RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7477
(237 letters)
>gnl|CDD|215564 PLN03082, PLN03082, Iron-sulfur cluster assembly; Provisional.
Length = 163
Score = 108 bits (270), Expect = 2e-29
Identities = 51/117 (43%), Positives = 79/117 (67%), Gaps = 5/117 (4%)
Query: 85 PTLSPYSTSSPSEKPVSASTLKDLVIHDSCIKKLKEI-----STDGSFLRIIVEGGGCSG 139
+ + S+ S P S+++L + + D+CI++LKE+ S + LR+ VE GGCSG
Sbjct: 32 SSSALKEASTSSSSPSSSASLDAVHMTDNCIRRLKELQTSEPSAEDKMLRLSVETGGCSG 91
Query: 140 FQYKFELDTQVSDEDRVYEKSGCKVVIDQTSLEYVQGSVIEYHQELIRSAFQISNNP 196
FQY FELD + + +DRV+EK G K+V+D S ++V+G+ ++Y +ELIRSAF +S NP
Sbjct: 92 FQYVFELDDKTNSDDRVFEKDGVKLVVDNISYDFVKGATVDYVEELIRSAFVVSTNP 148
Score = 71.5 bits (175), Expect = 1e-15
Identities = 35/85 (41%), Positives = 54/85 (63%), Gaps = 5/85 (5%)
Query: 5 PTVSPYSTSSPSEKPVSASTLKDLVIHDSCIKKLKEI-----STDGSFLRIIVEGGGCSG 59
+ + S+ S P S+++L + + D+CI++LKE+ S + LR+ VE GGCSG
Sbjct: 32 SSSALKEASTSSSSPSSSASLDAVHMTDNCIRRLKELQTSEPSAEDKMLRLSVETGGCSG 91
Query: 60 FQYKFELDTQVSDEDRVYEKSGCKI 84
FQY FELD + + +DRV+EK G K+
Sbjct: 92 FQYVFELDDKTNSDDRVFEKDGVKL 116
>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 = 100 bits (251), Expect = 3e-27
Identities = 38/94 (40%), Positives = 56/94 (59%), Gaps = 5/94 (5%)
Query: 112 DSCIKKLKEI----STDGSFLRIIVEGGGCSGFQYKFELDTQVSDEDRVYEKSGCKVVID 167
DS K++K + LR+ V+GGGCSG QY E D + +++D V+E+ G KVV+D
Sbjct: 4 DSAAKRIKALLAGEGEPNLGLRVGVKGGGCSGLQYGLEFDDEPNEDDEVFEQDGVKVVVD 63
Query: 168 QTSLEYVQGSVIEYHQELIRSAFQISNNPQVEQG 201
SL Y+ GS I+Y +EL+ S F + NP +
Sbjct: 64 PKSLPYLDGSEIDYVEELLGSGFTFT-NPNAKGT 96
Score = 62.6 bits (153), Expect = 8e-13
Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 4/57 (7%)
Query: 32 DSCIKKLKEI----STDGSFLRIIVEGGGCSGFQYKFELDTQVSDEDRVYEKSGCKI 84
DS K++K + LR+ V+GGGCSG QY E D + +++D V+E+ G K+
Sbjct: 4 DSAAKRIKALLAGEGEPNLGLRVGVKGGGCSGLQYGLEFDDEPNEDDEVFEQDGVKV 60
>gnl|CDD|223393 COG0316, sufA, Fe-S cluster assembly scaffold protein
[Posttranslational modification, protein turnover,
chaperones].
