RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 029926
(185 letters)
>gnl|CDD|178534 PLN02948, PLN02948, phosphoribosylaminoimidazole carboxylase.
Length = 577
Score = 105 bits (264), Expect = 8e-27
Identities = 42/73 (57%), Positives = 50/73 (68%)
Query: 111 DTPIVGIIMESDSDLPVMNDAARTLSDFGVPYEIKILSPHQNRKGALSYALSAKERGIKI 170
TP+VGIIM SDSDLP M DAA L FGVPYE+ I+S H+ + SYA SA RG+++
Sbjct: 409 GTPLVGIIMGSDSDLPTMKDAAEILDSFGVPYEVTIVSAHRTPERMFSYARSAHSRGLQV 468
Query: 171 IIVGDGVEAHLSG 183
II G G AHL G
Sbjct: 469 IIAGAGGAAHLPG 481
>gnl|CDD|144362 pfam00731, AIRC, AIR carboxylase. Members of this family catalyze
the decarboxylation of
1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate
(AIR). This family catalyze the sixth step of de novo
purine biosynthesis. Some members of this family contain
two copies of this domain.
Length = 150
Score = 94.1 bits (235), Expect = 6e-25
Identities = 38/73 (52%), Positives = 50/73 (68%)
Query: 113 PIVGIIMESDSDLPVMNDAARTLSDFGVPYEIKILSPHQNRKGALSYALSAKERGIKIII 172
P VGIIM SDSDLP M AA+ L +FG+PYE++++S H+ + YA A+ RGIK+II
Sbjct: 1 PKVGIIMGSDSDLPTMEKAAKVLKEFGIPYEVRVVSAHRTPERLFEYAKEAEARGIKVII 60
Query: 173 VGDGVEAHLSGTL 185
G G AHL G +
Sbjct: 61 AGAGGAAHLPGMV 73
>gnl|CDD|214965 smart01001, AIRC, AIR carboxylase. Members of this family catalyse
the decarboxylation of
1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate
(AIR). This family catalyse the sixth step of de novo
purine biosynthesis. Some members of this family contain
two copies of this domain.
Length = 152
Score = 93.8 bits (234), Expect = 8e-25
Identities = 39/71 (54%), Positives = 50/71 (70%)
Query: 113 PIVGIIMESDSDLPVMNDAARTLSDFGVPYEIKILSPHQNRKGALSYALSAKERGIKIII 172
P+VGIIM S SDLPVM +AA+TL +FG+PYE+ + S H+ YA A++RGIK+II
Sbjct: 1 PLVGIIMGSTSDLPVMEEAAKTLEEFGIPYEVGVASAHRTPDRLFEYAKEAEDRGIKVII 60
Query: 173 VGDGVEAHLSG 183
G G AHL G
Sbjct: 61 AGAGGAAHLPG 71
>gnl|CDD|223119 COG0041, PurE, Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase
[Nucleotide transport and metabolism].
Length = 162
Score = 93.1 bits (232), Expect = 2e-24
Identities = 36/73 (49%), Positives = 46/73 (63%)
Query: 111 DTPIVGIIMESDSDLPVMNDAARTLSDFGVPYEIKILSPHQNRKGALSYALSAKERGIKI 170
P VGIIM S SD M AA L +FGVPYE++++S H+ + YA A+ERG+K+
Sbjct: 1 MPPKVGIIMGSKSDWDTMKKAAEILEEFGVPYEVRVVSAHRTPEKMFEYAEEAEERGVKV 60
Query: 171 IIVGDGVEAHLSG 183
II G G AHL G
Sbjct: 61 IIAGAGGAAHLPG 73
>gnl|CDD|130230 TIGR01162, purE, phosphoribosylaminoimidazole carboxylase, PurE
protein. Phosphoribosylaminoimidazole carboxylase is a
fusion protein in plants and fungi, but consists of two
non-interacting proteins in bacteria, PurK and PurE.
This model represents PurK, an N5-CAIR mutase [Purines,
pyrimidines, nucleosides, and nucleotides, Purine
ribonucleotide biosynthesis].
