RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 026745
(234 letters)
>gnl|CDD|216656 pfam01709, Transcrip_reg, Transcriptional regulator. This is a
family of transcriptional regulators. In mammals, it
activates the transcription of mitochondrially-encoded
COX1. In bacteria, it negatively regulates the
quorum-sensing response regulator by binding to its
promoter region.
Length = 234
Score = 199 bits (508), Expect = 3e-64
Identities = 82/213 (38%), Positives = 117/213 (54%), Gaps = 14/213 (6%)
Query: 20 VKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRAS-EKGQEAFIEKVYEVYGYGGV 78
K GGP+P N L +EKAK ++PKD +ER IK+ S E + E YE YG GGV
Sbjct: 32 AKMGGPDPEGNPRLRLAIEKAKAANMPKDNIERAIKKGSGGLDGENYEEIRYEGYGPGGV 91
Query: 79 SIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDI 138
+I+VE LTD R+ A VR GG + + GSV + F R V+ + D+D+LL+
Sbjct: 92 AIIVECLTDNRNRTAADVRHAFSKNGGNLGETGSVSYMFDRKGVIVFEKEGVDEDELLEA 151
Query: 139 ALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELL 198
AL+AGAEDV E ED + +V++ ++ + L EAG+ E ++
Sbjct: 152 ALEAGAEDVEE----EDGS--------IEVITDPTDFEAVKKALEEAGLEIE-SAEITMI 198
Query: 199 PITTIEVDDEAMELNKELIAKLLELDDVDAVYT 231
P T+E+D+E E ++LI L +LDDV VY
Sbjct: 199 PQNTVELDEEDAEKLEKLIDALEDLDDVQNVYH 231
>gnl|CDD|223295 COG0217, COG0217, Uncharacterized conserved protein [Function
unknown].
Length = 241
Score = 166 bits (424), Expect = 1e-51
Identities = 83/213 (38%), Positives = 120/213 (56%), Gaps = 14/213 (6%)
Query: 20 VKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRAS-EKGQEAFIEKVYEVYGYGGV 78
K+GGP+P SN L +EKAK ++PKD +ER IK+AS K + E YE YG GGV
Sbjct: 36 AKQGGPDPESNPRLRTAIEKAKAANMPKDNIERAIKKASGGKDGANYEEIRYEGYGPGGV 95
Query: 79 SIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDI 138
+I+VE LTD R+ + VR GG + +PGSV + F R V+ ++ + D+D+LL+
Sbjct: 96 AIIVEALTDNRNRTASNVRSAFNKNGGNLGEPGSVSYMFDRKGVIVVEKNEIDEDELLEA 155
Query: 139 ALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELL 198
A++AGAEDV E DE E V + +++ + L AG E+ ++
Sbjct: 156 AIEAGAEDVEE--------DEGSIE----VYTEPEDFNKVKEALEAAGYEIESA-ELTMI 202
Query: 199 PITTIEVDDEAMELNKELIAKLLELDDVDAVYT 231
P T+E+DDE E ++LI L + DDV VY
Sbjct: 203 PQNTVELDDEDAEKLEKLIDALEDDDDVQNVYH 235
>gnl|CDD|234640 PRK00110, PRK00110, hypothetical protein; Validated.
Length = 245
Score = 163 bits (415), Expect = 4e-50
Identities = 78/215 (36%), Positives = 118/215 (54%), Gaps = 20/215 (9%)
Query: 20 VKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRAS-EKGQEAFIEKVYEVYGYGGV 78
K GG +P N L ++KAK ++PKD +ER IK+ + E + E YE YG GGV
Sbjct: 36 AKLGGGDPEGNPRLRLAIDKAKAANMPKDNIERAIKKGTGELDGANYEEIRYEGYGPGGV 95
Query: 79 SIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDI 138
+I+VE LTD R+ A VR GG + + GSV + F R V I D+D+L++
Sbjct: 96 AIIVEALTDNRNRTAAEVRHAFSKNGGNLGETGSVSYMFDRKGV--IVIEPLDEDELMEA 153
Query: 139 ALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSEL- 197
AL+AGAEDV TD++ ++V++ +++ + L AG+ E+ +E+
Sbjct: 154 ALEAGAEDVE--------TDDE----SFEVITAPEDFEAVRDALEAAGLEAES---AEVT 198
Query: 198 -LPITTIEVDDEAMELNKELIAKLLELDDVDAVYT 231
+P T+E+D+E E +LI L +LDDV VY
Sbjct: 199 MIPQNTVELDEETAEKLLKLIDALEDLDDVQNVYH 233
>gnl|CDD|237084 PRK12378, PRK12378, hypothetical protein; Provisional.
