RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11096
(554 letters)
>gnl|CDD|216231 pfam00995, Sec1, Sec1 family.
Length = 554
Score = 393 bits (1013), Expect = e-131
Identities = 180/600 (30%), Positives = 294/600 (49%), Gaps = 118/600 (19%)
Query: 22 MKILLLDKQTTSIVSMVFTQSEILQREVYMFEKIEISTQCDYENMKHLKCIALLRPTKEN 81
K+L+LDK+TT I+S V T S++L+ V + E IE E + L I +RPT+EN
Sbjct: 1 WKVLVLDKETTKILSSVLTVSDLLEHGVTLVENIE----NKREPLPDLPAIYFIRPTEEN 56
Query: 82 IALLCKELKNPKFGSYYIYFTNIIPKADIKTLAEYDEQESVREIEELYADYLPILPHFFS 141
+ + +LKNPK+ SY+I+FTN + ++ ++ LAE D E V++++E+Y D++P+ FS
Sbjct: 57 VDRIIDDLKNPKYKSYHIFFTNSLSRSLLERLAEADVAELVKQVKEIYLDFIPLESDLFS 116
Query: 142 LNIPLCS---NGHFWDPVHLVRSSQGLIALLLSLNKNPVIRYQASSEMTKRLAEKVKETI 198
L +P D L R ++GL +LLL+L + P+IRYQ +S +RLAEK+ + +
Sbjct: 117 LELPNSFRDLYSPDGDESDLERIAEGLFSLLLTLGEIPIIRYQGNSA-AERLAEKLAQLL 175
Query: 199 IKEEKLFDMRQGD-----AVPVLLIIDRTCDPITPLLSQWTYQAMLHELLTINNNRVDLS 253
+ LFD PVLLI+DR+ D ITPLL QWTYQAM+H+LL I NNRV L
Sbjct: 176 QENLDLFDADNPSTPPSKPRPVLLILDRSIDLITPLLHQWTYQAMVHDLLGIKNNRVTLD 235
Query: 254 HVSGISPDLKQVVVSYEHDDFYSSNLFMNYGEIGQTIKLLMDDFNKRAKRHEGVCDFYSS 313
G + K+ VV E+D F+ N +++ ++ + IK + ++ + K
Sbjct: 236 -TPGNGGESKKEVVLDENDPFWVENRHLHFPDVAEKIKKELKEYKEENK----------- 283
Query: 314 NLFMNYGEIGQTIKLLMDDFNKRAKSQQKVESIQDMKAFVENYPQFKMKK---------- 363
S +K +SI D+K FVE P+F+ +K
Sbjct: 284 ------------------------NSNKKKKSISDLKEFVEKLPEFQKEKGKLSLHLNLA 319
Query: 364 -------------------------------------LLTSGKIRDVEAVRLVMLYAIRY 386
LL + K+ + +RL++LY++
Sbjct: 320 EELMKQIKERKLDKVSELEQDLATGSDADKQKKDILELLNNPKVPLEDKLRLLLLYSL-R 378
Query: 387 EHHSNNDLSGLMDILRRIGVSESLVQMPLQVLDYSNEHSKYTHHNDSFSATQDVMVKKTQ 446
+ DL L +L G+ + + + S+ +FS +D + +
Sbjct: 379 DGGKGKDLEDLRKLLLHAGIGPEALNLVKNLEQLGGLLSR--TSGSNFSDLRDKLKLLVK 436
Query: 447 RFLK-DLKGVENVYTQHEPVLKDILDDLVKGKLKDTHFPYLDPYQGRSEGS--------- 496
K KGV+NV ++++P+LK IL+DL+KGKL +PY DP + G
Sbjct: 437 EVSKSLPKGVKNVLSRYKPLLKRILEDLIKGKLDTDSYPYFDPKLANASGPQGSLRSKRP 496
Query: 497 -------RWYQDIIVFMVGGTTYEECLCVHQMNTSSGNNARAILLGATTVHNSTSFMQQV 549
+ Q IIVF+VGG TY E +++++ N + +++G+T++ N SF++++
Sbjct: 497 TAAGQGRQPPQRIIVFVVGGVTYSEARALYELSKK--TNGKRVIIGSTSILNPESFLEEL 554
>gnl|CDD|227487 COG5158, SEC1, Proteins involved in synaptic transmission and
general secretion, Sec1 family [Intracellular
trafficking and secretion].