Length = 110
Score = 90.7 bits (226), Expect = 2e-23
Identities = 35/98 (35%), Positives = 60/98 (61%), Gaps = 5/98 (5%)
Query: 107 DLVIHDSCIKKLKEI----STDGSFLRIIVEGGGCSGFQYKFELDTQVSDEDRVYEKSGC 162
+ + D+ ++K + + LR+ V+GGGCSGFQY E D +++++D V+E+ G
Sbjct: 4 MITLTDAAAARVKALLAKEGEENLGLRVGVKGGGCSGFQYGLEFDDEINEDDTVFEQDGV 63
Query: 163 KVVIDQTSLEYVQGSVIEYHQELIRSAFQISNNPQVEQ 200
KVV+D SL Y++G+ I+Y ++L+ S F NP +
Sbjct: 64 KVVVDPKSLPYLEGTEIDYVEDLLGSGFTF-KNPNAKS 100
Score = 59.1 bits (144), Expect = 2e-11
Identities = 21/62 (33%), Positives = 38/62 (61%), Gaps = 4/62 (6%)
Query: 27 DLVIHDSCIKKLKEI----STDGSFLRIIVEGGGCSGFQYKFELDTQVSDEDRVYEKSGC 82
+ + D+ ++K + + LR+ V+GGGCSGFQY E D +++++D V+E+ G
Sbjct: 4 MITLTDAAAARVKALLAKEGEENLGLRVGVKGGGCSGFQYGLEFDDEINEDDTVFEQDGV 63
Query: 83 KI 84
K+
Sbjct: 64 KV 65
>gnl|CDD|184186 PRK13623, PRK13623, iron-sulfur cluster insertion protein ErpA;
Provisional.
Length = 115
Score = 85.4 bits (212), Expect = 2e-21
Identities = 39/92 (42%), Positives = 56/92 (60%), Gaps = 4/92 (4%)
Query: 107 DLVIHDSCIKKLKE-ISTDGSF---LRIIVEGGGCSGFQYKFELDTQVSDEDRVYEKSGC 162
LV D+ K+KE I +G+ LR+ + GGGCSGFQY F D QV+++D EK G
Sbjct: 9 PLVFTDAAAAKVKELIEEEGNPDLKLRVYITGGGCSGFQYGFTFDEQVNEDDTTIEKQGV 68
Query: 163 KVVIDQTSLEYVQGSVIEYHQELIRSAFQISN 194
+V+D SL+Y+ G+ ++Y + L S F I N
Sbjct: 69 TLVVDPMSLQYLVGAEVDYTEGLEGSRFVIKN 100
Score = 60.3 bits (147), Expect = 5e-12
Identities = 27/59 (45%), Positives = 36/59 (61%), Gaps = 4/59 (6%)
Query: 27 DLVIHDSCIKKLKE-ISTDGSF---LRIIVEGGGCSGFQYKFELDTQVSDEDRVYEKSG 81
LV D+ K+KE I +G+ LR+ + GGGCSGFQY F D QV+++D EK G
Sbjct: 9 PLVFTDAAAAKVKELIEEEGNPDLKLRVYITGGGCSGFQYGFTFDEQVNEDDTTIEKQG 67
>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 = 78.0 bits (193), Expect = 8e-19
Identities = 33/81 (40%), Positives = 50/81 (61%)
Query: 115 IKKLKEISTDGSFLRIIVEGGGCSGFQYKFELDTQVSDEDRVYEKSGCKVVIDQTSLEYV 174
IKKL ++ + LRI V GGCSGF Y + + + D V+E+ G VV+D+ SL Y+
Sbjct: 11 IKKLLDLEGGENGLRIGVRYGGCSGFSYGLTFEDEPDEGDEVFEQDGVTVVVDEKSLPYL 70
Query: 175 QGSVIEYHQELIRSAFQISNN 195
+G+ I++ +EL+ S F SN
Sbjct: 71 EGTEIDFVEELLGSGFTFSNP 91
Score = 47.6 bits (114), Expect = 1e-07
Identities = 19/50 (38%), Positives = 28/50 (56%)
Query: 35 IKKLKEISTDGSFLRIIVEGGGCSGFQYKFELDTQVSDEDRVYEKSGCKI 84
