RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1435
(171 letters)
>gnl|CDD|178203 PLN02593, PLN02593, adrenodoxin-like ferredoxin protein.
Length = 117
Score = 162 bits (413), Expect = 2e-52
Identities = 63/128 (49%), Positives = 84/128 (65%), Gaps = 12/128 (9%)
Query: 45 VNITFIDKDGKRREIKGKVGDNVLYLAHRYEIPMEGACEASLACTTCHVYVKHE-YLDAL 103
+++TF+DKDG+ R +K VG ++L AH +I +EGACE SLAC+TCHV V E + L
Sbjct: 1 ISVTFVDKDGEERTVKAPVGMSLLEAAHENDIELEGACEGSLACSTCHVIVMDEKVYNKL 60
Query: 104 PPAEEKEDDLLDLAPFLKDNSRLGCQNVMYNSRLGCQIILTKELEGIEVTLPKATRNFYV 163
P ++E+D+LDLA L + SRLGCQ+I EL+G+ + LP ATRNF V
Sbjct: 61 PEPTDEENDMLDLAFGLTE-----------TSRLGCQVIAKPELDGMRLALPAATRNFAV 109
Query: 164 DGHTPKPH 171
DGH PKPH
Sbjct: 110 DGHVPKPH 117
>gnl|CDD|131062 TIGR02007, fdx_isc, ferredoxin, 2Fe-2S type, ISC system. This
family consists of proteobacterial ferredoxins
associated with and essential to the ISC system of
2Fe-2S cluster assembly. This family is closely related
to (but excludes) eukaryotic (mitochondrial)
adrenodoxins, which are ferredoxins involved in electron
transfer to P450 cytochromes [Biosynthesis of cofactors,
prosthetic groups, and carriers, Other].
Length = 110
Score = 78.7 bits (194), Expect = 1e-19
Identities = 36/83 (43%), Positives = 52/83 (62%), Gaps = 1/83 (1%)
Query: 59 IKGKVGDNVLYLAHRYEIPMEGACEASLACTTCHVYVKHEYLDALPPAEEKEDDLLDLAP 118
++ K G+ +L +A I +E ACE S ACTTCH V+ E D+L A E+E+D+LD A
Sbjct: 18 VEAKPGETILDVALDNGIEIEHACEKSCACTTCHCIVR-EGFDSLEEASEQEEDMLDKAW 76
Query: 119 FLKDNSRLGCQNVMYNSRLGCQI 141
L+ +SRL CQ V+ + L +I
Sbjct: 77 GLEPDSRLSCQAVVADEDLVVEI 99
>gnl|CDD|223706 COG0633, Fdx, Ferredoxin [Energy production and conversion].
Length = 102
Score = 67.5 bits (165), Expect = 2e-15
Identities = 39/114 (34%), Positives = 52/114 (45%), Gaps = 15/114 (13%)
Query: 46 NITFIDKDGKRREIKGKV-GDNVLYLAHRYEIPMEGACEASLACTTCHVYVKHEYLDALP 104
I F+ DG+ + G+ +L A R IP+E AC AC TC V V + D +
Sbjct: 3 KIAFVTIDGEGDVTEAVNEGETLLEAAERNGIPIEYACRGG-ACGTCRVKVLEGF-DEVS 60
Query: 105 PAEEKEDDLLDLAPFLKDNSRLGCQNVMYNSRLGCQIILTKELEGIEVTLPKAT 158
P EE E+DLLD A NSRL CQ + +L+ V P+ T
Sbjct: 61 PPEESEEDLLDAAGLEG------------NSRLSCQCRVKGDLDIEVVEEPEYT 102
>gnl|CDD|185668 PTZ00490, PTZ00490, Ferredoxin superfamily; Provisional.
Length = 143
Score = 68.0 bits (166), Expect = 4e-15
Identities = 30/85 (35%), Positives = 42/85 (49%), Gaps = 11/85 (12%)
Query: 78 MEGACEASLACTTCHVYVKHEYLDALPPAEEKEDDLLDLAPFLKDNSRLGCQNVMYNSRL 137
+EG C + C TCHVY+ L E+E+D+L A +K+ SRL
Sbjct: 70 VEGTCNGCMQCATCHVYLSAASFKKLGGPSEEEEDVLAKALDVKE-----------TSRL 118
Query: 138 GCQIILTKELEGIEVTLPKATRNFY 162
CQ+ LT E++G+EV LP N
Sbjct: 119 ACQVDLTPEMDGLEVELPSYVTNRL 143
>gnl|CDD|238126 cd00207, fer2, 2Fe-2S iron-sulfur cluster binding domain.