Length = 235
Score = 156 bits (397), Expect = 1e-47
Identities = 75/212 (35%), Positives = 107/212 (50%), Gaps = 13/212 (6%)
Query: 20 VKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGYGGVS 79
K+GGP+P SN L V+E+AK+ +VPKD++ER IK+A G E + E YE +G GV
Sbjct: 34 AKQGGPDPESNPALRFVIERAKKANVPKDVIERAIKKAKGGGGEDYEEVRYEGFGPNGVM 93
Query: 80 IVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIA 139
++VE LTD + R+VA VR GG + GSV F F V + D D+ I
Sbjct: 94 VIVECLTDNVNRTVANVRSAFNKNGGNLGTSGSVAFMFDHKGVFVFEGDDEDELLEALID 153
Query: 140 LDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLP 199
D EDV E E+ T V + ++ + L AGI F E++P
Sbjct: 154 ADVDVEDVEE----EEGT--------ITVYTDPTDFHKVKKALEAAGIEFLVAE-LEMIP 200
Query: 200 ITTIEVDDEAMELNKELIAKLLELDDVDAVYT 231
+E+ E +E ++L+ L + DDV VY
Sbjct: 201 QNPVELSGEDLEQFEKLLDALEDDDDVQNVYH 232
>gnl|CDD|233240 TIGR01033, TIGR01033, DNA-binding regulatory protein, YebC/PmpR
family. This model describes a minimally characterized
protein family, restricted to bacteria excepting for
some eukaryotic sequences that have possible transit
peptides. YebC from E. coli is crystallized, and PA0964
from Pseudomonas aeruginosa has been shown to be a
sequence-specific DNA-binding regulatory protein
[Regulatory functions, DNA interactions].
Length = 238
Score = 154 bits (390), Expect = 2e-46
Identities = 76/213 (35%), Positives = 112/213 (52%), Gaps = 14/213 (6%)
Query: 20 VKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRA-SEKGQEAFIEKVYEVYGYGGV 78
K GG +P SN L +EKAK ++PKD +ER IK+ E + E YE Y GGV
Sbjct: 36 AKLGGGDPESNPRLRTAIEKAKAANMPKDNIERAIKKGAGELDGSNYEEITYEGYAPGGV 95
Query: 79 SIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDI 138
+I+VE LTD R+ + VR GG + +PGSV + F R V+ + + D++ L++
Sbjct: 96 AIIVECLTDNKNRTASEVRSAFNKNGGSLGEPGSVSYLFSRKGVIEVPKNEVDEEDLMEA 155
Query: 139 ALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELL 198
A++AGAED+ D D+D E V + + + L G P E ++
Sbjct: 156 AIEAGAEDI--------DVDDDEFE----VYTAPEELEKVKEALEAKGFPIE-SAEITMI 202
Query: 199 PITTIEVDDEAMELNKELIAKLLELDDVDAVYT 231
P+TT+++DDE E +LI L + DDV VY
Sbjct: 203 PLTTVDLDDEQAEKLLKLIDALEDDDDVQEVYH 235
>gnl|CDD|221101 pfam11382, DUF3186, Protein of unknown function (DUF3186). This
bacterial family of proteins has no known function.
