RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1882
(233 letters)
>gnl|CDD|216752 pfam01871, AMMECR1, AMMECR1. This family consists of several
AMMECR1 as well as several uncharacterized proteins. The
contiguous gene deletion syndrome AMME is characterized
by Alport syndrome, midface hypoplasia, mental
retardation and elliptocytosis and is caused by a
deletion in Xq22.3, comprising several genes including
COL4A5, FACL4 and AMMECR1. This family contains
sequences from several eukaryotic species as well as
archaebacteria and it has been suggested that the
AMMECR1 protein may have a basic cellular function,
potentially in either the transcription, replication,
repair or translation machinery.
Length = 172
Score = 174 bits (444), Expect = 2e-55
Identities = 58/177 (32%), Positives = 89/177 (50%), Gaps = 14/177 (7%)
Query: 44 MCFFCFDVLYCHLH---SLEPPNPPSGISNDAFPLFVTWKIGKDQRLRGCIGTFNAI-NL 99
+ + + +L LEPP N+ +FVT K K LRGCIGTF + L
Sbjct: 1 LVRLAREAIEAYLEGGKVLEPPPELPPKLNEKRGVFVTLK--KRGELRGCIGTFEPVRPL 58
Query: 100 HGGLREYAVTSAFKDSRFNPITVDEFSKLHVSVSILRHFEDGNDY-TDWKIGVHGIRIEF 158
+ E A+ +AF+D RF P+T +E L + VS+L E + D ++G HG+ IEF
Sbjct: 59 AEAVIEAAIAAAFEDPRFPPVTEEELPDLTIEVSVLSPPEPIDVDLEDLEVGRHGLIIEF 118
Query: 159 HNERGNKRTATYLPEVAPEQGWDQIQTIDSLLRKGGFKGPITPDIRCNIKLTRYQSE 215
G LP+VA EQGWD + + L RK G P + ++++ R++++
Sbjct: 119 GGYSG-----LLLPQVAVEQGWDPEEFLAHLCRKAGL--PPDAWLDEDVEIYRFEAQ 168
>gnl|CDD|224989 COG2078, AMMECR1, Uncharacterized conserved protein [Function
unknown].
Length = 203
Score = 113 bits (285), Expect = 3e-31
Identities = 44/182 (24%), Positives = 79/182 (43%), Gaps = 20/182 (10%)
Query: 45 CFFCFDVLYCHLHSLEPPNPPS--GISNDAFPLFVTW-KIGKDQRLRGCIGTFNAI-NLH 100
+ + +L + P + + +FVT K D LRGCIGT + L
Sbjct: 14 VRLAREAIENYLEGGKVIEPEPFPKLFQEKRGVFVTLEKYSPDGELRGCIGTPEPVKPLA 73
Query: 101 GGLREYAVTSAFKDSRFNPITVDEFSKLHVSVSILRHFE----DGNDYT-DWKIGVHGIR 155
+ + A+ +A D RF P++++E + V V+IL E + D ++G HG+
Sbjct: 74 EAIIKAAIEAALSDPRFPPVSLEELDDIVVEVTILTPPEEIDVPPEERPEDIEVGRHGLI 133
Query: 156 IEFHNERGNKRTATYLPEVAPEQGWDQIQTIDSLLRKGGFKGPITPDIRC--NIKLTRYQ 213
+E G LP+V E WD + ++ K G + D ++K+ R++
Sbjct: 134 VEKGIYSG-----LLLPQVPVEYRWDVEEFLEHTCEKAG----LPGDCWLDEDVKIYRFE 184
Query: 214 SE 215
++
Sbjct: 185 AQ 186
>gnl|CDD|234550 TIGR04335, AmmeMemoSam_A, AmmeMemoRadiSam system protein A.
