RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6082
(275 letters)
>gnl|CDD|227590 COG5265, ATM1, ABC-type transport system involved in Fe-S cluster
assembly, permease and ATPase components
[Posttranslational modification, protein turnover,
chaperones].
Length = 497
Score = 209 bits (534), Expect = 1e-64
Identities = 86/197 (43%), Positives = 129/197 (65%), Gaps = 12/197 (6%)
Query: 47 LRNAVFASVAQRSIRKIAKNVFLHLHNLDLAFHLNRQTGALSKIIDRGSRGINFVLSAMV 106
LR+ +F+ V Q ++R +A F HLH+L L FHL R+TG LS+ I+RG++GI +L ++
Sbjct: 1 LRDRLFSPVGQIAVRVLAYVTFFHLHSLSLRFHLERRTGGLSRAIERGTKGIETILRWIL 60
Query: 107 FNIVPTIFELALISSILSYKCGTLISSILSYKCGSEFSLLAVSCVGIYTAYTLSITQWRT 166
FNI+PT+ E++L++ IL G F+L + V +Y +T+ ++ WRT
Sbjct: 61 FNILPTLVEISLVAVILWRVYGW------------WFALTTLVTVILYLLFTVIVSDWRT 108
Query: 167 QFRVNMNKAENEAGNKAIDSLINYETVKYFNNEKFEADRYEGVLKKYEQAALKTSTSLAT 226
FR MN A+++A KAIDSL+N+ETVKYF NE++EA RY+ L+ YE+AA+K SL
Sbjct: 109 DFRRLMNNADSDANAKAIDSLLNFETVKYFGNEEYEAVRYDHALETYEKAAIKVHVSLLV 168
Query: 227 LNFGQSAIGKLMLTLVL 243
LNFGQ+AI L +++
Sbjct: 169 LNFGQTAIFSTGLRVMM 185
>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 = 69.6 bits (171), Expect = 6e-14
Identities = 39/228 (17%), Positives = 87/228 (38%), Gaps = 13/228 (5%)
Query: 16 LTNATDALIASATSIILGYGIARICSSGFNELRNAVFASVAQRSIRKIAKNVFLHLHNLD 75
L + +S S+ + + + + + QR +++ + + + L
Sbjct: 29 LIDGNGDERSSLISLAILLIAVGVLQGLLLQGSFYLGERLGQRIRKRLFRALLRQILGLP 88
Query: 76 LAFHLNRQTGALSKIIDRGSRGINFVLSAMVFNIVPTIFELALISSILSYKCGTLISSIL 135
++F G L+ + I L + +F +L + + G ++
Sbjct: 89 MSFFDTNSVGELTSRLTNDVSKIRDGLGDKLG-----LFFQSLATVV----GGFIVMFYY 139
Query: 136 SYKCGSEFSLLAVSCVGIYTAYTLSITQWRTQFRVNMNKAENEAGNKAIDSLINYETVKY 195
+K +L+ ++ + + + + + + KA +AG+ A +SL TVK
Sbjct: 140 GWK----LTLVLLAILPLLILLSAVLAKKLRKLNRKEQKAYAKAGSVAEESLSGIRTVKA 195
Query: 196 FNNEKFEADRYEGVLKKYEQAALKTSTSLATLNFGQSAIGKLMLTLVL 243
F E++E +RY+ L+ E+A +K + + I L L L
Sbjct: 196 FGREEYELERYDKALEDAEKAGIKKAITAGLSFGITQLISYLSYALAL 243
>gnl|CDD|224055 COG1132, MdlB, ABC-type multidrug transport system, ATPase and
permease components [Defense mechanisms].
