RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9486
(165 letters)
>gnl|CDD|223717 COG0644, FixC, Dehydrogenases (flavoproteins) [Energy production
and conversion].
Length = 396
Score = 84.0 bits (208), Expect = 1e-19
Identities = 41/145 (28%), Positives = 61/145 (42%), Gaps = 27/145 (18%)
Query: 2 HILSGAVIDPIALNELLPDWKDLGAPLNTPVQEDKFAYLTKSKRIGIPILPGMPMNNHGN 61
G + P AL EL+PD+ + + V + + + I +P+ G
Sbjct: 41 KPCCGGGLSPRALEELIPDFDEE---IERKVTGARIYFPGEKVAIEVPVGEG-------- 89
Query: 62 YVVRLGHVVKWLGEQAEAMGVEIYPGIPASEVLYHGDGSVKGIATGDVGIAKDGSPKDTF 121
Y+V KWL E+AE G E+YPG + V+ DG V G+ GD
Sbjct: 90 YIVDRAKFDKWLAERAEEAGAELYPGTRVTGVIREDDGVVVGVRAGD------------- 136
Query: 122 ARGMELHAKVTIFAEGCHGHLTKSL 146
E+ AKV I A+G + L + L
Sbjct: 137 ---DEVRAKVVIDADGVNSALARKL 158
>gnl|CDD|182273 PRK10157, PRK10157, putative oxidoreductase FixC; Provisional.
Length = 428
Score = 43.0 bits (101), Expect = 2e-05
Identities = 35/136 (25%), Positives = 59/136 (43%), Gaps = 21/136 (15%)
Query: 13 ALNELLPDWKDLGAPLNTPVQEDKFAYLTKSKRIGIPILPGMPMN-NHGNYVVRLGHVVK 71
+L ++P + D AP+ + +K A++T+ + + G + + +Y V
Sbjct: 54 SLEHIIPGFAD-SAPVERLITHEKLAFMTEKSAMTMDYCNGDETSPSQRSYSVLRSKFDA 112
Query: 72 WLGEQAEAMGVEIYPGIPASEVLYHGDGSVKGI-ATGDVGIAKDGSPKDTFARGMELHAK 130
WL EQAE G ++ GI ++ DG V G+ A GDV + AK
Sbjct: 113 WLMEQAEEAGAQLITGIRVDNLVQR-DGKVVGVEADGDV-----------------IEAK 154
Query: 131 VTIFAEGCHGHLTKSL 146
I A+G + L + L
Sbjct: 155 TVILADGVNSILAEKL 170
>gnl|CDD|182194 PRK10015, PRK10015, oxidoreductase; Provisional.
Length = 429
Score = 38.4 bits (89), Expect = 8e-04
Identities = 34/122 (27%), Positives = 53/122 (43%), Gaps = 18/122 (14%)
Query: 26 APLNTPVQEDKFAYLTKSKRIGIPILPGMP-MNNHGNYVVRLGHVVKWLGEQAEAMGVEI 84
AP+ V +K ++LT+ + + P + H +Y V + WL EQAE G +
Sbjct: 66 APVERKVTREKISFLTEESAVTLDFHREQPDVPQHASYTVLRNRLDPWLMEQAEQAGAQF 125
Query: 85 YPGIPASEVLYHGDGSVKGIATGDVGIAKDGSPKDTFARGMELHAKVTIFAEGCHGHLTK 144
PG+ ++ G+ V G+ GD D L A V I A+G + L +
Sbjct: 126 IPGVRVDALVREGN-KVTGVQAGD----------DI------LEANVVILADGVNSMLGR 168
Query: 145 SL 146
SL
Sbjct: 169 SL 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 = 31.3 bits (71), Expect = 0.14
Identities = 11/59 (18%), Positives = 23/59 (38%), Gaps = 9/59 (15%)
Query: 54 MPMNNHGNYVVRLGHVVKWLGEQAEAMGVEIYPGIPASEVLYHGDGSVKGIATGDVGIA 112
+ M ++ + L + L E+A PG+ D + +G+ G + +A
Sbjct: 4 LAMPDYAEVAL-LPRLAPRLRERA--------PGLDLRLCPIGDDLAERGLEQGTIDLA 53
>gnl|CDD|178245 PLN02639, PLN02639, oxidoreductase, 2OG-Fe(II) oxygenase family
protein.