Length = 307
Score = 30.4 bits (69), Expect = 0.74
Identities = 35/220 (15%), Positives = 69/220 (31%), Gaps = 31/220 (14%)
Query: 24 GPNPTSNTVLAAVLEKAKELDVPKDIV--ERNIKRASEKGQEAFIEKVYEVY---GYGGV 78
G +L+ + ++ +L D + ER + FI + G
Sbjct: 25 GSGLLQENLLSGLEDEFSDLRTENDRLRAEREALNEQASAADQFIAALAPRLVAGRLTGK 84
Query: 79 SIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADK-DQLLD 137
S+ + D V AV E + G + G + + F D + D+L
Sbjct: 85 SVALVRTPDADDDDVDAVSEALTQAGATVV--GRI--------TLTDNFVDPESADKLKS 134
Query: 138 IALDAGAEDVIEPPVNEDDTDEDRAERYYKVV------STSDNYTDITTKLREAGIPFET 191
+ + + D + + ++++ + + LR+AG T
Sbjct: 135 VVNNDLKPAGDQLSTAAADPGSQAGDLLGAALLLNPPTASTEERSAVLAALRDAG--LIT 192
Query: 192 DNGSELLPITTIEV-------DDEAMELNKELIAKLLELD 224
+G + P V D +A L+ + LD
Sbjct: 193 YSGDTVGPADAAVVVGGDSAGDADANALDAAVARFARALD 232
>gnl|CDD|226857 COG4449, COG4449, Predicted protease of the Abi (CAAX) family
[General function prediction only].
Length = 827
Score = 29.6 bits (66), Expect = 1.6
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 11/69 (15%)
Query: 158 DEDRAERYYKVVSTSDNYTDITTKLREAGI--PFETDNGSELLPITTIE----VDD---- 207
+RY K+V+T N+T K +AG P + S++ P+ ++ VDD
Sbjct: 112 SNADLDRYLKLVTTDVNFTPAALKSEQAGNLLPNRLNGRSQVGPLQSLAGARPVDDVLVR 171
Query: 208 -EAMELNKE 215
++N
Sbjct: 172 FVQAQVNVP 180
>gnl|CDD|219605 pfam07847, DUF1637, Protein of unknown function (DUF1637). This
family contains many eukaryotic hypothetical proteins.
The region featured in this family is approximately 120
residues long. According to InterPro annotation, some
members of this family may belong to the cupin
superfamily.
Length = 194
Score = 28.4 bits (64), Expect = 2.2
Identities = 12/43 (27%), Positives = 15/43 (34%), Gaps = 3/43 (6%)
Query: 146 DVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIP 188
DV+ PP + DD R YY+ L E P
Sbjct: 140 DVLAPPYDPDD---GRDCTYYRDSPLPSGLPSEAAWLEEIPQP 179
>gnl|CDD|226048 COG3517, COG3517, Predicted component of the type VI protein
secretion system [Intracellular trafficking, secretion,
and vesicular transport].
Length = 495
Score = 28.9 bits (65), Expect = 2.5
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 39 KAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGYG 76
K + L++ KD + R+ ++A E Q +KVYE YG
Sbjct: 116 KIRVLNISKDELLRDFEKAPEFDQSGLFKKVYE-EEYG 152
>gnl|CDD|107298 cd06303, PBP1_LuxPQ_Quorum_Sensing, Periplasmic binding protein
(LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from
Vibrio harveyi and its close homologs. Periplasmic
binding protein (LuxP) of autoinducer-2 (AI-2) receptor
LuxPQ from Vibrio harveyi and its close homologs from
other bacteria. The members of this group are highly
homologous to a family of periplasmic pentose/hexose
sugar-binding proteins that function as the primary
receptors for chemotaxis and transport of many sugar
based solutes in bacteria and archaea, and that are
members of the type I periplasmic binding protein
superfamily. The Vibrio harveyi AI-2 receptor consists
of two polypeptides, LuxP and LuxQ: LuxP is a
periplasmic binding protein that binds AI-2 by clamping
it between two domains, LuxQ is an integral membrane
protein belonging to the two-component sensor kinase
family. Unlike AI-2 bound to the LsrB receptor in
Salmonella typhimurium, the Vibrio harveyi AI-2
signaling molecule has an unusual furanosyl borate
diester. Hence, many bacteria coordinate their gene
expression according to the local density of their
population by producing species specific AI-2. This
process of quorum sensing allows LuxPQ to control light
production as well as its motility behavior.