Length = 567
Score = 70.2 bits (172), Expect = 1e-13
Identities = 41/239 (17%), Positives = 94/239 (39%), Gaps = 13/239 (5%)
Query: 5 TGIVSDGALLELTNATDALIASATSIILGYGIARICSSGFNELRNAVFASVAQRSIRKIA 64
++ + + +A A + ++L + + L++ + + + Q+ + +
Sbjct: 29 LSLLLPLLIGRIIDALLADLGELLELLLLLLLLALLGGVLRALQSYLGSRLGQKIVADLR 88
Query: 65 KNVFLHLHNLDLAFHLNRQTGALSKIIDRGSRGINFVLSAMVFNIVPTIFELALISSILS 124
+++F L L L+F ++G L + ++ ++S ++ + +I L +L
Sbjct: 89 RDLFEKLLRLPLSFFDKAKSGDLISRLTNDVEAVSNLVSTVLVLVFTSILLLIGSLVLLF 148
Query: 125 YKCGTLISSILSYKCGSEFSLLAVSCVGIYTAYTLSITQWRTQFRVNMNKAENEAGNKAI 184
+S L + LL + + + + + R R + +A E + +
Sbjct: 149 S-----LSWRL-----ALILLLILPLLALVLSLL--ARKSRKLSR-RVREALGELNARLL 195
Query: 185 DSLINYETVKYFNNEKFEADRYEGVLKKYEQAALKTSTSLATLNFGQSAIGKLMLTLVL 243
+SL +K F E E R+E ++ +A L+ S A L + L LVL
Sbjct: 196 ESLSGIRVIKAFGAEDRELKRFEEANEELRRANLRASRLEALLAPLMLLLSSLGTVLVL 254
>gnl|CDD|225183 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
an N-terminal double-glycine peptidase domain [Defense
mechanisms].
Length = 709
Score = 51.1 bits (123), Expect = 3e-07
Identities = 42/224 (18%), Positives = 90/224 (40%), Gaps = 16/224 (7%)
Query: 21 DALIASATSIILGYGIARICSSGFNELRNAVFASVAQRSIRKIAKNVFLHLHNLDLAFHL 80
DA ++ T + +G +A + + LR + A + +R +++ F HL L L++
Sbjct: 187 DASRSTLTVLAIGLLLAALFEALLRLLRTYLIAHLGKRLDLELSGRFFRHLLRLPLSYFE 246
Query: 81 NRQTGALSKIIDRGSRGINFVLSAMVFNIVPTIFELALISSILSYKCGTLISSILSYKCG 140
R G + + + F+ +++ I+ +F L ++ + Y
Sbjct: 247 KRSVGEIISRVRELEQIREFLTGSILTLIIDLLFALIFLAVMFLY--------------S 292
Query: 141 SEFSLLAVSCVGIYTAYTLSITQWRTQFRVNMNKAENEAGNKA-IDSLINYETVKYFNNE 199
+ +L+ ++ + + TL I Q + + E+ ++++ ETVK E
Sbjct: 293 WKLTLIVLAAIPLNVLITL-IFQPLLRRKTRKLIEESAEQQSFLVETIKGIETVKALAAE 351
Query: 200 KFEADRYEGVLKKYEQAALKTSTSLATLNFGQSAIGKLMLTLVL 243
+++ L K KT LN +S + +L L+L
Sbjct: 352 PRFRSQWDNRLAKQVNIGFKTEKLALILNTIKSLLQQLSSVLIL 395
>gnl|CDD|131259 TIGR02204, MsbA_rel, ABC transporter, permease/ATP-binding protein.
This protein is related to a Proteobacterial ATP
transporter that exports lipid A and to eukaryotic
P-glycoproteins.
