RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9411
(118 letters)
>gnl|CDD|184186 PRK13623, PRK13623, iron-sulfur cluster insertion protein ErpA;
Provisional.
Length = 115
Score = 192 bits (489), Expect = 6e-65
Identities = 64/114 (56%), Positives = 85/114 (74%)
Query: 2 NENVKNNISITLTEVAIKKVSHLIKKKGNLNLKLRVFIQGGGCSGFQYGFMFDEHTNKDD 61
+ + + T+ A KV LI+++GN +LKLRV+I GGGCSGFQYGF FDE N+DD
Sbjct: 1 MMSDDVPLPLVFTDAAAAKVKELIEEEGNPDLKLRVYITGGGCSGFQYGFTFDEQVNEDD 60
Query: 62 IIFKKNGIQLLIDSVSYQYLIGSEIDYKDDLDGSKFVIKNPNAVTTCGCGSSFS 115
+K G+ L++D +S QYL+G+E+DY + L+GS+FVIKNPNA TTCGCGSSFS
Sbjct: 61 TTIEKQGVTLVVDPMSLQYLVGAEVDYTEGLEGSRFVIKNPNAKTTCGCGSSFS 114
>gnl|CDD|223393 COG0316, sufA, Fe-S cluster assembly scaffold protein
[Posttranslational modification, protein turnover,
chaperones].
Length = 110
Score = 156 bits (396), Expect = 7e-51
Identities = 57/106 (53%), Positives = 78/106 (73%)
Query: 11 ITLTEVAIKKVSHLIKKKGNLNLKLRVFIQGGGCSGFQYGFMFDEHTNKDDIIFKKNGIQ 70
ITLT+ A +V L+ K+G NL LRV ++GGGCSGFQYG FD+ N+DD +F+++G++
Sbjct: 5 ITLTDAAAARVKALLAKEGEENLGLRVGVKGGGCSGFQYGLEFDDEINEDDTVFEQDGVK 64
Query: 71 LLIDSVSYQYLIGSEIDYKDDLDGSKFVIKNPNAVTTCGCGSSFST 116
+++D S YL G+EIDY +DL GS F KNPNA ++CGCG SFS
Sbjct: 65 VVVDPKSLPYLEGTEIDYVEDLLGSGFTFKNPNAKSSCGCGESFSV 110
>gnl|CDD|232799 TIGR00049, TIGR00049, Iron-sulfur cluster assembly accessory
protein. Proteins in this subfamily appear to be
associated with the process of FeS-cluster assembly. The
HesB proteins are associated with the nif gene cluster
and the Rhizobium gene IscN has been shown to be
required for nitrogen fixation. Nitrogenase includes
multiple FeS clusters and many genes for their assembly.
The E. coli SufA protein is associated with SufS, a NifS
homolog and SufD which are involved in the FeS cluster
assembly of the FhnF protein. The Azotobacter protein
IscA (homologs of which are also found in E.coli) is
associated which IscS, another NifS homolog and IscU, a
nifU homolog as well as other factors consistent with a
role in FeS cluster chemistry. A homolog from Geobacter
contains a selenocysteine in place of an otherwise
invariant cysteine, further suggesting a role in redox
chemistry [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other].
Length = 105
Score = 150 bits (381), Expect = 1e-48
Identities = 54/105 (51%), Positives = 74/105 (70%)
Query: 12 TLTEVAIKKVSHLIKKKGNLNLKLRVFIQGGGCSGFQYGFMFDEHTNKDDIIFKKNGIQL 71
TLT+ A K++ L+ +G NL LRV ++GGGCSG QYG FD+ N+DD +F+++G+++
Sbjct: 1 TLTDSAAKRIKALLAGEGEPNLGLRVGVKGGGCSGLQYGLEFDDEPNEDDEVFEQDGVKV 60
Query: 72 LIDSVSYQYLIGSEIDYKDDLDGSKFVIKNPNAVTTCGCGSSFST 116
++D S YL GSEIDY ++L GS F NPNA TCGCG SFS
Sbjct: 61 VVDPKSLPYLDGSEIDYVEELLGSGFTFTNPNAKGTCGCGKSFSV 105
>gnl|CDD|110518 pfam01521, Fe-S_biosyn, Iron-sulphur cluster biosynthesis. This
family is involved in iron-sulphur cluster biosynthesis.
Its members include proteins that are involved in
nitrogen fixation such as the HesB and HesB-like
proteins.
