RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5108
(345 letters)
>gnl|CDD|132767 cd07306, Porin3_VDAC, Voltage-dependent anion channel of the outer
mitochondrial membrane. The voltage-dependent anion
channel (VDAC) regulates the flux of mostly anionic
metabolites through the outer mitochondrial membrane,
which is highly permeable to small molecules. VDAC is
the most abundant protein in the outer membrane, and
membrane potentials can toggle VDAC between open or
high-conducting and closed or low-conducting forms. VDAC
binds to and is regulated in part by hexokinase, an
interaction that renders mitochondria less susceptible
to pro-apoptotic signals, most likely by intefering with
VDAC's capability to respond to Bcl-2 family proteins.
While VDAC appears to play a key role in mitochondrially
induced cell death, a proposed involvement in forming
the mitochondrial permeability transition pore, which is
characteristic for damaged mitochondria and apoptosis,
has been challenged by more recent studies.
Length = 276
Score = 223 bits (570), Expect = 2e-71
Identities = 92/237 (38%), Positives = 142/237 (59%), Gaps = 6/237 (2%)
Query: 110 FNIDVIKIDLKTKTDSGVEFNSGGTAQLESGKIFGTLESKYKAKNYAGLTFSEKWNTDNV 169
+N K+D+KTKT +GVEF S G+ + ++GK+ G+LE+KYK GLT ++KWNTDNV
Sbjct: 19 YNFGAWKLDVKTKTPNGVEFTSTGSKKPDTGKVSGSLEAKYK---IKGLTLTQKWNTDNV 75
Query: 170 LTTEV--SSNIIDGARLAANTSFAPQTGDKTVKLSGEYKNSLAAVNLESEFKSLNPVISA 227
L TE+ + G +L +T+F P TG K+ KL YK+ +N + + P++ A
Sbjct: 76 LLTEITIEDLLAPGLKLTLDTTFPPNTGKKSGKLKAGYKHDPININADVDLNK-GPLVGA 134
Query: 228 AGVLGYNGWLCGYSLKFDSKDAKLKANRLSLGFVGSDFVFHTNVDDGKLFGGTVYQKLGP 287
+ VLGY G+L G + +D+ +K +LG+ DF +++GK G+ + K+ P
Sbjct: 135 SAVLGYKGFLLGAEVVYDTAKSKFTKYNFALGYTNGDFELSLKLNNGKTLRGSYFHKVSP 194
Query: 288 KLETGVQLAWSSESNDTKFAFGCKYDLENQASVRAKVNNASQIGLGYSQKLNDALSL 344
+L G ++ W S +N+T FA G +Y L+ A V+AKVNN Q+GL Y KL ++L
Sbjct: 195 RLAVGAKVTWYSGTNETTFAVGGQYALDPDALVKAKVNNDGQLGLSYQHKLRPGVTL 251
Score = 80.7 bits (200), Expect = 2e-17
Identities = 34/64 (53%), Positives = 47/64 (73%)
Query: 3 PPLYGDLGKHARDLFSKGYNIDVIKIDLKTKTDSGVEFNSGGTAQLESGKIFGTLESKYK 62
PP Y D+GK A+DL +KGYN K+D+KTKT +GVEF S G+ + ++GK+ G+LE+KYK
Sbjct: 1 PPTYFDIGKSAKDLLTKGYNFGAWKLDVKTKTPNGVEFTSTGSKKPDTGKVSGSLEAKYK 60
Query: 63 AKNY 66
K
Sbjct: 61 IKGL 64
>gnl|CDD|216515 pfam01459, Porin_3, Eukaryotic porin.
