RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5109
(145 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 = 136 bits (344), Expect = 2e-40
Identities = 65/145 (44%), Positives = 93/145 (64%), Gaps = 6/145 (4%)
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 AKNYAGLTFSEKWNTDNVLTTEV--SSNIIDGARLAANTSFAPQTGDKTVKLSGEYKNSL 120
GLT ++KWNTDNVL TE+ + G +L +T+F P TG K+ KL YK+
Sbjct: 61 ---IKGLTLTQKWNTDNVLLTEITIEDLLAPGLKLTLDTTFPPNTGKKSGKLKAGYKHDP 117
Query: 121 AAVNLESEFKSLNPVISAAGVLGYN 145
+N + + P++ A+ VLGY
Sbjct: 118 ININADVDLNK-GPLVGASAVLGYK 141
>gnl|CDD|216515 pfam01459, Porin_3, Eukaryotic porin.
Length = 272
Score = 115 bits (289), Expect = 2e-32
Identities = 53/146 (36%), Positives = 75/146 (51%), Gaps = 6/146 (4%)
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 KAKNYAGLTFSEKWNTDNVLTTEVSSN--IIDGARLAANTSFAPQTGDKTVKLSGEYKNS 119
K GLT + KW+TDN L+T + N + G +L +T P TG K+ KL EYK
Sbjct: 61 K---DKGLTLTLKWDTDNDLSTNATVNDQLAPGLKLKLSTQLVPGTGKKSAKLELEYKGD 117
Query: 120 LAAVNLESEFKSLNPVISAAGVLGYN 145
+L+ P++ + + G
Sbjct: 118 DFTASLKVGL-LKGPIVVGSALQGVT 142
>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 = 59.6 bits (144), Expect = 2e-11
Identities = 64/147 (43%), Positives = 86/147 (58%), Gaps = 16/147 (10%)
Query: 6 YGDLGKHARDLFSKGYNIDVIKIDLKTKTDSGVEFNSGGTAQLESG----KIFGTLESKY 61
Y +LGK ARDLF+KGY IK+D+KTK++ EF S G+A E+ K+ G+LE+KY
Sbjct: 2 YAELGKSARDLFTKGYG-GGIKLDVKTKSEL--EFTSSGSANTETIESTTKVGGSLETKY 58
Query: 62 KAKNYAGLTFSEKWNTDNVLTTE--VSSNIIDGARLAANTSFAPQTGDKTVKLSGEYK-- 117
+ Y GLTF+EKWNTDN L E V + G + ++SF+P TG K K+ YK
Sbjct: 59 RWSPY-GLTFTEKWNTDNTLGLEITVEDQLSRGLKSTFDSSFSPNTGKKNAKIKTGYKRI 117
Query: 118 NSLAAVNLESEFKSLNPVISAAGVLGY 144
N V+ + P+I A VLGY
Sbjct: 118 NLGCDVDFDIA----GPLIRGALVLGY 140
>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 = 29.2 bits (65), Expect = 0.38
Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 7/82 (8%)
Query: 31 KTKTDSGVEFNSGGTAQLESGKI---FGTLESKYKAKNYAGLTFSEKWNTDNVLTTEV-- 85
K T + VE N GG AQLE + F T +K+ K+ FS++ DN+L+ +
Sbjct: 9 KNITPTSVERNFGGVAQLEVERAKLSFETFGNKFLLKDV--FMFSDQSLGDNILSYTLLK 66
Query: 86 SSNIIDGARLAANTSFAPQTGD 107
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 = 30.0 bits (68), Expect = 0.45
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 94 RLAANTSFAPQTGDKTVKLSG 114
+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 = 28.5 bits (63), Expect = 1.2
Identities = 22/57 (38%), Positives = 27/57 (47%), Gaps = 5/57 (8%)
Query: 42 SGGTAQLESGKIFGTLESKYKAKNYA----GLTFSEKWNTDNVLTTEVSSNIIDGAR 94
+ G E KI L S Y+ KNYA G TF E ++ V TE + DGAR
Sbjct: 392 TAGVEISEVNKILDKLVSLYE-KNYASAPAGKTFQECYDVKTVTPTEEYMQVYDGAR 447
>gnl|CDD|239124 cd02659, peptidase_C19C, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin
molecules from polyubiquinated peptides by cleavage of
isopeptide bonds. They hydrolyze bonds involving the
carboxyl group of the C-terminal Gly residue of
ubiquitin. The purpose of the de-ubiquitination is
thought to be editing of the ubiquitin conjugates,
which could rescue them from degradation, as well as
recycling of the ubiquitin. The ubiquitin/proteasome
system is responsible for most protein turnover in the
mammalian cell, and with over 50 members, family C19 is
one of the largest families of peptidases in the human
genome.