Length = 582
Score = 230 bits (589), Expect = 2e-68
Identities = 165/594 (27%), Positives = 283/594 (47%), Gaps = 62/594 (10%)
Query: 1 MNVVRAIKQYVIKMTEQSGPG--MKILLLDKQTTSIVSMVFTQSEILQREVYMFEKIEIS 58
M+++ K ++ P K+LLLDK TTSI+S + T SE+L+ + + + IE
Sbjct: 2 MDLLELQKNKILDEIFLVQPANIWKVLLLDKDTTSILSSLITTSELLEHGITLVDLIE-- 59
Query: 59 TQCDYENMKHLKCIALLRPTKENIALLCKELKN--PKFGSYYIYFTNIIPKADIKTLAEY 116
E + L I +RPTKENI L+ ++L+ P + +Y+I F N + ++ ++ LAE
Sbjct: 60 --NKREPISDLPAIYFVRPTKENIDLILEDLEQWDPFYLNYHISFLNTVTESLLELLAES 117
Query: 117 DEQESVREIEELYADYLPILPHFFSLNIP--LCSNGHFWDPVHLVRSSQGLIALLLSLNK 174
E + + E+Y D+ + FSLN+P + L++ GL +L +SL +
Sbjct: 118 GVFEKILSVYEIYLDFFVLESDLFSLNLPESFLESSLPSTTEALIKIVNGLFSLCVSLGR 177
Query: 175 NPVIRYQASSEMTKRLAEKVKETIIKEEKL-FDMRQGDAV--PVLLIIDRTCDPITPLLS 231
P+IRY + + +A+K+ + I E + FD P+L+I+DR+ DPITPLL
Sbjct: 178 IPIIRYS-GGKNAEHMAKKLSDEIRNELSINFDGVVSKNPLRPILIILDRSLDPITPLLH 236
Query: 232 QWTYQAMLHELLTINNNRVDLSHVSGISPDLKQVVVSYEHDDFYSSNLFMNYGEIGQTIK 291
QWTYQAMLH+LL INNN V + S P K+ +S + D F++ N F+N+GE+G+ +K
Sbjct: 237 QWTYQAMLHDLLGINNNIVTIPSSSVNGP-EKKFSLSDKDDPFWNDNKFLNFGEVGEKLK 295
Query: 292 LLMDDFNKRAKRHEGVCDFYSSNLFMNYGEIGQTIKLLMDDFNKRAKSQQKVESIQD--M 349
K AK + + +I + + L + KR++S K ++ +
Sbjct: 296 -------KLAKELKTKAQLRHKENAKSVNDIKEFVDKL-PELQKRSRSLNKHLTLASELL 347
Query: 350 KAFVENYPQ--FKMKKLLTSGK---------IRDVEA-------VRLVMLYAIRYEHHSN 391
K E Y ++++ L++G I +E+ +RL++LY++ +
Sbjct: 348 KVVEERYLDDFSEIEQNLSTGNDVKSDISDLIELLESGVEEDDKLRLLILYSLTKD--GL 405
Query: 392 NDLSGLMDILRRIGVS---ESLVQMPLQVLDYSNEHSKYT--HHNDSFSATQDVMVKKTQ 446
+ +LR G + Q ++ + + SK D S Q
Sbjct: 406 IKDIDELRLLRIQGYGIEALNFFQRLKELGFLTLKDSKTISLKRGDKDSLFQWFNTYSLS 465
Query: 447 RFLKDLKGVENVYTQHEPVLKDILDDLVKGKLKDTHFPYLDPYQGRSEGSRW-------- 498
R + + +ENVY+ P+ KDI DL+ +L + R +
Sbjct: 466 REHQGVPDLENVYSGLIPLKKDIPIDLLVRRLFEPLKSSQQ-QSLRLSRPKGRSRSNKKI 524
Query: 499 -YQDIIVFMVGGTTYEECLCVHQMNTSSGNNARAILLGATTVHNSTSFMQQVRS 551
Q I+VF++GG TYEE ++++N S + I+ G+T + F+ +V+
Sbjct: 525 PQQRILVFVIGGVTYEELRVLYELNESQNS--VRIIYGSTEILTPAEFLDEVKR 576
>gnl|CDD|224567 COG1653, UgpB, ABC-type sugar transport system, periplasmic
component [Carbohydrate transport and metabolism].
