RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12536
(205 letters)
>gnl|CDD|233335 TIGR01271, CFTR_protein, cystic fibrosis transmembrane conductor
regulator (CFTR). The model describes the cystis
fibrosis transmembrane conductor regulator (CFTR) in
eukaryotes. The principal role of this protein is
chloride ion conductance. The protein is predicted to
consist of 12 transmembrane domains. Mutations or
lesions in the genetic loci have been linked to the
aetiology of asthma, bronchiectasis, chronic obstructive
pulmonary disease etc. Disease-causing mutations have
been studied by 36Cl efflux assays in vitro cell
cultures and electrophysiology, all of which point to
the impairment of chloride channel stability and not the
biosynthetic processing per se [Transport and binding
proteins, Anions].
Length = 1490
Score = 91.9 bits (228), Expect = 1e-21
Identities = 57/177 (32%), Positives = 87/177 (49%), Gaps = 27/177 (15%)
Query: 12 LVALIVVDLLIDHQYDLAVQALGMELRVAGCSLIYRKALRLSKTALGDTTVGQVVNLLSN 71
L L +V L+ H + LGM++R+A SLIY+K L+LS L + GQ+V+LLSN
Sbjct: 128 LCLLFIVRTLLLHPAIFGLHHLGMQMRIALFSLIYKKTLKLSSRVLDKISTGQLVSLLSN 187
Query: 72 DVNRFDTA-------------CIFLHHLINRL--------------LGAKKMYLGKKTSE 104
++N+FD I L LI L L + LG+K
Sbjct: 188 NLNKFDEGLALAHFVWIAPLQVILLMGLIWELLEVNGFCGLGFLILLALFQACLGQKMMP 247
Query: 105 LRLKTALRTDERVRLMNEIISGIQVIKMYAWERSFASMVRNARKKEIQQIRGSTYIK 161
R K A + ER+ + +EII IQ +K Y WE + +++N R+ E++ R Y++
Sbjct: 248 YRDKRAGKISERLAITSEIIENIQSVKAYCWEEAMEKIIKNIRQDELKLTRKIAYLR 304
>gnl|CDD|188098 TIGR00957, MRP_assoc_pro, multi drug resistance-associated protein
(MRP). This model describes multi drug
resistance-associated protein (MRP) in eukaryotes. The
multidrug resistance-associated protein is an integral
membrane protein that causes multidrug resistance when
overexpressed in mammalian cells. It belongs to ABC
transporter superfamily. The protein topology and
function was experimentally demonstrated by epitope
tagging and immunofluorescence. Insertion of tags in the
critical regions associated with drug efflux, abrogated
its function. The C-terminal domain seem to highly
conserved [Transport and binding proteins, Other].
Length = 1522
Score = 87.3 bits (216), Expect = 4e-20
Identities = 52/170 (30%), Positives = 84/170 (49%), Gaps = 27/170 (15%)
Query: 21 LIDHQYDLAVQALGMELRVAGCSLIYRKALRLSKTALGDTTVGQVVNLLSNDVNRFDTAC 80
LI HQY GM ++ A +YRKAL ++ +A +TVG++VNL+S D RF
Sbjct: 373 LILHQYFHICFVSGMRIKTAVMGAVYRKALVITNSARKSSTVGEIVNLMSVDAQRFMDLA 432
Query: 81 IFLHHLINR-------------------LLGAKKMYL--------GKKTSELRLKTALRT 113
+++ + + L G M L KT ++
Sbjct: 433 TYINMIWSAPLQVILALYFLWLNLGPSVLAGVAVMVLMVPLNAVMAMKTKTYQVAHMKSK 492
Query: 114 DERVRLMNEIISGIQVIKMYAWERSFASMVRNARKKEIQQIRGSTYIKGV 163
D R++LMNEI++GI+V+K+YAWE +F V R++E++ ++ S Y+ V
Sbjct: 493 DNRIKLMNEILNGIKVLKLYAWELAFLDKVEGIRQEELKVLKKSAYLHAV 542
>gnl|CDD|215595 PLN03130, PLN03130, ABC transporter C family member; Provisional.
