RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17300
(152 letters)
>gnl|CDD|235000 PRK02106, PRK02106, choline dehydrogenase; Validated.
Length = 560
Score = 96.4 bits (241), Expect = 5e-24
Identities = 43/140 (30%), Positives = 70/140 (50%), Gaps = 11/140 (7%)
Query: 3 ASSIFLRAIKDKNTVQVSKNSEVTKLCFDETKTKVTGVEFRNPQGKTIKVNANREVVLAA 62
A+ +L + + + ++ ++ F+ + GVE+ G A REV+L+A
Sbjct: 202 AARAYLDPALKRPNLTIVTHALTDRILFE--GKRAVGVEYER-GGGRETARARREVILSA 258
Query: 63 NSINSVRILQQSGVGDAALLSKYNIPLVKNLPGVGKRLSLHPMFFGLSYTFTKTPVSSYT 122
+INS ++LQ SG+G A L + IP+V +LPGVG+ L H + + Y + PVS Y
Sbjct: 259 GAINSPQLLQLSGIGPAEHLKELGIPVVHDLPGVGENLQDH-LEVYIQYECKQ-PVSLYP 316
Query: 123 INE------IIYEYLTQRTG 136
+ I E+L TG
Sbjct: 317 ALKWWNKPKIGAEWLFTGTG 336
>gnl|CDD|233581 TIGR01810, betA, choline dehydrogenase. Choline dehydrogenase
catalyzes the conversion of exogenously supplied choline
into the intermediate glycine betaine aldehyde, as part
of a two-step oxidative reaction leading to the
formation of osmoprotectant betaine. This enzymatic
system can be found in both gram-positive and
gram-negative bacteria. As in Escherichia coli ,
Staphylococcus xylosus , and Sinorhizobium meliloti,
this enzyme is found associated in a transciptionally
co-induced gene cluster with betaine aldehyde
dehydrogenase, the second catalytic enzyme in this
reaction. Other gram-positive organisms have been shown
to employ a different enzymatic system, utlizing a
soluable choline oxidase or type III alcohol
dehydrogenase instead of choline dehydrogenase. This
enzyme is a member of the GMC oxidoreductase family
(pfam00732 and pfam05199), sharing a common
evoluntionary origin and enzymatic reaction with alcohol
dehydrogenase. Outgrouping from this model, Caulobacter
crescentus shares sequence homology with choline
dehydrogenase, yet other genes participating in this
enzymatic reaction have not currently been identified
[Cellular processes, Adaptations to atypical
conditions].
Length = 532
Score = 87.2 bits (216), Expect = 9e-21
Identities = 42/119 (35%), Positives = 66/119 (55%), Gaps = 5/119 (4%)
Query: 3 ASSIFLRAIKDKNTVQVSKNSEVTKLCFDETKTKVTGVEFRNPQGKTIKVNANREVVLAA 62
A+ +L + ++V + VTK+ F+ + TGVEF+ K AN+EV+L+A
Sbjct: 195 AARAYLHPAMKRPNLEVQTRAFVTKINFE--GNRATGVEFKKGGRKE-HTEANKEVILSA 251
Query: 63 NSINSVRILQQSGVGDAALLSKYNIPLVKNLPGVGKRLSLHPMFFGLSYTFTKTPVSSY 121
+INS ++LQ SG+GDA L + I +LPGVG+ L H + + + + PVS Y
Sbjct: 252 GAINSPQLLQLSGIGDAEHLRELGIEPRIHLPGVGENLQDH-LEVYVQHACKQ-PVSLY 308
>gnl|CDD|225186 COG2303, BetA, Choline dehydrogenase and related flavoproteins
[Amino acid transport and metabolism].
Length = 542
Score = 81.7 bits (202), Expect = 6e-19
Identities = 41/135 (30%), Positives = 66/135 (48%), Gaps = 7/135 (5%)
Query: 7 FLRAIKDKNTVQVSKNSEVTKLCFDETKTKVTGVEFRNPQGKTIKV-NANREVVLAANSI 65
+L+ + + + + V ++ + + GVE G TI+ A REVVLAA +I
Sbjct: 208 YLKPALKRPNLTLLTGARVRRILLE--GDRAVGVEVEIGDGGTIETAVAAREVVLAAGAI 265
Query: 66 NSVRILQQSGVGDAALLSKYNIPLVKNLPGVGKRLSLHP---MFFGLSYTFTKTPVSSYT 122
NS ++L SG+G A L ++ I +V LPGVG+ L H + F + + +S ++
Sbjct: 266 NSPKLLLLSGIGPADHLLEHGIDVVGRLPGVGQNLQDHLEIYVAFEATEPTNDSVLSLFS 325
Query: 123 INEI-IYEYLTQRTG 136
I YL R G
Sbjct: 326 KLGIGADRYLLTRDG 340
>gnl|CDD|216089 pfam00732, GMC_oxred_N, GMC oxidoreductase. This family of
proteins bind FAD as a cofactor.