IKKL ++ + LRI V GGCSGF Y + + + D V+E+ G +
Sbjct: 11 IKKLLDLEGGENGLRIGVRYGGCSGFSYGLTFEDEPDEGDEVFEQDGVTV 60
>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 = 58.3 bits (141), Expect = 2e-11
Identities = 26/72 (36%), Positives = 43/72 (59%), Gaps = 1/72 (1%)
Query: 128 LRIIVEGGGCSGFQYKFELDTQVSDEDRVYEKSGCKVVIDQTSLEYVQGSVIEYHQELIR 187
LR+ V+ GCSG Y E + + +D V+E G K+VID SL+Y+ G+ +++ +E +
Sbjct: 24 LRLGVKTSGCSGMAYVLEFVDEPTPDDIVFEDKGVKIVIDGKSLQYLDGTQLDFVKEGLN 83
Query: 188 SAFQISNNPQVE 199
F+ NP V+
Sbjct: 84 EGFKF-TNPNVK 94
Score = 34.8 bits (80), Expect = 0.007
Identities = 15/37 (40%), Positives = 21/37 (56%)
Query: 48 LRIIVEGGGCSGFQYKFELDTQVSDEDRVYEKSGCKI 84
LR+ V+ GCSG Y E + + +D V+E G KI
Sbjct: 24 LRLGVKTSGCSGMAYVLEFVDEPTPDDIVFEDKGVKI 60
>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 = 57.1 bits (138), Expect = 7e-11
Identities = 20/82 (24%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 115 IKKLKEISTDGSFLRIIVEGGGCSGFQYKFELDTQVSDEDRVYEKSGCKVVIDQTSLEYV 174
I++L + +R+ V+ GC+G +Y +L ++ +D + E G KV + ++ ++
Sbjct: 13 IRELVAKRPEAVGIRLGVKKTGCAGMEYVLDLVSEPKKDDDLIEHDGAKVFVAPEAVLFI 72
Query: 175 QGSVIEYHQELIRSAFQISNNP 196
G+ +++ + +R F+ NNP
Sbjct: 73 LGTQVDFVRTTLRQGFKF-NNP 93
Score = 39.0 bits (91), Expect = 3e-04
Identities = 13/50 (26%), Positives = 27/50 (54%)
Query: 35 IKKLKEISTDGSFLRIIVEGGGCSGFQYKFELDTQVSDEDRVYEKSGCKI 84
I++L + +R+ V+ GC+G +Y +L ++ +D + E G K+
Sbjct: 13 IRELVAKRPEAVGIRLGVKKTGCAGMEYVLDLVSEPKKDDDLIEHDGAKV 62
>gnl|CDD|181914 PRK09502, iscA, iron-sulfur cluster assembly protein; Provisional.
Length = 107
Score = 56.4 bits (136), Expect = 1e-10
Identities = 26/71 (36%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 128 LRIIVEGGGCSGFQYKFELDTQVSDEDRVYEKSGCKVVIDQTSLEYVQGSVIEYHQELIR 187
LR+ V GCSG Y E + + ED V+E G KVV+D SL+++ G+ +++ +E +
Sbjct: 26 LRLGVRTSGCSGMAYVLEFVDEPTPEDIVFEDKGVKVVVDGKSLQFLDGTQLDFVKEGLN 85
Query: 188 SAFQISNNPQV 198
F+ NP V
Sbjct: 86 EGFKF-TNPNV 95
Score = 34.5 bits (79), Expect = 0.011
Identities = 15/37 (40%), Positives = 20/37 (54%)
Query: 48 LRIIVEGGGCSGFQYKFELDTQVSDEDRVYEKSGCKI 84
LR+ V GCSG Y E + + ED V+E G K+
Sbjct: 26 LRLGVRTSGCSGMAYVLEFVDEPTPEDIVFEDKGVKV 62
>gnl|CDD|181915 PRK09504, sufA, iron-sulfur cluster assembly scaffold protein;
Provisional.