Length = 91
Score = 109 bits (275), Expect = 9e-33
Identities = 36/92 (39%), Positives = 59/92 (64%), Gaps = 1/92 (1%)
Query: 11 ITLTEVAIKKVSHLIKKKGNLNLKLRVFIQGGGCSGFQYGFMFDEHTNKDDIIFKKNGIQ 70
ITLT+ A K + L+ +G LR+ ++ GGCSGF YG F++ ++ D +F+++G+
Sbjct: 1 ITLTDAAAKHIKKLLDLEGG-ENGLRIGVRYGGCSGFSYGLTFEDEPDEGDEVFEQDGVT 59
Query: 71 LLIDSVSYQYLIGSEIDYKDDLDGSKFVIKNP 102
+++D S YL G+EID+ ++L GS F NP
Sbjct: 60 VVVDEKSLPYLEGTEIDFVEELLGSGFTFSNP 91
>gnl|CDD|215564 PLN03082, PLN03082, Iron-sulfur cluster assembly; Provisional.
Length = 163
Score = 102 bits (255), Expect = 6e-29
Identities = 43/107 (40%), Positives = 73/107 (68%), Gaps = 2/107 (1%)
Query: 10 SITLTEVAIKKVSHLIKKKGNLNLK-LRVFIQGGGCSGFQYGFMFDEHTNKDDIIFKKNG 68
++ +T+ I+++ L + + K LR+ ++ GGCSGFQY F D+ TN DD +F+K+G
Sbjct: 54 AVHMTDNCIRRLKELQTSEPSAEDKMLRLSVETGGCSGFQYVFELDDKTNSDDRVFEKDG 113
Query: 69 IQLLIDSVSYQYLIGSEIDYKDDLDGSKFVIK-NPNAVTTCGCGSSF 114
++L++D++SY ++ G+ +DY ++L S FV+ NP+AV C C SSF
Sbjct: 114 VKLVVDNISYDFVKGATVDYVEELIRSAFVVSTNPSAVGGCSCKSSF 160
>gnl|CDD|131052 TIGR01997, sufA_proteo, FeS assembly scaffold SufA. This model
represents the SufA protein of the SUF system of
iron-sulfur cluster biosynthesis. This system performs
FeS biosynthesis even during oxidative stress and tends
to be absent in obligate anaerobic and microaerophilic
bacteria [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other].
Length = 107
Score = 79.5 bits (196), Expect = 1e-20
Identities = 29/104 (27%), Positives = 55/104 (52%), Gaps = 1/104 (0%)
Query: 11 ITLTEVAIKKVSHLIKKKGNLNLKLRVFIQGGGCSGFQYGFMFDEHTNKDDIIFKKNGIQ 70
ITLT+ A + L+ K+ + +R+ ++ GC+G +Y KDD + + +G +
Sbjct: 3 ITLTDAAAIHIRELVAKRPEA-VGIRLGVKKTGCAGMEYVLDLVSEPKKDDDLIEHDGAK 61
Query: 71 LLIDSVSYQYLIGSEIDYKDDLDGSKFVIKNPNAVTTCGCGSSF 114
+ + + +++G+++D+ F NPNA + CGCG SF
Sbjct: 62 VFVAPEAVLFILGTQVDFVRTTLRQGFKFNNPNATSACGCGESF 105
>gnl|CDD|213674 TIGR02011, IscA, iron-sulfur cluster assembly protein IscA. This
model represents the IscA component of the ISC system
for iron-sulfur cluster assembly. The ISC system
consists of IscRASU, HscAB and an Isc-specific
ferredoxin. IscA previously was believed to act as a
scaffold and now is seen as an iron donor protein. This
clade is limited to the proteobacteria [Biosynthesis of
cofactors, prosthetic groups, and carriers, Other].
Length = 105
Score = 78.7 bits (194), Expect = 2e-20
Identities = 38/104 (36%), Positives = 58/104 (55%), Gaps = 1/104 (0%)
Query: 11 ITLTEVAIKKVSHLIKKKGNLNLKLRVFIQGGGCSGFQYGFMFDEHTNKDDIIFKKNGIQ 70
ITLT+ A +V+ + +G LR+ ++ GCSG Y F + DDI+F+ G++
Sbjct: 1 ITLTDSAAARVNTFLANRGK-GFGLRLGVKTSGCSGMAYVLEFVDEPTPDDIVFEDKGVK 59
Query: 71 LLIDSVSYQYLIGSEIDYKDDLDGSKFVIKNPNAVTTCGCGSSF 114
++ID S QYL G+++D+ + F NPN CGCG SF
Sbjct: 60 IVIDGKSLQYLDGTQLDFVKEGLNEGFKFTNPNVKDECGCGESF 103
>gnl|CDD|181914 PRK09502, iscA, iron-sulfur cluster assembly protein; Provisional.