Length = 576
Score = 41.6 bits (98), Expect = 3e-04
Identities = 54/231 (23%), Positives = 96/231 (41%), Gaps = 40/231 (17%)
Query: 23 LIASATSIILGYGIARICSSGFN----ELRNAVFA---------------------SVAQ 57
LI +A ++ L Y + + GF+ L N FA + +
Sbjct: 28 LITAAATLSLPYAVRLMIDHGFSKDSSGLLNRYFAFLLVVALVLALGTAARFYLVTWLGE 87
Query: 58 RSIRKIAKNVFLHLHNLDLAFHLNRQTGALSKIIDRGSRGINFVLSAMVFNIVPTIFELA 117
R + I + VF HL +L +F ++G +++ R + + S ++ + +A
Sbjct: 88 RVVADIRRAVFAHLISLSPSFFDKNRSG---EVVSRLTTDTTLLQS-----VIGSSLSMA 139
Query: 118 LISSILSYKCGTLISSILSYKCGSEFSLLAVSCVGIYTAYTLSITQW-RTQFRVNMNKAE 176
L + L G ++ I S K S LLAV V L + R R + ++
Sbjct: 140 L-RNALMCIGGLIMMFITSPKLTS-LVLLAVPLV---LLPILLFGRRVRKLSRESQDRIA 194
Query: 177 NEAGNKAIDSLINYETVKYFNNEKFEADRYEGVLKKYEQAALKTSTSLATL 227
+AG+ A ++L TV+ F +E E R+ G ++K +AA + + A L
Sbjct: 195 -DAGSYAGETLGAIRTVQAFGHEDAERSRFGGAVEKAYEAARQRIRTRALL 244
>gnl|CDD|233209 TIGR00958, 3a01208, Conjugate Transporter-2 (CT2) Family protein.
[Transport and binding proteins, Other].
Length = 711
Score = 35.9 bits (83), Expect = 0.023
Identities = 52/245 (21%), Positives = 94/245 (38%), Gaps = 27/245 (11%)
Query: 5 TGIVSDGALLELTNATDALIASATSIILGYGIARICSSGFNELRNAVFASVAQRSIRKIA 64
TG V D T D + S I + I SS LR F R +I
Sbjct: 184 TGRVID------TLGGDKGPPALASAIFFMCLLSIASSVSAGLRGGSFNYTMARINLRIR 237
Query: 65 KNVFLHLHNLDLAFHLNRQTGALSKIIDRGSRGINFVLSAMVFNIVPTIFELALISSILS 124
+++F L DL F +TG ++ R S + ++ N+ + L+ +
Sbjct: 238 EDLFRSLLRQDLGFFDENKTG---ELTSRLSSDTQTMSRSLSLNV--NVLLRNLVMLLGL 292
Query: 125 YKCGTLISSILSYKCGSEFSLLAVSCVG----IYTAYTLSITQWRTQFRVNMNKAENEAG 180
+S L+ +L+ + V ++ +++ Q +A +A
Sbjct: 293 LGFMLWLSPRLTM-----VTLINLPLVFLAEKVFGKRYQLLSE-ELQ------EAVAKAN 340
Query: 181 NKAIDSLINYETVKYFNNEKFEADRYEGVLKKYEQAALKTSTSLATLNFGQSAIGKLMLT 240
A ++L TV+ F E+ EA R++ L++ Q + + + A + S +G L+
Sbjct: 341 QVAEEALSGMRTVRSFAAEEGEASRFKEALEETLQLNKRKALAYAGYLWTTSVLGMLIQV 400
Query: 241 LVLNL 245
LVL
Sbjct: 401 LVLYY 405
>gnl|CDD|233596 TIGR01846, type_I_sec_HlyB, type I secretion system ABC
transporter, HlyB family. Type I protein secretion is a
system in some Gram-negative bacteria to export proteins
(often proteases) across both inner and outer membranes
to the extracellular medium. This is one of three
proteins of the type I secretion apparatus. Targeted
proteins are not cleaved at the N-terminus, but rather
carry signals located toward the extreme C-terminus to
direct type I secretion [Protein fate, Protein and
peptide secretion and trafficking].