Length = 280
Score = 28.5 bits (64), Expect = 2.6
Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 7/58 (12%)
Query: 166 YKVVSTSD----NYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAK 219
Y SD N T +L E IP+E + I+ ++ +LN+ L +K
Sbjct: 6 YPGQQISDYWVRNIASFTARLEELNIPYELT---QFSSRPGIDHRLQSQQLNEALQSK 60
>gnl|CDD|216078 pfam00716, Peptidase_S21, Assemblin (Peptidase family S21).
Length = 326
Score = 28.5 bits (64), Expect = 2.7
Identities = 23/114 (20%), Positives = 37/114 (32%), Gaps = 25/114 (21%)
Query: 108 ADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYK 167
+ FR + A+++ LL +A A + EP D Y
Sbjct: 130 RTLEWAIAPFRD-------LSPAEREALLSLAKQALGDSAWEPSFPSDT---------YV 173
Query: 168 VVSTS-------DNYTDITTKLREAGIPFETD-NGSELLPITTIEVDDEAMELN 213
+++ + D + T R AGI T SE +T DE +
Sbjct: 174 LLAKAVDAMFIRDRLPKLKTDRRVAGIKGHTYLKASESPGLTAAC-HDEVVASK 226
>gnl|CDD|223946 COG1014, PorG, Pyruvate:ferredoxin oxidoreductase and related
2-oxoacid:ferredoxin oxidoreductases, gamma subunit
[Energy production and conversion].
Length = 203
Score = 28.1 bits (63), Expect = 2.9
Identities = 15/62 (24%), Positives = 23/62 (37%), Gaps = 14/62 (22%)
Query: 20 VKKGGPNPTSNTVLAAVL-------------EKAKELDVPKDIVERNIKRASEKGQEAFI 66
++ G +NTV+ E+A + +VE N+K A E G E
Sbjct: 135 AEEAGGRIIANTVMLGAFAALTGIVPELEALEEAIKARFKGKVVEANLK-AFEAGYEEAE 193
Query: 67 EK 68
E
Sbjct: 194 EV 195
>gnl|CDD|115305 pfam06635, NolV, Nodulation protein NolV. This family consists
of several nodulation protein NolV sequences from
different Rhizobium species. The function of this
family is unclear.
Length = 207
Score = 28.1 bits (62), Expect = 3.3
Identities = 14/56 (25%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 2 QRKQSCIRGWGRKSYLRNVKKG---GPNPTSNTVLAAVLEKAKELDVPKDIVERNI 54
+R +RGW R +Y R + +G G + + A + + EL K ++E+ +
Sbjct: 40 ERHLQHVRGWARAAYERELAQGHAEGAKAGAEEMAALIAQATAELAQRKAVLEQEL 95
>gnl|CDD|201667 pfam01215, COX5B, Cytochrome c oxidase subunit Vb.
Length = 136
Score = 27.6 bits (61), Expect = 3.8
Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 13/78 (16%)
Query: 17 LRNVKKGGPNPTSNTVLAAVLEKAKELDVPKDI-----VERNIKRASEKGQEAF-IEKVY 70
L + P +++ A VP D+ +ER A+ KG++ F I+ +
Sbjct: 17 LAFARG----PNGVSLIGPG---ASGGGVPTDLEQATGLEREELLAALKGRDPFDIKPLD 69
Query: 71 EVYGYGGVSIVVEVLTDK 88
G I+VE + +
Sbjct: 70 ASKGTLKDPIIVESIDNY 87
>gnl|CDD|240349 PTZ00295, PTZ00295, glucosamine-fructose-6-phosphate
aminotransferase; Provisional.