Length = 334
Score = 28.0 bits (63), Expect = 1.7
Identities = 10/52 (19%), Positives = 15/52 (28%), Gaps = 1/52 (1%)
Query: 30 LKTKTDSGVEFNSGGTAQLESGKIFG-TLESKYKAKNYAGLTFSEKWNTDNV 80
+ N L+ +F ES K T S W++ N
Sbjct: 32 YSIPPTEDDDDNKSVPLALQRLFLFLQLSESPVKTTELTDKTRSFGWDSLNT 83
>gnl|CDD|185085 PRK15131, PRK15131, mannose-6-phosphate isomerase; Provisional.
Length = 389
Score = 26.5 bits (59), Expect = 5.5
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 76 NTDNVLTTEVSSNIIDGARLAANTSFAPQTGDK 108
N+DNVL ++ ID L AN F + ++
Sbjct: 268 NSDNVLRAGLTPKYIDIPELVANVKFEAKPANQ 300
>gnl|CDD|235982 PRK07259, PRK07259, dihydroorotate dehydrogenase 1B; Reviewed.
Length = 301
Score = 26.3 bits (59), Expect = 6.6
Identities = 7/18 (38%), Positives = 11/18 (61%), Gaps = 2/18 (11%)
Query: 128 EFKSLNPVISAAGVLGYN 145
+ K NPV+ A+G G+
Sbjct: 10 KLK--NPVMPASGTFGFG 25
>gnl|CDD|234432 TIGR03991, alt_bact_glmU, UDP-N-acetylglucosamine
diphosphorylase/glucosamine-1-phosphate
N-acetyltransferase. The MJ_1101 protein from
Methanococcus jannaschii has been characterized as the
GlmU enzyme catalyzing the final two steps of UDP-GlcNAc
biosynthesis. Homologs of this enzyme are identified in
a number of bacterial organisms and modeled here. A
number of these are observed in proximity to the GlmS
and GlmM genes, and phylogenetic profiling by PPP
identifies the LEPBI_I0518 gene in Leptospira biflexa as
a likely Glm-system candidate. Multiple sequence
alignments of these bacterial homologs with their
archaeal counterparts reveals significant structural
differences, necessitating the construction of separate
models.
Length = 337
Score = 26.1 bits (58), Expect = 7.8
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 5/35 (14%)
Query: 86 SSNIIDGARLAANTSFAPQTGDKTVKLSGEYKNSL 120
+ + GAR+ TS P T K+ GE +NS+
Sbjct: 168 GARVKAGARIYGGTSIGP-----TCKIGGEVENSI 197
>gnl|CDD|185131 PRK15209, PRK15209, long polar fimbrial protein LpfA; Provisional.
Length = 174
Score = 25.7 bits (56), Expect = 8.1
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 95 LAANTSFAPQTGDKTVKLSGEYKNSLAAVNLESE 128
L + + FA ++GD TVK +GE ++ V+ +S+
Sbjct: 13 LTSTSVFAAESGDGTVKFTGEIVDAPCVVSTDSQ 46
>gnl|CDD|225975 COG3443, COG3443, Predicted periplasmic or secreted protein
[General function prediction only].
Length = 193
Score = 25.5 bits (56), Expect = 9.5
Identities = 15/59 (25%), Positives = 20/59 (33%), Gaps = 13/59 (22%)
Query: 14 RDLFSKGYNIDVIKIDLKTKTDSGVEFNSGGTAQLESGKIFGTLESKYKAKNYAGLTFS 72
+ + KGY DV +I + T V F G KY Y LT+
Sbjct: 71 KAYYRKGYKTDVERIGIDGDT---VTFFKNGK----------PTSGKYAYDGYKILTYK 116
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
0.310 0.129 0.357
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,990,541
Number of extensions: 581961
Number of successful extensions: 344
Number of sequences better than 10.0: 1
Number of HSP's gapped: 338
Number of HSP's successfully gapped: 19
Length of query: 145
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 57
Effective length of database: 7,034,450
Effective search space: 400963650
Effective search space used: 400963650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 54 (24.6 bits)