RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9408
(219 letters)
>gnl|CDD|224997 COG2086, FixA, Electron transfer flavoprotein, beta subunit [Energy
production and conversion].
Length = 260
Score = 217 bits (555), Expect = 2e-71
Identities = 95/229 (41%), Positives = 137/229 (59%), Gaps = 11/229 (4%)
Query: 1 MSINPFDEIAIESAIRLRESSNKIKEIIAISCGNKKCKEILQIAMAMGVDRAILIETDTI 60
+SINPFD A+E A+RL+E E+ ++ G + +E L+ A+AMG DRAILI
Sbjct: 33 LSINPFDLNAVEEALRLKEK-GYGGEVTVLTMGPPQAEEALREALAMGADRAILITDRAF 91
Query: 61 LQS--LSVAKLLQVIVKKENPQLVILGKQSIDSDNNQTGQMLAALLNWPQATFASKIVLK 118
+ L+ AK L VKK P LV+ GKQ+ID D Q G +LA LL WPQ T+ SKI +
Sbjct: 92 AGADPLATAKALAAAVKKIGPDLVLTGKQAIDGDTGQVGPLLAELLGWPQVTYVSKIEIV 151
Query: 119 KNNKILVTQEIEDGKETILLSLPAIITTDLRMNEPRYVTLMNIIKARKKNINIFKIDELN 178
K+ V +E+E G ET+ LPA++T DLR+NEPRY +L I+ A+KK + + + +L
Sbjct: 152 DGGKVTVERELEGGLETVEAPLPAVVTVDLRINEPRYPSLPGIMAAKKKPVKKWSLADLG 211
Query: 179 VNINT---GLNIIKVKESHKNNLGIKVKNVIE-----LIDKLKNEAKII 219
+N+ L ++KV + G+KVK+ E L++KLK E I+
Sbjct: 212 LNVGLAGSPLKVVKVTPPPERKAGVKVKDGPEEIAAELVEKLKEEGVIL 260
>gnl|CDD|238847 cd01714, ETF_beta, The electron transfer flavoprotein (ETF) serves
as a specific electron acceptor for various
mitochondrial dehydrogenases. ETF transfers electrons to
the main respiratory chain via ETF-ubiquinone
oxidoreductase. ETF is an heterodimer that consists of
an alpha and a beta subunit which binds one molecule of
FAD per dimer . A similar system also exists in some
bacteria. The homologous pair of proteins (FixA/FixB)
are essential for nitrogen fixation. The beta subunit
protein is distantly related to and forms a heterodimer
with the alpha subunit.
Length = 202
Score = 200 bits (512), Expect = 1e-65
Identities = 78/175 (44%), Positives = 110/175 (62%), Gaps = 5/175 (2%)
Query: 1 MSINPFDEIAIESAIRLRESSNKIKEIIAISCGNKKCKEILQIAMAMGVDRAILIETDTI 60
+ INP+DE A+E A+RL+E E+ +S G + +E L+ A+AMG DRAIL+
Sbjct: 31 LIINPYDEYAVEEALRLKEKYGG--EVTVVSMGPPQAEEALREALAMGADRAILVSDRAF 88
Query: 61 LQS--LSVAKLLQVIVKKENPQLVILGKQSIDSDNNQTGQMLAALLNWPQATFASKIVLK 118
+ L+ AK L +KK L++ GKQSID D Q G +LA LL WPQ T+ SKI +
Sbjct: 89 AGADTLATAKALAAAIKKIGVDLILTGKQSIDGDTGQVGPLLAELLGWPQITYVSKIEI- 147
Query: 119 KNNKILVTQEIEDGKETILLSLPAIITTDLRMNEPRYVTLMNIIKARKKNINIFK 173
+ K+ V +E+E G ET+ + LPA+IT DL +NEPRY +L I+KA+KK I +
Sbjct: 148 EGGKVTVERELEGGVETVEVKLPAVITVDLGINEPRYPSLPGIMKAKKKPIEVVS 202
>gnl|CDD|214890 smart00893, ETF, Electron transfer flavoprotein domain. Electron
transfer flavoproteins (ETFs) serve as specific electron
acceptors for primary dehydrogenases, transferring the
electrons to terminal respiratory systems. They can be
functionally classified into constitutive,
"housekeeping" ETFs, mainly involved in the oxidation of
fatty acids (Group I), and ETFs produced by some
prokaryotes under specific growth conditions, receiving
electrons only from the oxidation of specific substrates
(Group II). ETFs are heterodimeric proteins composed of
an alpha and beta subunit, and contain an FAD cofactor
and AMP. ETF consists of three domains: domains I and II
are formed by the N- and C-terminal portions of the
alpha subunit, respectively, while domain III is formed
by the beta subunit. Domains I and III share an almost
identical alpha-beta-alpha sandwich fold, while domain
II forms an alpha-beta-alpha sandwich similar to that of
bacterial flavodoxins. FAD is bound in a cleft between
domains II and III, while domain III binds the AMP
molecule. Interactions between domains I and III
stabilise the protein, forming a shallow bowl where
domain II resides. This entry represents the N-terminal
domain of both the alpha and beta subunits from Group I
and Group II ETFs.