Length = 640
Score = 28.1 bits (63), Expect = 4.8
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 171 TSDNYTDITTKLREAGIPFETDNGSEL 197
T +NY ++ ++L GI F ++ SE+
Sbjct: 132 TIENYVELKSELIAKGIKFRSETDSEV 158
>gnl|CDD|153004 pfam12570, DUF3750, Protein of unknown function (DUF3750). This
family of proteins is found in bacteria. Proteins in
this family are typically between 175 and 265 amino
acids in length.
Length = 129
Score = 26.8 bits (60), Expect = 5.0
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 25 PNPTSNTVLAAVLEKAKELDV 45
P P SNT +A VL + ELD+
Sbjct: 98 PGPNSNTFVAWVLRQVPELDL 118
>gnl|CDD|235668 PRK06007, fliF, flagellar MS-ring protein; Reviewed.
Length = 542
Score = 27.9 bits (63), Expect = 5.0
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 166 YKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIEVD-DEAMELNKELIAK 219
Y +S D I L +AGIP++ + TI V D+ EL +L ++
Sbjct: 54 YSNLSDQD-AGQIVAALDQAGIPYKVADDG-----GTILVPADKVDELRLKLASE 102
>gnl|CDD|236490 PRK09376, rho, transcription termination factor Rho; Provisional.
Length = 416
Score = 27.8 bits (63), Expect = 5.1
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 9/53 (16%)
Query: 33 LAAVLEKAKELDVP-------KDIVERNIKRASEKGQEAFIEKVYEVY--GYG 76
L+ +LE A+EL + ++++ +K +EKG + F E V E+ G+G
Sbjct: 11 LSELLELAEELGIENASRLRKQELIFAILKAQAEKGGDIFGEGVLEILPDGFG 63
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 27.8 bits (61), Expect = 5.7
Identities = 14/59 (23%), Positives = 26/59 (44%)
Query: 151 PVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEA 209
+ E+ + ED VSTSD D+ ++ I E ++ +E + + DE+
Sbjct: 417 AIAEETSREDELSFDDSDVSTSDENEDVDFTGKKGAINNEDESDNEEVAFDSDSQFDES 475
>gnl|CDD|227277 COG4941, COG4941, Predicted RNA polymerase sigma factor containing
a TPR repeat domain [Transcription].
Length = 415
Score = 27.8 bits (62), Expect = 6.2
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 180 TKLREAGIPFETDNGSEL 197
++REAGIPFE EL
Sbjct: 162 ARIREAGIPFEVPGPQEL 179
>gnl|CDD|148673 pfam07209, DUF1415, Protein of unknown function (DUF1415). This
family consists of several hypothetical bacterial
proteins of around 180 residues in length. The function
of this family is unknown.
Length = 174
Score = 26.7 bits (60), Expect = 7.6
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 46 PKDIVERNIKRASEKGQEAFIE 67
P+ I ERNI G+E +
Sbjct: 152 PESIPERNIATLRRLGREGWKA 173
>gnl|CDD|203351 pfam05922, Inhibitor_I9, Peptidase inhibitor I9. This family
includes the proteinase B inhibitor from Saccharomyces
cerevisiae and the activation peptides from peptidases
of the subtilisin family. The subtilisin propeptides are
known to function as molecular chaperones, assisting in
the folding of the mature peptidase, but have also been
shown to act as 'temporary inhibitors'.
Length = 76
Score = 25.3 bits (56), Expect = 8.3
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 209 AMELNKELIAKLLELDDVDAVYTDQI 234
A +L +E KL + DV+ V DQ+
Sbjct: 47 AAKLTEEEAEKLRKHPDVEYVEPDQV 72
>gnl|CDD|238315 cd00562, NifX_NifB, This CD represents a family of iron-molybdenum
cluster-binding proteins that includes NifB, NifX, and
NifY, all of which are involved in the synthesis of an
iron-molybdenum cofactor (FeMo-co) that binds the active
site of the dinitrogenase enzyme. This domain is a
predicted small-molecule-binding domain (SMBD) with an
alpha/beta fold that is present either as a stand-alone
domain (e.g. NifX and NifY) or fused to another
conserved domain (e.g. NifB) however, its function is
still undetermined.The SCOP database suggests that this
domain is most similar to structures within the
ribonuclease H superfamily. This conserved domain is
represented in two of the three major divisions of life
(bacteria and archaea).