Length = 156
Score = 86.9 bits (216), Expect = 4e-22
Identities = 39/69 (56%), Positives = 49/69 (71%)
Query: 115 VGIIMESDSDLPVMNDAARTLSDFGVPYEIKILSPHQNRKGALSYALSAKERGIKIIIVG 174
VGIIM SDSDLP M AA L +FG+PYE++++S H+ + L YA A+ERGIK+II G
Sbjct: 1 VGIIMGSDSDLPTMKKAADILEEFGIPYELRVVSAHRTPELMLEYAKEAEERGIKVIIAG 60
Query: 175 DGVEAHLSG 183
G AHL G
Sbjct: 61 AGGAAHLPG 69
>gnl|CDD|224605 COG1691, COG1691, NCAIR mutase (PurE)-related proteins [General
function prediction only].
Length = 254
Score = 32.0 bits (73), Expect = 0.12
Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 8/82 (9%)
Query: 104 NANGDSTDTPIVGIIMESDSDLPVMNDAARTLSDFGVP----YEIKILSPHQNRKGALSY 159
+ N + VG++ SDLPV +AA T + GV Y++ + H+ LS
Sbjct: 109 DPNYEPKKGGKVGVLSAGTSDLPVAEEAAVTAEELGVEVQKVYDVGVAGIHR----LLSA 164
Query: 160 ALSAKERGIKIIIVGDGVEAHL 181
K ++IV G+E L
Sbjct: 165 LKRLKIEDADVLIVVAGMEGAL 186
>gnl|CDD|223840 COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell
envelope biogenesis, outer membrane].
Length = 475
Score = 32.3 bits (74), Expect = 0.12
Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 10/83 (12%)
Query: 105 ANGDSTDTPIVGIIMESDSDLPVMN-------DAARTLSD--FGVPYEIKILSPHQNRKG 155
+ D + P +G I E +D+ ++ D A L+D G+ K +R+
Sbjct: 369 GDRDKSKRPDMGAIAEQLADIVIVTSDNPRSEDPAVILADILAGIEAPEKYEIIE-DREE 427
Query: 156 ALSYALSAKERGIKIIIVGDGVE 178
A+ AL + G ++I G G E
Sbjct: 428 AIRKALDLAKEGDVVLIAGKGHE 450
>gnl|CDD|233074 TIGR00655, PurU, formyltetrahydrofolate deformylase. This model
describes formyltetrahydrofolate deformylases. The
enzyme is a homohexamer. Sequences from a related enzyme
formyl tetrahydrofolate-specific enzyme,
phosphoribosylglycinamide formyltransferase, serve as an
outgroup for phylogenetic analysis. Putative members of
this family, scoring below the trusted cutoff, include a
sequence from Rhodobacter capsulatus that lacks an
otherwise conserved C-terminal region [Purines,
pyrimidines, nucleosides, and nucleotides, Purine
ribonucleotide biosynthesis].
Length = 280
Score = 29.3 bits (66), Expect = 0.91
Identities = 24/69 (34%), Positives = 33/69 (47%), Gaps = 10/69 (14%)
Query: 117 IIMESDSDLPVMNDAARTLS-DFGVPYEIKILSPHQNR----KGALSYALSAKERGIKII 171
++ + DL V+ + LS DF Y KI++ H + GA Y A ERG+KII
Sbjct: 155 LLKQYQVDLVVLAKYMQILSPDFVKRYPNKIINIHHSFLPAFIGANPYQ-RAYERGVKII 213
Query: 172 IVGDGVEAH 180
G AH
Sbjct: 214 ----GATAH 218
>gnl|CDD|178528 PLN02940, PLN02940, riboflavin kinase.
Length = 382
Score = 28.3 bits (63), Expect = 2.2
Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 1/68 (1%)
Query: 112 TPIVGIIMESDSDLPVMNDAARTLSDFGVPYEIKILSPHQNRKGALSYALSAKERGIKII 171
TP++ + LP N + L GVP + SP N + +S KE +I
Sbjct: 82 TPLLSEQWCNIKALPGANRLIKHLKSHGVPMALASNSPRANIEAKISCHQGWKE-SFSVI 140
Query: 172 IVGDGVEA 179
+ GD VE
Sbjct: 141 VGGDEVEK 148
>gnl|CDD|197223 cd09124, PLDc_like_TrmB_middle, Middle phospholipase D-like domain
of the transcriptional regulator TrmB and similar
proteins. Middle phospholipase D (PLD)-like domain of
the transcriptional regulator TrmB and similar proteins.
