RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781064|ref|YP_003065477.1| FeS assembly scaffold SufA
[Candidatus Liberibacter asiaticus str. psy62]
(116 letters)
>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.
Length = 107
Score = 139 bits (352), Expect = 2e-34
Identities = 53/108 (49%), Positives = 78/108 (72%), Gaps = 2/108 (1%)
Query: 4 IVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDG 63
++T+T+AA I+E+V + +A GIR+ +KK GCAG+EY++DLV+ P DDLIE DG
Sbjct: 2 VITLTDAAAIHIRELV-AKRPEAVGIRLGVKKTGCAGMEYVLDLVS-EPKKDDDLIEHDG 59
Query: 64 VKVWIDSASLLYMLGTEIDFKTEKLYSGFVFHNPNQVSACGCGQSVEI 111
KV++ ++L++LGT++DF L GF F+NPN SACGCG+S E+
Sbjct: 60 AKVFVAPEAVLFILGTQVDFVRTTLRQGFKFNNPNATSACGCGESFEL 107
>gnl|CDD|161681 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.
Length = 105
Score = 123 bits (312), Expect = 8e-30
Identities = 46/103 (44%), Positives = 67/103 (65%), Gaps = 1/103 (0%)
Query: 6 TMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGVK 65
T+T++A RIK ++ G+R+ +K GGC+GL+Y ++ D P + D++ E+DGVK
Sbjct: 1 TLTDSAAKRIKALLAGEGEPNLGLRVGVKGGGCSGLQYGLEFD-DEPNEDDEVFEQDGVK 59
Query: 66 VWIDSASLLYMLGTEIDFKTEKLYSGFVFHNPNQVSACGCGQS 108
V +D SL Y+ G+EID+ E L SGF F NPN CGCG+S
Sbjct: 60 VVVDPKSLPYLDGSEIDYVEELLGSGFTFTNPNAKGTCGCGKS 102
>gnl|CDD|131066 TIGR02011, IscA, iron-sulfur cluster assembly protein IscA. This
clade is limited to the proteobacteria.
Length = 105
Score = 95.3 bits (237), Expect = 3e-21
Identities = 44/107 (41%), Positives = 66/107 (61%), Gaps = 2/107 (1%)
Query: 5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGV 64
+T+T++A R+ + N +GK G+R+ +K GC+G+ Y+++ V D P D + E GV
Sbjct: 1 ITLTDSAAARVNTFLAN-RGKGFGLRLGVKTSGCSGMAYVLEFV-DEPTPDDIVFEDKGV 58
Query: 65 KVWIDSASLLYMLGTEIDFKTEKLYSGFVFHNPNQVSACGCGQSVEI 111
K+ ID SL Y+ GT++DF E L GF F NPN CGCG+S +
Sbjct: 59 KIVIDGKSLQYLDGTQLDFVKEGLNEGFKFTNPNVKDECGCGESFHV 105
>gnl|CDD|181914 PRK09502, iscA, iron-sulfur cluster assembly protein; Provisional.
Length = 107
Score = 91.5 bits (227), Expect = 5e-20
Identities = 40/107 (37%), Positives = 66/107 (61%), Gaps = 2/107 (1%)
Query: 5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGV 64
+T++++A R+ + ++GK G+R+ ++ GC+G+ Y+++ V D P D + E GV
Sbjct: 3 ITLSDSAAARVNTFL-ANRGKGFGLRLGVRTSGCSGMAYVLEFV-DEPTPEDIVFEDKGV 60
Query: 65 KVWIDSASLLYMLGTEIDFKTEKLYSGFVFHNPNQVSACGCGQSVEI 111
KV +D SL ++ GT++DF E L GF F NPN CGCG+S +
Sbjct: 61 KVVVDGKSLQFLDGTQLDFVKEGLNEGFKFTNPNVKDECGCGESFHV 107
>gnl|CDD|181915 PRK09504, sufA, iron-sulfur cluster assembly scaffold protein;
Provisional.