Length = 337
Score = 31.3 bits (71), Expect = 0.19
Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 9/57 (15%)
Query: 68 HVVKWLGEQAEAMGVEIYPGIPASEVLY----HGDGSVKGIATGDVGIA-----KDG 115
++ LGEQ + M V YP P E+ Y H D + I D +A KDG
Sbjct: 180 YIKNVLGEQGQHMAVNYYPPCPEPELTYGLPAHTDPNALTILLQDQQVAGLQVLKDG 236
>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 = 30.0 bits (68), Expect = 0.48
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 69 VVKWLGEQAEAMGVEIYPGIPASEVLYHGDG 99
+++ L AEA+GVEI G + + G G
Sbjct: 149 LLRALARAAEALGVEILEGTEVTGLEREGGG 179
>gnl|CDD|182262 PRK10139, PRK10139, serine endoprotease; Provisional.
Length = 455
Score = 29.9 bits (67), Expect = 0.55
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 77 AEAMGVEIYPGIPASEVLYHGDGSVKGIATGDVGIAKDGSPKDTFARGMELHAKV 131
A+A +++ G SEVL + + G+ GD+ + +G P ++FA EL +++
Sbjct: 281 AKAFNLDVQRGAFVSEVLPNSGSAKAGVKAGDIITSLNGKPLNSFA---ELRSRI 332
>gnl|CDD|235977 PRK07233, PRK07233, hypothetical protein; Provisional.
Length = 434
Score = 28.7 bits (65), Expect = 1.3
Identities = 15/43 (34%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 73 LGEQAEAMGVEIYPGIPASEVLYHGDGSVKGIATGDVGIAKDG 115
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 = 2.2
Identities = 15/71 (21%), Positives = 32/71 (45%)
Query: 68 HVVKWLGEQAEAMGVEIYPGIPASEVLYHGDGSVKGIATGDVGIAKDGSPKDTFARGMEL 127
+ KW+ +A+G+ ++ GI ++ G + + G + G +D AR + +
Sbjct: 84 RLPKWMLPVLDAVGLAVFVGIGVNKAFNAEAGPLVAVCMGVITGVGGGIIRDVLAREIPM 143
Query: 128 HAKVTIFAEGC 138
+ I+A C
Sbjct: 144 ILRTEIYATAC 154
>gnl|CDD|218614 pfam05503, Pox_G7, Poxvirus G7-like.
Length = 363
Score = 28.1 bits (63), Expect = 2.5
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 1 GHILSGAVIDPIALNELLPD 20
GH+L GAV PI NE + D
Sbjct: 287 GHVLDGAVSSPITKNETVAD 306
>gnl|CDD|222428 pfam13872, AAA_34, P-loop containing NTP hydrolase pore-1.
Length = 303
Score = 27.9 bits (63), Expect = 2.7
Identities = 17/67 (25%), Positives = 22/67 (32%), Gaps = 9/67 (13%)
Query: 20 DWKDLGAPLN--TPVQEDKFAYLTKSKRIGI-----PILPGMPMNNHGNYVVRLGHVVKW 72
D +DLG P+ K + K GI L RL +V W
Sbjct: 110 DLRDLGGERIDIVPLSRFKQGKPIRLKE-GILFTTYATLRSESQAGGK-KRSRLDQIVDW 167
Query: 73 LGEQAEA 79
LGE +
Sbjct: 168 LGEDFDG 174
>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 = 26.4 bits (59), Expect = 3.1
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 69 VVKWLGEQAEAMGVEIYPGIPASEVLYHGDGSVKGIATGD 108
+ K L E+ E G+E+ E+ +GDG V + TGD
Sbjct: 42 IAKILQEKLEKNGIEVLLNTTVEEIEGNGDGVVVKLKTGD 81
>gnl|CDD|236802 PRK10942, PRK10942, serine endoprotease; Provisional.