Members of this protein family belong to the same domain
family as AMMECR1, a mammalian protein named for AMME -
Alport syndrome, Mental Retardation, Midface hypoplasia,
and Elliptocytosis. Members of the present family occur
as part of a three gene system with a homolog of the
mammalian protein Memo (Mediator of ErbB2-driven cell
MOtility), and an uncharacterized radical SAM enzyme.
Length = 175
Score = 109 bits (274), Expect = 5e-30
Identities = 50/178 (28%), Positives = 74/178 (41%), Gaps = 25/178 (14%)
Query: 50 DVLYCHLHSLEPPNPPSGISNDAFPL----FVTWKIGKDQRLRGCIGTFNAI-NLHGGLR 104
+ L + P FVT + K+ LRGCIGT A L +
Sbjct: 9 QAIESALANGRLP-DIEPELPPKLNEKGGCFVT--LHKNGELRGCIGTIEADRPLVEDVA 65
Query: 105 EYAVTSAFKDSRFNPITVDEFSKLHVSVSILRH-----FEDGNDY-TDWKIGVHGIRIEF 158
E A+ +AFKD RF P+T DE +L + VS+L ED + + + G G+ +
Sbjct: 66 ENAIAAAFKDPRFPPLTEDELDRLTIEVSVLSPPEPLPVEDEEELLEELRPGRDGLIL-- 123
Query: 159 HNERGNKRTATYLPEVAPEQGWDQIQTIDSLLRKGGFKGPITPDI-RCNIKLTRYQSE 215
E G +R +LP+V E D + L K G + PD + + R+ E
Sbjct: 124 --EDGGRR-GLFLPQVWEELP-DPETFLRHLCLKAG----LPPDAWKDPTTIYRFTVE 173
>gnl|CDD|232909 TIGR00296, TIGR00296, uncharacterized protein, PH0010 family.
Members of this functionally uncharacterized protein
family have been crystallized from Pyrococcus
Horikoshii, Methanosarcina Mazei, and Sulfolobus
Tokodaii [Unknown function, General].
Length = 200
Score = 106 bits (265), Expect = 2e-28
Identities = 51/162 (31%), Positives = 78/162 (48%), Gaps = 15/162 (9%)
Query: 46 FFCFDVLYCHLH---SLEPPNPPSGISNDAFPLFVTWKIGKDQRLRGCIGTFNAIN-LHG 101
+ + HL+ S + N+ +F+T K ++ LRGCIGT + L
Sbjct: 14 RYARYAIESHLNGGKSSRLYPDLPIVFNEKRGVFITLKKKGNKHLRGCIGTPEPVMPLIE 73
Query: 102 GLREYAVTSAFKDSRFNPITVDEFSKLHVSVSILRHFE-----DGNDY-TDWKIGVHGIR 155
+ E A+++A +D RF P+ ++E + V VSIL E DY D +IG HG+
Sbjct: 74 AIEEAAISAATEDPRFPPVQLEELDDIKVEVSILTPPETIFVGGPKDYPFDIEIGRHGLI 133
Query: 156 IEFHNERGNKRTATYLPEVAPEQGWDQIQTIDSLLRKGGFKG 197
+EF +RG LP+VA E GWD + + +L K G
Sbjct: 134 VEFGPKRG-----LLLPQVAVEYGWDAEEFLANLCMKAGLPP 170
>gnl|CDD|234839 PRK00801, PRK00801, hypothetical protein; Provisional.
Length = 201
Score = 58.1 bits (141), Expect = 1e-10
Identities = 38/132 (28%), Positives = 66/132 (50%), Gaps = 13/132 (9%)
Query: 59 LEPPNPPSGISNDAFPLFVTWKIGKDQRLRGCIGTFNAIN-LHGGLREYAVTSAFKDSRF 117
+EPP + + +FVT + K LRGCIG + L + + A+++A +D RF
Sbjct: 30 IEPPKDLPPVFWEKRGVFVT--LNKHGVLRGCIGFPYPDSPLVEAIIDSAISAATRDPRF 87
Query: 118 NPITVDEFSKLHVSVSILRHFE--DGNDYT---DWKIGVHGIRIEFHNERGNKRTATYLP 172
P+ ++E ++ V V++L E +G ++G HG+ ++ G LP
Sbjct: 88 PPVKLEEMDEITVEVTVLTPPELIEGPPEELPEKIEVGRHGLIVKKGIYSG-----LLLP 142
Query: 173 EVAPEQGWDQIQ 184
+VAPE G+D +
Sbjct: 143 QVAPEWGFDSEE 154
>gnl|CDD|235170 PRK03881, PRK03881, hypothetical protein; Provisional.