Length = 1622
Score = 78.2 bits (193), Expect = 5e-17
Identities = 49/181 (27%), Positives = 83/181 (45%), Gaps = 28/181 (15%)
Query: 16 IVVDLLIDHQYDLAVQALGMELRVAGCSLIYRKALRLSKTALGDTTVGQVVNLLSNDVNR 75
+V+ +L + QY V +G LR + ++RK+LRL+ T G++ NL++ D
Sbjct: 351 VVLGVLCEAQYFQNVMRVGFRLRSTLVAAVFRKSLRLTHEGRKKFTSGKITNLMTTDAEA 410
Query: 76 FDTACIFLHHL-------------------INRLLGA--------KKMYLGKKTSELRLK 108
C LH L + L+G+ + ++ K +L +
Sbjct: 411 LQQICQQLHTLWSAPFRIIIAMVLLYQQLGVASLIGSLMLVLMFPIQTFIISKMQKLTKE 470
Query: 109 TALRTDERVRLMNEIISGIQVIKMYAWERSFASMVRNARKKEIQQIRGSTYIKGVLLSFI 168
RTD+R+ LMNE+++ + +K YAWE SF S V+ R E+ R + + SFI
Sbjct: 471 GLQRTDKRIGLMNEVLAAMDTVKCYAWENSFQSKVQTVRDDELSWFRKAQLL-SAFNSFI 529
Query: 169 I 169
+
Sbjct: 530 L 530
>gnl|CDD|215640 PLN03232, PLN03232, ABC transporter C family member; Provisional.
Length = 1495
Score = 69.6 bits (170), Expect = 5e-14
Identities = 43/167 (25%), Positives = 76/167 (45%), Gaps = 27/167 (16%)
Query: 16 IVVDLLIDHQYDLAVQALGMELRVAGCSLIYRKALRLSKTALGDTTVGQVVNLLSNDVNR 75
+ +L + QY V +G LR + I+ K+LRL+ A + G+V N+++ D N
Sbjct: 351 VTFGVLCESQYFQNVGRVGFRLRSTLVAAIFHKSLRLTHEARKNFASGKVTNMITTDANA 410
Query: 76 FDTACIFLHHL-------------INRLLGAKKMY--------------LGKKTSELRLK 108
LH L + + LG ++ + +K +L +
Sbjct: 411 LQQIAEQLHGLWSAPFRIIVSMVLLYQQLGVASLFGSLILFLLIPLQTLIVRKMRKLTKE 470
Query: 109 TALRTDERVRLMNEIISGIQVIKMYAWERSFASMVRNARKKEIQQIR 155
TD+RV ++NEI++ + +K YAWE+SF S ++ R +E+ R
Sbjct: 471 GLQWTDKRVGIINEILASMDTVKCYAWEKSFESRIQGIRNEELSWFR 517
>gnl|CDD|240327 PTZ00243, PTZ00243, ABC transporter; Provisional.
Length = 1560
Score = 63.6 bits (155), Expect = 7e-12
Identities = 51/190 (26%), Positives = 83/190 (43%), Gaps = 37/190 (19%)
Query: 3 LTAPTACWA----LVALIVVDLLID----HQYDLAVQALGMELRVAGCSLIYRKALRLSK 54
L A A W LV + + LI H++ G++ R A +LI+ K +S
Sbjct: 274 LDADNATWGRGLGLVLTLFLTQLIQSVCLHRFYYISIRCGLQYRSALNALIFEKCFTISS 333
Query: 55 TALG--DTTVGQVVNLLSNDV---NRFDTACIFLHH----------LINRLLGAKKM--- 96
+L D G+++N++S DV N F C++L L++RL+G +
Sbjct: 334 KSLAQPDMNTGRIINMMSTDVERINSFMQYCMYLWSSPMVLLLSILLLSRLVGWCALMAV 393
Query: 97 -----------YLGKKTSELRLKTALRTDERVRLMNEIISGIQVIKMYAWERSFASMVRN 145
+ K R K A D RV+ NE SGI++ K AWE F + + +
Sbjct: 394 AVLLVTLPLNGAIMKHQMAARRKIAKAADARVKATNEFFSGIRIAKFMAWEPCFVANIED 453
Query: 146 ARKKEIQQIR 155
R +E++ +R
Sbjct: 454 KRARELRYLR 463
>gnl|CDD|216049 pfam00664, ABC_membrane, ABC transporter transmembrane region.