Length = 107
Score = 76.8 bits (189), Expect = 1e-19
Identities = 35/107 (32%), Positives = 60/107 (56%), Gaps = 1/107 (0%)
Query: 9 ISITLTEVAIKKVSHLIKKKGNLNLKLRVFIQGGGCSGFQYGFMFDEHTNKDDIIFKKNG 68
+SITL++ A +V+ + +G LR+ ++ GCSG Y F + +DI+F+ G
Sbjct: 1 MSITLSDSAAARVNTFLANRGK-GFGLRLGVRTSGCSGMAYVLEFVDEPTPEDIVFEDKG 59
Query: 69 IQLLIDSVSYQYLIGSEIDYKDDLDGSKFVIKNPNAVTTCGCGSSFS 115
+++++D S Q+L G+++D+ + F NPN CGCG SF
Sbjct: 60 VKVVVDGKSLQFLDGTQLDFVKEGLNEGFKFTNPNVKDECGCGESFH 106
>gnl|CDD|181915 PRK09504, sufA, iron-sulfur cluster assembly scaffold protein;
Provisional.
Length = 122
Score = 61.7 bits (150), Expect = 2e-13
Identities = 32/104 (30%), Positives = 55/104 (52%), Gaps = 1/104 (0%)
Query: 11 ITLTEVAIKKVSHLIKKKGNLNLKLRVFIQGGGCSGFQYGFMFDEHTNKDDIIFKKNGIQ 70
+TLT A + L+ K+ + +R+ ++ GC+GF Y +KDD++F+ +G +
Sbjct: 18 LTLTPAAAAHIRELMAKQPGM-KGVRLGVKQTGCAGFGYVLDSVSEPDKDDLVFEHDGAK 76
Query: 71 LLIDSVSYQYLIGSEIDYKDDLDGSKFVIKNPNAVTTCGCGSSF 114
L + + ++ G+E+DY + F NP A CGCG SF
Sbjct: 77 LFVPLQAMPFIDGTEVDYVREGLNQIFKFHNPKAQNECGCGESF 120
>gnl|CDD|132384 TIGR03341, YhgI_GntY, IscR-regulated protein YhgI. IscR
(TIGR02010) is an iron-sulfur cluster-binding
transcriptional regulator (see Genome Property
GenProp0138). Members of this protein family include
YhgI, whose expression is under control of IscR, and
show sequence similarity to IscA, a known protein of
iron-sulfur cluster biosynthesis. These two lines of
evidence strongly suggest a role as an iron-sulfur
cluster biosynthesis protein. An older study designated
this protein GntY and suggested a role for it and for
the product of an adjacent gene, based on
complementation studies, in gluconate utilization
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 190
Score = 43.1 bits (102), Expect = 4e-06
Identities = 29/97 (29%), Positives = 47/97 (48%), Gaps = 5/97 (5%)
Query: 11 ITLTEVAIKKVSHLIKKKGNLNLKLRVFIQGGGCSGFQYGFMF---DEHTNKDDIIFKKN 67
IT+TE A ++ L+ K+ N +RVF+ G + + DE DI + N
Sbjct: 1 ITITEAAQAYLAKLLAKQ-NEGTGIRVFVVNPGTPYAECCVSYCPPDE-VEPSDIKLEFN 58
Query: 68 GIQLLIDSVSYQYLIGSEIDYKDDLDGSKFVIKNPNA 104
G +D++S +L + ID+ D G + +K PNA
Sbjct: 59 GFSAYVDALSAPFLEDAVIDFVTDRMGGQLTLKAPNA 95
>gnl|CDD|183027 PRK11190, PRK11190, Fe/S biogenesis protein NfuA; Provisional.
Length = 192
Score = 38.8 bits (91), Expect = 1e-04
Identities = 16/45 (35%), Positives = 24/45 (53%)
Query: 60 DDIIFKKNGIQLLIDSVSYQYLIGSEIDYKDDLDGSKFVIKNPNA 104
D K +G +D +S +L +EID+ D GS+ +K PNA
Sbjct: 52 TDTELKFDGFSAYVDELSAPFLEDAEIDFVTDQLGSQLTLKAPNA 96
>gnl|CDD|188182 TIGR01911, HesB_rel_seleno, HesB-like selenoprotein. This model
represents a family of small proteins related to HesB
and its close homologs, which are likely to be
invovlved in iron-sulfur cluster assembly (See
TIGR00049 and pfam01521). Several members are
selenoproteins, with a TGA codon and Sec residue that
aligns to the conserved Cys of the HesB domain. A
variable Cys/Ser/Gly-rich C-terminal region is not
included in the seed alignment and model [Unknown
function, General].
Length = 92
Score = 31.0 bits (70), Expect = 0.050
Identities = 14/65 (21%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 11 ITLTEVAIKKVSHLIKKKGNLNLKLRVFIQGGGCSGFQYGFMFDEHTNKDDIIFKKNGIQ 70
+ +++ A ++ +KK N +R++ +G G G ++G N++D + N
Sbjct: 4 VVMSDEAYEEFLDFLKKNNQDNNVVRIYFEGFGUGGPKFGIAIA-EPNENDELIYINDFT 62
Query: 71 LLIDS 75
ID
Sbjct: 63 FYIDP 67
>gnl|CDD|185216 PRK15316, PRK15316, RatA-like protein; Provisional.