Length = 185
Score = 136 bits (345), Expect = 1e-40
Identities = 59/179 (32%), Positives = 89/179 (49%), Gaps = 19/179 (10%)
Query: 1 MSINPFDEIAIESAIRLRESSNKIKEIIAISCGNKKCKEILQIAMAMGVDRAILIETDTI 60
INP D A+E+A RL+E E+ A+ G +E L+ A+AMG D+ L++ D +
Sbjct: 7 ALINPVDLEALEAARRLKEKG----EVTAVVVGPPAAEEALREALAMGADKVYLVDDDAL 62
Query: 61 LQSLS---VAKLLQVIVKKENPQLVILGKQSIDSDNNQTGQMLAALLNWPQATFASKIVL 117
+ +A+ L ++K+E P LV+ G SD Q LAALL PQ T +K+ +
Sbjct: 63 AGYDTLATLAEALAALIKEEKPDLVLAGAT---SDGKQLAPRLAALLGVPQITDVTKLEV 119
Query: 118 KKNNKILVTQEIEDG---KETILLSLPAIIT--TDLRMNEP--RYVTLMNIIKARKKNI 169
+ V + G E + LPA+IT P Y +L+ I+KA+KK I
Sbjct: 120 --DGDTFVRRIYGGGAIATEVVEADLPAVITVRPGAFEPAPRDGYPSLVEIMKAKKKPI 176
>gnl|CDD|238943 cd01985, ETF, The electron transfer flavoprotein (ETF) serves as a
specific electron acceptor for various mitochondrial
dehydrogenases. ETF transfers electrons to the main
respiratory chain via ETF-ubiquinone oxidoreductase. ETF
is an heterodimer that consists of an alpha and a beta
subunit which binds one molecule of FAD per dimer . A
similar system also exists in some bacteria. The
homologous pair of proteins (FixA/FixB) are essential
for nitrogen fixation. The alpha subunit of ETF is
structurally related to the bacterial nitrogen fixation
protein fixB which could play a role in a redox process
and feed electrons to ferredoxin. The beta subunit
protein is distantly related to and forms a heterodimer
with the alpha subunit.
Length = 181
Score = 132 bits (334), Expect = 6e-39
Identities = 55/169 (32%), Positives = 84/169 (49%), Gaps = 12/169 (7%)
Query: 1 MSINPFDEIAIESAIRLRESSNKIKEIIAISCGNKKCKEILQIAMAMGVDRAILIETDTI 60
+ +NP D A+E+A+RL+E E+ A+ G + L+ A+AMG D+ +L+E +
Sbjct: 15 LVLNPLDLEAVEAALRLKEYGG---EVTALVIGPPAAEVALREALAMGADKVLLVEDPAL 71
Query: 61 LQSLS--VAKLLQVIVKKENPQLVILGKQSIDSDNNQTGQMLAALLNWPQATFASKIVLK 118
AK L ++KKE P L++ G SI Q +AALL PQ + +K+ +
Sbjct: 72 AGYDPEATAKALAALIKKEKPDLILAGATSI---GKQLAPRVAALLGVPQISDVTKLEI- 127
Query: 119 KNNKILVTQEIEDGK--ETILLS-LPAIITTDLRMNEPRYVTLMNIIKA 164
+ VT+ I G ET+ LPA+IT EPRY + K
Sbjct: 128 DGGDLTVTRPIYAGNGLETVESPDLPAVITVRPGAFEPRYPSGPGKKKP 176
>gnl|CDD|216243 pfam01012, ETF, Electron transfer flavoprotein domain. This family
includes the homologous domain shared between the alpha
and beta subunits of the electron transfer flavoprotein.
