RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 025859
(247 letters)
>gnl|CDD|178408 PLN02812, PLN02812, 5-formyltetrahydrofolate cyclo-ligase.
Length = 211
Score = 350 bits (899), Expect = e-124
Identities = 150/219 (68%), Positives = 177/219 (80%), Gaps = 9/219 (4%)
Query: 18 ESIFQQKRILRSQVRKTLKSMDPSLRSHEDNAIQKIVLEAPWFKSSQRLCAYISCSALRE 77
+ I +QK+ LR +VR+ LK++ P R+ ED AIQ +LE PWFKSS+RLCAY+SC+ LRE
Sbjct: 1 DEIREQKKALRKEVRRALKALSPEQRAQEDAAIQSRLLELPWFKSSKRLCAYVSCAKLRE 60
Query: 78 VDTSKLLSQILQIPNADGDTKTRKKLYVPRVEDKNSHMRMFHISSI-DDLIANSMNILEP 136
VDTSK+LS+ILQ P K+LYVPRVEDKNS+MRM HI+ + DDL+ANSMNILEP
Sbjct: 61 VDTSKILSEILQNP--------DKRLYVPRVEDKNSNMRMLHITDMADDLVANSMNILEP 112
Query: 137 APVDADGNEREDVMQANEPVDLFLLPGLAFDRSGRRLGRGGGYYDTFLKKYQELAKERNW 196
PVDADGN REDV+QA EP+DL LLPGLAFDRSGRRLGRGGGYYDTFL KYQELAKE+ W
Sbjct: 113 TPVDADGNPREDVLQAPEPLDLLLLPGLAFDRSGRRLGRGGGYYDTFLSKYQELAKEKGW 172
Query: 197 RQPLFVALSYSLQIMDEGIISATPKDMPVDALVSPSGVI 235
+QPL VALSYS QI+DEG + D+ VDALV+PSGVI
Sbjct: 173 KQPLLVALSYSPQILDEGSVPVDETDVLVDALVTPSGVI 211
>gnl|CDD|233985 TIGR02727, MTHFS_bact, 5,10-methenyltetrahydrofolate synthetase.
This enzyme, 5,10-methenyltetrahydrofolate synthetase,
is also called 5-formyltetrahydrofolate cycloligase.
Function of bacterial proteins in this family was
inferred originally from the known activity of
eukaryotic homologs. Recently, activity was shown
explicitly for the member from Mycoplasma pneumonia.
Members of this family from alpha- and
gamma-proteobacteria, designated ygfA, are often found
in an operon with 6S structural RNA, and show a similar
pattern of high expression during stationary phase. The
function may be to deplete folate to slow 1-carbon
biosynthetic metabolism [Central intermediary
metabolism, One-carbon metabolism].
Length = 179
Score = 127 bits (321), Expect = 8e-37
Identities = 64/210 (30%), Positives = 106/210 (50%), Gaps = 33/210 (15%)
Query: 24 KRILRSQVRKTLKSMDPSLRSHEDNAIQKIVLEAPWFKSSQRLCAYISCSALR-EVDTSK 82
K+ LR ++ + K++ + R +AI K +L +K+++ + Y+ LR EVDT
Sbjct: 1 KKELRKKLLEARKALSSAERKAASSAIAKRLLALIEWKNAKTIALYLP---LRGEVDTRP 57
Query: 83 LLSQILQIPNADGDTKTRKKLYVPRVEDKNSHMRMFHISSIDD-LIANSMNILEPAPVDA 141
L+ Q+L+ K++ +P+V+ M F I S + L ILEP
Sbjct: 58 LIEQLLKEG---------KRVALPKVDGDGKEMLFFRIWSPEQPLTKGPFGILEP---VG 105
Query: 142 DGNEREDVMQANEPVDLFLLPGLAFDRSGRRLGRGGGYYDTFLKKYQELAKERNWRQPLF 201
D E + +DL ++PG+AFDR G RLG GGGYYD FL + + +
Sbjct: 106 DLEEPVPPDE----IDLIIVPGVAFDRRGYRLGYGGGYYDRFLARL----------KGIT 151
Query: 202 VALSYSLQIMDEGIISATPKDMPVDALVSP 231
+ L++ Q++DE + P D+PVDA+++
Sbjct: 152 IGLAFDFQLVDE--LPREPHDVPVDAIITE 179
>gnl|CDD|223290 COG0212, COG0212, 5-formyltetrahydrofolate cyclo-ligase [Coenzyme
metabolism].