Length = 272
Score = 185 bits (472), Expect = 6e-57
Identities = 75/239 (31%), Positives = 121/239 (50%), Gaps = 7/239 (2%)
Query: 110 FNIDVIKIDLKTKTDSGVEFNSGGTAQLESGKIFGTLESKYKAKNYAGLTFSEKWNTDNV 169
++ D K+D+ TK+ GV F G+ L G G E+KYK GLT + KW+TDN
Sbjct: 20 YHFDGAKLDVTTKSPLGVAFTVSGSKSLGGGLSSGDFEAKYK---DKGLTLTLKWDTDND 76
Query: 170 LTTEVSSN--IIDGARLAANTSFAPQTGDKTVKLSGEYKNSLAAVNLESEFKSLNPVISA 227
L+T + N + G +L +T P TG K+ KL EYK +L+ P++
Sbjct: 77 LSTNATVNDQLAPGLKLKLSTQLVPGTGKKSAKLELEYKGDDFTASLKVGL-LKGPIVVG 135
Query: 228 AGVLGYNGWLCGYSLKFDSKDAKLKANRLSLGFVGSDFVFHTNV-DDGKLFGGTVYQKLG 286
+ + G G G +D+ KL +LG+ D++ + + G + + Y K+
Sbjct: 136 SALQGVTGLALGAEAVYDTASGKLTKYNAALGYAARDYIASLTLNNKGDVLTASYYHKVS 195
Query: 287 PKLETGVQLAWSSESNDTKFAFGCKYDLENQASVRAKVNNASQIGLGYSQKLNDALSLN 345
KLE G +L W+ SN+T G KYDL+ +V+AKV++ ++GL ++L ++L
Sbjct: 196 DKLEVGAELTWNFSSNETTTTVGYKYDLDPSTTVKAKVDSNGKVGLLLEKRLRPGVTLT 254
Score = 74.2 bits (183), Expect = 3e-15
Identities = 28/64 (43%), Positives = 36/64 (56%)
Query: 2 APPLYGDLGKHARDLFSKGYNIDVIKIDLKTKTDSGVEFNSGGTAQLESGKIFGTLESKY 61
P Y D+GK ARDL +K Y+ D K+D+ TK+ GV F G+ L G G E+KY
Sbjct: 1 NPGTYEDIGKEARDLLNKDYHFDGAKLDVTTKSPLGVAFTVSGSKSLGGGLSSGDFEAKY 60
Query: 62 KAKN 65
K K
Sbjct: 61 KDKG 64
>gnl|CDD|132765 cd07303, Porin3, Eukaryotic porin family that forms channels in the
mitochondrial outer membrane. The porin family 3
contains two sub-families that play vital roles in the
mitochondrial outer membrane, a translocase for unfolded
pre-proteins (Tom40) and the voltage-dependent anion
channel (VDAC) that regulates the flux of mostly anionic
metabolites through the outer mitochondrial membrane.
Length = 274
Score = 121 bits (304), Expect = 3e-32
Identities = 95/239 (39%), Positives = 139/239 (58%), Gaps = 16/239 (6%)
Query: 115 IKIDLKTKTDSGVEFNSGGTAQLESG----KIFGTLESKYKAKNYAGLTFSEKWNTDNVL 170
IK+D+KTK++ EF S G+A E+ K+ G+LE+KY+ Y GLTF+EKWNTDN L
Sbjct: 21 IKLDVKTKSEL--EFTSSGSANTETIESTTKVGGSLETKYRWSPY-GLTFTEKWNTDNTL 77
Query: 171 TTE--VSSNIIDGARLAANTSFAPQTGDKTVKLSGEYK--NSLAAVNLESEFKSLNPVIS 226
E V + G + ++SF+P TG K K+ YK N V+ + P+I
Sbjct: 78 GLEITVEDQLSRGLKSTFDSSFSPNTGKKNAKIKTGYKRINLGCDVDFDIA----GPLIR 133
Query: 227 AAGVLGYNGWLCGYSLKFDSKDAKLKAN-RLSLGFVGSDFVFHTNVDDGKLFGGTVYQKL 285
A VLGY GWL GY + F++ ++N + ++F HTNV+DG FGG++Y K+
Sbjct: 134 GALVLGYEGWLAGYQMVFETVSRVTQSNFAVGYKTDYNEFQAHTNVNDGTEFGGSIYHKV 193
Query: 286 GPKLETGVQLAWSSESNDTKFAFGCKYDLENQASVRAKVNNASQIGLGYSQKLNDALSL 344
KLE GV LA ++ +++T+F KY ++ A A VNN+S +GLGY+Q L + L
Sbjct: 194 NDKLEVGVNLAATAGNSNTRFGIAAKYQVDPDACFSASVNNSSLVGLGYTQTLKPGIKL 252
Score = 34.9 bits (80), Expect = 0.040
Identities = 62/311 (19%), Positives = 101/311 (32%), Gaps = 49/311 (15%)
Query: 6 YGDLGKHARDLFSKGYNIDVIKIDLKTKTDSGVEFNSGGTAQLESGKIFGTLESKYKAKN 65
Y +LGK ARDLF+KGY IK+D+KTK++ EF S G+A E+ + + + K
Sbjct: 2 YAELGKSARDLFTKGYG-GGIKLDVKTKSEL--EFTSSGSANTETIESTTKVGGSLETKY 58