Length = 218
Score = 56.9 bits (138), Expect = 1e-10
Identities = 26/82 (31%), Positives = 36/82 (43%), Gaps = 16/82 (19%)
Query: 25 VTKLCFDETKTKVTGVEFRNPQGKTIKVN--ANREVVLAANSINSVRILQQSGVGDAALL 82
K+ + GVE R G IK A +EVV+AA ++N+ +L +SG+G
Sbjct: 150 AEKIIILGRGGRAVGVEAR-DGGGGIKRLITAAKEVVVAAGALNTPPLLLRSGLGKNPH- 207
Query: 83 SKYNIPLVKNLPGVGKRLSLHP 104
VGK L LHP
Sbjct: 208 ------------PVGKNLQLHP 217
>gnl|CDD|234421 TIGR03970, Rv0697, dehydrogenase, Rv0697 family. This model
describes a set of dehydrogenases belonging to the
glucose-methanol-choline oxidoreductase (GMC
oxidoreductase) family. Members of the present family
are restricted to Actinobacterial genome contexts
containing also members of families TIGR03962 and
TIGR03969 (the mycofactocin system), and are proposed to
be uniform in function.
Length = 487
Score = 54.8 bits (132), Expect = 2e-09
Identities = 32/99 (32%), Positives = 48/99 (48%), Gaps = 6/99 (6%)
Query: 19 VSKNSEVTKLCFDETKTKVTGVEFRNPQGKTIKVNANREVVLAANSINSVRILQQSGVGD 78
V ++ V ++ F + T+ GVE G + A+R VVL A ++ S +L SG+G
Sbjct: 212 VEADTRVVRILF--SGTRAVGVEVLGDGGPRT-LRADR-VVLCAGAVESAHLLLLSGIGP 267
Query: 79 AALLSKYNIPLVKNLPGVGKRLSLHPMFFGLSYTFTKTP 117
A L I +V +LP VG HP + L Y + T
Sbjct: 268 AEQLRAAGIAVVLDLP-VGSDFVDHPE-WVLPYRWRPTH 304
>gnl|CDD|215420 PLN02785, PLN02785, Protein HOTHEAD.
Length = 587
Score = 54.4 bits (131), Expect = 2e-09
Identities = 33/104 (31%), Positives = 57/104 (54%), Gaps = 6/104 (5%)
Query: 8 LRAIKDKNTVQVSKNSEVTKLCFD--ETKTKVTGVEFRNPQGKT----IKVNANREVVLA 61
L A + N ++V ++ V K+ FD + + TGV F++ G + N E++L+
Sbjct: 226 LLAAGNPNKLRVLLHATVQKIVFDTSGKRPRATGVIFKDENGNQHQAFLSNNKGSEIILS 285
Query: 62 ANSINSVRILQQSGVGDAALLSKYNIPLVKNLPGVGKRLSLHPM 105
A +I S ++L SG+G L K+ IP+V + VGK ++ +PM
Sbjct: 286 AGAIGSPQMLLLSGIGPKKELKKHKIPVVLHNEHVGKGMADNPM 329
>gnl|CDD|180854 PRK07121, PRK07121, hypothetical protein; Validated.
Length = 492
Score = 33.7 bits (78), Expect = 0.026
Identities = 18/46 (39%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 17 VQVSKNSEVTKLCFDETKTKVTGVEFRNPQGKTIKVNANREVVLAA 62
VQ+ ++ T+L D+ +V GVE R G+T+ + A + VVLAA
Sbjct: 192 VQIRYDTRATRLIVDDDG-RVVGVEARRY-GETVAIRARKGVVLAA 235
>gnl|CDD|216412 pfam01285, TEA, TEA/ATTS domain family.
Length = 424
Score = 33.6 bits (77), Expect = 0.029
Identities = 14/26 (53%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 120 SYTINEIIYEYLTQRTGKRRRKFTRK 145
SY NE+I Y+ RTGK R TRK
Sbjct: 84 SYGRNELIARYIKLRTGKTR---TRK 106
>gnl|CDD|180919 PRK07282, PRK07282, acetolactate synthase catalytic subunit;
Reviewed.