Iron-sulfur proteins play an important role in electron
transfer processes and in various enzymatic reactions.
The family includes plant and algal ferredoxins, which
act as electron carriers in photosynthesis and
ferredoxins, which participate in redox chains (from
bacteria to mammals). Fold is ismilar to thioredoxin.
Length = 84
Score = 41.2 bits (97), Expect = 1e-05
Identities = 21/83 (25%), Positives = 33/83 (39%), Gaps = 9/83 (10%)
Query: 47 ITFIDKDGKRREIKGKVGDNVLYLAHRYEIPMEGACEASLACTTCHVYVKHEYLDALPPA 106
+T G E++ G+ +L A I + +C A AC TC V V +D P+
Sbjct: 1 VTINVP-GSGVEVEVPEGETLLDAAREAGIDIPYSCRAG-ACGTCKVEVVEGEVDQSDPS 58
Query: 107 EEKEDDLLDLAPFLKDNSRLGCQ 129
E++ + L CQ
Sbjct: 59 LLDEEE-------AEGGYVLACQ 74
>gnl|CDD|215725 pfam00111, Fer2, 2Fe-2S iron-sulfur cluster binding domain.
Length = 77
Score = 35.2 bits (81), Expect = 0.002
Identities = 21/81 (25%), Positives = 27/81 (33%), Gaps = 9/81 (11%)
Query: 50 IDKDGKRREIKGKVGDNVLYLAHR-YEIPMEGACEASLACTTCHVYVKHEYLDALPPAEE 108
+ DGK I+ G+ L A I + +C C TC V V +
Sbjct: 1 VTIDGKGVTIEVPDGETTLLDAAEEAGIDIPYSCRGG-GCGTCAVKVLEG--EVQSDQSF 57
Query: 109 KEDDLLDLAPFLKDNSRLGCQ 129
EDD L L CQ
Sbjct: 58 LEDDELA-----AGYVVLACQ 73
>gnl|CDD|130996 TIGR01941, nqrF, NADH:ubiquinone oxidoreductase,
Na(+)-translocating, F subunit. This model represents
the NqrF subunit of the six-protein, Na(+)-pumping
NADH-quinone reductase of a number of marine and
pathogenic Gram-negative bacteria. This oxidoreductase
complex functions primarily as a sodium ion pump
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 405
Score = 30.1 bits (68), Expect = 0.51
Identities = 25/107 (23%), Positives = 41/107 (38%), Gaps = 17/107 (15%)
Query: 46 NITFIDKDGKRREIKGKVGDNVLYLAHRYEIPMEGACEASLACTTCHVYVKHEYLDALPP 105
+IT D + + I G +L I + AC C C V V + LP
Sbjct: 31 DITIGINDDEEKSITVPAGGKLLNTLASNGIFISSACGGGGTCGQCRVRVVEGGGEILPT 90
Query: 106 AEEKEDDLLDLAPFLKDNSRLGCQNVMYNSRLGCQIILTKELEGIEV 152
+L+ F K ++ G RL CQ+ + +++ IE+
Sbjct: 91 ---------ELSHFSKREAKEGW-------RLSCQVKVKQDMS-IEI 120
>gnl|CDD|178988 PRK00364, groES, co-chaperonin GroES; Reviewed.
Length = 95
Score = 27.0 bits (61), Expect = 2.2
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 50 IDKDGKRREIKGKVGDNVLY 69
+G+R + KVGD VL+
Sbjct: 48 RLDNGERVPLDVKVGDKVLF 67
>gnl|CDD|217969 pfam04216, FdhE, Protein involved in formate dehydrogenase
formation. The function of these proteins is unknown.
They may possibly be involved in the formation of
formate dehydrogenase.
Length = 283
Score = 28.1 bits (63), Expect = 2.5
Identities = 14/34 (41%), Positives = 16/34 (47%), Gaps = 4/34 (11%)
Query: 87 ACTTCHVYVKHEYLDALPPAEEKEDDL----LDL 116
C TCH Y+K + P E DDL LDL
Sbjct: 233 TCDTCHSYLKILDQEKDPDLEPVADDLASLALDL 266
>gnl|CDD|197951 smart00883, Cpn10, Chaperonin 10 Kd subunit. The chaperonins are
'helper' molecules required for correct folding and
subsequent assembly of some proteins. These are
required for normal cell growth, and are
stress-induced, acting to stabilise or protect
disassembled polypeptides under heat-shock conditions.