Length = 191
Score = 123 bits (311), Expect = 5e-35
Identities = 60/212 (28%), Positives = 95/212 (44%), Gaps = 28/212 (13%)
Query: 24 KRILRSQVRKTLKSMDPSLRSHEDNAIQKIVLEAPWFKSSQRLCAYISCSALREVDTSKL 83
K LR + + ++ P R D I K++ K ++ + Y+ + E+DT L
Sbjct: 5 KSALRKLLLERRIALSPEERHEADQRIAKLLASLIEVKKAKTIALYVPFN--GEIDTRPL 62
Query: 84 LSQILQIPNADGDTKTRKKLYVPRVEDKNSHMRMFHISSIDDLIANSMNILEPAPVDADG 143
+ Q L+ G K+L +P++ D + + LI N ILEP
Sbjct: 63 IRQALR----RG-----KRLLLPKLRDYKLLFLRYIPDPLQPLIKNRFGILEP------- 106
Query: 144 NEREDVMQANEPVDLFLLPGLAFDRSGRRLGRGGGYYDTFLKKYQELAKERNWRQPLFVA 203
+DL L+P +AFD+ G RLG GGGYYD +L + R+ V
Sbjct: 107 -GEYGRKIPPPEIDLVLVPLVAFDKQGYRLGYGGGYYDRYLANLR-------GRKTPTVG 158
Query: 204 LSYSLQIMDEGIISATPKDMPVDALVSPSGVI 235
++Y Q++D P D+P+DA+V+ GVI
Sbjct: 159 IAYDCQLVDHLPRE--PHDVPLDAIVTEEGVI 188
>gnl|CDD|216717 pfam01812, 5-FTHF_cyc-lig, 5-formyltetrahydrofolate cyclo-ligase
family. 5-formyltetrahydrofolate cyclo-ligase or
methenyl-THF synthetase EC:6.3.3.2 catalyzes the
interchange of 5-formyltetrahydrofolate (5-FTHF) to
5-10-methenyltetrahydrofolate, this requires ATP and
Mg2+. 5-FTHF is used in chemotherapy where it is
clinically known as Leucovorin.
Length = 182
Score = 120 bits (302), Expect = 8e-34
Identities = 57/209 (27%), Positives = 97/209 (46%), Gaps = 28/209 (13%)
Query: 24 KRILRSQVRKTLKSMDPSLRSHEDNAIQKIVLEAPWFKSSQRLCAYISCSALREVDTSKL 83
K+ LR Q+ +++ R+ A+ + + + ++R+ Y+S E+DT +L
Sbjct: 1 KQELRKQLLAKRRALSEEERAAASRALHQKLPSFVGAQKAKRVALYVSVK--GEIDTREL 58
Query: 84 LSQILQIPNADGDTKTRKKLYVPRVEDKNSHMRMFHIS-SIDDLIANSMNILEPAPVDAD 142
+ +L+ K + +PR + + L + + EP +
Sbjct: 59 IELLLEE---------GKLVLLPRPRPDSGLVVRITPYYPETGLPSGPYGLPEPI----E 105
Query: 143 GNEREDVMQANEPVDLFLLPGLAFDRSGRRLGRGGGYYDTFLKKYQELAKERNWRQPLFV 202
+RE A +DL L+PG+AFDR G RLGRGGGYYD +L + Q PL V
Sbjct: 106 EEQREL---ALNQIDLVLVPGVAFDRQGYRLGRGGGYYDRYLARLQ-------GHGPLTV 155
Query: 203 ALSYSLQIMDEGIISATPKDMPVDALVSP 231
L+Y Q+++ + P D+PVD +V+
Sbjct: 156 GLAYDEQLVER--LPQEPHDVPVDEIVTE 182
>gnl|CDD|182385 PRK10333, PRK10333, 5-formyltetrahydrofolate cyclo-ligase family
protein; Provisional.