Length = 160
Score = 105 bits (265), Expect = 6e-29
Identities = 49/156 (31%), Positives = 72/156 (46%), Gaps = 11/156 (7%)
Query: 2 SINPFDEIAIESAIRLRESSNKIKEIIAISCGNKKCKEILQIAMAMGVDRAILIETDTIL 61
+NP D A+E+A RL E+ E+ A+ G + + AMG D+ L+E +
Sbjct: 12 KLNPVDLEALEAARRLAEALGG--EVTAVVVGPVE-AAAEALLAAMGADKVYLVEDPALA 68
Query: 62 QSLS--VAKLLQVIVKKENPQLVILGKQSIDSDNNQTGQMLAALLNWPQATFASKIVLKK 119
A L ++KKE P LV+ G SI D LAALL P T + + + +
Sbjct: 69 GYDPEAYAAALAALIKKEGPDLVLAGATSIGKD---LAPRLAALLGAPLITDVTALEV-E 124
Query: 120 NNKILVTQEIEDGKE--TILLSLPAIITTDLRMNEP 153
K+ VT+ I G T+ L PA++T EP
Sbjct: 125 GGKLTVTRPIYGGNAIATVKLPDPAVLTVRPGAFEP 160
>gnl|CDD|179569 PRK03359, PRK03359, putative electron transfer flavoprotein FixA;
Reviewed.
Length = 256
Score = 66.7 bits (163), Expect = 2e-13
Identities = 51/186 (27%), Positives = 93/186 (50%), Gaps = 13/186 (6%)
Query: 3 INPFDEIAIESAIRLRESSNKIKEIIAISCGNKKC------KEILQIAMAMGVDRAILIE 56
I+ +D AIE+A +L++ + + + + A+S G K K++L + G D I++
Sbjct: 34 ISQYDLNAIEAACQLKQQAAEAQ-VTALSVGGKALTNAKGRKDVL----SRGPDELIVVI 88
Query: 57 TDTILQSL--SVAKLLQVIVKKENPQLVILGKQSIDSDNNQTGQMLAALLNWPQATFASK 114
D Q+L A L +K L++ G S D Q G ++ +LN P SK
Sbjct: 89 DDQFEQALPQQTASALAAAAQKAGFDLILCGDGSSDLYAQQVGLLVGEILNIPAINGVSK 148
Query: 115 IVLKKNNKILVTQEIEDGKETILLSLPAIITTDLRMNEPRYVTLMNIIKARKKNINIFKI 174
I+ ++ + V +E+ED ET+ + LPA+I +N P+ ++ I+ A KK + ++
Sbjct: 149 IISLTDDTLTVERELEDEVETLSIPLPAVIAVSTDINSPQIPSMKAILGAAKKPVQVWSA 208
Query: 175 DELNVN 180
++ N
Sbjct: 209 ADIGFN 214
>gnl|CDD|183455 PRK12342, PRK12342, hypothetical protein; Provisional.