Type I chaperonins present in eubacteria, mitochondria
and chloroplasts require the concerted action of 2
proteins, chaperonin 60 (cpn60) and chaperonin 10
(cpn10). The 10 kDa chaperonin (cpn10 - or groES in
bacteria) exists as a ring-shaped oligomer of between
six to eight identical subunits, while the 60 kDa
chaperonin (cpn60 - or groEL in bacteria) forms a
structure comprising 2 stacked rings, each ring
containing 7 identical subunits. These ring structures
assemble by self-stimulation in the presence of
Mg2+-ATP. The central cavity of the cylindrical cpn60
tetradecamer provides as isolated environment for
protein folding whilst cpn-10 binds to cpn-60 and
synchronizes the release of the folded protein in an
Mg2+-ATP dependent manner. The binding of cpn10 to
cpn60 inhibits the weak ATPase activity of cpn60.
Length = 93
Score = 26.2 bits (59), Expect = 3.8
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 50 IDKDGKRREIKGKVGDNVLY 69
++G+R + KVGD VL+
Sbjct: 47 RLENGERVPLDVKVGDKVLF 66
>gnl|CDD|225166 COG2257, COG2257, Uncharacterized homolog of the cytoplasmic
domain of flagellar protein FhlB [Function unknown].
Length = 92
Score = 26.2 bits (58), Expect = 4.8
Identities = 4/20 (20%), Positives = 13/20 (65%)
Query: 60 KGKVGDNVLYLAHRYEIPME 79
KG++ + ++ A + +P++
Sbjct: 30 KGEIAEKIIEKAKEHGVPIQ 49
>gnl|CDD|130625 TIGR01562, FdhE, formate dehydrogenase accessory protein FdhE.
This model describes an accessory protein required for
the assembly of formate dehydrogenase of certain
proteobacteria although not present in the final
complex. The exact nature of the function of FdhE in the
assembly of the complex is unknown, but considering the
presence of selenocysteine, molybdopterin, iron-sulfur
clusters and cytochrome b556, it is likely to have
something to do with the insertion of cofactors. The
only sequence scoring between trusted and noise is that
from Aquifex aeolicus, which shows certain structural
differences from the proteobacterial forms in the
alignment. However it is notable that A. aeolicus also
has a sequence scoring above trusted to the alpha
subunit of formate dehydrogenase (TIGR01553).
Length = 305
Score = 26.4 bits (58), Expect = 8.9
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 88 CTTCHVYVKHEYLDALPPAEEKEDDLLDLA 117
C +C Y+K Y + P A+ DDL LA
Sbjct: 255 CDSCQGYLKILYQEKDPHADAVADDLASLA 284
>gnl|CDD|238197 cd00320, cpn10, Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10
cooperates with chaperonin 60 (cpn60 or GroEL), an
ATPase, to assist the folding and assembly of proteins
and is found in eubacterial cytosol, as well as in the
matrix of mitochondria and chloroplasts. It forms
heptameric rings with a dome-like structure, forming a
lid to the large cavity of the tetradecameric cpn60
cylinder and thereby tightly regulating release and
binding of proteins to the cpn60 surface.
Length = 93
Score = 25.2 bits (56), Expect = 9.0
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 50 IDKDGKRREIKGKVGDNVLY 69
+++G+R + KVGD VL+
Sbjct: 47 RNENGERVPLSVKVGDKVLF 66
>gnl|CDD|225426 COG2871, NqrF, Na+-transporting NADH:ubiquinone oxidoreductase,
subunit NqrF [Energy production and conversion].
Length = 410
Score = 26.3 bits (58), Expect = 9.5
Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 17/77 (22%)
Query: 76 IPMEGACEASLACTTCHVYVKHEYLDALPPAEEKEDDLLDLAPFLKDNSRLGCQNVMYNS 135
I + AC +C C V VK + LP +L+ K ++ G
Sbjct: 66 IFISSACGGGGSCGQCKVRVKKGGGEILPT---------ELSHISKREAKEGW------- 109
Query: 136 RLGCQIILTKELEGIEV 152
RL CQ+ + +++ +EV
Sbjct: 110 RLSCQVNVKHDMD-LEV 125
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 0.139 0.433
Gapped
Lambda K H
0.267 0.0876 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,846,292
Number of extensions: 788444
Number of successful extensions: 691
Number of sequences better than 10.0: 1
Number of HSP's gapped: 680
Number of HSP's successfully gapped: 23
Length of query: 171
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 81
Effective length of database: 6,945,742
Effective search space: 562605102
Effective search space used: 562605102
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: 55 (24.7 bits)