TrmB acts as a bifunctional sugar-sensing
transcriptional regulator which controls two operons
encoding maltose/trehalose and maltodextrin ABC
transporters of Pyrococcus fruiosus. It functions as a
dimer. Full length TrmB includes an N-terminal
DNA-binding domain, a C-terminal sugar-binding domain
and middle region that has been named as a PLD-like
domain. The middle domain displays homology to PLD
enzymes, which contain one or two HKD motifs
(H-x-K-x(4)-D, where x represents any amino acid
residue) per chain. The HKD motif characterizes the PLD
superfamily. Due to the lack of key residues related to
PLD activity in the PLD-like domain, members of this
subfamily are unlikely to carry PLD activity.
Length = 126
Score = 27.3 bits (61), Expect = 2.5
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 142 YEIKILSPHQNRKGALSYALSAKERGIKIIIV 173
EI I P + + L A ERG+K++I+
Sbjct: 24 EEIYISLPSEELEELLEELEKAAERGVKVVII 55
>gnl|CDD|223859 COG0788, PurU, Formyltetrahydrofolate hydrolase [Nucleotide
transport and metabolism].
Length = 287
Score = 28.0 bits (63), Expect = 2.7
Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 10/69 (14%)
Query: 117 IIMESDSDLPVMNDAARTLS-DFGVPYEIKILSPHQNR----KGALSYALSAKERGIKII 171
++ E +DL V+ + LS DF + KI++ H + GA Y A ERG+K+I
Sbjct: 161 LLEEYGADLVVLARYMQILSPDFVERFPGKIINIHHSFLPAFIGANPYH-QAYERGVKLI 219
Query: 172 IVGDGVEAH 180
G AH
Sbjct: 220 ----GATAH 224
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain
[Unknown function, General].
Length = 499
Score = 28.3 bits (63), Expect = 3.0
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 7/68 (10%)
Query: 107 GDSTDTPI-VGIIMESDSDLPVMNDAARTLSDFGVPYEIKILSPHQNRKGALSYALSAKE 165
G D PI +GI+ S+ A+ L ++ E+ + + KG L A++
Sbjct: 73 GGRFDLPIAIGILAASEQL------DAKNLGEYLFLGELALDGKLRGIKGVLPAIALAQK 126
Query: 166 RGIKIIIV 173
G K IIV
Sbjct: 127 SGRKFIIV 134
>gnl|CDD|205719 pfam13541, ChlI, Subunit ChlI of Mg-chelatase.
Length = 121
Score = 27.0 bits (61), Expect = 3.2
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 154 KGALSYALSAKERGIKIIIV 173
+GAL AL+A++ G K +IV
Sbjct: 98 RGALPIALAARKLGFKGLIV 117
>gnl|CDD|215357 PLN02665, PLN02665, pectinesterase family protein.
Length = 366
Score = 27.7 bits (62), Expect = 3.7
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 5/53 (9%)
Query: 121 SDSDLPVMNDAARTLSDFGVPYEIKILSPHQNRKGALSYALSAKERGIKIIIV 173
SD P+ D ++ F + P+ RKG L AL A E +II V
Sbjct: 25 SDDTTPIPADKSQLNQWFQ-----ANVKPYAQRKGTLDPALEAAEAAPRIIKV 72
>gnl|CDD|197753 smart00481, POLIIIAc, DNA polymerase alpha chain like domain. DNA
polymerase alpha chain like domain, incl. family of
hypothetical proteins.
Length = 67
Score = 26.1 bits (58), Expect = 3.7
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 122 DSDLPVMNDAARTLSDFGVPYEIKILSPHQNRKGALSYALSAKERGIKIIIVGDGVEA 179
D L + + + G+ I ++ H N GA+ + +AK+ GIK II G+EA
Sbjct: 12 DGALSPE-ELVKRAKELGLKA-I-AITDHGNLFGAVEFYKAAKKAGIKPII---GLEA 63
>gnl|CDD|200477 cd11338, AmyAc_CMD, Alpha amylase catalytic domain found in
cyclomaltodextrinases and related proteins.
Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase
(NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC
3.2.1.133) catalyze the hydrolysis of alpha-(1,4)
glycosidic linkages on a number of substrates including
cyclomaltodextrins (CDs), pullulan, and starch. These
enzymes hydrolyze CDs and starch to maltose and pullulan
to panose by cleavage of alpha-1,4 glycosidic bonds
whereas alpha-amylases essentially lack activity on CDs
and pullulan. They also catalyze transglycosylation of
oligosaccharides to the C3-, C4- or C6-hydroxyl groups
of various acceptor sugar molecules. Since these
proteins are nearly indistinguishable from each other,
they are referred to as cyclomaltodextrinases (CMDs).
The Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 389
Score = 27.4 bits (62), Expect = 4.2
Identities = 8/15 (53%), Positives = 12/15 (80%), Gaps = 2/15 (13%)
Query: 163 AKERGIKIIIVGDGV 177
A +RGI++I+ DGV
Sbjct: 112 AHKRGIRVIL--DGV 124
>gnl|CDD|224409 COG1492, CobQ, Cobyric acid synthase [Coenzyme metabolism].
Length = 486
Score = 27.6 bits (62), Expect = 4.6
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 4/27 (14%)
Query: 163 AKERGIKIIIVGD----GVEAHLSGTL 185
A+ +I+VGD GV A L GTL
Sbjct: 153 AEIADAPVILVGDIDRGGVFASLYGTL 179
>gnl|CDD|236113 PRK07847, PRK07847, amidophosphoribosyltransferase; Provisional.
Length = 510
Score = 27.6 bits (62), Expect = 4.7
Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 2/70 (2%)
Query: 66 RTVSQGTIPVLASSNGSATSTRKDYSSVREPSTVFEEENANGDSTDTPIVGIIMESDSDL 125
R + G L NG+ +T + + R+ + + G +TDT +V ++ +
Sbjct: 113 RATAAGGGVALGH-NGNLVNTAELAARARDRGLIRGR-DPAGATTDTDLVTALLAHGAAD 170
Query: 126 PVMNDAARTL 135
+ AA L
Sbjct: 171 STLEQAALEL 180
>gnl|CDD|239152 cd02751, MopB_DMSOR-like, The MopB_DMSOR-like CD contains
dimethylsulfoxide reductase (DMSOR), biotin sulfoxide
reductase (BSOR), trimethylamine N-oxide reductase
(TMAOR) and other related proteins. DMSOR catalyzes the
reduction of DMSO to dimethylsulfide, but its cellular
location and oligomerization state are
organism-dependent. For example, in Rhodobacter
sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa
monomeric soluble protein found in the periplasmic
space; in E. coli, it is membrane-bound and exists as a
heterotrimer. BSOR catalyzes the reduction of biotin
sulfixode to biotin, and is unique among Mo enzymes
because no additional auxiliary proteins or cofactors
are required. TMAOR is similar to DMSOR, but its only
natural substrate is TMAO. Also included in this group
is the pyrogallol-phloroglucinol transhydroxylase from
Pelobacter acidigallici. Members of the MopB_DMSOR-like
CD belong to the molybdopterin_binding (MopB)
superfamily of proteins.
Length = 609
Score = 27.2 bits (61), Expect = 5.6
Identities = 22/112 (19%), Positives = 38/112 (33%), Gaps = 23/112 (20%)
Query: 69 SQGTIPVLASSNGSATSTRKDYSS----VREPSTVFEEENANGDSTDTPIVGIIMESDSD 124
+Q + + G + YS+ V P V +E ++ I SD
Sbjct: 117 AQSLLHRFLNLIGGYLGSYGTYSTGAAQVILPHVVGSDEVYEQGTSWDDIA-----EHSD 171
Query: 125 LPVM--NDAARTL-SDFGVPYEIKILSPHQNRKGALSYALSAKERGIKIIIV 173
L V+ + +T G P G+ Y AK+ G++ I +
Sbjct: 172 LVVLFGANPLKTRQGGGGGP-----------DHGSYYYLKQAKDAGVRFICI 212
>gnl|CDD|233039 TIGR00594, polc, DNA-directed DNA polymerase III (polc). All
proteins in this family for which functions are known
are DNA polymerases. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1022
Score = 27.3 bits (61), Expect = 6.1
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 147 LSPHQNRKGALSYALSAKERGIKIIIVGDGVEAH 180
L+ H N GA+ + + K+ GIK II G EA+
Sbjct: 36 LTDHGNMFGAVEFYKACKKAGIKPII---GCEAY 66
>gnl|CDD|238920 cd01945, ribokinase_group_B, Ribokinase-like subgroup B. Found in
bacteria and plants, this subgroup is part of the
ribokinase/pfkB superfamily. Its oligomerization state
is unknown at this time. .
