RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 027202
(226 letters)
>gnl|CDD|178408 PLN02812, PLN02812, 5-formyltetrahydrofolate cyclo-ligase.
Length = 211
Score = 258 bits (662), Expect = 4e-88
Identities = 110/162 (67%), Positives = 131/162 (80%), Gaps = 9/162 (5%)
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 APVDADGNEREDVMQANEPVDLFLLPGLAFDRSGRRLGRGGG 178
PVDADGN REDV+QA EP+DL LLPGLAFDRSGRRLGRGGG
Sbjct: 113 TPVDADGNPREDVLQAPEPLDLLLLPGLAFDRSGRRLGRGGG 154
>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 = 102 bits (256), Expect = 2e-27
Identities = 49/157 (31%), Positives = 78/157 (49%), Gaps = 21/157 (13%)
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 DGNEREDVMQANEPVDLFLLPGLAFDRSGRRLGRGGG 178
D E + +DL ++PG+AFDR G RLG GGG
Sbjct: 106 DLEEPVPPDE----IDLIIVPGVAFDRRGYRLGYGGG 138
>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 = 88.6 bits (220), Expect = 5e-22
Identities = 40/156 (25%), Positives = 70/156 (44%), Gaps = 19/156 (12%)
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 GNEREDVMQANEPVDLFLLPGLAFDRSGRRLGRGGG 178
+RE A +DL L+PG+AFDR G RLGRGGG
Sbjct: 106 EEQREL---ALNQIDLVLVPGVAFDRQGYRLGRGGG 138
>gnl|CDD|223290 COG0212, COG0212, 5-formyltetrahydrofolate cyclo-ligase [Coenzyme
metabolism].
Length = 191
Score = 88.5 bits (220), Expect = 8e-22
Identities = 42/155 (27%), Positives = 66/155 (42%), Gaps = 19/155 (12%)
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 NEREDVMQANEPVDLFLLPGLAFDRSGRRLGRGGG 178
+DL L+P +AFD+ G RLG GGG
Sbjct: 107 -GEYGRKIPPPEIDLVLVPLVAFDKQGYRLGYGGG 140
>gnl|CDD|182385 PRK10333, PRK10333, 5-formyltetrahydrofolate cyclo-ligase family
protein; Provisional.
Length = 182
Score = 41.8 bits (98), Expect = 7e-05
Identities = 29/103 (28%), Positives = 52/103 (50%), Gaps = 17/103 (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 PAPVDADGNEREDVMQANEPVDLFLLPGLAFDRSGRRLGRGGG 178
P +D DV+ + +D+ + P +AFD G+RLG GGG
Sbjct: 97 PK-LDV-----RDVLPLSR-LDVLITPLVAFDEYGQRLGMGGG 132
>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 = 29.9 bits (68), Expect = 0.98
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|182392 PRK10342, PRK10342, glycerate kinase I; Provisional.
Length = 381
Score = 29.5 bits (66), Expect = 1.3
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 167 DRSGRRLGRGGGSTKSLQRKEIGG-NPSLLLCHI 199
D +G +G GGGS +L +I G +P L C I
Sbjct: 155 DANGNEIGFGGGSLNTLNDIDISGLDPRLKDCVI 188
>gnl|CDD|235213 PRK04044, rps5p, 30S ribosomal protein S5P; Reviewed.
Length = 211
Score = 28.0 bits (63), Expect = 3.6
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|236406 PRK09197, PRK09197, fructose-bisphosphate aldolase; Provisional.
Length = 350
Score = 27.8 bits (63), Expect = 4.2
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|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 = 4.2
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|235165 PRK03826, PRK03826, 5'-nucleotidase; Provisional.
Length = 195
Score = 27.3 bits (61), Expect = 5.1
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|238476 cd00946, FBP_aldolase_IIA, Class II Type A,
Fructose-1,6-bisphosphate (FBP) aldolases. The enzyme
catalyses the zinc-dependent, reversible aldol
condensation of dihydroxyacetone phosphate with
glyceraldehyde-3-phosphate to form
fructose-1,6-bisphosphate. FBP aldolase is homodimeric
and used in gluconeogenesis and glycolysis. The type A
and type B Class II FBPA's differ in the presence and
absence of distinct indels in the sequence that result
in differing loop lengths in the structures.
Length = 345
Score = 27.3 bits (61), Expect = 7.1
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 89 QIPNADGDTKTRKKLYVPRV 108
QI N +G K KK Y PRV
Sbjct: 300 QIGNPEGPDKPNKKYYDPRV 319
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 0.133 0.383
Gapped
Lambda K H
0.267 0.0735 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,181,361
Number of extensions: 1026146
Number of successful extensions: 766
Number of sequences better than 10.0: 1
Number of HSP's gapped: 757
Number of HSP's successfully gapped: 22
Length of query: 226
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 133
Effective length of database: 6,812,680
Effective search space: 906086440
Effective search space used: 906086440
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: 57 (25.7 bits)