Length = 433
Score = 33.4 bits (76), Expect = 0.27
Identities = 14/79 (17%), Positives = 24/79 (30%), Gaps = 1/79 (1%)
Query: 437 TQDVMVKKTQRFLKDLKGV-ENVYTQHEPVLKDILDDLVKGKLKDTHFPYLDPYQGRSEG 495
Q ++ K L K ++ Y + P L L + + + L +
Sbjct: 339 AQAELLAKVTGGLPVRKSAYDDPYDKEAPALLKALAEALATAVPAPPIAGLPVFNPIELA 398
Query: 496 SRWYQDIIVFMVGGTTYEE 514
Y I + G EE
Sbjct: 399 DITYDAIEAILTGQKDPEE 417
>gnl|CDD|240430 PTZ00473, PTZ00473, Plasmodium Vir superfamily; Provisional.
Length = 420
Score = 32.9 bits (75), Expect = 0.43
Identities = 30/142 (21%), Positives = 52/142 (36%), Gaps = 25/142 (17%)
Query: 228 PLLSQWTYQAMLHELLTINNNRVD-----LSHVSGISPDLKQVVV---SYEHDDFYSSNL 279
P L+ W +L I N + +S VS + K+ + S + +L
Sbjct: 19 PFLANW-PDYHFEDLRGIYNATYESICEEISSVSDYNKVNKENCIKFFSILENIVRRGDL 77
Query: 280 FMNYGEIGQTIKLLMDDFNKRAKRHEGVCDFYSSNL--FMNYGEIGQTI-KLLMDDFNKR 336
N + DF + + D +S++L F I K ++ +FNK
Sbjct: 78 KKNDD--------IWKDFVEWFYNKQEKFDVFSNHLESFNYD--FEYLIQKNILKNFNKF 127
Query: 337 AK---SQQKVESIQDMKAFVEN 355
K + ++E I + F EN
Sbjct: 128 KKLYENNYELEDIMKLFYFTEN 149
>gnl|CDD|176462 cd01357, Aspartase, Aspartase. This subgroup contains Escherichia
coli aspartase (L-aspartate ammonia-lyase), Bacillus
aspartase and related proteins. It is a member of the
Lyase class I family, which includes both aspartase
(L-aspartate ammonia-lyase) and fumarase class II
enzymes. Members of this family for the most part
catalyze similar beta-elimination reactions in which a
C-N or C-O bond is cleaved with the release of fumarate
as one of the products. These proteins are active as
tetramers. The four active sites of the homotetrameric
enzyme are each formed by residues from three different
subunits. Aspartase catalyzes the reversible deamination
of aspartic acid.
Length = 450
Score = 30.6 bits (70), Expect = 2.6
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 9/53 (16%)
Query: 157 HLVRSSQGLIALLLSLNKNPVIRYQASSEMTKRLAE---KVKETIIKEEKLFD 206
V +S G++ L NP I Y+A++E+ K E V+E ++ EE L
Sbjct: 395 EYVENSIGIVTAL-----NPYIGYEAAAEIAKEALETGRSVRE-LVLEEGLLT 441
>gnl|CDD|233990 TIGR02740, TraF-like, TraF-like protein. This protein is related
to the F-type conjugation system pilus assembly proteins
TraF (TIGR02739)and TrbB (TIGR02738) both of which
exhibit a thioredoxin fold. The protein represented by
this model has the same length and architecture as TraF,
but lacks the CXXC-motif found in TrbB and believed to
be responsible for the disulfide isomerase activity of
that protein.