Length = 566
Score = 31.7 bits (72), Expect = 0.14
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 10/59 (16%)
Query: 54 ANREVVLAANSIN---SVRILQQSGVGDAALLSKYNIPLVKNLPGVGKRLSLHPMFFGL 109
A + V+LA IN + L A +Y IP+V L G G + HP+F G+
Sbjct: 210 AKKPVILAGGGINYAEAATELN-------AFAERYQIPVVTTLLGQGTIATSHPLFLGM 261
>gnl|CDD|236076 PRK07710, PRK07710, acetolactate synthase catalytic subunit;
Reviewed.
Length = 571
Score = 30.9 bits (70), Expect = 0.26
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 5/46 (10%)
Query: 84 KYNIPLVKNLPGVGKRLSLHPMFFGLSYTFTKTPVSSYTINEIIYE 129
+ IP+V L G+G + HP+F G++ +YT N +YE
Sbjct: 241 QQEIPVVHTLLGLGGFPADHPLFLGMAGMH-----GTYTANMALYE 281
>gnl|CDD|233583 TIGR01813, flavo_cyto_c, flavocytochrome c. This model describes a
family of redox proteins related to the succinate
dehydrogenases and fumarate reductases of E. coli,
mitochondria, and other well-characterized systems. A
member of this family from Shewanella frigidimarina
NCIMB400 is characterized as a water-soluble periplasmic
protein with four heme groups, a non-covalently bound
FAD, and essentially unidirectional fumarate reductase
activity. At least seven distinct members of this family
are found in Shewanella oneidensis, a species able to
use a wide variety of pathways for respiraton [Energy
metabolism, Electron transport].
Length = 439
Score = 30.4 bits (69), Expect = 0.30
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 13 DKNTVQVSKNSEVTKLCFDETKTKVTGVEFRNPQGKTIKVNANREVVLA 61
K + NS+V L D+ T V GV + +GK I + A + VVLA
Sbjct: 141 KKEGIDTRLNSKVEDLIQDDQGT-VVGVVVKG-KGKGIYIKAAKAVVLA 187
>gnl|CDD|128703 smart00426, TEA, TEA domain.
Length = 68
Score = 27.2 bits (60), Expect = 1.1
Identities = 13/27 (48%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 120 SYTINEIIYEYLTQRTGKRRRKFTRKR 146
Y NE+I Y+ RTGK R TRK+
Sbjct: 37 MYGRNELIARYIKLRTGKTR---TRKQ 60
>gnl|CDD|183955 PRK13292, PRK13292, trifunctional NADH dehydrogenase I subunit
B/C/D; Provisional.
Length = 788
Score = 28.2 bits (63), Expect = 1.9
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 97 GKRLSLHPMFFGLSYTF 113
G+ SL PMFFGLS F
Sbjct: 19 GRANSLWPMFFGLSCCF 35
>gnl|CDD|215553 PLN03052, PLN03052, acetate--CoA ligase; Provisional.
Length = 728
Score = 28.1 bits (63), Expect = 2.2
Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 81 LLSKYNIPLVKNLPGVGKRLSLHPMFFGLSYT 112
+L P + P G+ L+L P+ FG S T
Sbjct: 538 ILDDSGNPYPDDAPCTGE-LALFPLMFGASST 568
>gnl|CDD|223981 COG1053, SdhA, Succinate dehydrogenase/fumarate reductase,
flavoprotein subunit [Energy production and conversion].
Length = 562
Score = 28.1 bits (63), Expect = 2.3
Identities = 11/55 (20%), Positives = 22/55 (40%), Gaps = 1/55 (1%)
Query: 9 RAIKDKNTVQVSKNSEVTKLCFDETKTKVTGVEFRNPQGKTIKVNANREVVLAAN 63
+ + +++ V L D+ V GV R+ + + V + V+LA
Sbjct: 146 EQLLKFSGIEIFDEYFVLDLLVDDGG-GVAGVVARDLRTGELYVFRAKAVILATG 199
>gnl|CDD|235729 PRK06185, PRK06185, hypothetical protein; Provisional.
Length = 407
Score = 27.5 bits (62), Expect = 2.7
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 5/47 (10%)
Query: 22 NSEVTKLCFDETKTKVTGVEFRNPQGKTIKVNANREVVLAANSINSV 68
+EVT L + + VTGV R P G ++ A ++V+ A+ +S
Sbjct: 129 GAEVTGLIEEGGR--VTGVRARTPDG-PGEIRA--DLVVGADGRHSR 170
>gnl|CDD|180584 PRK06481, PRK06481, fumarate reductase flavoprotein subunit;
Validated.