Length = 122
Score = 88.3 bits (219), Expect = 4e-19
Identities = 39/104 (37%), Positives = 65/104 (62%), Gaps = 2/104 (1%)
Query: 5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGV 64
+T+T AA I+E++ Q +G+R+ +K+ GCAG Y++D V++ P D + E DG
Sbjct: 18 LTLTPAAAAHIRELM-AKQPGMKGVRLGVKQTGCAGFGYVLDSVSE-PDKDDLVFEHDGA 75
Query: 65 KVWIDSASLLYMLGTEIDFKTEKLYSGFVFHNPNQVSACGCGQS 108
K+++ ++ ++ GTE+D+ E L F FHNP + CGCG+S
Sbjct: 76 KLFVPLQAMPFIDGTEVDYVREGLNQIFKFHNPKAQNECGCGES 119
>gnl|CDD|184186 PRK13623, PRK13623, iron-sulfur cluster insertion protein ErpA;
Provisional.
Length = 115
Score = 74.6 bits (184), Expect = 5e-15
Identities = 42/108 (38%), Positives = 60/108 (55%), Gaps = 5/108 (4%)
Query: 6 TMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDL-IEKDGV 64
T+AA ++KE++ +R+ + GGC+G +Y D V+ DD IEK GV
Sbjct: 11 VFTDAAAAKVKELIEEEGNPDLKLRVYITGGGCSGFQYGFTF--DEQVNEDDTTIEKQGV 68
Query: 65 KVWIDSASLLYMLGTEIDFKTEKLY-SGFVFHNPNQVSACGCGQSVEI 111
+ +D SL Y++G E+D+ TE L S FV NPN + CGCG S I
Sbjct: 69 TLVVDPMSLQYLVGAEVDY-TEGLEGSRFVIKNPNAKTTCGCGSSFSI 115
>gnl|CDD|178631 PLN03082, PLN03082, Iron-sulfur cluster assembly; Provisional.
Length = 163
Score = 71.1 bits (174), Expect = 6e-14
Identities = 41/114 (35%), Positives = 68/114 (59%), Gaps = 7/114 (6%)
Query: 3 DIVTMTEAAVYRIKEIVFNSQGKAQG--IRISLKKGGCAGLEYMVDLVTDNPVDGDDLI- 59
D V MT+ + R+KE+ S+ A+ +R+S++ GGC+G +Y+ +L D+ + DD +
Sbjct: 53 DAVHMTDNCIRRLKEL-QTSEPSAEDKMLRLSVETGGCSGFQYVFEL--DDKTNSDDRVF 109
Query: 60 EKDGVKVWIDSASLLYMLGTEIDFKTEKLYSGFVFH-NPNQVSACGCGQSVEIK 112
EKDGVK+ +D+ S ++ G +D+ E + S FV NP+ V C C S +K
Sbjct: 110 EKDGVKLVVDNISYDFVKGATVDYVEELIRSAFVVSTNPSAVGGCSCKSSFMVK 163
>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.
Length = 190
Score = 38.5 bits (90), Expect = 4e-04
Identities = 24/95 (25%), Positives = 46/95 (48%), Gaps = 2/95 (2%)
Query: 5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDL-IEKDG 63
+T+TEAA + +++ Q + GIR+ + G E V + V+ D+ +E +G
Sbjct: 1 ITITEAAQAYLAKLL-AKQNEGTGIRVFVVNPGTPYAECCVSYCPPDEVEPSDIKLEFNG 59
Query: 64 VKVWIDSASLLYMLGTEIDFKTEKLYSGFVFHNPN 98
++D+ S ++ IDF T+++ PN
Sbjct: 60 FSAYVDALSAPFLEDAVIDFVTDRMGGQLTLKAPN 94
>gnl|CDD|183027 PRK11190, PRK11190, Fe/S biogenesis protein NfuA; Provisional.
Length = 192
Score = 29.6 bits (67), Expect = 0.16
Identities = 24/95 (25%), Positives = 45/95 (47%), Gaps = 2/95 (2%)
Query: 5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDL-IEKDG 63
+T+++AA +++ +Q + IR+ + G E V + V+ D ++ DG
Sbjct: 2 ITISDAAQAHFAKLL-ANQEEGTQIRVFVINPGTPNAECGVSYCPPDAVEATDTELKFDG 60
Query: 64 VKVWIDSASLLYMLGTEIDFKTEKLYSGFVFHNPN 98
++D S ++ EIDF T++L S PN
Sbjct: 61 FSAYVDELSAPFLEDAEIDFVTDQLGSQLTLKAPN 95
>gnl|CDD|130966 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.
