LAEAIEARGGEIRLGTPVTSVVIDGGG-VTGVEVDGEEEDFDA 245
>gnl|CDD|182564 PRK10578, PRK10578, hypothetical protein; Provisional.
Length = 207
Score = 27.9 bits (62), Expect = 0.91
Identities = 15/71 (21%), Positives = 32/71 (45%)
Query: 19 HVVKWLGEQAEAMGVEIYPGIPASEVLYHGDGSVKGIATGDVGIAKDGSPKDTFARGMEL 78
+ KW+ +A+G+ ++ GI ++ G + + G + G +D AR + +
Sbjct: 84 RLPKWMLPVLDAVGLAVFVGIGVNKAFNAEAGPLVAVCMGVITGVGGGIIRDVLAREIPM 143
Query: 79 HAKVTIFAEGC 89
+ I+A C
Sbjct: 144 ILRTEIYATAC 154
>gnl|CDD|236802 PRK10942, PRK10942, serine endoprotease; Provisional.
Length = 473
Score = 27.8 bits (62), Expect = 1.1
Identities = 18/48 (37%), Positives = 26/48 (54%)
Query: 26 EQAEAMGVEIYPGIPASEVLYHGDGSVKGIATGDVGIAKDGSPKDTFA 73
E A+AM V+ G S+VL + + GI GDV + +G P +FA
Sbjct: 300 ELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFA 347
>gnl|CDD|216325 pfam01140, Gag_MA, Matrix protein (MA), p15. The matrix protein,
p15, is encoded by the gag gene. MA is involved in
pathogenicity.
Length = 129
Score = 27.1 bits (60), Expect = 1.1
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 56 ATGDVGIAKDGSPKDTFARGMELHAKVTIFAEGCHGH 92
T VG ++G TF + L K +F+ G HGH
Sbjct: 43 PTFGVGWPQEG----TFNLDVILQVKDIVFSPGPHGH 75
>gnl|CDD|227557 COG5232, SEC62, Preprotein translocase subunit Sec62
[Intracellular trafficking and secretion].
Length = 259
Score = 27.2 bits (60), Expect = 1.6
Identities = 8/37 (21%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 13 YVVRLGHVVKWLGEQAEAMG----VEIYPGIPASEVL 45
+ R +++WL + + ++Y G+PA +L
Sbjct: 54 ELFRCKRILRWLNSEEYTLRHRRRPKVYRGVPAVAIL 90
>gnl|CDD|178500 PLN02912, PLN02912, oxidoreductase, 2OG-Fe(II) oxygenase family
protein.
Length = 348
Score = 26.5 bits (58), Expect = 2.5
Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 19 HVVKWLGEQAEAMGVEIYPGIPASEVLY----HGDGSV 52
V LG+ + M + YP P E+ Y H D ++
Sbjct: 187 RVSNTLGKHGQHMAINYYPPCPQPELTYGLPGHKDANL 224
>gnl|CDD|215691 pfam00070, Pyr_redox, Pyridine nucleotide-disulphide
oxidoreductase. This family includes both class I and
class II oxidoreductases and also NADH oxidases and
peroxidases. This domain is actually a small NADH
binding domain within a larger FAD binding domain.
Length = 82
Score = 25.2 bits (56), Expect = 3.1
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 20 VVKWLGEQAEAMGVEIYPGIPASEVLYHGDGSVKGIATGD 59
+ K L E+ E G+E+ E+ +GDG V + TGD
Sbjct: 42 IAKILQEKLEKNGIEVLLNTTVEEIEGNGDGVVVKLKTGD 81
>gnl|CDD|223647 COG0574, PpsA, Phosphoenolpyruvate synthase/pyruvate phosphate
dikinase [Carbohydrate transport and metabolism].
Length = 740
Score = 26.2 bits (58), Expect = 3.4
Identities = 14/45 (31%), Positives = 19/45 (42%)
Query: 34 EIYPGIPASEVLYHGDGSVKGIATGDVGIAKDGSPKDTFARGMEL 78
++P L G G+ GIA+G V I D S + G L
Sbjct: 325 LLHPVEDRGRALLKGIGASPGIASGRVKIILDVSEMEKLEHGDIL 369
>gnl|CDD|219864 pfam08491, SE, Squalene epoxidase. This domain is found in
squalene epoxidase (SE) and related proteins which are
found in taxonomically diverse groups of eukaryotes and
also in bacteria. SE was first cloned from
Saccharomyces cerevisiae where it was named ERG1. It
contains a putative FAD binding site and is a key
enzyme in the sterol biosynthetic pathway. Putative
transmembrane regions are found to the protein's
C-terminus.
Length = 276
Score = 25.8 bits (57), Expect = 4.5
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 79 HAKVTIFAEGCHGHLTKSLSS 99
A +TI +GC KSLS
Sbjct: 1 FAPLTIVCDGCFSKFRKSLSD 21
>gnl|CDD|220021 pfam08798, CRISPR_assoc, CRISPR associated protein. This domain
forms an anti-parallel beta strand structure with
flanking alpha helical regions.