This family represents a unit of six transmembrane
helices. Many members of the ABC transporter family
(pfam00005) have two such regions.
Length = 274
Score = 51.5 bits (124), Expect = 4e-08
Identities = 32/169 (18%), Positives = 58/169 (34%), Gaps = 28/169 (16%)
Query: 12 LVALIVVDLLIDHQYDLAVQALGMELRVAGCSLIYRKALRLSKTALGDTTVGQVVNLLSN 71
L+A+ V+ L+ + LG +R + R+ L L + +VG++ + L+N
Sbjct: 47 LIAVGVLQGLLLQGSFYLGERLGQRIRKRLFRALLRQILGLPMSFFDTNSVGELTSRLTN 106
Query: 72 DVNRFDTAC-----IFLHHLIN--------RLLGAK---------------KMYLGKKTS 103
DV++ +F L G K L KK
Sbjct: 107 DVSKIRDGLGDKLGLFFQSLATVVGGFIVMFYYGWKLTLVLLAILPLLILLSAVLAKKLR 166
Query: 104 ELRLKTALRTDERVRLMNEIISGIQVIKMYAWERSFASMVRNARKKEIQ 152
+L K + + E +SGI+ +K + E A + +
Sbjct: 167 KLNRKEQKAYAKAGSVAEESLSGIRTVKAFGREEYELERYDKALEDAEK 215
>gnl|CDD|224055 COG1132, MdlB, ABC-type multidrug transport system, ATPase and
permease components [Defense mechanisms].
Length = 567
Score = 37.0 bits (86), Expect = 0.004
Identities = 31/188 (16%), Positives = 66/188 (35%), Gaps = 32/188 (17%)
Query: 11 ALVALIVVDLLIDHQYDLAVQALGMELRVAGCSLIYRKALRLSKTALGDTTVGQVVNLLS 70
+ V+ L + Q + +LR ++ K LRL + G +++ L+
Sbjct: 61 LALLGGVLRALQSYLGSRLGQKIVADLRRD----LFEKLLRLPLSFFDKAKSGDLISRLT 116
Query: 71 NDVNR-FDTACIFLHHLINR---LLGAKKM------------------------YLGKKT 102
NDV + L + L+G+ + L +K+
Sbjct: 117 NDVEAVSNLVSTVLVLVFTSILLLIGSLVLLFSLSWRLALILLLILPLLALVLSLLARKS 176
Query: 103 SELRLKTALRTDERVRLMNEIISGIQVIKMYAWERSFASMVRNARKKEIQQIRGSTYIKG 162
+L + E + E +SGI+VIK + E A ++ + ++ ++
Sbjct: 177 RKLSRRVREALGELNARLLESLSGIRVIKAFGAEDRELKRFEEANEELRRANLRASRLEA 236
Query: 163 VLLSFIIF 170
+L ++
Sbjct: 237 LLAPLMLL 244
>gnl|CDD|184209 PRK13650, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 279
Score = 35.5 bits (82), Expect = 0.012
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 175 IFIKNIKAKWLPDQPDYTLNDITLDVKNAE 204
I +KN+ K+ DQ YTLND++ VK E
Sbjct: 5 IEVKNLTFKYKEDQEKYTLNDVSFHVKQGE 34
>gnl|CDD|217728 pfam03787, RAMPs, RAMP superfamily. The molecular function of
these proteins is not yet known. However, they have been
identified and called the RAMP (Repair Associated
Mysterious Proteins) superfamily. The members of this
family have no known function they are around 300 amino
acids in length and have several conserved motifs.