Length = 506
Score = 27.5 bits (61), Expect = 2.8
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 22 NSEVTKLCFDETKTKVTGVEFRNPQGKTIKVNANREVV 59
N++VTK+ E KVTGV+ + +T +++ VV
Sbjct: 210 NADVTKI--TEKDGKVTGVKVKINGKETKTISSKAVVV 245
>gnl|CDD|202354 pfam02700, PurS, Phosphoribosylformylglycinamidine (FGAM)
synthase. This family forms a component of the de novo
purine biosynthesis pathway.
Length = 80
Score = 25.5 bits (57), Expect = 5.1
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 43 RNPQGKTIKVNANREVVLAANSINSVRI 70
+PQG+ IK +R L + VRI
Sbjct: 14 LDPQGEAIKKALHR---LGYEGVEDVRI 38
>gnl|CDD|200458 cd11319, AmyAc_euk_AmyA, Alpha amylase catalytic domain found in
eukaryotic Alpha-amylases (also called
1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC
3.2.1.1) catalyzes the hydrolysis of alpha-(1,4)
glycosidic linkages of glycogen, starch, related
polysaccharides, and some oligosaccharides. This group
includes eukaryotic alpha-amylases including proteins
from fungi, sponges, and protozoans. The Alpha-amylase
family comprises the largest family of glycoside
hydrolases (GH), with the majority of enzymes acting on
starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 375
Score = 26.8 bits (60), Expect = 5.9
Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 8/51 (15%)
Query: 77 GDAALLSKYNIPLVKNLPGVGKRLSLHPMFFGLSYTFTKTPVSSYTINEII 127
GD + Y L GV L+ +P+++ L F T S + + I
Sbjct: 234 GDPNYVCPY----QNYLDGV---LN-YPLYYPLVDAFQSTKGSMSALVDTI 276
>gnl|CDD|117498 pfam08931, DUF1913, Domain of unknown function (DUF1913). This
domain has no known function. It is found in a various
putative receptor proteins from Lactococcus
bacteriophages.
Length = 146
Score = 26.0 bits (57), Expect = 7.7
Identities = 12/37 (32%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 15 NTVQVSKNSEVTKLCFDETKTKVTGVEFR-NPQGKTI 50
N V ++ S V K+C D T TGV P +
Sbjct: 108 NGVDINNGSGVLKVCIDIVTTNGTGVTSVEPPSQVST 144
>gnl|CDD|184335 PRK13802, PRK13802, bifunctional indole-3-glycerol phosphate
synthase/tryptophan synthase subunit beta; Provisional.
Length = 695
Score = 26.5 bits (58), Expect = 7.9
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 36 KVTGVEFRNPQGKTIKVNANREVVLAANSINSVRILQQSGVGDAALLSKY 85
KV G+ RN K +KV+ N+ LAA+ + V + +SGV A + Y
Sbjct: 182 KVIGINARNL--KDLKVDVNKYNELAADLPDDVIKVAESGVFGAVEVEDY 229
>gnl|CDD|237550 PRK13899, PRK13899, type IV secretion system protein VirB3;
Provisional.
Length = 97
Score = 25.1 bits (55), Expect = 9.0
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 98 KRLSLHPMFFGLSYTF 113
K L+ PM FG+SY F
Sbjct: 12 KGLTRPPMIFGVSYKF 27
>gnl|CDD|181416 PRK08415, PRK08415, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 274
Score = 25.9 bits (57), Expect = 9.1
Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 11/49 (22%)
Query: 48 KTIKVNANREVVLAANSINSVRILQQSGVGDAALLSKYN---IPLVKNL 93
K I+VNA ++A I + L SG+GD ++ K+N PL KN+
Sbjct: 178 KGIRVNA-----ISAGPI---KTLAASGIGDFRMILKWNEINAPLKKNV 218
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
0.318 0.133 0.365
Gapped
Lambda K H
0.267 0.0577 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,492,266
Number of extensions: 661371
Number of successful extensions: 655
Number of sequences better than 10.0: 1
Number of HSP's gapped: 651
Number of HSP's successfully gapped: 35
Length of query: 152
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 64
Effective length of database: 7,034,450
Effective search space: 450204800
Effective search space used: 450204800
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 (21.7 bits)
S2: 55 (25.3 bits)