Length = 694
Score = 31.6 bits (72), Expect = 0.48
Identities = 31/152 (20%), Positives = 54/152 (35%), Gaps = 34/152 (22%)
Query: 47 LRNAVFASVAQRSIRKIAKNVFLHLHNLDLAFHLNRQTG-------------------AL 87
LR +FA + R ++ ++ HL L L + +R+ G AL
Sbjct: 198 LRTYLFAHLTSRIDVELGARLYRHLLGLPLGYFESRRVGDTVARVRELEQIRNFLTGSAL 257
Query: 88 SKIIDRGSRGINFVLSAMVFNIVPTIFELALISSILSYKCGTLISSILSYKCGSEF---- 143
+ ++D V A++F PT+ + + S + + IL + +F
Sbjct: 258 TVVLD---LLFVVVFLAVMFFYSPTLTGVVIGSLVCYALLSVFVGPILRKRVEDKFERSA 314
Query: 144 ---SLLAVSCVGIYTAYTLSIT-----QWRTQ 167
S L S GI T + +W Q
Sbjct: 315 AATSFLVESVTGIETIKATATEPQFQNRWDRQ 346
>gnl|CDD|130261 TIGR01193, bacteriocin_ABC, ABC-type bacteriocin transporter. This
model describes ABC-type bacteriocin transporter. The
amino terminal domain (pfam03412) processes the
N-terminal leader peptide from the bacteriocin while
C-terminal domains resemble ABC transporter membrane
protein and ATP-binding cassette domain. In general,
bacteriocins are agents which are responsible for
killing or inhibiting the closely related species or
even different strains of the same species. Bacteriocins
are usually encoded by bacterial plasmids. Bacteriocins
are named after the species and hence in literature one
encounters various names e.g., leucocin from Leuconostic
geldium; pedicocin from Pedicoccus acidilactici; sakacin
from Lactobacillus sake etc [Protein fate, Protein and
peptide secretion and trafficking, Protein fate, Protein
modification and repair, Transport and binding proteins,
Other].
Length = 708
Score = 31.2 bits (71), Expect = 0.56
Identities = 50/218 (22%), Positives = 88/218 (40%), Gaps = 23/218 (10%)
Query: 30 IILGYGIARICSSGFNELRNAVFASVAQRSIRKIAKNVFLHLHNLDLAFHLNRQTGALSK 89
I +G IA I + ++ + + QR I + HL L ++F R+TG +
Sbjct: 198 ISIGLIIAYIIQQILSYIQIFLLNVLGQRLSIDIILSYIKHLFELPMSFFSTRRTG---E 254
Query: 90 IIDRGSRGINFVLSAMVFNIVPTIFELALISSILSYKCGTLISSILSYKCGSEFSLLAVS 149
I+ R + S+++ + TI L L IL ++ L + F L +S
Sbjct: 255 IVSRFTDA-----SSIIDALASTILSLFLDMWIL-----VIVGLFLVRQNMLLFLLSLLS 304
Query: 150 CVGIYTAYTLSITQWRTQFRVNMNKAENEA--GNKAIDSLINYETVKYFNNEKFEADRYE 207
+ +Y + RT ++N + + A + I+ L ET+K +E + +
Sbjct: 305 -IPVYAVIIILFK--RTFNKLNHDAMQANAVLNSSIIEDLNGIETIKSLTSEAERYSKID 361
Query: 208 GVLKKYEQAALKTSTSLATLNFGQSAIGKLMLTLVLNL 245
Y L S + GQ AI K + L+LN+
Sbjct: 362 SEFGDY----LNKSFKYQKADQGQQAI-KAVTKLILNV 394
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 28.7 bits (64), Expect = 4.4
Identities = 17/66 (25%), Positives = 25/66 (37%), Gaps = 19/66 (28%)
Query: 163 QWRTQFRVNMNKAE-----------------NEAGNKAIDSLIN--YETVKYFNNEKFEA 203
Q++T F V NK + NE A+ L YE + F+A
Sbjct: 576 QYKTPFVVAANKIDLIPGWNISEDEPFLLNFNEQDQHALTELEIKLYELIGKLYELGFDA 635
Query: 204 DRYEGV 209
DR++ V
Sbjct: 636 DRFDRV 641
>gnl|CDD|225272 COG2409, COG2409, Predicted drug exporters of the RND superfamily
[General function prediction only].