Length = 467
Score = 54.1 bits (131), Expect = 1e-08
Identities = 27/77 (35%), Positives = 38/77 (49%), Gaps = 4/77 (5%)
Query: 61 PPNPPSGISNDAFPLFVTWKIGKDQRLRGCIGTF--NAINLHGGLREYAVTSAFKDSRFN 118
P P + N +FV+ K KD LRGCIGT N+ + A+++ +D RF
Sbjct: 323 PDYLPEEMLNRRAGVFVSLK--KDGELRGCIGTIFPTRENIAEEIIRNAISAGTEDPRFP 380
Query: 119 PITVDEFSKLHVSVSIL 135
P+ DE L SV +L
Sbjct: 381 PVEEDELDDLVYSVDVL 397
>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR). This
family consists of several bovine specific leukaemia
virus receptors which are thought to function as
transmembrane proteins, although their exact function is
unknown.
Length = 561
Score = 33.1 bits (75), Expect = 0.099
Identities = 33/112 (29%), Positives = 45/112 (40%), Gaps = 31/112 (27%)
Query: 61 PPNPPSGISNDAFPLFVTWKIGKDQRLRGCIGTFNAIN------------LHGGLREYAV 108
P P G+SN+A +F I Q+L+G + +F A N LH Y +
Sbjct: 399 PFQLPPGVSNEAQFVFTIQSIVMAQKLKGTL-SFIAKNDEGSTHEKLDFKLHFTCTSYLI 457
Query: 109 TSAFKDSRFNPITVDEFSKLHVSVSILRHFEDGNDYTDWKIGVHGIRIEFHN 160
T+ P D F+KL E G D + I V GI + FHN
Sbjct: 458 TT--------PCYSDAFAKL---------LESG-DLSMSSIKVDGIDMSFHN 491
>gnl|CDD|183276 PRK11688, PRK11688, hypothetical protein; Provisional.
Length = 154
Score = 32.1 bits (74), Expect = 0.10
Identities = 30/110 (27%), Positives = 40/110 (36%), Gaps = 52/110 (47%)
Query: 99 LHGGLREYAVTSAFKDS------------RFNPITVDE----FSK-----LHV------- 130
LHGG V ++ D R I+ +E S+ L V
Sbjct: 58 LHGG-----VIASVLDVAGGLVCVGGILARHEDISEEELRQRLSRLGTIDLRVDYLRPGR 112
Query: 131 ------SVSILRHFEDGNDYTDWKIGVHGIRIEFHNERGN---KRTATYL 171
+ S+LR GN K+ V R+E HNE+G TATYL
Sbjct: 113 GERFTATSSVLRA---GN-----KVAV--ARMELHNEQGVHIASGTATYL 152
>gnl|CDD|173850 cd01161, VLCAD, Very long chain acyl-CoA dehydrogenase. VLCAD is
an acyl-CoA dehydrogenase (ACAD), which is found in the
mitochondria of eukaryotes and in some bacteria. It
catalyzes the alpha,beta dehydrogenation of the
corresponding trans-enoyl-CoA by FAD, which becomes
reduced. The reduced form of ACAD is reoxidized in the
oxidative half-reaction by electron-transferring
flavoprotein (ETF), from which the electrons are
transferred to the mitochondrial respiratory chain
coupled with ATP synthesis. VLCAD acts as a homodimer.