Length = 182
Score = 57.2 bits (138), Expect = 4e-10
Identities = 42/159 (26%), Positives = 75/159 (47%), Gaps = 26/159 (16%)
Query: 77 EVDTSKLLSQILQIPNADGDTKTRKKLYVPRVEDKNSHMRMF-HISSIDDLIANSMNILE 135
E+DT L+ Q+ + K++Y+P + ++ +F + +L+ N + I E
Sbjct: 46 ELDTQPLIEQLWR---------AGKRVYLPVLHPFSAGNLLFLNYHPQSELVMNRLKIHE 96
Query: 136 PAPVDADGNEREDVMQANEPVDLFLLPGLAFDRSGRRLGRGGGYYDTFLKKYQELAKERN 195
P +D DV+ + +D+ + P +AFD G+RLG GGG+YD L+ N
Sbjct: 97 PK-LDV-----RDVLPLSR-LDVLITPLVAFDEYGQRLGMGGGFYDRTLQ---------N 140
Query: 196 WRQPLFVALSYSLQIMDEGIISATPKDMPVDALVSPSGV 234
W+ + Y+ + D+P+ A+V+PS V
Sbjct: 141 WQHYKTQPVGYAHDCQLVEKLPVEEWDIPLPAVVTPSKV 179
>gnl|CDD|191103 pfam04821, TIMELESS, Timeless protein. The timeless gene in
Drosophila melanogaster and its homologues in a number
of other insects and mammals (including human) are
involved in circadian rhythm control. This family
includes a related proteins from a number of fungal
species.
Length = 266
Score = 30.7 bits (70), Expect = 0.64
Identities = 29/112 (25%), Positives = 42/112 (37%), Gaps = 38/112 (33%)
Query: 21 FQQKRILRSQVRKTLKSM--DPSLRSHEDNAIQKIVLEAPWFKSSQRLCAYISCSALREV 78
F ++L++ VR L S+ RS DN I +++L
Sbjct: 105 FLDAKVLKALVRILLPSLAVPWEDRSERDNLIIELIL----------------------- 141
Query: 79 DTSKLLSQILQIPNADGDTKTRKKLYVPRVEDKNSHMRM---FHISSIDDLI 127
LL IL IP + + + R ED +SH FH IDDL+
Sbjct: 142 ---LLLRNILHIP-PNPEAEKRGD------EDASSHDATIWAFHQQGIDDLL 183
>gnl|CDD|215282 PLN02511, PLN02511, hydrolase.
Length = 388
Score = 29.0 bits (65), Expect = 2.2
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 12/52 (23%)
Query: 150 MQANEPVDLFLLPGLAFDRSGRRLGRGGGYYDTFLKKYQELAKERNWRQPLF 201
+ A+ PV L LLPGL GG D++++ A+ + WR +F
Sbjct: 96 LPADAPV-LILLPGLT-----------GGSDDSYVRHMLLRARSKGWRVVVF 135
>gnl|CDD|235213 PRK04044, rps5p, 30S ribosomal protein S5P; Reviewed.
Length = 211
Score = 28.0 bits (63), Expect = 4.5
Identities = 13/45 (28%), Positives = 18/45 (40%), Gaps = 18/45 (40%)
Query: 120 ISSIDDLIANSMNILEPAPVDADGNEREDVMQANEPVDLFLLPGL 164
I+SID++ + + I EP VD LLP L
Sbjct: 24 ITSIDEIFDSGLPIKEPEIVDV------------------LLPDL 50
>gnl|CDD|187571 cd05261, CAPF_like_SDR_e, capsular polysaccharide assembling
protein (CAPF) like, extended (e) SDRs. This subgroup
of extended SDRs, includes some members which have been
identified as capsular polysaccharide assembling
proteins, such as Staphylococcus aureus Cap5F which is
involved in the biosynthesis of N-acetyl-l-fucosamine, a
constituent of surface polysaccharide structures of S.