Length = 937
Score = 28.2 bits (63), Expect = 5.3
Identities = 25/90 (27%), Positives = 37/90 (41%), Gaps = 9/90 (10%)
Query: 98 INFVLSAMVFNIVPTIFELA---LISSILSYKCGTLISSILSYKCG---SEFSLLAVSCV 151
I VL +V IV A LI+ LS I ++L+Y G S F+L + +
Sbjct: 192 ITLVLILVVLLIVYRSVITAFLPLITVGLSLLVAQGIVALLAYAFGLGVSTFALSLLVAL 251
Query: 152 GI--YTAYTLSITQWRTQFRVNMNKAENEA 179
GI T Y L + R + + + A
Sbjct: 252 GIGAGTDYALFLVS-RYREELREGQDREAA 280
>gnl|CDD|143495 cd06821, PLPDE_III_D-TA, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme D-Threonine Aldolase.
D-threonine aldolase (D-TA, EC 4.3.1.18) reversibly
catalyzes the aldol cleavage of D-threonine into glycine
and acetaldehyde, and the synthesis of D-threonine from
glycine and acetaldehyde. Its activity is present in
several genera of bacteria but not in fungi. It requires
PLP and a divalent cation such as Co2+, Ni2+, Mn2+, or
Mg2+ as cofactors for catalytic activity and thermal
stability. Members of this subfamily show similarity to
bacterial alanine racemase (AR), a fold type III
PLP-dependent enzyme which contains an N-terminal
PLP-binding TIM-barrel domain and a C-terminal
beta-sandwich domain. 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. Based on its similarity to
AR, it is possible that low specificity D-TAs also form
dimers in solution. Experimental data show that the
monomeric form of low specificity D-TAs exhibit full
catalytic activity.
Length = 361
Score = 28.0 bits (63), Expect = 5.6
Identities = 13/43 (30%), Positives = 20/43 (46%)
Query: 111 PTIFELALISSILSYKCGTLISSILSYKCGSEFSLLAVSCVGI 153
I L L + I +KC T+ + + + G+ LLA VG
Sbjct: 46 AEIVRLQLEAGITKFKCATIAEAEMLAEAGAPDVLLAYPLVGP 88
>gnl|CDD|183106 PRK11375, PRK11375, allantoin permease; Provisional.
Length = 484
Score = 27.4 bits (61), Expect = 9.2
Identities = 13/30 (43%), Positives = 23/30 (76%), Gaps = 1/30 (3%)
Query: 108 NIVPTIFELALIS-SILSYKCGTLISSILS 136
NI+P +++A ++ + L+YK G LI+SI+S
Sbjct: 329 NIIPAGYQIAALAPTKLTYKNGVLIASIIS 358
>gnl|CDD|131258 TIGR02203, MsbA_lipidA, lipid A export permease/ATP-binding protein
MsbA. This family consists of a single polypeptide
chain transporter in the ATP-binding cassette (ABC)
transporter family, MsbA, which exports lipid A. It may
also act in multidrug resistance. Lipid A, a part of
lipopolysaccharide, is found in the outer leaflet of the
outer membrane of most Gram-negative bacteria. Members
of this family are restricted to the Proteobacteria
(although lipid A is more broadly distributed) and often
are clustered with lipid A biosynthesis genes [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides, Transport and
binding proteins, Other].
Length = 571
Score = 27.4 bits (61), Expect = 9.7
Identities = 17/79 (21%), Positives = 37/79 (46%)
Query: 171 NMNKAENEAGNKAIDSLINYETVKYFNNEKFEADRYEGVLKKYEQAALKTSTSLATLNFG 230
+ + + A ++L Y VK F + +E R++ V + + A+K +++ + +
Sbjct: 184 EIQNSMGQVTTVAEETLQGYRVVKLFGGQAYETRRFDAVSNRNRRLAMKMTSAGSISSPI 243
Query: 231 QSAIGKLMLTLVLNLQSFE 249
I L L +VL + F+
Sbjct: 244 TQLIASLALAVVLFIALFQ 262
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
0.321 0.134 0.382
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,270,097
Number of extensions: 1229607
Number of successful extensions: 1110
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1104
Number of HSP's successfully gapped: 24
Length of query: 275
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 179
Effective length of database: 6,679,618
Effective search space: 1195651622
Effective search space used: 1195651622
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 (21.9 bits)
S2: 58 (26.0 bits)