Length = 271
Score = 29.7 bits (67), Expect = 3.9
Identities = 10/30 (33%), Positives = 14/30 (46%)
Query: 53 EKIEISTQCDYENMKHLKCIALLRPTKENI 82
E S EN+ L+ A+ PT EN+
Sbjct: 73 ELAPFSVAWLRENLPELRDKAIDNPTPENV 102
>gnl|CDD|223351 COG0274, DeoC, Deoxyribose-phosphate aldolase [Nucleotide transport
and metabolism].
Length = 228
Score = 29.1 bits (66), Expect = 4.7
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 63 YENMKHLKCI--ALLRP--TKENIALLCKELKNPKFGSYYIY 100
M+ K I LL+P T+E+IA LC E K F + +
Sbjct: 3 ASRMQLAKLIDHTLLKPDATEEDIARLCAEAKEYGFAAVCVN 44
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 29.5 bits (67), Expect = 5.3
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 14/52 (26%)
Query: 416 QVLDYSNEHSKYTH--------------HNDSFSATQDVMVKKTQRFLKDLK 453
QV D + E +K+TH H + FS QD++V R L+ +K
Sbjct: 88 QVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIK 139
>gnl|CDD|237031 PRK12273, aspA, aspartate ammonia-lyase; Provisional.
Length = 472
Score = 29.3 bits (67), Expect = 6.1
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 9/59 (15%)
Query: 158 LVRSSQGLIALLLSLNKNPVIRYQASSEMTKRLAE---KVKETIIKEEKLFDMRQGDAV 213
V +S G++ L NP I Y+ ++E+ K E V+E ++ E L + D +
Sbjct: 403 YVENSIGIVTAL-----NPYIGYENAAEIAKEALETGKSVRE-LVLERGLLTEEELDDI 455
>gnl|CDD|173885 cd08520, PBP2_NikA_DppA_OppA_like_21, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 468
Score = 29.2 bits (66), Expect = 7.0
Identities = 14/28 (50%), Positives = 19/28 (67%), Gaps = 3/28 (10%)
Query: 113 LAEYDE---QESVREIEELYADYLPILP 137
L E D +E V EI+ELYA+ LP++P
Sbjct: 424 LQEMDPEKRKELVFEIQELYAEELPMIP 451
>gnl|CDD|236203 PRK08255, PRK08255, salicylyl-CoA 5-hydroxylase; Reviewed.
Length = 765
Score = 28.8 bits (65), Expect = 8.6
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 113 LAEYDEQESVREIEELYADYL 133
L E ++ES+ E+L+ADYL
Sbjct: 214 LDEMSQEESIAFCEKLFADYL 234
>gnl|CDD|237798 PRK14714, PRK14714, DNA polymerase II large subunit; Provisional.
Length = 1337
Score = 28.9 bits (65), Expect = 9.6
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 62 DYENMKHLKCIALLRPTKENIALLCKELKNPKFGSYYIYFTNIIPKADIKTLAE 115
D + ++ + L RPT E A E P YY Y + I ++ LA+
Sbjct: 459 DVQALEDKPFVDLTRPTVEEAAHWATEYGAP-LHPYYTYLWHDISVEQVRALAD 511
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 0.135 0.390
Gapped
Lambda K H
0.267 0.0715 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,049,942
Number of extensions: 2761020
Number of successful extensions: 2542
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2520
Number of HSP's successfully gapped: 32
Length of query: 554
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 452
Effective length of database: 6,413,494
Effective search space: 2898899288
Effective search space used: 2898899288
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: 62 (27.7 bits)