Length = 254
Score = 60.9 bits (148), Expect = 3e-11
Identities = 50/181 (27%), Positives = 89/181 (49%), Gaps = 8/181 (4%)
Query: 3 INPFDEIAIESAIRLRESSNKIKEIIAISCGNKKCK--EILQIAMAMGVDRAILIETDTI 60
I+ FD AIE+A +L + EI A++ G + ++ + ++ G L++ +
Sbjct: 33 ISQFDLNAIEAASQLATDGD---EIAALTVGGSLLQNSKVRKDVLSRGPHSLYLVQDAQL 89
Query: 61 LQSLS--VAKLLQVIVKKENPQLVILGKQSIDSDNNQTGQMLAALLNWPQATFASKIVLK 118
+L AK L ++K L++ G+ S D Q G +L LL P SKI +
Sbjct: 90 EHALPLDTAKALAAAIEKIGFDLLLFGEGSGDLYAQQVGLLLGELLQLPVINAVSKIQRQ 149
Query: 119 KNNKILVTQEIEDGKETILLSLPAIITTDLRMNEPRYVTLMNIIKARKKNINIFKIDELN 178
NK++V + +ED E + LSLPA++ +N PR ++ I+ A KK + ++ ++
Sbjct: 150 -GNKLIVERTLEDDVEVLELSLPAVLCVTSDINVPRIPSMKAILGAGKKPVTQWQASDIG 208
Query: 179 V 179
Sbjct: 209 W 209
>gnl|CDD|234414 TIGR03953, rplD_bact, 50S ribosomal protein L4,
bacterial/organelle. Members of this protein family are
ribosomal protein L4. This model recognizes bacterial
and most organellar forms, but excludes homologs from
the eukaryotic cytoplasm and from archaea [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 188
Score = 30.6 bits (70), Expect = 0.42
Identities = 13/51 (25%), Positives = 26/51 (50%)
Query: 10 AIESAIRLRESSNKIKEIIAISCGNKKCKEILQIAMAMGVDRAILIETDTI 60
A+ SA+ + K+ + K K++ +I +G+D+ +LI TD +
Sbjct: 93 ALRSALSEKAREGKLVVVDDFDLEEPKTKDLAKILKNLGLDKKVLIVTDEV 143
>gnl|CDD|238848 cd01715, ETF_alpha, The electron transfer flavoprotein (ETF)
serves as a specific electron acceptor for various
mitochondrial dehydrogenases. ETF transfers electrons
to the main respiratory chain via ETF-ubiquinone
oxidoreductase. ETF is an heterodimer that consists of
an alpha and a beta subunit which binds one molecule of
FAD per dimer . A similar system also exists in some
bacteria. The homologous pair of proteins (FixA/FixB)
are essential for nitrogen fixation. The alpha subunit
of ETF is structurally related to the bacterial
nitrogen fixation protein fixB which could play a role
in a redox process and feed electrons to ferredoxin.
Length = 168
Score = 30.2 bits (69), Expect = 0.47
Identities = 17/77 (22%), Positives = 34/77 (44%), Gaps = 4/77 (5%)
Query: 12 ESAIRLRESSNKIK-EIIAISCGNKKCKEILQIAMAMGVDRAILIETDTILQSLS--VAK 68
E + ++ K+ E+ A+ G+ + + A G D+ ++ E + L+ A
Sbjct: 15 ELTLEAVTAARKLGGEVTALVIGSG-AEAVAAALKAYGADKVLVAEDPALAHYLAEPYAP 73
Query: 69 LLQVIVKKENPQLVILG 85
L + KKE P ++ G
Sbjct: 74 ALVALAKKEKPSHILAG 90
>gnl|CDD|130619 TIGR01556, rhamnosyltran, L-rhamnosyltransferase. This model
subfamily is comprised of gamma proteobacteria whose
proteins function as L-rhamnosyltransferases in the
synthesis of their respective surface polysaccharides.
Rhamnolipids are glycolipids containing mono- or di-
L-rhamnose molecules. Rhamnolipid synthesis occurs by
sequential glycosyltransferase reactions involving two
distinct rhamnosyltransferase enzymes. In P.aeruginosa,
the synthesis of mono-rhamnolipids is catalyzed by
rhamnosyltransferase 1, and proceeds by a
glycosyltransfer reaction catalyzed by
rhamnosyltransferase 2 to yield di-rhamnolipids [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 281
Score = 27.8 bits (62), Expect = 4.6
Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 41 LQIAMAMGVDRAILIETDTILQSLSVAKLLQVIVKKENPQLVILGKQSIDSD 92
L + GV +L++ D+ + +A + ++ EN Q LG + D
Sbjct: 66 LDASFRRGVQGVLLLDQDSRPGNAFLAAQWK-LLSAENGQACALGPRFFDRG 116
>gnl|CDD|113590 pfam04824, Rad21_Rec8, Conserved region of Rad21 / Rec8 like
protein. This family represents a conserved region
found in eukaryotic cohesins of the Rad21, Rec8 and Scc1
families. Members of this family mediate sister
chromatid cohesion during mitosis and meiosis, as part
of the cohesin complex. Cohesion is necessary for
homologous recombination (including double-strand break
repair) and correct chromatid segregation. These
proteins may also be involved in chromosome
condensation. Dissociation at the metaphase to anaphase
transition causes loss of cohesion and chromatid
segregation.