Length = 473
Score = 27.4 bits (61), Expect = 3.9
Identities = 18/48 (37%), Positives = 26/48 (54%)
Query: 75 EQAEAMGVEIYPGIPASEVLYHGDGSVKGIATGDVGIAKDGSPKDTFA 122
E A+AM V+ G S+VL + + GI GDV + +G P +FA
Sbjct: 300 ELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFA 347
>gnl|CDD|180734 PRK06855, PRK06855, aminotransferase; Validated.
Length = 433
Score = 27.2 bits (61), Expect = 4.7
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 5/32 (15%)
Query: 10 DPIALNELLPDW-KDLGAPLNTPVQEDK-FAY 39
DPIA E +PDW K++ A L V +DK + Y
Sbjct: 41 DPIAKGEKIPDWMKEIVAEL---VMDDKSYGY 69
>gnl|CDD|227557 COG5232, SEC62, Preprotein translocase subunit Sec62
[Intracellular trafficking and secretion].
Length = 259
Score = 26.8 bits (59), Expect = 5.1
Identities = 8/37 (21%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 62 YVVRLGHVVKWLGEQAEAMG----VEIYPGIPASEVL 94
+ R +++WL + + ++Y G+PA +L
Sbjct: 54 ELFRCKRILRWLNSEEYTLRHRRRPKVYRGVPAVAIL 90
>gnl|CDD|222972 PHA03080, PHA03080, putative virion core protein; Provisional.
Length = 366
Score = 26.9 bits (60), Expect = 5.9
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 1 GHILSGAVIDPIALNELLPD 20
GH+L GAV P+ N + D
Sbjct: 287 GHVLDGAVTSPLTKNATIVD 306
>gnl|CDD|220298 pfam09582, AnfO_nitrog, Iron only nitrogenase protein AnfO
(AnfO_nitrog). Proteins in this entry include Anf1 from
Rhodobacter capsulatus (Rhodopseudomonas capsulata) and
AnfO from Azotobacter vinelandii. They are found
exclusively in species which contain the iron-only
nitrogenase, and are encoded immediately downstream of
the structural genes for the nitrogenase enzyme in these
species.
Length = 201
Score = 26.5 bits (59), Expect = 6.7
Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 9/45 (20%)
Query: 43 SKRIGIPILPGMPMNNHGNY---VVRLGHVVKWLGEQAEAMGVEI 84
SK++ IP L +G + + HV W + +A+G++
Sbjct: 152 SKQVLIPFL------ENGGFNELEILCSHVPPWFEAELDALGLKA 190
>gnl|CDD|223647 COG0574, PpsA, Phosphoenolpyruvate synthase/pyruvate phosphate
dikinase [Carbohydrate transport and metabolism].
Length = 740
Score = 26.6 bits (59), Expect = 8.8
Identities = 14/45 (31%), Positives = 19/45 (42%)
Query: 83 EIYPGIPASEVLYHGDGSVKGIATGDVGIAKDGSPKDTFARGMEL 127
++P L G G+ GIA+G V I D S + G L
Sbjct: 325 LLHPVEDRGRALLKGIGASPGIASGRVKIILDVSEMEKLEHGDIL 369
>gnl|CDD|176682 cd07261, Glo_EDI_BRP_like_11, This conserved domain belongs to a
superfamily including the bleomycin resistance protein,
glyoxalase I, and type I ring-cleaving dioxygenases.
This protein family belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
superfamily contains members with or without domain
swapping.
Length = 114
Score = 25.6 bits (57), Expect = 9.2
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 4 LSGAVIDPIALNELLPDWKDLGAP-LNTPVQEDKFAY 39
L+ V D A++ L +W+ G + P + D F Y
Sbjct: 63 LAFMVDDGAAVDALYAEWQAKGVKIIQEPTEMD-FGY 98
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
0.317 0.139 0.426
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,517,596
Number of extensions: 776039
Number of successful extensions: 694
Number of sequences better than 10.0: 1
Number of HSP's gapped: 690
Number of HSP's successfully gapped: 36
Length of query: 165
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 75
Effective length of database: 6,945,742
Effective search space: 520930650
Effective search space used: 520930650
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: 55 (24.8 bits)