Length = 92
Score = 29.1 bits (65), Expect = 0.24
Identities = 23/90 (25%), Positives = 38/90 (42%), Gaps = 2/90 (2%)
Query: 3 DIVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKD 62
IV M++ A K+ + + IRI GC G M +L+ D +GD++ +
Sbjct: 2 KIVAMSDDAYEEFKDFLKENDIDNDVIRIHFAGMGCMGP--MFNLIADEEKEGDEIEKIH 59
Query: 63 GVKVWIDSASLLYMLGTEIDFKTEKLYSGF 92
+ ID + G I+ E +GF
Sbjct: 60 DLTFLIDKNLIDQFGGFSIECAEENFGAGF 89
>gnl|CDD|72638 pfam09222, Fim-adh_lectin, Fimbrial adhesin F17-AG, lectin domain.
Members of this family are carbohydrate-specific lectin
domains found in bacterial fimbrial adhesins. They adopt
a compact, elongated structure consisting of a
beta-sandwich with two major sheets: one consisting of
five long strands in mixed orientations, and a front
sheet with four antiparallel strands, forming an
immunoglobin-like fold.
Length = 170
Score = 28.9 bits (64), Expect = 0.26
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 6/68 (8%)
Query: 33 LKKGGCAGLEYMVDLVTDNPVDGDD---LIEKDGVKVWIDSASLLYMLGTEIDFKT-EKL 88
+ G C GL+ VDL +DG L E+ G+ +W+ + Y GT + + E +
Sbjct: 47 ISGGFCVGLDGKVDLPVVGSLDGQSIYGLTEEVGLLIWMGDTN--YSRGTAMSGNSWENV 104
Query: 89 YSGFVFHN 96
+SG+ N
Sbjct: 105 FSGWCVGN 112
>gnl|CDD|178732 PLN03190, PLN03190, aminophospholipid translocase; Provisional.
Length = 1178
Score = 26.8 bits (59), Expect = 1.2
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 1/69 (1%)
Query: 14 RIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGVKVWIDSASL 73
++ +I+ NS K + R SL+ + G D V + ID SL
Sbjct: 769 KMTQIIINSNSK-ESCRKSLEDALVMSKKLTTVSGISQNTGGSSAAASDPVALIIDGTSL 827
Query: 74 LYMLGTEID 82
+Y+L +E++
Sbjct: 828 VYVLDSELE 836
>gnl|CDD|180640 PRK06608, PRK06608, threonine dehydratase; Provisional.
Length = 338
Score = 26.7 bits (59), Expect = 1.4
Identities = 12/21 (57%), Positives = 13/21 (61%)
Query: 68 IDSASLLYMLGTEIDFKTEKL 88
+ S SL MLG EI FK E L
Sbjct: 27 VHSESLNEMLGHEIFFKVESL 47
>gnl|CDD|181426 PRK08444, PRK08444, hypothetical protein; Provisional.
Length = 353
Score = 25.8 bits (57), Expect = 2.4
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 5/46 (10%)
Query: 54 DGDDLIEKDGVKVW-IDSASLLYMLGTEIDFKTEKLYSGFVFHNPN 98
+ + L +++ VK++ +D L+ LG D K KL+ V+ N N
Sbjct: 9 NNERLNQEEAVKLYDLD----LFTLGKYADKKRTKLHGKKVYFNVN 50
>gnl|CDD|161885 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble
position of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer.
Length = 442
Score = 25.5 bits (56), Expect = 2.7
Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 5/62 (8%)
Query: 4 IVTMTEAAVYRIKEIVFNSQGKAQGIRISL-----KKGGCAGLEYMVDLVTDNPVDGDDL 58
I+ ++ I + + N A G+RI C E + V N G+D+
Sbjct: 11 IIRLSGPDSLSILKKITNKLNTASGMRIQYGHIIDSNNKCKDDELLFKFVAPNSYTGEDV 70
Query: 59 IE 60
IE
Sbjct: 71 IE 72
>gnl|CDD|149840 pfam08902, DUF1848, Domain of unknown function (DUF1848). This
family of proteins are functionally uncharacterized. The
C-terminus contains a cluster of cysteines that are
similar to the iron-sulfur cluster found at the
N-terminus of pfam04055.