Length = 2683
Score = 30.8 bits (69), Expect = 0.15
Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 5/88 (5%)
Query: 27 KKGNLNLKLRVFIQGGGCSGFQYGFMFDEHTNKDDIIFKKNGIQLLIDSVSYQYLIGSEI 86
KK L+ V +G M + T D +FK+ LL+ +S G
Sbjct: 1123 KKATLDTIFTVVTSPDSDKAKMWGHMPETVTAADGTVFKR---PLLLKELSST--SGRTA 1177
Query: 87 DYKDDLDGSKFVIKNPNAVTTCGCGSSF 114
+D+ D ++F + ++ GCGS +
Sbjct: 1178 IAEDNEDWAQFTQAQAISTSSNGCGSEY 1205
>gnl|CDD|227178 COG4841, COG4841, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 95
Score = 27.8 bits (62), Expect = 0.74
Identities = 27/97 (27%), Positives = 42/97 (43%), Gaps = 11/97 (11%)
Query: 11 ITLTEVAIK-KVSHLIKKKGNLNLKLRVFIQGGGCS----GFQYGFMFDEHTNKDDIIFK 65
I +T+ A+K L ++GN K+R F++ GGCS GF G E + +
Sbjct: 3 IEVTDQALKWFKEELDLEEGN---KVRFFVRYGGCSSLQQGFSLGVA-KEVPKEIGYKQE 58
Query: 66 KNGIQLLIDSVSYQYLIGSE--IDYKDDLDGSKFVIK 100
+G+ I+ Y + +DY D D F K
Sbjct: 59 YDGLTFFIEEKDLWYFDDHDLKVDYSPDTDEISFSYK 95
>gnl|CDD|131559 TIGR02507, MtrF, tetrahydromethanopterin S-methyltransferase, F
subunit. This small protein (MtrF) is one of eight
subunits of the N5-methyltetrahydromethanopterin:
coenzyme M methyltransferase in methanogenic archaea.
This methyltranferase is membrane-associated enzyme
complex that uses methy-transfer reaction to drive
sodium-ion pump. Archaea domain, have evolved
energy-yielding pathways marked by one-carbon
biochemistry featuring novel cofactors and enzymes.
This transferase is involved in the transfer of
'methyl' group from N5-methyltetrahydromethanopterin to
coenzyme M. In an accompanying reaction, methane is
produced by two-electron reduction of the methyl moiety
in methyl-coenzyme M by another enzyme methyl-coenzyme
M reductase.
Length = 65
Score = 25.2 bits (55), Expect = 4.4
Identities = 11/40 (27%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 17 AIKKVSHLIKKKGNL---NLKLRVFIQGGGCSGFQYGFMF 53
+IK + I + L ++ L +Q +G YGF+F
Sbjct: 12 SIKSLVEAIDYRVQLITRDIGLASGVQTTTITGLAYGFLF 51
>gnl|CDD|143256 cd05848, Ig1_Contactin-5, First Ig domain of contactin-5.
Ig1_Contactin-5: First Ig domain of the neural cell
adhesion molecule contactin-5. Contactins are comprised
of six Ig domains followed by four fibronectin type III
(FnIII) domains, anchored to the membrane by
glycosylphosphatidylinositol. The different contactins
show different expression patterns in the central
nervous system. In rats, a lack of contactin-5 (NB-2)
results in an impairment of the neuronal activity in the
auditory system. Contactin-5 is expressed specifically
in the postnatal nervous system, peaking at about 3
weeks postnatal. Contactin-5 is highly expressed in the
adult human brain in the occipital lobe and in the
amygdala; lower levels of expression have been detected
in the corpus callosum, caudate nucleus, and spinal
cord.
Length = 94
Score = 24.9 bits (54), Expect = 6.5
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 7/39 (17%)
Query: 77 SYQYLI-GSEIDYKDD-----LDGSKFVIKNPNAVTTCG 109
+Y++L G+EID + D +DG+ +I NP+ V G
Sbjct: 35 TYRWLRNGTEIDTESDYRYSLIDGN-LIISNPSEVKDSG 72
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
0.318 0.138 0.398
Gapped
Lambda K H
0.267 0.0746 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,849,570
Number of extensions: 521363
Number of successful extensions: 444
Number of sequences better than 10.0: 1
Number of HSP's gapped: 439
Number of HSP's successfully gapped: 27
Length of query: 118
Length of database: 10,937,602
Length adjustment: 81
Effective length of query: 37
Effective length of database: 7,344,928
Effective search space: 271762336
Effective search space used: 271762336
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 (21.7 bits)
S2: 53 (24.2 bits)