Length = 409
Score = 30.5 bits (69), Expect = 0.68
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 96 AINLHGGL---REYAVTSAFKDSRFNPI--TVDEFSKLHVSVSILRH 137
AI +HGG+ REY V +D R I +E +L ++++ L+H
Sbjct: 361 AIQIHGGMGFMREYGVERVLRDLRIFRIFEGTNEILRLFIALTGLQH 407
>gnl|CDD|173849 cd01160, LCAD, Long chain acyl-CoA dehydrogenase. LCAD is an
acyl-CoA dehydrogenases (ACAD), which is found in the
mitochondria of eukaryotes and in some prokaryotes. It
catalyzes the alpha, beta dehydrogenation of the
corresponding trans-enoyl-CoA by FAD, which becomes
reduced. The reduced form of LCAD is reoxidized in the
oxidative half-reaction by electron-transferring
flavoprotein (ETF), from which the electrons are
transferred to the mitochondrial respiratory chain
coupled with ATP synthesis. LCAD acts as a homodimer.
Length = 372
Score = 30.2 bits (68), Expect = 0.84
Identities = 12/28 (42%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 96 AINLHGG---LREYAVTSAFKDSRFNPI 120
+ LHGG +REY + A++D+R PI
Sbjct: 328 CVQLHGGWGYMREYPIARAYRDARVQPI 355
>gnl|CDD|233680 TIGR02001, gcw_chp, conserved hypothetical protein,
proteobacterial. This model represents a conserved
hypothetical protein about 240 residues in length found
so far in Proteobacteria including Shewanella
oneidensis, Ralstonia solanacearum, and Colwellia
psychrerythraea, usually as part of a paralogous family.
The function is unknown.
Length = 243
Score = 29.3 bits (66), Expect = 1.3
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 128 LHVSVSILRHFEDGNDYTDWKIGV 151
LHV S + Y+DW +G+
Sbjct: 177 LHVGYSDGDADGAVDSYSDWSVGL 200
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 29.9 bits (68), Expect = 1.3
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 7/40 (17%)
Query: 116 RFNPITVDEFSKLHVSVSILR----HFED--GNDYTDWKI 149
RF + VDE S + +++ILR +E G TD +
Sbjct: 324 RFQKVLVDEPS-VEDTIAILRGLKERYEAHHGVRITDEAL 362
>gnl|CDD|133382 cd01107, HTH_BmrR, Helix-Turn-Helix DNA binding domain of the BmrR
transcription regulator. Helix-turn-helix (HTH)
multidrug-efflux transporter transcription regulator,
BmrR and YdfL of Bacillus subtilis, and related
proteins; N-terminal domain. Bmr is a membrane protein
which causes the efflux of a variety of toxic substances
and antibiotics. BmrR is comprised of two distinct
domains that harbor a regulatory (effector-binding) site
and an active (DNA-binding) site. The conserved
N-terminal domain contains a winged HTH motif that
mediates DNA binding, while the C-terminal domain binds
coactivating, toxic compounds. BmrR shares the
N-terminal DNA binding domain with other transcription
regulators of the MerR superfamily that promote
transcription by reconfiguring the spacer between the
-35 and -10 promoter elements.
Length = 108
Score = 27.5 bits (62), Expect = 2.6
Identities = 8/22 (36%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 120 ITVDEFSKL-HVSVSILRHFED 140
T+ EF+KL ++S+ LR+++
Sbjct: 1 FTIGEFAKLSNLSIKALRYYDK 22
>gnl|CDD|143498 cd06825, PLPDE_III_VanT, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, VanT and similar proteins.