Query: 66 YAGWLCGYSLKFDSKDAKLKANRLSLGFV-----GSDFVFHTNVSSRQIFNIDVIKIDLK 120
Y L F K L + G F ++ S + K
Sbjct: 59 R---WSPYGLTFTEKWNTDNTLGLEITVEDQLSRGLKSTFDSSFSPNTGKK------NAK 109
Query: 121 TKTDS-GVEFNSGGTAQLESGKIFGTLESKYKAKNYAGLTFSEKWNTDNVLTTEVSSNII 179
KT + + I G L Y+ +
Sbjct: 110 IKTGYKRINLGCDVDFDIAGPLIRGALVLGYE-------------------------GWL 144
Query: 180 DGARLAANTSFAPQTGDKTVKLSGEYKNSLAAVNLESEFKSLNPVISAAGVLGYNGWL-C 238
G ++ T + V +Y A N+ + I N L
Sbjct: 145 AGYQMVFETVSRVTQSNFAVGYKTDYNEFQAHTNVN-DGTEFGGSIYHK----VNDKLEV 199
Query: 239 GYSLKFDSKDAKLKANRLSLGFVGSDFVFHTNVDDGKLFGGTVYQKLGPKLETGVQLAWS 298
G +L + ++ + + V D F +V++ L G Q L P ++ +
Sbjct: 200 GVNLAATAGNSNTRFGIAAKYQVDPDACFSASVNNSSLVGLGYTQTLKPGIKLTLSALLD 259
Query: 299 SESNDTKFAFG 309
++ K G
Sbjct: 260 HKAGGHKLGLG 270
>gnl|CDD|132766 cd07305, Porin3_Tom40, Translocase of outer mitochondrial membrane
40 (Tom40). Tom40 forms a channel in the mitochondrial
outer membrane with a pore about 1.5 to 2.5 nanometers
wide. It functions as a transport channel for unfolded
protein chains and forms a complex with Tom5, Tom6,
Tom7, and Tom22. The primary receptors Tom20 and Tom70
recruit the unfolded precursor protein from the
mitochondrial-import stimulating factor (MSF) or
cytosolic Hsc70. The precursor passes through the Tom40
channel and through another channel in the inner
membrane, formed by Tim23, to be finally translocated
into the mitochondrial matrix. The process depends on a
proton motive force across the inner membrane and
requires a contact site where the outer and inner
membranes come close. Tom40 is also involved in
inserting outer membrane proteins into the membrane,
most likely not via a lateral opening in the pore, but
by transfering precursor proteins to an outer membrane
sorting and assembly machinery.
Length = 279
Score = 42.6 bits (101), Expect = 1e-04
Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 282 YQKLGPKLETGVQLAWSSESNDTKFAFGCKYDLENQASVRAKVNNASQIGLGYSQKLNDA 341
Y+KL KL+ GV+L + + ++ G +YD Q+ R +++ ++ ++L
Sbjct: 196 YRKLSDKLQLGVELELNLRTRESTATLGYQYDFR-QSRFRGSIDSNGKVSAVLEKRLPLP 254
Query: 342 LSLN 345
LSL
Sbjct: 255 LSLL 258
Score = 31.4 bits (72), Expect = 0.62
Identities = 28/122 (22%), Positives = 49/122 (40%), Gaps = 13/122 (10%)
Query: 234 NGWLCGYSLKFDS--KDAKLKANRLSLGFVGSDFVFH---TNVDDGKLFG---GTVYQKL 285
+ K + +D+K ++L L + G DF N D G + Q +
Sbjct: 86 HQLGDRLRSKLQAQLQDSKFNMSQLELDYRGDDFTASLKLANPDILNETGIYVASYLQSV 145
Query: 286 GPKLETGVQLAW--SSESNDTKFAFGCKYDLEN-QASVRAKVNNASQIGLGYSQKLNDAL 342
PKL G +L + + + ++ +Y N AS ++ + L Y +KL+D L
Sbjct: 146 TPKLALGGELVYQRVPGNGISVLSYAARYTAGNWIAS--GQLGAQGGLHLSYYRKLSDKL 203
Query: 343 SL 344
L
Sbjct: 204 QL 205
>gnl|CDD|151771 pfam11330, DUF3132, Protein of unknown function (DUF3132). This
viral family of proteins are 55kDa. No function is
currently known.