Length = 55
Score = 25.4 bits (56), Expect = 6.2
Identities = 11/33 (33%), Positives = 13/33 (39%), Gaps = 2/33 (6%)
Query: 98 QMLAALLNWPQA--TFASKIVLKKNNKILVTQE 128
L A +A F +VLK I V QE
Sbjct: 9 SQLPAGTTRKEAARLFYELLVLKTEGAIDVKQE 41
>gnl|CDD|133017 cd02526, GT2_RfbF_like, RfbF is a putative dTDP-rhamnosyl
transferase. Shigella flexneri RfbF protein is a
putative dTDP-rhamnosyl transferase. dTDP rhamnosyl
transferases of Shigella flexneri add rhamnose sugars
to N-acetyl-glucosamine in the O-antigen tetrasaccharide
repeat. Lipopolysaccharide O antigens are important
virulence determinants for many bacteria. The variations
of sugar composition, the sequence of the sugars and the
linkages in the O antigen provide structural diversity
of the O antigen.
Length = 237
Score = 26.9 bits (60), Expect = 7.3
Identities = 24/104 (23%), Positives = 41/104 (39%), Gaps = 12/104 (11%)
Query: 3 INPFDEIAI-----ESAIRLRESSNKIKEIIAISCGN-----KKCKEILQIAMAMGVDRA 52
D++ + + I LR N K I I G K ++ A+ G D
Sbjct: 21 AEQVDKVVVVDNSSGNDIELRLRLNSEK-IELIHLGENLGIAKALNIGIKAALENGADYV 79
Query: 53 ILIETDTILQSLSVAKLLQ-VIVKKENPQLVILGKQSIDSDNNQ 95
+L + D++ V KLL I+ +N + +G + ID +
Sbjct: 80 LLFDQDSVPPPDMVEKLLAYKILSDKNSNIGAVGPRIIDRRTGE 123
>gnl|CDD|131391 TIGR02338, gimC_beta, prefoldin, beta subunit, archaeal.
Chaperonins are cytosolic, ATP-dependent molecular
chaperones, with a conserved toroidal architecture, that
assist in the folding of nascent and/or denatured
polypeptide chains. The group I chaperonin system
consists of GroEL and GroES, and is found (usually) in
bacteria and organelles of bacterial origin. The group
II chaperonin system, called the thermosome in Archaea
and TRiC or CCT in the Eukaryota, is structurally
similar but only distantly related. Prefoldin, also
called GimC, is a complex in Archaea and Eukaryota, that
works with group II chaperonins. Members of this protein
family are the archaeal clade of the beta class of
prefoldin subunit. Closely related, but outside the
scope of this family are the eukaryotic beta-class
prefoldin subunits, Gim-1,3,4 and 6. The alpha class
prefoldin subunits are more distantly related.
Length = 110
Score = 26.2 bits (58), Expect = 7.5
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 3/80 (3%)
Query: 76 KENPQLVILGKQSIDSDNNQTGQMLAALLNWPQATFASKIV---LKKNNKILVTQEIEDG 132
++ Q V KQ +++ + + L L P T K V L K +K QE+++
Sbjct: 16 QQQLQAVATQKQQVEAQLKEAEKALEELERLPDDTPVYKSVGNLLVKTDKEEAIQELKEK 75
Query: 133 KETILLSLPAIITTDLRMNE 152
KET+ L + + + R+ E
Sbjct: 76 KETLELRVKTLQRQEERLRE 95
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
0.316 0.134 0.351
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,879,551
Number of extensions: 1049133
Number of successful extensions: 1240
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1214
Number of HSP's successfully gapped: 61
Length of query: 219
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 126
Effective length of database: 6,812,680
Effective search space: 858397680
Effective search space used: 858397680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.7 bits)