Length = 284
Score = 26.9 bits (60), Expect = 6.2
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 155 GALSYALSAKERGIKIIIVGDG 176
AL A A+ RGI I + DG
Sbjct: 139 AALHLAQEARARGIPIPLDLDG 160
>gnl|CDD|107205 cd01562, Thr-dehyd, Threonine dehydratase: The first step in amino
acid degradation is the removal of nitrogen. Although
the nitrogen atoms of most amino acids are transferred
to alpha-ketoglutarate before removal, the alpha-amino
group of threonine can be directly converted into NH4+.
The direct deamination is catalyzed by threonine
dehydratase, in which pyridoxal phosphate (PLP) is the
prosthetic group. Threonine dehydratase is widely
distributed in all three major phylogenetic divisions.
Length = 304
Score = 26.7 bits (60), Expect = 7.3
Identities = 12/36 (33%), Positives = 14/36 (38%), Gaps = 9/36 (25%)
Query: 147 LSPHQNRKG---------ALSYALSAKERGIKIIIV 173
LS + KG A A +AK GI IV
Sbjct: 59 LSEEERAKGVVAASAGNHAQGVAYAAKLLGIPATIV 94
>gnl|CDD|143587 cd07197, nitrilase, Nitrilase superfamily, including nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes.
This superfamily (also known as the C-N hydrolase
superfamily) contains hydrolases that break
carbon-nitrogen bonds; it includes nitrilases, cyanide
dihydratases, aliphatic amidases, N-terminal amidases,
beta-ureidopropionases, biotinidases, pantotheinase,
N-carbamyl-D-amino acid amidohydrolases, the glutaminase
domain of glutamine-dependent NAD+ synthetase,
apolipoprotein N-acyltransferases, and
N-carbamoylputrescine amidohydrolases, among others.
These enzymes depend on a Glu-Lys-Cys catalytic triad,
and work through a thiol acylenzyme intermediate.
Members of this superfamily generally form homomeric
complexes, the basic building block of which is a
homodimer. These oligomers include dimers, tetramers,
hexamers, octamers, tetradecamers, octadecamers, as well
as variable length helical arrangements and
homo-oligomeric spirals. These proteins have roles in
vitamin and co-enzyme metabolism, in detoxifying small
molecules, in the synthesis of signaling molecules, and
in the post-translational modification of proteins. They
are used industrially, as biocatalysts in the fine
chemical and pharmaceutical industry, in cyanide
remediation, and in the treatment of toxic effluent.
This superfamily has been classified previously in the
literature, based on global and structure-based sequence
analysis, into thirteen different enzyme classes
(referred to as 1-13). This hierarchy includes those
thirteen classes and a few additional subfamilies. A
putative distant relative, the plasmid-borne TraB
family, has not been included in the hierarchy.
Length = 253
Score = 26.5 bits (59), Expect = 7.7
Identities = 12/41 (29%), Positives = 17/41 (41%), Gaps = 3/41 (7%)
Query: 143 EIKILSPHQNRKGALSYALSAKERGIKIIIVGDGVEAHLSG 183
KI N AL A E+G +I++ E L+G
Sbjct: 7 APKIGDVEANLAKALRLIKEAAEQGADLIVLP---ELFLTG 44
>gnl|CDD|235404 PRK05319, rplD, 50S ribosomal protein L4; Provisional.
Length = 205
Score = 26.2 bits (59), Expect = 8.9
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 153 RKGALSYALSAKERGIKIIIV 173
R+ AL ALS K R ++++V
Sbjct: 105 RRLALRSALSEKAREGRLVVV 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
0.317 0.132 0.367
Gapped
Lambda K H
0.267 0.0817 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,976,525
Number of extensions: 794106
Number of successful extensions: 928
Number of sequences better than 10.0: 1
Number of HSP's gapped: 925
Number of HSP's successfully gapped: 40
Length of query: 185
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 94
Effective length of database: 6,901,388
Effective search space: 648730472
Effective search space used: 648730472
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: 56 (25.2 bits)