Length = 102
Score = 26.1 bits (58), Expect = 8.5
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 2/47 (4%)
Query: 189 FETDNGSELLPITTIEVDDEAMELNKE-LIAKLLELDDVDAVYTDQI 234
+E + G L + E + L A+LL L+ DAV I
Sbjct: 25 YEVEPGGIKL-VEVRENPAACGGGGEGKLAARLLALEGCDAVLVGGI 70
>gnl|CDD|239094 cd02411, archeal_30S_S3_KH, K homology RNA-binding domain (KH) of
the archaeal 30S small ribosomal subunit S3 protein. S3
is part of the head region of the 30S ribosomal
subunit and is believed to interact with mRNA as it
threads its way from the latch into the channel. The
KH motif is a beta-alpha-alpha-beta-beta unit that
folds into an alpha-beta structure with a three
stranded beta-sheet interupted by two contiguous
helices. In general, KH binds single-stranded RNA or
DNA. It is found in a wide variety of proteins
including ribosomal proteins, transcription factors and
post-transcriptional modifiers of mRNA.
Length = 85
Score = 25.7 bits (57), Expect = 8.6
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 45 VPKDIVERNIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKIT 90
V + V +KR ++EK E GYGG+ I+ L +IT
Sbjct: 1 VERKFVNEGVKRTMID---EYLEKELERAGYGGMEILRTPLGTQIT 43
>gnl|CDD|176237 cd08276, MDR7, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 336
Score = 27.1 bits (61), Expect = 8.8
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 67 EKVYEVYGYGGVSIVVEVL-TDKITRSVAAVR 97
E+V ++ G GV VVEV + +S+ AV
Sbjct: 219 EEVLKLTGGRGVDHVVEVGGPGTLAQSIKAVA 250
>gnl|CDD|233962 TIGR02645, ARCH_P_rylase, putative thymidine phosphorylase.
Members of this family are closely related to
characterized examples of thymidine phosphorylase (EC
2.4.2.4) and pyrimidine nucleoside phosphorylase (RC
2.4.2.2). Most examples are found in the archaea, but
other examples in Legionella pneumophila str. Paris and
Rhodopseudomonas palustris CGA009.
Length = 493
Score = 27.1 bits (60), Expect = 8.8
Identities = 10/38 (26%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 76 GGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSV 113
G + +EVLT ++ S ++ +V+ GG + G++
Sbjct: 200 AGTADTMEVLT-RVALSAEEIKRIVEKVGGCLVWGGAL 236
>gnl|CDD|223923 COG0854, PdxJ, Pyridoxal phosphate biosynthesis protein [Coenzyme
metabolism].
Length = 243
Score = 26.8 bits (60), Expect = 8.8
Identities = 24/94 (25%), Positives = 35/94 (37%), Gaps = 19/94 (20%)
Query: 133 DQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIP---F 189
+++L IAL V P + +E E V D D +L+ AGI F
Sbjct: 74 EEMLAIALKTKPHQVTLVP---EKREEVTTEGGLDVAGQLDKLRDAVRRLKNAGIRVSLF 130
Query: 190 ETDNGSELLPITTIEVDDEAMELNKELIAKLLEL 223
I+ D E +E E+ A +EL
Sbjct: 131 -------------IDPDPEQIEAAAEVGAPRIEL 151
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
0.314 0.134 0.368
Gapped
Lambda K H
0.267 0.0742 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,257,468
Number of extensions: 1221722
Number of successful extensions: 1535
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1520
Number of HSP's successfully gapped: 63
Length of query: 234
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 140
Effective length of database: 6,768,326
Effective search space: 947565640
Effective search space used: 947565640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (25.7 bits)