Length = 122
Score = 48.2 bits (115), Expect = 2e-07
Identities = 24/108 (22%), Positives = 52/108 (48%), Gaps = 3/108 (2%)
Query: 92 TSSPSEKPVSASTLKDLVIHDSCIKKLKEISTDGSFLRIIVEGGGCSGFQYKFELDTQVS 151
T +P + TL I++L +R+ V+ GC+GF Y + ++
Sbjct: 7 TFNPDDFAWQGLTLTPAAAAH--IRELMAKQPGMKGVRLGVKQTGCAGFGYVLDSVSEPD 64
Query: 152 DEDRVYEKSGCKVVIDQTSLEYVQGSVIEYHQELIRSAFQISNNPQVE 199
+D V+E G K+ + ++ ++ G+ ++Y +E + F+ +NP+ +
Sbjct: 65 KDDLVFEHDGAKLFVPLQAMPFIDGTEVDYVREGLNQIFKF-HNPKAQ 111
Score = 39.0 bits (91), Expect = 4e-04
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 2/73 (2%)
Query: 12 TSSPSEKPVSASTLKDLVIHDSCIKKLKEISTDGSFLRIIVEGGGCSGFQYKFELDTQVS 71
T +P + TL I++L +R+ V+ GC+GF Y + ++
Sbjct: 7 TFNPDDFAWQGLTLTPAAAAH--IRELMAKQPGMKGVRLGVKQTGCAGFGYVLDSVSEPD 64
Query: 72 DEDRVYEKSGCKI 84
+D V+E G K+
Sbjct: 65 KDDLVFEHDGAKL 77
>gnl|CDD|181288 PRK08204, PRK08204, hypothetical protein; Provisional.
Length = 449
Score = 31.1 bits (71), Expect = 0.45
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 185 LIRSAFQISNNPQVEQGNLTKGDHFISPSNITRIRPRL 222
LIR ++ +P + G+L +GD I I + P +
Sbjct: 5 LIRGGTVLTMDPAI--GDLPRGDILIEGDRIAAVAPSI 40
>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 = 28.7 bits (64), Expect = 0.76
Identities = 15/76 (19%), Positives = 31/76 (40%), Gaps = 1/76 (1%)
Query: 117 KLKEISTDGSFLRIIVEGGGCSGFQYKFELDTQVSDEDRVYEKSGCKVVIDQTSLEYVQG 176
LK+ + D + +RI EG G G ++ + +++ +Y ID ++ G
Sbjct: 17 FLKKNNQDNNVVRIYFEGFGUGGPKFGIAIAEPNENDELIYIND-FTFYIDPNLIDQFLG 75
Query: 177 SVIEYHQELIRSAFQI 192
I +E ++
Sbjct: 76 FNITLREENFGKGLKL 91
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 27.7 bits (61), Expect = 7.9
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 183 QELIRSAFQISNNPQVEQGNLTKGDHFISPSNITRIRPRLSYRISPGIDSVCF 235
+EL+ A ++ + +V+Q N+ D + +IR L+ ISPG+ S+C+
Sbjct: 2275 KELLVKAGELIDEDKVKQINIAGLD-------VVKIRSPLTCEISPGVCSLCY 2320
>gnl|CDD|215137 PLN02246, PLN02246, 4-coumarate--CoA ligase.
Length = 537
Score = 27.3 bits (61), Expect = 8.3
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 4/63 (6%)
Query: 81 GCKIPTLSPYSTSSPSEKPVSASTLKDLVIHDSC-IKKLKEISTDGSFLRIIVEGG--GC 137
G T +P+ T + K AS K L+I SC + KLK ++ D + ++ GC
Sbjct: 99 GAVTTTANPFYTPAEIAKQAKASGAK-LIITQSCYVDKLKGLAEDDGVTVVTIDDPPEGC 157
Query: 138 SGF 140
F
Sbjct: 158 LHF 160
Score = 27.3 bits (61), Expect = 9.5
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 4/58 (6%)
Query: 6 TVSPYSTSSPSEKPVSASTLKDLVIHDSC-IKKLKEISTDGSFLRIIVEGG--GCSGF 60
T +P+ T + K AS K L+I SC + KLK ++ D + ++ GC F
Sbjct: 104 TANPFYTPAEIAKQAKASGAK-LIITQSCYVDKLKGLAEDDGVTVVTIDDPPEGCLHF 160
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
0.314 0.133 0.380
Gapped
Lambda K H
0.267 0.0690 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,672,694
Number of extensions: 1065205
Number of successful extensions: 598
Number of sequences better than 10.0: 1
Number of HSP's gapped: 596
Number of HSP's successfully gapped: 28
Length of query: 237
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 143
Effective length of database: 6,768,326
Effective search space: 967870618
Effective search space used: 967870618
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (25.8 bits)