This subfamily is composed of Enterococcus gallinarum
VanT and similar proteins. VanT is a membrane-bound
serine racemase (EC 5.1.1.18) that is essential for
vancomycin resistance in Enterococcus gallinarum. It
converts L-serine into its D-enantiomer (D-serine) for
peptidoglycan synthesis. The C-terminal region of this
protein contains a PLP-binding TIM-barrel domain
followed by beta-sandwich domain, which is homologous to
the fold type III PLP-dependent enzyme, bacterial
alanine racemase (AR). AR exists as homodimers with
active sites that lie at the interface between the TIM
barrel domain of one subunit and the beta-sandwich
domain of the other subunit. On the basis of this
similarity, it has been suggested that dimer formation
of VanT is required for its catalytic activity, and that
it catalyzes the racemization of serine in a
mechanistically similar manner to that of alanine by
bacterial AR. Some biochemical evidence indicates that
VanT also exhibits alanine racemase activity and plays a
role in the racemization of L-alanine. VanT contains a
unique N-terminal transmembrane domain, which may
function as an L-serine transporter. VanT serine
racemases are not related to eukaryotic serine
racemases, which are fold type II PLP-dependent enzymes.
Length = 368
Score = 27.7 bits (62), Expect = 5.2
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 10/48 (20%)
Query: 190 LRKGGFKGPI-----TPDIRCNIKLTRY---QSELVSVSYQDYLNHWK 229
LR+ G KG I TP +R +L +Y Q+ L+S +Y + L+ +
Sbjct: 67 LREAGIKGEILILGYTPPVRAK-ELKKYSLTQT-LISEAYAEELSKYA 112
>gnl|CDD|220347 pfam09694, Gcw_chp, Bacterial protein of unknown function
(Gcw_chp). This entry represents a conserved
hypothetical protein about 240 residues in length found
so far in Proteobacteria including Shewanella oneidensis
and Ralstonia solanacearum, usually as part of a
paralogous family. The function is unknown.
Length = 226
Score = 27.4 bits (61), Expect = 6.0
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 128 LHVSVSILRHFEDGNDYTDWKIGV 151
HV +R+ YTDWKIG+
Sbjct: 157 AHVGYQDVRNGFTAYSYTDWKIGL 180
>gnl|CDD|235821 PRK06522, PRK06522, 2-dehydropantoate 2-reductase; Reviewed.
Length = 304
Score = 27.1 bits (61), Expect = 7.6
Identities = 9/37 (24%), Positives = 13/37 (35%), Gaps = 2/37 (5%)
Query: 168 ATYLPEVAPEQGWDQIQTIDSLLRKGGFKGPITPDIR 204
+ E E + + LL G +PDIR
Sbjct: 142 RLKIGEPDGESA--AAEALADLLNAAGLDVEWSPDIR 176
>gnl|CDD|182159 PRK09946, PRK09946, hypothetical protein; Provisional.
Length = 270
Score = 27.1 bits (60), Expect = 7.6
Identities = 10/33 (30%), Positives = 13/33 (39%), Gaps = 4/33 (12%)
Query: 118 NPITVDEFSKLHVSVSI----LRHFEDGNDYTD 146
IT + + V + LRHF G Y D
Sbjct: 1 MIITRADLREWRVGAVMYRWFLRHFPRGGSYAD 33
>gnl|CDD|225389 COG2833, COG2833, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 268
Score = 27.0 bits (60), Expect = 7.8
Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 3/49 (6%)
Query: 177 EQGWDQIQTIDSLLRK---GGFKGPITPDIRCNIKLTRYQSELVSVSYQ 222
+G D T L+R KGP D R T+ + + + Q
Sbjct: 219 RRGLDPAATFRELVRAYFRFILKGPFNIDARAKAGFTQSEYDSIEAFEQ 267
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
0.320 0.138 0.445
Gapped
Lambda K H
0.267 0.0793 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,784,368
Number of extensions: 1087821
Number of successful extensions: 727
Number of sequences better than 10.0: 1
Number of HSP's gapped: 709
Number of HSP's successfully gapped: 23
Length of query: 233
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 139
Effective length of database: 6,768,326
Effective search space: 940797314
Effective search space used: 940797314
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: 57 (25.6 bits)