aureus. This subgroup has the characteristic active site
tetrad and NAD-binding motif of extended SDRs. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal extension
of approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 248
Score = 27.7 bits (62), Expect = 5.3
Identities = 9/39 (23%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 105 VPRVEDKNSHMRMFHISSIDDLIANSMNILEPAPVDADG 143
++ D + + + +I DD++ + +LE AP + G
Sbjct: 158 PIQINDPAAELTLVYI---DDVVDELIQLLEGAPTYSGG 193
>gnl|CDD|236406 PRK09197, PRK09197, fructose-bisphosphate aldolase; Provisional.
Length = 350
Score = 27.5 bits (62), Expect = 6.6
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 89 QIPNADGDTKTRKKLYVPRV 108
Q+ N +G+ K KK Y PRV
Sbjct: 304 QVGNPEGEDKPNKKYYDPRV 323
>gnl|CDD|184975 PRK15014, PRK15014, 6-phospho-beta-glucosidase BglA; Provisional.
Length = 477
Score = 27.7 bits (61), Expect = 7.6
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 9/47 (19%)
Query: 156 VDLFL-LPGLAFDRSGRRLGRGGGYYDTFLKKYQELAKERNWRQPLF 201
VD F+ + F+R ++ Y+ TF E+ +RNWR PLF
Sbjct: 152 VDFFVRFAEVVFERYKHKVK----YWMTF----NEINNQRNWRAPLF 190
>gnl|CDD|235165 PRK03826, PRK03826, 5'-nucleotidase; Provisional.
Length = 195
Score = 26.9 bits (60), Expect = 8.1
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 12/68 (17%)
Query: 9 NPE-EKE-HDLESIFQQKRILRSQVRKTLKS-MDPSLRSHE-DNAIQKIVLEAPWFKSSQ 64
NPE E +E I +QK L + + L+ P L SH + IV K +
Sbjct: 85 NPEIAHEYKKIEKIAEQK--LLDMLPEELQEDFRPLLDSHAASEEEKAIV------KQAD 136
Query: 65 RLCAYISC 72
LCAY+ C
Sbjct: 137 ALCAYLKC 144
>gnl|CDD|240198 cd05693, S1_Rrp5_repeat_hs1_sc1, S1_Rrp5_repeat_hs1_sc1: Rrp5 is
a trans-acting factor important for biogenesis of both
the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has
two distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of
A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1)
and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in
eukaryotes but not in prokaryotes or archaea.
Length = 100
Score = 26.0 bits (58), Expect = 8.4
Identities = 10/37 (27%), Positives = 21/37 (56%)
Query: 1 MSQSNDSSNPEEKEHDLESIFQQKRILRSQVRKTLKS 37
+ + ++ + EE+ DLE +F +++R +V KS
Sbjct: 47 LDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLDKS 83
>gnl|CDD|234425 TIGR03974, rSAM_six_Cys, SCIFF radical SAM maturase. Members of
this protein family are predicted radical SAM enzymes
universally associated with Six Cysteines in Forty-Five
protein, or SCIFF (family TIGR03973), a predicted
ribosomal natural product precursor that is nearly
universal in the class Clostridia. Similarity of this
family to radical SAM maturases (PqqE and subtilosin A
maturase) found in the vicinity of other peptide
precursors suggests this protein is the SCIFF radical
SAM maturase [Cellular processes, Biosynthesis of
natural products].
Length = 451
Score = 27.2 bits (61), Expect = 9.9
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 176 GGGYYDTFLKKYQELAKERN 195
G G YD + K+Q+L + R
Sbjct: 230 GKGSYDLIVPKFQKLVESRG 249
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 0.375
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,603,432
Number of extensions: 1191538
Number of successful extensions: 983
Number of sequences better than 10.0: 1
Number of HSP's gapped: 971
Number of HSP's successfully gapped: 24
Length of query: 247
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 153
Effective length of database: 6,768,326
Effective search space: 1035553878
Effective search space used: 1035553878
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 (21.6 bits)
S2: 58 (26.1 bits)