Length = 212
Score = 25.3 bits (56), Expect = 5.4
Identities = 10/45 (22%), Positives = 15/45 (33%), Gaps = 3/45 (6%)
Query: 19 HVVKWLGEQAEAMGVEIYPGIP---ASEVLYHGDGSVKGIATGDV 60
+ WL + EA G E+ +P E + I V
Sbjct: 131 EQLAWLQRRGEAAGFELLAVLPQVDGYERRQFRKKRGRRITLSSV 175
>gnl|CDD|180419 PRK06134, PRK06134, putative FAD-binding dehydrogenase; Reviewed.
Length = 581
Score = 25.5 bits (56), Expect = 5.6
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 24 LGEQAEAMGVEIYPGIPASEVLYHGDGSVKGIATG 58
L + AE +GV I+ PA E+L DG V G
Sbjct: 223 LLKSAEDLGVRIWESAPARELLRE-DGRVAGAVVE 256
>gnl|CDD|224154 COG1233, COG1233, Phytoene dehydrogenase and related proteins
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 487
Score = 25.5 bits (56), Expect = 6.3
Identities = 15/48 (31%), Positives = 19/48 (39%)
Query: 18 GHVVKWLGEQAEAMGVEIYPGIPASEVLYHGDGSVKGIATGDVGIAKD 65
G +V L E A G EI G S++L G V + I D
Sbjct: 224 GALVDALAELAREHGGEIRTGAEVSQILVEGGKGVGVRTSDGENIEAD 271
>gnl|CDD|238519 cd01086, MetAP1, Methionine Aminopeptidase 1. 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 = 238
Score = 25.1 bits (56), Expect = 7.4
Identities = 13/29 (44%), Positives = 14/29 (48%), Gaps = 5/29 (17%)
Query: 38 GIPASEVLYHGDGSVKGIATGDVGIAKDG 66
GIP VL GD I DVG+ DG
Sbjct: 69 GIPDDRVLKDGD-----IVNIDVGVELDG 92
>gnl|CDD|172486 PRK13984, PRK13984, putative oxidoreductase; Provisional.
Length = 604
Score = 25.1 bits (55), Expect = 8.9
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 26 EQAEAMGVEIYPGIPASEVLYHGDGSVKGIAT 57
E+ GV IYPG EV+ + VKG+
Sbjct: 470 EEGLEEGVVIYPGWGPMEVVIE-NDKVKGVKF 500
>gnl|CDD|238952 cd01994, Alpha_ANH_like_IV, This is a subfamily of Adenine
nucleotide alpha hydrolases superfamily.Adeninosine
nucleotide alpha hydrolases superfamily includes N
type ATP PPases and ATP sulphurylases. It forms a
apha/beta/apha fold which binds to Adenosine group.
This subfamily of proteins is predicted to bind ATP.
This domainhas a strongly conserved motif SGGKD at the
N terminus.
Length = 194
Score = 24.9 bits (55), Expect = 9.4
Identities = 17/76 (22%), Positives = 26/76 (34%), Gaps = 25/76 (32%)
Query: 10 HGNYVVRLGHV--------------VKWLGEQAEAMGVEIY----PGIPASEV--LYH-- 47
G+ VV L ++ + L QAEAMG+ + G EV L
Sbjct: 22 EGHEVVALLNLTPEEGSSMMYHTVNHELLELQAEAMGIPLIRIEISGEEEDEVEDLKELL 81
Query: 48 ---GDGSVKGIATGDV 60
+ V + G +
Sbjct: 82 RKLKEEGVDAVVFGAI 97
>gnl|CDD|179379 PRK02155, ppnK, NAD(+)/NADH kinase family protein; Provisional.
Length = 291
Score = 24.9 bits (55), Expect = 9.8
Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 8/59 (13%)
Query: 6 PMNNHGNYVVRLGHVVKWLGEQAEAMGVEIYPGIPASEVLYH--------GDGSVKGIA 56
P+ + ++ + G V + + A +G+ YP + E+ GDG++ GI
Sbjct: 22 PLESLAAFLAKRGFEVVFEADTARNIGLTGYPALTPEEIGARADLAVVLGGDGTMLGIG 80
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 0.137 0.421
Gapped
Lambda K H
0.267 0.0732 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,129,872
Number of extensions: 429577
Number of successful extensions: 432
Number of sequences better than 10.0: 1
Number of HSP's gapped: 430
Number of HSP's successfully gapped: 40
Length of query: 101
Length of database: 10,937,602
Length adjustment: 67
Effective length of query: 34
Effective length of database: 7,965,884
Effective search space: 270840056
Effective search space used: 270840056
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 (21.7 bits)
S2: 53 (24.2 bits)