Length = 264
Score = 24.9 bits (55), Expect = 4.5
Identities = 6/16 (37%), Positives = 9/16 (56%)
Query: 96 NPNQVSACGCGQSVEI 111
+ Q CGC +S +I
Sbjct: 234 DKGQRKECGCVESRDI 249
>gnl|CDD|177494 PHA02878, PHA02878, ankyrin repeat protein; Provisional.
Length = 477
Score = 24.8 bits (54), Expect = 4.8
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 10/61 (16%)
Query: 42 EYMVDLVTDNPVDGDDLIEKDGVKVWIDSASLLYMLGTEIDFKTEKLYSG---FVFHNPN 98
+DLV + DD+IE + K LL G +I+ K + + N +
Sbjct: 128 IQTIDLVYIDKKSKDDIIEAEITK-------LLLSYGADINMKDRHKGNTALHYATENKD 180
Query: 99 Q 99
Q
Sbjct: 181 Q 181
>gnl|CDD|179992 PRK05286, PRK05286, dihydroorotate dehydrogenase 2; Reviewed.
Length = 344
Score = 24.7 bits (55), Expect = 5.0
Identities = 5/16 (31%), Positives = 8/16 (50%)
Query: 88 LYSGFVFHNPNQVSAC 103
+YSG ++ P V
Sbjct: 317 IYSGLIYEGPGLVKEI 332
>gnl|CDD|180889 PRK07217, PRK07217, replication factor A; Reviewed.
Length = 311
Score = 24.6 bits (54), Expect = 5.5
Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 10/74 (13%)
Query: 2 SDIVTMTEAAVYRIKEIVFNS-QGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIE 60
SD+ + E Y +K +V + QG R S+K +E +L D V GDD +E
Sbjct: 123 SDLPELEEGKSYLLKNVVTDEYQG-----RFSVKLNRTTSIE---ELDEDIEV-GDDEVE 173
Query: 61 KDGVKVWIDSASLL 74
+G V I S S L
Sbjct: 174 VEGALVDIQSGSGL 187
>gnl|CDD|184036 PRK13407, bchI, magnesium chelatase subunit I; Provisional.
Length = 334
Score = 24.4 bits (53), Expect = 5.9
Identities = 7/25 (28%), Positives = 19/25 (76%)
Query: 42 EYMVDLVTDNPVDGDDLIEKDGVKV 66
+++VDL+ D G++++E++G+ +
Sbjct: 142 DHIVDLLLDVAQSGENVVEREGLSI 166
>gnl|CDD|184379 PRK13896, PRK13896, cobyrinic acid a,c-diamide synthase;
Provisional.
Length = 433
Score = 24.3 bits (53), Expect = 6.7
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 41 LEYMVDLVTDNPVDGDDLIEKDGV 64
L D+VT +PV GD L + DGV
Sbjct: 255 LRERADVVTFSPVAGDPLPDCDGV 278
>gnl|CDD|178069 PLN02450, PLN02450, 1-aminocyclopropane-1-carboxylate synthase.
Length = 468
Score = 23.9 bits (52), Expect = 8.5
Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 8/30 (26%)
Query: 81 IDFKTEK--------LYSGFVFHNPNQVSA 102
+DF T K +YSG VF +P VS
Sbjct: 217 VDFITAKNIHLISDEIYSGTVFDSPGFVSV 246
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.319 0.137 0.398
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,840,825
Number of extensions: 104111
Number of successful extensions: 205
Number of sequences better than 10.0: 1
Number of HSP's gapped: 194
Number of HSP's successfully gapped: 31
Length of query: 116
Length of database: 5,994,473
Length adjustment: 81
Effective length of query: 35
Effective length of database: 4,244,225
Effective search space: 148547875
Effective search space used: 148547875
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 (21.7 bits)
S2: 50 (23.1 bits)