Length = 92
Score = 28.6 bits (64), Expect = 0.74
Identities = 10/47 (21%), Positives = 15/47 (31%), Gaps = 1/47 (2%)
Query: 154 IRGSTYIKGVLLSFIIFHTRSIFIKNIKAKWLPDQPDYTLNDITLDV 200
I GS+ IKG LL I + + + L +
Sbjct: 33 IPGSS-IKGALLELIPPGLGFLEFLDNLDDEDLELLKELLKLLLNFG 78
>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 29.8 bits (67), Expect = 1.2
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 55 TALGDTTVG-QVVNLLSNDVNRFDTACIFLHHLINRLLGAKKMYLGKKTSELRLKTALRT 113
T +G T V Q+ L ++ RFD + H ++RL+GA Y+G L ++
Sbjct: 497 TGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAVIKH 556
Query: 114 DERVRLMNEI 123
V L++EI
Sbjct: 557 PHAVLLLDEI 566
>gnl|CDD|131701 TIGR02653, Lon_rel_chp, conserved hypothetical protein. This model
describes a protein family of unknown function, about
690 residues in length, in which some members show
C-terminal sequence similarity to pfam05362, which is
the Lon protease C-terminal proteolytic domain, from
MEROPS family S16. However, the annotated catalytic
sites of E. coli Lon protease are not conserved in
members of this family. Members have a motif
GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif
GxxGxGK[ST] [Hypothetical proteins, Conserved].
Length = 675
Score = 27.9 bits (62), Expect = 4.4
Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 9/58 (15%)
Query: 23 DHQYDLAVQ---------ALGMELRVAGCSLIYRKALRLSKTALGDTTVGQVVNLLSN 71
+H Y L V + +A CS + ++ ++ LG T+G V+N + +
Sbjct: 562 EHDYHLHVVDLHNTGPSTEASLAALIALCSALLKRPVQEQMVILGSMTIGGVINPVQD 619
>gnl|CDD|227267 COG4930, COG4930, Predicted ATP-dependent Lon-type protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 683
Score = 27.6 bits (61), Expect = 5.0
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 9/58 (15%)
Query: 23 DHQYDLAVQ---------ALGMELRVAGCSLIYRKALRLSKTALGDTTVGQVVNLLSN 71
+H+Y L V A + +A CS++ K ++ LG T+G V+N + +
Sbjct: 570 EHEYHLHVVELHNTGPSTATSLAALIALCSVLLAKPVQEQMVVLGSMTLGGVINPVQD 627
>gnl|CDD|172473 PRK13970, PRK13970, hydroxyproline-2-epimerase; Provisional.
Length = 311
Score = 27.3 bits (60), Expect = 5.3
Identities = 12/38 (31%), Positives = 23/38 (60%)
Query: 56 ALGDTTVGQVVNLLSNDVNRFDTACIFLHHLINRLLGA 93
+LG T+ + ++L+ + +R+ TACI + L+GA
Sbjct: 26 SLGGGTMAERRDVLAREHDRYRTACILEPRGSDVLVGA 63
>gnl|CDD|219433 pfam07500, TFIIS_M, Transcription factor S-II (TFIIS), central
domain. Transcription elongation by RNA polymerase II
is regulated by the general elongation factor TFIIS.
This factor stimulates RNA polymerase II to transcribe
through regions of DNA that promote the formation of
stalled ternary complexes. TFIIS is composed of three
structural domains, termed I, II, and III. The two
C-terminal domains (II and III), this domain and
pfam01096 are required for transcription activity.
Length = 115
Score = 25.7 bits (57), Expect = 9.0
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 107 LKTALRTDERVRLMNEIISGIQVIKMYAWERSFASMVRNARKKEIQQIR 155
LK D R +++N IS +++ M E AS + KKE ++I
Sbjct: 63 LKDPKNPDLRRKVLNGEISPERLVNMSPEE--LAS---DELKKEREEIE 106
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
0.325 0.137 0.398
Gapped
Lambda K H
0.267 0.0792 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,391,187
Number of extensions: 976656
Number of successful extensions: 1102
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1100
Number of HSP's successfully gapped: 29
Length of query: 205
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 113
Effective length of database: 6,857,034
Effective search space: 774844842
Effective search space used: 774844842
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 57 (25.6 bits)