Length = 124
Score = 28.8 bits (64), Expect = 1.6
Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 7/82 (8%)
Query: 120 KTKTDSGVEFNSGGTAQLESGKI---FGTLESKYKAKNYAGLTFSEKWNTDNVLTTEV-- 174
K T + VE N GG AQLE + F T +K+ K+ FS++ DN+L+ +
Sbjct: 9 KNITPTSVERNFGGVAQLEVERAKLSFETFGNKFLLKDV--FMFSDQSLGDNILSYTLLK 66
Query: 175 SSNIIDGARLAANTSFAPQTGD 196
IDG R A + + G+
Sbjct: 67 EEGHIDGMRTAGDDVLLEKDGE 88
>gnl|CDD|234283 TIGR03623, TIGR03623, probable DNA repair protein. Members of this
protein family are bacterial proteins of about 900 amino
acids in length. Members show extended homology to
proteins in TIGR02786, the AddB protein of double-strand
break repair via homologous recombination. Members of
this family, therefore, may be DNA repair proteins.
Length = 874
Score = 29.6 bits (67), Expect = 2.5
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 183 RLAANTSFAPQTGDKTVKLSG 203
+LAA T F P+T + +++ G
Sbjct: 443 QLAAETLFQPETPEAPIQVLG 463
>gnl|CDD|114111 pfam05369, MtmB, Monomethylamine methyltransferase MtmB.
Monomethylamine methyltransferase of the archaebacterium
Methanosarcina barkeri contains a novel amino acid,
pyrrolysine, encoded by the termination codon UAG. The
structure reveals a homohexamer comprised of individual
subunits with a TIM barrel fold.
Length = 457
Score = 29.3 bits (65), Expect = 3.6
Identities = 22/57 (38%), Positives = 27/57 (47%), Gaps = 5/57 (8%)
Query: 131 SGGTAQLESGKIFGTLESKYKAKNYA----GLTFSEKWNTDNVLTTEVSSNIIDGAR 183
+ G E KI L S Y+ KNYA G TF E ++ V TE + DGAR
Sbjct: 392 TAGVEISEVNKILDKLVSLYE-KNYASAPAGKTFQECYDVKTVTPTEEYMQVYDGAR 447
>gnl|CDD|129353 TIGR00251, TIGR00251, TIGR00251 family protein. [Hypothetical
proteins, Conserved].
Length = 87
Score = 27.1 bits (60), Expect = 4.5
Identities = 16/56 (28%), Positives = 25/56 (44%)
Query: 221 LNPVISAAGVLGYNGWLCGYSLKFDSKDAKLKANRLSLGFVGSDFVFHTNVDDGKL 276
+ P S ++GYN W +K + + KANR + F G F + G+L
Sbjct: 14 VQPKASKDSIVGYNEWRKRVEVKIKAPPVEGKANRELIKFFGEIFGVDVEIVSGEL 69
>gnl|CDD|235982 PRK07259, PRK07259, dihydroorotate dehydrogenase 1B; Reviewed.
Length = 301
Score = 28.6 bits (65), Expect = 4.6
Identities = 8/24 (33%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 217 EFKSLNPVISAAGVLGYNGWLCGY 240
+ K NPV+ A+G G+ G +
Sbjct: 10 KLK--NPVMPASGTFGFGGEYARF 31
>gnl|CDD|218886 pfam06082, DUF940, Bacterial putative lipoprotein (DUF940). This
family consists of hypothetical bacterial proteins
several of which are described as putative lipoproteins.
Length = 661
Score = 28.1 bits (63), Expect = 7.8
Identities = 22/84 (26%), Positives = 29/84 (34%), Gaps = 25/84 (29%)
Query: 273 DGKLFGGTVYQ----KLGPKLETGVQLAWSSESND-------------TKFAFGCKYDLE 315
D LFGG YQ L K E + ND + F FG Y L
Sbjct: 164 DAALFGGVEYQTPWEPLRLKAEY--------DGNDYSAEFAGRGLEQDSPFNFGAVYRLT 215
Query: 316 NQASVRAKVNNASQIGLGYSQKLN 339
+ A + + +G G S + N
Sbjct: 216 DGADLSLSYERGNTLGFGISLRTN 239
>gnl|CDD|216360 pfam01202, SKI, Shikimate kinase.
Length = 158
Score = 27.2 bits (61), Expect = 9.6
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 82 AKLKANRLSLGFVGSDFVF--HTNVSSRQIFNID 113
+L A L L F+ +D T +S +IF +
Sbjct: 9 GRLLAKALGLPFIDTDQEIEKRTGMSIAEIFEEE 42
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
0.313 0.132 0.378
Gapped
Lambda K H
0.267 0.0547 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,617,096
Number of extensions: 1518774
Number of successful extensions: 846
Number of sequences better than 10.0: 1
Number of HSP's gapped: 831
Number of HSP's successfully gapped: 25
Length of query: 345
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 247
Effective length of database: 6,590,910
Effective search space: 1627954770
Effective search space used: 1627954770
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: 59 (26.9 bits)